diff options
Diffstat (limited to 'release_docs')
| -rw-r--r-- | release_docs/COPYING | 16 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_0-1_8_0_rc3.txt | 3376 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_10.txt | 6562 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_10_0-1_12_0.txt | 1183 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_12.txt | 628 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_13.txt | 3194 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_8.txt | 14439 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_8_0-1_10_0.txt | 1739 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_9.txt | 6 | ||||
| -rw-r--r-- | release_docs/INSTALL | 473 | ||||
| -rw-r--r-- | release_docs/INSTALL_CMake.txt | 959 | ||||
| -rw-r--r-- | release_docs/INSTALL_Cygwin.txt | 194 | ||||
| -rw-r--r-- | release_docs/INSTALL_VMS.txt | 77 | ||||
| -rw-r--r-- | release_docs/INSTALL_Warnings.txt | 469 | ||||
| -rw-r--r-- | release_docs/INSTALL_Windows.txt | 6 | ||||
| -rw-r--r-- | release_docs/INSTALL_parallel | 212 | ||||
| -rw-r--r-- | release_docs/README_HDF5_CMake | 25 | ||||
| -rw-r--r-- | release_docs/README_HPC | 206 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 2091 | ||||
| -rw-r--r-- | release_docs/USING_CMake_Examples.txt | 106 | ||||
| -rw-r--r-- | release_docs/USING_HDF5_CMake.txt | 291 | ||||
| -rw-r--r-- | release_docs/USING_HDF5_VS.txt | 57 |
22 files changed, 31761 insertions, 4548 deletions
diff --git a/release_docs/COPYING b/release_docs/COPYING deleted file mode 100644 index 6903daf..0000000 --- a/release_docs/COPYING +++ /dev/null @@ -1,16 +0,0 @@ - - Copyright by The HDF Group and - The Board of Trustees of the University of Illinois. - All rights reserved. - - The files and subdirectories in this directory are part of HDF5. - The full HDF5 copyright notice, including terms governing use, - modification, and redistribution, is contained in the files COPYING - and Copyright.html. COPYING can be found at the root of the source - code distribution tree; Copyright.html can be found at the root - level of an installed copy of the electronic HDF5 document set and - is linked from the top-level documents page. It can also be found - at http://www.hdfgroup.org/HDF5/doc/Copyright.html. If you do not - have access to either file, you may request a copy from - help@hdfgroup.org. - diff --git a/release_docs/HISTORY-1_0-1_8_0_rc3.txt b/release_docs/HISTORY-1_0-1_8_0_rc3.txt index 964d374..3669f4d 100644 --- a/release_docs/HISTORY-1_0-1_8_0_rc3.txt +++ b/release_docs/HISTORY-1_0-1_8_0_rc3.txt @@ -1,7 +1,7 @@ HDF5 HISTORY ============ This file contains history of the HDF5 libraries releases starting with -HDF5-1.0.0 and ending with HDF5-1.8.0-rc3 (the state of the code before i +HDF5-1.0.0 and ending with HDF5-1.8.0-rc3 (the state of the code before the HDF5 1.8.0 release). CONTENTS @@ -27,7 +27,7 @@ CONTENTS 4. Changes from Release 1.0.0 to Release 1.0.1 3. Changes from the Beta 1.0.0 Release to Release 1.0.0 2. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release -1. Changes from the First Alpha 1.0.0 Release to the +1. Changes from the First Alpha 1.0.0 Release to the Second Alpha 1.0.0 Release [Search on the string '%%%%' for per-release section breaks.] @@ -35,15 +35,15 @@ CONTENTS %%%%1.8.0-rc3%%%% Changes from 1.6.0 to 1.8.0-rc3 -HDF5 version 1.8.0-rc3 +HDF5 version 1.8.0-rc3 ================================================================================ INTRODUCTION This document describes the differences between HDF5-1.6.* and -Hdf5 1.8.0 release candidate "HDF5-1.8.0-rc3", and contains information -on the platforms tested and known problems in HDF5-1.8.0-rc3. +Hdf5 1.8.0 release candidate "HDF5-1.8.0-rc3", and contains information +on the platforms tested and known problems in HDF5-1.8.0-rc3. For more details check the HISTORY.txt file in the HDF5 source. @@ -51,7 +51,7 @@ Links to HDF5 1.8.0-rc3 source code, documentation, and additional materials can be found on THG's development server (www.hdfgroup.uiuc.edu) at the following location: http://www.hdfgroup.uiuc.edu/HDF5/release/beta/obtain518.html -User documentation for the beta can be accessed directly at this location: +User documentation for the beta can be accessed directly at this location: http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ New features of the upcoming 1.8.0 release are described in @@ -66,7 +66,7 @@ and will be listed in the "HDF5 Software Changes" document: For more information, see the HDF5 home page: - + http://www.hdfgroup.org/HDF5/ If you have any questions or comments, please send them to the HDF Help Desk: @@ -89,120 +89,120 @@ New Features Configuration: -------------- - Removed stream-vfd from the HDF5 library. - AKC 2007/11/19. - - Updated versions of autotools. HDF5 now uses automake 1.10.0, - autoconf 2.61, and libtool 1.5.22. MAM - 2007/7/25. + - Updated versions of autotools. HDF5 now uses automake 1.10.0, + autoconf 2.61, and libtool 1.5.22. MAM - 2007/7/25. - Changed default fortran compiler to g95 when gcc is used. - AKC - 2007/2/17. + 2007/2/17. - 'make check-vfd' can now be run from the top level directory. Not all - tests that 'make check' invokes work with certain Virtual File Drivers, - so those tests have been skipped. - MAM 2006/7/17 + tests that 'make check' invokes work with certain Virtual File Drivers, + so those tests have been skipped. - MAM 2006/7/17 - Added the variable HDF5TestExpress to control how long tests run. - Setting it to a value between 0 and 3 controls how thoroughly the - library is tested, with 0 being an "exhaustive run" and 3 being a - very quick "smoke test." 1 (a "full run") is the default. - -JML 2006/6/21 + Setting it to a value between 0 and 3 controls how thoroughly the + library is tested, with 0 being an "exhaustive run" and 3 being a + very quick "smoke test." 1 (a "full run") is the default. + -JML 2006/6/21 - If both shared and static libraries are installed, now both will be - tested during 'make install'. -MAM 2006/06/21 - - Added support to explicity enable stream_vfd or shared libraries - when using parallel via the '--enable-stream_vfd' and - '--enable-shared' options, respectively. If not explicity defined, - These settings default to enabled when parallel is not used, - and disabled when parallel is used. -MAM 2006/06/17 + tested during 'make install'. -MAM 2006/06/21 + - Added support to explicitly enable stream_vfd or shared libraries + when using parallel via the '--enable-stream_vfd' and + '--enable-shared' options, respectively. If not explicitly defined, + These settings default to enabled when parallel is not used, + and disabled when parallel is used. -MAM 2006/06/17 - Remove the flexible parallel code and the --enable-fphdf5 - configure option, it was never up to production standards - anyway. -QAK 2006/4/20 + configure option, it was never up to production standards + anyway. -QAK 2006/4/20 - Added a macro hdf5_mpi_special_collective_io_works to filter out - some mpi-io packages that don't support collective IO for no IO - contributions in some processes. -KY 2006/2/16 - - Added -shlib option to link against installed shared libraries to - h5c++ and h5fc. -JML 2005/11/1 - - Added --enable-build-all option to configure, which only developers - should need to use. -JML 2005/10/24 - - Configure uses the 'TR' variable to let the user override the path - to the 'tr' utility. -JML 2005/10/17 - - Configure can recognize -lmpich as a form of MPI library. -AKC- - 2005/9/28. + some mpi-io packages that don't support collective IO for no IO + contributions in some processes. -KY 2006/2/16 + - Added -shlib option to link against installed shared libraries to + h5c++ and h5fc. -JML 2005/11/1 + - Added --enable-build-all option to configure, which only developers + should need to use. -JML 2005/10/24 + - Configure uses the 'TR' variable to let the user override the path + to the 'tr' utility. -JML 2005/10/17 + - Configure can recognize -lmpich as a form of MPI library. -AKC- + 2005/9/28. - MD5 checksumming has been added to snapshot releases. Release - tarballs will be accompanied by .md5 checksum files, which can - be verified using the md5sum utility. -JML 2005/9/6 + tarballs will be accompanied by .md5 checksum files, which can + be verified using the md5sum utility. -JML 2005/9/6 - Some configure flags are incompatible (e.g., the C++ APIs cannot - be built using the parallel version of HDF5). configure will now - output errors when some common incompatible features are used - together. -JML 2005/9/6 + be built using the parallel version of HDF5). configure will now + output errors when some common incompatible features are used + together. -JML 2005/9/6 - A new API function, H5Tis_hard(), was added to the library. It - checks if a conversion function is a compiler (hard) conversion. - SLU - 2005/9/6 - - t_mpi will run the test_mpio_derived_dtype by default unless it is - known not working (indicated by macro H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS - not defined.) -AKC- 2005/8/23. - - Test execution has changed in a number of ways: - When make is invoked in parallel (using -j), sequential tests - are now executed as parallel make targets. This should make them - finish more quickly on machines with multiple processors. - Since test output is garbled when they are executed by parallel make, - tests now dump their output to foo.log files and foo.logsh files - (for test scripts). These logs are printed to the screen only - when a test fails or when all tests in the current directory have - completed successfully. - When tests pass, they will create a foo.chkexe file. - This prevents the test from executing again until the test or - main library changes. - All files generated by tests (*.chkexe, *.log, and any *.h5 files - created) can be removed by invoking 'make check-clean'. - Sequential and parallel library tests can now be invoked separately. - 'make check-s' will execute only sequential tests, and 'make check-p' - will execute only parallel tests. 'make check' will still execute - all tests. - -JML 2005/08/03 + checks if a conversion function is a compiler (hard) conversion. + SLU - 2005/9/6 + - t_mpi will run the test_mpio_derived_dtype by default unless it is + known not working (indicated by macro H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS + not defined.) -AKC- 2005/8/23. + - Test execution has changed in a number of ways: + When make is invoked in parallel (using -j), sequential tests + are now executed as parallel make targets. This should make them + finish more quickly on machines with multiple processors. + Since test output is garbled when they are executed by parallel make, + tests now dump their output to foo.log files and foo.logsh files + (for test scripts). These logs are printed to the screen only + when a test fails or when all tests in the current directory have + completed successfully. + When tests pass, they will create a foo.chkexe file. + This prevents the test from executing again until the test or + main library changes. + All files generated by tests (*.chkexe, *.log, and any *.h5 files + created) can be removed by invoking 'make check-clean'. + Sequential and parallel library tests can now be invoked separately. + 'make check-s' will execute only sequential tests, and 'make check-p' + will execute only parallel tests. 'make check' will still execute + all tests. + JML - 2005/08/03 - On windows, all.zip is deprecated. users should read INSTALL_Windows.txt to know the details. Reasons to deprecate all.zip: - 1. Avoid confliction for windows programmers + 1. Avoid confliction for windows programmers 2. Decrease size of CVS tree by adding all.zip - 3. Avoid using winzip as the intermediate step + 3. Avoid using winzip as the intermediate step --KY 2005/04/22 - - When HDF5 is created as a shared library, it now uses libtool's - shared library versioning scheme. -JML 2005/04/18 - - HDF5 now uses automake 1.9.5 to generate Makefiles.in. - This has a number of effects on users: - The Fortran compiler should be set using the environment - variable $FC, not $F9X. F9X still works, but is depreciated. - The output of make may be different. This should be only a - cosmetic effect. - make depened (or make dep) is no longer recognized, since automake - handles dependency tracking. - Some new configure options exist. --enable-dependency-tracking - and --disable-dependency-tracking are used to control automake's - dependency tracking. Dependencies are on by default *on most - platforms and compilers*. If --enable-dependency-tracking is - used, they will be enabled on any platform. However, this can - slow down builds or even cause build errors in some cases. - Likewise, --disable-dependency-tracking can speed up builds and - avoid some build errors. - Some make targets have alternate names. make check-install and - make installcheck do the same thing, for instance. - pmake on IRIX can be invoked from the root directory, but the - -V flag must be used to invoke it in any subdirectory or it - will give an error about undefined variables. - JML 2005/01 - 2005/03 - - Hardware conversion between long double and integers is also added. - SLU 2005/02/10 - - Started to support software conversion between long double and - integers. Hardware conversion will come very soon. SLU - 2005/1/6 - - Intel v8.0 compiler would infinite loop when compiling some test - code with -O3 option. Changed enable-production default compiler - option to -O2. AKC - 2004/12/06 - - Long double is assumed to be a supported C data type. It is a - stanadard C89 type. AKC - 2004/10/22 - - The IA64 will use ecc as the C++ compiler by default. + - When HDF5 is created as a shared library, it now uses libtool's + shared library versioning scheme. -JML 2005/04/18 + - HDF5 now uses automake 1.9.5 to generate Makefiles.in. + This has a number of effects on users: + The Fortran compiler should be set using the environment + variable $FC, not $F9X. F9X still works, but is depreciated. + The output of make may be different. This should be only a + cosmetic effect. + make depend (or make dep) is no longer recognized, since automake + handles dependency tracking. + Some new configure options exist. --enable-dependency-tracking + and --disable-dependency-tracking are used to control automake's + dependency tracking. Dependencies are on by default *on most + platforms and compilers*. If --enable-dependency-tracking is + used, they will be enabled on any platform. However, this can + slow down builds or even cause build errors in some cases. + Likewise, --disable-dependency-tracking can speed up builds and + avoid some build errors. + Some make targets have alternate names. make check-install and + make installcheck do the same thing, for instance. + pmake on IRIX can be invoked from the root directory, but the + -V flag must be used to invoke it in any subdirectory or it + will give an error about undefined variables. + JML 2005/01 - 2005/03 + - Hardware conversion between long double and integers is also added. + SLU 2005/02/10 + - Started to support software conversion between long double and + integers. Hardware conversion will come very soon. SLU - 2005/1/6 + - Intel v8.0 compiler would infinite loop when compiling some test + code with -O3 option. Changed enable-production default compiler + option to -O2. AKC - 2004/12/06 + - Long double is assumed to be a supported C data type. It is a + stanadard C89 type. AKC - 2004/10/22 + - The IA64 will use ecc as the C++ compiler by default. - Added some initial support for making valgrind/Purify (or similar memory checking products) happier by initializing buffers to zero and disabling the internal free list code. To take advantage of this, use the "--enable-using-memchecker" configure option when building the library. QAK - 2004/07/23 - Fixed the long compile time of H5detect.c when v7.x Intel Compiler - is used with optimization NOT off. AKC - 2004/05/20 - - Fixed configure setting of C++ for OSF1 platform. AKC - 2004/01/06 + is used with optimization NOT off. AKC - 2004/05/20 + - Fixed configure setting of C++ for OSF1 platform. AKC - 2004/01/06 - Prefix default is changed from /usr/local to `pwd`/hdf5. AKC - 2003/07/09 @@ -214,8 +214,8 @@ New Features be used as the "location ID". If a file ID is used, the attribute operation will occur on the root group of the file. - QAK - 2007/02/09 - - Enabled the CORE driver to read an existing file depending on - the setting of the backing_store for H5Pset_fapl_core and file + - Enabled the CORE driver to read an existing file depending on + the setting of the backing_store for H5Pset_fapl_core and file open flags. - SLU - 2006/11/30 - Added new H5Gget_info_by_idx() routine to query the information about a group according to the order within an index. @@ -273,7 +273,7 @@ New Features - Added H5Fget_intent to get the "intent" of a file (whether it was opened with read-write access or read-only. -JML 2006/8/23 - - Added Link Access Property Lists. They currently contain two + - Added Link Access Property Lists. They currently contain two properties, nlinks (H5Pget/set_nlinks) and elink_prefix (H5Pget/set_elink_prefix). nlinks controls how many soft and user-defined traversals are allowed before HDF5 assumes it has @@ -281,47 +281,47 @@ New Features The elink_prefix is a filesystem path that is prefixed to the names of any external link files opened using this LAPL. -JML 2006/8/23 - - Add H5L link APIs. Old APIs (H5Glink, H5Gmove, etc.) are still - supported but deprecated. - New APIs are: - H5Llink - create a link to an object given its ID - H5Lmove - just like H5Gmove2 - H5Lcopy - copy a link without copying the underlying object - H5Lcreate_hard - like H5Glink2 for hard links - H5Lcreate_soft - like H5Glink2 for soft links - H5Ldelete - just like H5Gunlink - H5Lget_val - just like H5Gget_linkval - H5Lget_info - gets link-specific info (like H5Gget_objinfo) - - In addition, H5Gcreate_anon, H5Tcommit_anon, and H5Dcreate_anon - no longer create links to objects; objects must be manually linked - using H5Llink or they will be deleted when the ID is closed. - - Link Creation Property Lists can be used to pass character - encoding (ASCII or UTF-8) for link names and to set the Intermediate - Group Creation Flag: - H5Pset_char_encoding, H5Pget_char_encoding - H5Pset_copy_object, H5Pget_copy_object - -JML 2006/7/5 - - Added managements of collective IO supports for chunking storage - inside parallel HDF5 - 1) Implemented One IO with collective mode for all chunks in the - application by building one MPI derived datatype accross all - chunks. - 2) Implemented the decision-making support to do collective IO inside - MPI-IO per chunk. - 3) Added the decision-making support to do one IO accross all chunks - or to do multiple IOs with each IO per chunk. - 4) Added the support to handle the case some processes won't do any IOs in - collectively. - 5) Some MPI-IO package(mpich 1.2.6 or lower, e.g.) cannot handle - collective IO correctly for the case when some processes have no - contributions to IOs, a special macro is added to change - collective IO mode to independent IO mode inside HDF5 library. - - Currently we find that MPICH at Linux and vender MPI-IO package at NCSA - Altix cannot handle this case. - + - Add H5L link APIs. Old APIs (H5Glink, H5Gmove, etc.) are still + supported but deprecated. + New APIs are: + H5Llink - create a link to an object given its ID + H5Lmove - just like H5Gmove2 + H5Lcopy - copy a link without copying the underlying object + H5Lcreate_hard - like H5Glink2 for hard links + H5Lcreate_soft - like H5Glink2 for soft links + H5Ldelete - just like H5Gunlink + H5Lget_val - just like H5Gget_linkval + H5Lget_info - gets link-specific info (like H5Gget_objinfo) + + In addition, H5Gcreate_anon, H5Tcommit_anon, and H5Dcreate_anon + no longer create links to objects; objects must be manually linked + using H5Llink or they will be deleted when the ID is closed. + + Link Creation Property Lists can be used to pass character + encoding (ASCII or UTF-8) for link names and to set the Intermediate + Group Creation Flag: + H5Pset_char_encoding, H5Pget_char_encoding + H5Pset_copy_object, H5Pget_copy_object + -JML 2006/7/5 + - Added managements of collective IO supports for chunking storage + inside parallel HDF5 + 1) Implemented One IO with collective mode for all chunks in the + application by building one MPI derived datatype across all + chunks. + 2) Implemented the decision-making support to do collective IO inside + MPI-IO per chunk. + 3) Added the decision-making support to do one IO across all chunks + or to do multiple IOs with each IO per chunk. + 4) Added the support to handle the case some processes won't do any IOs in + collectively. + 5) Some MPI-IO package(mpich 1.2.6 or lower, e.g.) cannot handle + collective IO correctly for the case when some processes have no + contributions to IOs, a special macro is added to change + collective IO mode to independent IO mode inside HDF5 library. + + Currently we find that MPICH at Linux and vendor MPI-IO package at NCSA + Altix cannot handle this case. + "hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works='no'}" has been added at the end of file <ia64-linux-gnui> and <linux-gnulibc1>. @@ -329,30 +329,30 @@ New Features If MPI-IO packages at your Linux and Altix support this case, please comment out the last line and report to us at help@hdfgroup.org. We can tune in our configuration to - support this. - + support this. + KY - 2006/02/16 - - Added character encoding to attribute creation property lists. + - Added character encoding to attribute creation property lists. JML - 2006/01/02 - - Added H5Gcopy() routine to copy objects between while keeping - data in compressed form. QAK - 2005/11/06 - - Added H5Sextent_equal() routine. QAK - 2005/11/06 - - Added HSYS_ERROR which retrieves the system error message and pushes - it to the error stack. This gives more information of the failed - system call. AKC - 2005/08/04 - - Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to - allow querying for objects in file that were opened with a particular - file ID, instead of all objects opened in file with any file ID. - QAK - 2005/06/01 - - Added H5T_CSET_UTF8 character set to mark datatypes that use the - UTF-8 Unicode character encoding. Added tests to ensure that - library handles UTF-8 object names, attributes, etc. -JL 2005/05/13 - - HDF5 supports collective MPI-IO for irregular selection with HDF5 - dataset. Irregular selection is when users use H5Sselect_hyperslab - more than once for the same dataset. - Currently, not all MPI-IO packages support complicated MPI derived + - Added H5Gcopy() routine to copy objects between while keeping + data in compressed form. QAK - 2005/11/06 + - Added H5Sextent_equal() routine. QAK - 2005/11/06 + - Added HSYS_ERROR which retrieves the system error message and pushes + it to the error stack. This gives more information of the failed + system call. AKC - 2005/08/04 + - Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to + allow querying for objects in file that were opened with a particular + file ID, instead of all objects opened in file with any file ID. + QAK - 2005/06/01 + - Added H5T_CSET_UTF8 character set to mark datatypes that use the + UTF-8 Unicode character encoding. Added tests to ensure that + library handles UTF-8 object names, attributes, etc. -JL 2005/05/13 + - HDF5 supports collective MPI-IO for irregular selection with HDF5 + dataset. Irregular selection is when users use H5Sselect_hyperslab + more than once for the same dataset. + Currently, not all MPI-IO packages support complicated MPI derived datatype used in the implementation of irregular - selection INSIDE HDF5. + selection INSIDE HDF5. 1) DEC 5.x is not supporting complicated derived datatype. 2) For AIX 5.1, if your poe version number is 3.2.0.19 or lower, @@ -362,57 +362,57 @@ New Features and UNCOMMENT this line before the configure. check poe version with the following command: lpp -l all | grep ppe.poe - 3) For Linux cluster, + 3) For Linux cluster, if mpich version is 1.2.5 or lower, collective irregular selection IO is not supported, internally independent IO is used. 4) For IRIX 6.5, if C compiler version is 7.3 or lower, collective irregular selection IO is not supported, internally independent IO is used. 5) For platforms which internally used mpich, if the - mpich version is 1.2.5 or lower, please find the + mpich version is 1.2.5 or lower, please find the corresponding config file and add hdf5_mpi_complex_derived_datatype_works='no' at the end of the configuration file. For example, at NCSA - SGI Altix, the internal mpich library is 1.2.5. So + SGI Altix, the internal mpich library is 1.2.5. So hdf5_mpi_complex_derived_datatype_works='no' should be added at the end of the config file ia64-linux-gnu. KY - 2005/09/12 - We also found not all MPI-IO packages support collective IO with one + We also found not all MPI-IO packages support collective IO with one or more processes to have no contributions to IO. - For mpich version 1.2.6 or lower and all IRIX machine, + For mpich version 1.2.6 or lower and all IRIX machine, if the library checks that there are no IO contributions for some processes, collective IO request is replaced with independent inside HDF5. KY - 2006/05/04 - - - HDF5 N-bit filter - HDF5 support N-bit filter from this version, - The N-Bit filter is used effectively for compressing data of N-Bit - datatype as well as compound and array datatype with N-Bit fields. - KY - 2005/04/15 + + - HDF5 N-bit filter + HDF5 support N-bit filter from this version, + The N-Bit filter is used effectively for compressing data of N-Bit + datatype as well as compound and array datatype with N-Bit fields. + KY - 2005/04/15 - HDF5 scaleoffset filter - HDF5 supports scaleoffset filter for users to do data - compression through HDF5 library. - Scale-Offset compression performs a scale and/or offset operation - on each data value and truncates the resulting value to a minimum - number of bits and then stores the data. - Scaleoffset filter supports floating-point and integer datatype. - Please check the HDF5 reference manual for this. - KY - 2005/06/06 + HDF5 supports scaleoffset filter for users to do data + compression through HDF5 library. + Scale-Offset compression performs a scale and/or offset operation + on each data value and truncates the resulting value to a minimum + number of bits and then stores the data. + Scaleoffset filter supports floating-point and integer datatype. + Please check the HDF5 reference manual for this. + KY - 2005/06/06 - Retired SRB vfd (--with-srb). Functions H5Pset_fapl_srb and - H5Pget_fapl_srb were removed. EIP - 2005/04/07 - - Retired GASS vfd (--with-gass). Functions H5Pset_fapl_gass and - H5Pget_fapl_gass are removed too. AKC - 2005/3/3 + H5Pget_fapl_srb were removed. EIP - 2005/04/07 + - Retired GASS vfd (--with-gass). Functions H5Pset_fapl_gass and + H5Pget_fapl_gass are removed too. AKC - 2005/3/3 - Pablo was removed from the source code EIP - 2005/01/21 - Modified registration of SZIP to dynamically detect the presence or absence of the encoder. Changed configure and Makefiles, and tests to dynamically detect encoder. BEM - 2004/11/02 - - Added function H5Pget_data_transform, together with the previously - added H5Pset_data_transform, to support the data transform - feature. AKC - 2004/10/26 - - Compound datatype has been enhanced with a new feature of size + - Added function H5Pget_data_transform, together with the previously + added H5Pset_data_transform, to support the data transform + feature. AKC - 2004/10/26 + - Compound datatype has been enhanced with a new feature of size adjustment. The size can be increased and decreased(without - cutting the last member) as long as it doesn't go down to zero. + cutting the last member) as long as it doesn't go down to zero. No API change is involved. SLU - 2004/10/1 - Put back 6 old error API functions to be backward compatible with version 1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, @@ -421,14 +421,14 @@ New Features H5Eclear_stack, H5Eset_auto_stack, H5Eget_auto_stack. SLU - 2004/9/2 - 4 new API functions, H5Tencode, H5Tdecode, H5Sencode, H5Sdecode were - added to the library. Given object ID, these functions encode and - decode HDF5 objects(data type and space) information into and from + added to the library. Given object ID, these functions encode and + decode HDF5 objects(data type and space) information into and from binary buffer. SLU - 2004/07/21 - - Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for + - Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for SZIP compression. Now there is no restriction on the size and shape of the - chunk except that the total number of elements in the chunk cannot be - bigger than 'pixels_per_block' parameter provided by the user. - EIP - 2004/07/21 + chunk except that the total number of elements in the chunk cannot be + bigger than 'pixels_per_block' parameter provided by the user. + EIP - 2004/07/21 - Added support for SZIP without encoder. Added H5Zget_filter_info and changed H5Pget_filter and H5Pget_filter_by_id to support this change. JL/NF - 2004/06/30 @@ -442,20 +442,20 @@ New Features - Added support for user defined identifier types. NF/JL - 2004/06/29 - A new API function H5Fget_filesize was added. It returns the actual file size of the opened file. SLU - 2004/06/24 - - New Feature of Data transformation is added. AKC - 2004/05/03. - - New exception handler for datatype conversion is put in to + - New Feature of Data transformation is added. AKC - 2004/05/03. + - New exception handler for datatype conversion is put in to replace the old overflow callback function. This exception handler is set through H5Pset_type_conv_cb function. SLU - 2004/4/27 - Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2, - will suppress all library version mismatch warning messages. - AKC - 2004/4/14 - - A new type of dataspace, null dataspace(dataspace without any + will suppress all library version mismatch warning messages. + AKC - 2004/4/14 + - A new type of dataspace, null dataspace(dataspace without any element) was added. SLU - 2004/3/24 - Data type conversion(software) from integer to float was added. - SLU - 2004/3/13 + SLU - 2004/3/13 - Data type conversion(software) from float to integer was added. - Conversion from integer to float will be added later. + Conversion from integer to float will be added later. SLU -2004/2/4 - Added new H5Premove_filter routine to remove I/O pipeline filters from dataset creation property lists. PVN - 2004/01/26 @@ -469,7 +469,7 @@ New Features object's object header. QAK 2003/10/06 - Added new H5Fget_freespace() routine to query the free space in a given file. QAK 2003/10/06 - - Added backward compatability with v1.6 for new Error API. SLU - + - Added backward compatibility with v1.6 for new Error API. SLU - 2003/09/24 - Changed 'objno' field in H5G_stat_t structure from 'unsigned long[2]' to 'haddr_t'. QAK - 2003/08/08 @@ -484,39 +484,39 @@ New Features Parallel Library: ----------------- - - Added mpich2 as a testing "platform" informally. AKC - 2005/9/28. - - A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation - setting was not extendible, either explicitly by H5Dextend or - implicitly by writing to unallocated chunks. Library now allocates - more space when needed or directed if the file is opened by parallel - mode, independent of what the dataset allocation mode is. - CC/AKC - 2005/08/29. + - Added mpich2 as a testing "platform" informally. AKC - 2005/9/28. + - A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation + setting was not extendible, either explicitly by H5Dextend or + implicitly by writing to unallocated chunks. Library now allocates + more space when needed or directed if the file is opened by parallel + mode, independent of what the dataset allocation mode is. + CC/AKC - 2005/08/29. - Allow compressed, chunked datasets to be read in parallel. QAK - 2004/10/04 - Add options of using atomicity and file-sync to test_mpio_1wMr. AKC - 2003/11/13 - Added parallel test, test_mpio_1wMr, which tests if the - underlaying parallel I/O system is conforming to the POSIX + underlying parallel I/O system is conforming to the POSIX write/read requirement. AKC - 2003/11/12 Fortran Library: ---------------- - added support for shared Fortran libraries. -JML 2005/09/20 - added missing h5tget_member_class_f function - EIP 2005/04/06 - - added new functions h5fget_name_f and h5fget_filesize_f + EIP 2005/04/06 + - added new functions h5fget_name_f and h5fget_filesize_f EIP 2004/07/08 - h5dwrite/read_f and h5awrite/read_f functions only accept dims parameter - of the type INTEGER(HSIZE_T). + of the type INTEGER(HSIZE_T). - added support for native integers of 8 bytes (i.e. when special - compiler flag is specified to set native fortran integers to 8 bytes, - for example, -i8 flag for PGI and Absoft Fortran compilers, - -qintsize=8 flag for IBM xlf compiler). + compiler flag is specified to set native fortran integers to 8 bytes, + for example, -i8 flag for PGI and Absoft Fortran compilers, + -qintsize=8 flag for IBM xlf compiler). EIP 2005/06/20 - added support for "big" REAL and DOUBLE PRECISION types - (usually the size is specified by compilers flags like - -r8, -r16, etc.) - Known problem: multi file test fails when REAL is 16 bytes. + (usually the size is specified by compilers flags like + -r8, -r16, etc.) + Known problem: multi file test fails when REAL is 16 bytes. EIP 2005/09/8 C++ Library: @@ -539,41 +539,41 @@ New Features Tools: ------ - h5repack and h5diff changed command line parameter syntax to be - similar to h5dump, adding also long switch names. PVN - 2008/1/16 - - h5repack now supports adding multiple filters to all objects. - PVN - 2008/1/16 - - h5dump lists groups and attributes in requested orders (by name and - creation order, both ascending and descending). PVN - 2007/10/5 + similar to h5dump, adding also long switch names. PVN - 2008/1/16 + - h5repack now supports adding multiple filters to all objects. + PVN - 2008/1/16 + - h5dump lists groups and attributes in requested orders (by name and + creation order, both ascending and descending). PVN - 2007/10/5 - h5import imports string (text) data. PVN - 2007/10/5 - h52gif and gif2h5: Both these tools were revised to include the High - Level Image API support, and tests were added to /hl/tools/gif2h5. - PVN - 2007/04/13 + Level Image API support, and tests were added to /hl/tools/gif2h5. + PVN - 2007/04/13 - h5dump: added support for double long type H5T_NATIVE_LDOUBLE. PVN - 2007/03/13 + 2007/03/13 - h5dump: added support for binary output, see usage. PVN 2007/03/13 - h5repack: added support for the new nbit and scaleoffset filters. - PVN - 2007/05/07 + PVN - 2007/05/07 - h5repack: now uses the API function H5Ocopy (of the tool h5copy) to - recreate objects if there is not a user input for changes. PVN - - 2007/05/07 + recreate objects if there is not a user input for changes. PVN - + 2007/05/07 - h5repack: added support for reading and repacking by hyperslabs for - large files. PVN - 2007/03/01 + large files. PVN - 2007/03/01 - h5repack: a new option allows the copy using the file type (default) - instead of the previous conversion to native type. PVN - 2007/03/01 + instead of the previous conversion to native type. PVN - 2007/03/01 - h5repack: output the percentage of compression used. PVN - 2007/03/01 - h5diff: added support for -p option for unsigned long_long data. PVN - - 2007/02/26 + 2007/02/26 - h5diff: added support for comparing dataset regions. PVN - 2007/02/20 - h5diff: added support for reading and comparing by hyperslabs for large files. - PVN - 2007/02/20 + PVN - 2007/02/20 - h5diff: printing of dataset dimensions along with dataset name. PVN -2007/02/19 - h5dump now uses the new API function H5Rget_name to display the name - of the dataset referenced instead of its ID. PVN - 2007/02/19 + of the dataset referenced instead of its ID. PVN - 2007/02/19 - Added new tool, h5mkgrp. QAK - 2007/02/14 - Added new tool, h5copy. PVN - 2006/7/15 - - Removed obsolete pdb2hdf5 tool from tools/misc -JML 2005/10/24 - - Added build_h5perf_alone.sh that builds h5perf by standalone mode. - AKC - 2005/09/18. + - Removed obsolete pdb2hdf5 tool from tools/misc -JML 2005/10/24 + - Added build_h5perf_alone.sh that builds h5perf by standalone mode. + AKC - 2005/09/18. - Sped up h5dump on files with large numbers of objects. QAK - 2005/08/25 - Added a standalone mode for building h5perf. AKC - 2005/08/12 @@ -584,8 +584,8 @@ New Features available for h5dump and h5ls. RPM & QAK - 2004/02/01 - Added option --vfd= to h5ls to allow a VFL driver to be selected by a user. RPM & QAK - 2004/02/01 - - Added option -showconfig to compiler tools (h5cc,h5fc,h5c++). - AKC - 2004/01/08 + - Added option -showconfig to compiler tools (h5cc,h5fc,h5c++). + AKC - 2004/01/08 - Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc" respectively if library is built in parallel mode. WCW - 2003/11/04 @@ -601,25 +601,25 @@ New Features ------ - Fortran interfaces for the Image, Table and Lite APIs. PVN - 2007/5/1 - New HDF5 Dimension Scale API (H5DS) allows dimension scales to be - created in an HDF5 file and associated with specific datasets. PVN - 2007/5/1 + created in an HDF5 file and associated with specific datasets. PVN - 2007/5/1 - There are two new functions in the Lite library, H5LTtext_to_dtype and H5LTdtype_to_text. H5LTtext_to_dtype creates a HDF5 data type given a text description; H5LTdtype_to_text converts a data type - to text description. Only DDL definition is supported as text - desciption now. SLU - 2006/05/17 + to text description. Only DDL definition is supported as text + description now. SLU - 2006/05/17 - Added Packet Table API for creating tables with less overhead than H5TB API. Added C++ wrapper for Packet Tables. See documentation. JML - 2004/03/28 - - Documentation - ------------- - - The documentation for this release is largely complete, but - trails the source code. A few of the newer functions are + + Documentation + ------------- + - The documentation for this release is largely complete, but + trails the source code. A few of the newer functions are not yet documented. FMB - 2007/04/18 - The user documents for this release can be accessed directly at this location: http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ - The most recent document versions (updated daily) in the + The most recent document versions (updated daily) in the 1.8 development branch can be accessed at this location: http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/ FMB - 2007/04/18 @@ -628,19 +628,19 @@ New Features Support for new platforms, languages and compilers. ======================================= - Added support for Free-BSD on amd64 with GNU C and Fortran compilers - 4.2.1 + 4.2.1 EIP - 2007/06/25 - Added support for sequential and parallel libraries for Intel 64 Linux - cluster (abe.ncsa.uiuc.edu). Among three MPICH packages available on - this machine, only Open MPI works. The VMI has seg fault in hyperslab.c - and bittests.c tests. The MVAPICH2 complained about mpd not running - the parallel test. (see Known Problems section for more info) + cluster (abe.ncsa.uiuc.edu). Among three MPICH packages available on + this machine, only Open MPI works. The VMI has seg fault in hyperslab.c + and bittests.c tests. The MVAPICH2 complained about mpd not running + the parallel test. (see Known Problems section for more info) EIP - 2007/06/25 - Added support for HPUX11.23 for both 32 and 64-bit; HDF5 C++ - Added support for 64-bit Windows with Visual Studio .NET and 2005. SJW - 2007/06/25 - - Added suport for HPUX11.23 for both 32 and 64-bit; HDF5 C++ - shared library is not supported with +DD64 flag. + - Added support for HPUX11.23 for both 32 and 64-bit; HDF5 C++ + shared library is not supported with +DD64 flag. EIP - 2006/06/22 - Added support for VAX floating numbers for Alpha Open VMS 7.3.2 EIP - 2006/05/05 @@ -655,7 +655,7 @@ Support for new platforms, languages and compilers. - HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran compiler version 8.1. This is a default compiler. - HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler - version 8.2; set F9X environment varibale to f95, for example + version 8.2; set F9X environment variable to f95, for example setenv F9X f95 Use --disable-shared --enable-static configure flags when Absoft compiler is used. @@ -700,7 +700,7 @@ Bug Fixes since HDF5-1.6.0 release - Re-open the file - Delete one of the attributes on the object - Add a smaller attribute to the object - - Delete the smaller atttribute on the object + - Delete the smaller attribute on the object - Add a larger attribute on the object After this, the number of header messages stored for the object @@ -746,9 +746,9 @@ Bug Fixes since HDF5-1.6.0 release - Fixed bug where unmounted files could cause the library to go into an infinite loop when shutting down. QAK - 2005/06/30 - The library didn't save the information of family driver in file. - The original file member size was lost after file was closed (see - bug #213). This has been fixed by saving driver name and member - file size in the superblock. SLU - 2005/6/24 + The original file member size was lost after file was closed (see + bug #213). This has been fixed by saving driver name and member + file size in the superblock. SLU - 2005/6/24 - Fixed bug with hyperslab selections that use selection offsets and operate on chunked datasets going into infinite loop or dumping core. QAK - 2005/06/17 @@ -762,22 +762,22 @@ Bug Fixes since HDF5-1.6.0 release particular file ID being closed, instead of operating on all open file IDs for a given file. QAK - 2005/06/01 - For family driver, the library didn't save member size in file. - When file is reopened, the size of 1st member file determine the - member size. Now member size is saved in file and is used to - define member file size. Wrong file access property of member size - will result in a failure. Using any other driver except family - will cause library to return error. So is multi driver. SLU - - 2005/05/24 + When file is reopened, the size of 1st member file determine the + member size. Now member size is saved in file and is used to + define member file size. Wrong file access property of member size + will result in a failure. Using any other driver except family + will cause library to return error. So is multi driver. SLU - + 2005/05/24 - Fixed error in opening object in group that was opened in mounted - file which has been unmounted. QAK - 2005/03/17 + file which has been unmounted. QAK - 2005/03/17 - Fixed a racing condition in MPIPOSIX virtual file drive close - function. Now all processes must completed the close before any - of them is returned. This prevents some "faster" processes start - accessing the file for another purpose (e.g., open with truncate) - while other "slower" processes have not closed the same file with - the previous purpose. AKC - 2005/03/01 - - H5Tget_member_value calls for enum datatype didn't return correct - value if H5Tenum_valueof was called first. It's fixed. SLU - + function. Now all processes must completed the close before any + of them is returned. This prevents some "faster" processes start + accessing the file for another purpose (e.g., open with truncate) + while other "slower" processes have not closed the same file with + the previous purpose. AKC - 2005/03/01 + - H5Tget_member_value calls for enum datatype didn't return correct + value if H5Tenum_valueof was called first. It's fixed. SLU - 2005/02/08 - For variable-length string, H5Tget_class returned H5T_STRING as its class. But H5Tdetect_class and H5Tget_member_class considered it @@ -785,24 +785,24 @@ Bug Fixes since HDF5-1.6.0 release as H5T_STRING. SLU - 2005/02/08 - The byte order of 1-byte integer types was fixed as little endian even on a big-endian machine. This has been corrected. SLU - - 2005/02/07 + 2005/02/07 - Fix segmentation fault when calling H5Fflush with an attribute that hasn't had a value written to it open. QAK - 2004/10/18 - - Back up supporting bitfield and time types in H5Tget_native_type. - Leave it to future support. The function simply returns error - message of "not support" for bitfield and time types. + - Back up supporting bitfield and time types in H5Tget_native_type. + Leave it to future support. The function simply returns error + message of "not support" for bitfield and time types. SLU - 2004/10/5 - Fixed address check in Core VFL driver to avoid spurious address/size overflows for odd valued addresses and/or sizes. QAK - 2004/09/27 - - Fixed parallel bug in which some processes attempted collective - I/O while others did independent I/O. Bug appeared when some - processes used point selections, and others didn't. JRM - 2004/9/15 + - Fixed parallel bug in which some processes attempted collective + I/O while others did independent I/O. Bug appeared when some + processes used point selections, and others didn't. JRM - 2004/9/15 - Corrected error where dataset region references were written in an incorrect way on Cray machines. PVN & QAK - 2004/09/13 - - The H5Tget_native_type now determines the native type for integers - based on the precision. This is to avoid cases of wrongly converting - an int to a short in machines that have a short of 8 bytes but with - 32bit precision (e.g Cray SV1). PVN - 2004/09/07 + - The H5Tget_native_type now determines the native type for integers + based on the precision. This is to avoid cases of wrongly converting + an int to a short in machines that have a short of 8 bytes but with + 32bit precision (e.g Cray SV1). PVN - 2004/09/07 - Changed H5Dread() to not overwrite data in an application's buffer with garbage when accessing a chunked dataset with an undefined fill value and an unwritten chunk is uncountered. QAK - 2004/08/25 @@ -844,18 +844,18 @@ Bug Fixes since HDF5-1.6.0 release variable-length string as field. SLU - 2004/06/10 - Fixed potential file corruption bug when a block of metadata could overlap the end of the internal metadata accumulator buffer and - the buffer would be extended correctly, but would incorrectly + the buffer would be extended correctly, but would incorrectly change it's starting address. QAK - 2004/06/09 - Opaque datatype with no tag failed for some operations. Fixed. - SLU - 2004/6/3 + SLU - 2004/6/3 - Fixed potential file corruption bug where dimensions that were too large (a value greater than could be represented in 32-bits) could cause the incorrect amount of space to be allocated in a file for the raw data for the dataset. QAK - 2004/06/01 - - Fixed dtypes "sw long double -> double" failure in QSC class + - Fixed dtypes "sw long double -> double" failure in QSC class machines. AKC - 2004/4/16 - Fixed problem with fletcher32 filter when converting data of different - endianess. PVN - 2004/03/10 + endianness. PVN - 2004/03/10 - Fixed problem with H5Tget_native_type() not handling opaque fields correctly. QAK - 2004/01/31 - Fixed several errors in B-tree deletion code which could cause a @@ -903,7 +903,7 @@ Bug Fixes since HDF5-1.6.0 release but were interspersed with dimensions that could not be flattened were not correctly handled, causing core dumps. QAK - 2003/10/25 - Fixed incorrect datatype of the third parameter to the Fortran90 - h5pset(get)_cache_f subroutine (INTEGER to INTEGER(SIZE_T)) + h5pset(get)_cache_f subroutine (INTEGER to INTEGER(SIZE_T)) EIP - 2003/10/13 - Fixed problems with accessing variable-length data datatypes on Crays. QAK - 2003/10/10 @@ -970,8 +970,8 @@ Bug Fixes since HDF5-1.6.0 release Configuration ------------- - - Configure can now use any tr command. No more need for - defining variable TR nor is it supported. -AKC 2006/05/19 + - Configure can now use any tr command. No more need for + defining variable TR nor is it supported. -AKC 2006/05/19 - Parallel I/O with the MPI-I/O driver will no longer work if the filesystem is not POSIX compliant. The "HDF5_MPI_1_METAWRITE" environment variable has been removed. QAK - 2004/01/30 @@ -991,27 +991,27 @@ Bug Fixes since HDF5-1.6.0 release Tools ----- - Fixed h5dump regarding the display of blocks in hyperslab - selections. PVN 2008/01/16 + selections. PVN 2008/01/16 - Fixed h5diff regarding the display of NaN (Not a Number) - values. PVN 2008/01/16 - - Fixed h5dump regarding the parsing of binary output parameters. - PVN 2008/01/16 - - Fixed memory problems in h52gif and gif2h5. PVN 2008/01/16 - - Fixed h5repack dealing with NULL references. PVN 2008/01/16 + values. PVN 2008/01/16 + - Fixed h5dump regarding the parsing of binary output parameters. + PVN 2008/01/16 + - Fixed memory problems in h52gif and gif2h5. PVN 2008/01/16 + - Fixed h5repack dealing with NULL references. PVN 2008/01/16 - Fixed h5dump & h5ls to display attributes in "name" order, rather - than the order they are encountered in the object header. - QAK - 2007/10/04 + than the order they are encountered in the object header. + QAK - 2007/10/04 - Fixed h5dump regarding the display of named datatypes - attributes. PVN 2007/03/13 + attributes. PVN 2007/03/13 - Fixed h5dump regarding the display of group comments. PVN - 2007/03/13 - - Fixed h5dump regarding the display of hardlinks pointing - to the root group. PVN 2007/03/13 + 2007/03/13 + - Fixed h5dump regarding the display of hardlinks pointing + to the root group. PVN 2007/03/13 - Fixed h5diff percentage option -p. PVN 2007/03/05 - Fixed h5dump that caused array indices greater than 2 ^32-1 - not to be printed correctly - PVN 2007/2/19 + not to be printed correctly - PVN 2007/2/19 - Fixed h5dump to print attributes data in ASCII if -r option is used. - AKC - 2004/11/18 + AKC - 2004/11/18 - Fixed space utilization reported in h5ls to correct error in formula used. QAK - 2004/10/22 - Fixed h5redeploy which sometimes complain too many argument for the @@ -1023,14 +1023,14 @@ Bug Fixes since HDF5-1.6.0 release H5Tget_native_type() internally. QAK - 2003/08/25 - Documentation - ------------- + Documentation + ------------- F90 APIs -------- - h5pget_driver_f was returning information that could not be - interpreted by fortran application program; fixed. EIP - 2005/04/10 + interpreted by fortran application program; fixed. EIP - 2005/04/10 Platforms Tested @@ -1041,7 +1041,7 @@ Platforms marked with * were not tested for hdf5-1.8.0-rc* release * AIX 5.2 (32/64 bit) xlc 8.0.0.11 xlC 8.0 - xlf 10.01.0000.0 + xlf 10.01.0000.0 mpcc_r 6.0.0.8 mpxlf_r 8.1.1.7 * AIX 5.3 (32/64 bit) xlc 7.0.0.8 @@ -1065,9 +1065,9 @@ Platforms marked with * were not tested for hdf5-1.8.0-rc* release HP F90 v2.9.2 HP aC++/ANSI C B3910B A.06.00 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m - F90 MIPSpro 7.4.4m + F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m - + * Linux 2.6.9 (RHEL4) Intel 10.0 compilers (abe.ncsa.uiuc.edu) Linux 2.4.21-47 gcc 3.2.3 20030502 @@ -1077,10 +1077,10 @@ Platforms marked with * were not tested for hdf5-1.8.0-rc* release Intel 9.1 (icc, ifort, icpc) Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, g95 (GCC 4.0.3) (smirom) PGI 6.2-5 (pgcc, pgf90, pgCC) - Intel 9.1 (icc, iort, icpc) - Linux 2.6.5-7.252.1-rtgfx #1 + Intel 9.1 (icc, iort, icpc) + Linux 2.6.5-7.252.1-rtgfx #1 SMP ia64 Intel(R) C++ Version 9.0 - (cobalt) Intel(R) Fortran Itanium(R) Version 9.0 + (cobalt) Intel(R) Fortran Itanium(R) Version 9.0 SGI MPI SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 @@ -1088,29 +1088,29 @@ Platforms marked with * were not tested for hdf5-1.8.0-rc* release * SunOS 5.10 i86pc Sun C 5.7 Sun Fortran 95 8.1 Sun C++ 5.7 - SunOS 5.10 cc: Sun C 5.8 - (linew) f90: Sun Fortran 95 8.2 - CC: Sun C++ 5.8 + SunOS 5.10 cc: Sun C 5.8 + (linew) f90: Sun Fortran 95 8.2 + CC: Sun C++ 5.8 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre - (tungsten) gcc 3.2.2 20030222 + (tungsten) gcc 3.2.2 20030222 Intel(R) C++ Version 9.0 Intel(R) Fortran Compiler Version 9.0 IA-64 Linux 2.4.21.SuSE_292.til1 ia64 (NCSA tg-login) gcc 3.2.2 Intel(R) C++ Version 8.1 Intel(R) Fortran Compiler Version 8.1 - mpich-gm-1.2.5..10-intel-r2 - Windows XP - Visual Studio .NET + mpich-gm-1.2.5..10-intel-r2 + Windows XP + Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) - MinGW(native gcc compiler and g95) - Windows XP x64 - Visual Studio 2005 w/ Intel Fortran 9.1 - Windows Vista - Visual Studio 2005 + MinGW(native gcc compiler and g95) + Windows XP x64 + Visual Studio 2005 w/ Intel Fortran 9.1 + Windows Vista + Visual Studio 2005 - MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 + MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) * Alpha Open VMS 7.3 @@ -1125,7 +1125,7 @@ Supported Configuration Features Summary x = not working in this release dna = does not apply ( ) = footnote appears below second table - <blank> = testing incomplete on this feature or platform + <blank> = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel @@ -1149,57 +1149,57 @@ RedHat EL3 W PGI (3) n y n y y n SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y SuSe x86_64 Int (3,12) n y(13) n y y n SuSe x86_64 PGI (3,12) n y(8) n y y y -Linux 2.4 Xeon C +Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y n -Linux 2.6 SuSE ia64 C +Linux 2.6 SuSE ia64 C Intel (3,7) y y y y y n -Linux 2.6 SGI Altix +Linux 2.6 SGI Altix ia64 Intel (3) y y y y y y Alpha OpenVMS 7.3.2 n y n y n n -Platform Shared Shared Shared static- Thread- - C libs F90 libs C++ libs exec safe -Solaris2.8 64-bit y y y x y -Solaris2.8 32-bit y y y x y -Solaris2.10 64-bit y x y -Solaris2.10 32-bit y x y -IRIX64_6.5 64-bit y y n y y -IRIX64_6.5 32-bit y dna y y y -HPUX11.00 y n y x n -HPUX11.23-32bit y n n y n -HPUX11.23-64bit y dna n y n -Cray XT3 (16) n n n n n -AIX-5.2 & 5.3 32-bit n n n y n -AIX-5.2 & 5.3 64-bit n n n y n -Windows XP y y(15) y y y -Windows XP x64 y y(15) y y y -Windows Vista y n n y y -Mac OS X 10.3 y y n +Platform Shared Shared Shared static- Thread- + C libs F90 libs C++ libs exec safe +Solaris2.8 64-bit y y y x y +Solaris2.8 32-bit y y y x y +Solaris2.10 64-bit y x y +Solaris2.10 32-bit y x y +IRIX64_6.5 64-bit y y n y y +IRIX64_6.5 32-bit y dna y y y +HPUX11.00 y n y x n +HPUX11.23-32bit y n n y n +HPUX11.23-64bit y dna n y n +Cray XT3 (16) n n n n n +AIX-5.2 & 5.3 32-bit n n n y n +AIX-5.2 & 5.3 64-bit n n n y n +Windows XP y y(15) y y y +Windows XP x64 y y(15) y y y +Windows Vista y n n y y +Mac OS X 10.3 y y n Mac OS X 10.4 PowerPC -FreeBSD 4.11 y n y y y -RedHat EL3 W (3) y y(10) y y y -RedHat EL3 W Intel (3) y y y y n -RedHat EL3 W PGI (3) y y y y n -SuSe x86_64 W GNU (3,12) y y y y y -SuSe x86_64 W Int (3,12) y y y y(14) n -SuSe x86_64 W PGI (3,12) y y y y(14) n -Linux 2.4 Xeon C - Lustre Intel (6) y y y y n -Linux 2.4 SuSE - ia64 C Intel (7) y y y y n -Linux 2.4 SGI Altix - ia64 Intel y y n -Alpha OpenVMS 7.3.2 n n n y n +FreeBSD 4.11 y n y y y +RedHat EL3 W (3) y y(10) y y y +RedHat EL3 W Intel (3) y y y y n +RedHat EL3 W PGI (3) y y y y n +SuSe x86_64 W GNU (3,12) y y y y y +SuSe x86_64 W Int (3,12) y y y y(14) n +SuSe x86_64 W PGI (3,12) y y y y(14) n +Linux 2.4 Xeon C + Lustre Intel (6) y y y y n +Linux 2.4 SuSE + ia64 C Intel (7) y y y y n +Linux 2.4 SGI Altix + ia64 Intel y y n +Alpha OpenVMS 7.3.2 n n n y n Notes: (1) Using mpich 1.2.6. (1a) Using mpich2 1.0.6. (2) Using mpt and mpich 1.2.6. - (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. + (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. - (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre + (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers (8) pgf90 @@ -1209,7 +1209,7 @@ Alpha OpenVMS 7.3.2 n n n y n (12) AMD Opteron x86_64 (13) ifort (14) Yes with C and Fortran, but not with C++ - (15) Using Visual Studio 2005 or Cygwin + (15) Using Visual Studio 2005 or Cygwin (16) Not tested for this release. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. @@ -1218,14 +1218,14 @@ Alpha OpenVMS 7.3.2 n n n y n Known Problems ============== -* We discovered two problems when running collective IO parallel HDF5 tests - with chunking storage on ChaMPIon MPI compiler on tungsten, a linux +* We discovered two problems when running collective IO parallel HDF5 tests + with chunking storage on ChaMPIon MPI compiler on tungsten, a linux cluster at NCSA. - Under some complex selection cases, + Under some complex selection cases, 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates wrong derived data type and corrupt data may be generated. - This only happens when turning on collective IO with chunking storage + This only happens when turning on collective IO with chunking storage with some complex selections. We haven't found these problems on other MPI-IO compilers. If you encounter these problems, you may use Independent IO instead. @@ -1241,22 +1241,22 @@ Known Problems * For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel tests failed with MPI-IO file locking message. AKC - 2007/6/25. * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use - -mp -O1 compilation flags to build the libraries. Higher level of optimization - causes failures in several HDF5 library tests. + -mp -O1 compilation flags to build the libraries. Higher level of optimization + causes failures in several HDF5 library tests. * For HPUX 11.23 many tools tests failed for 64-bit version when linked to the shared libraries (tested for 1.8.0-beta2) -* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass +* For SNL, Red Storm: only parallel HDF5 is supported. The serial tests pass and the parallel tests also pass with lots of non-fatal error messages. * For LLNL, uP: both serial and parallel pass. Zeus: serial passes but parallel fails with a known proglem in MPI. ubgl: serial passes but - parallel fails. -* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test + parallel fails. +* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test * configuring with --enable-debug=all produces compiler errors on most platforms. Users who want to run HDF5 in debug mode should use --enable-debug rather than --enable-debug=all to enable debugging information on most modules. * On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long - double to (unsigned) long long and from (unsigned)long long to long double. + double to (unsigned) long long and from (unsigned)long long to long double. * On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3 optimization flag. * On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to @@ -1270,23 +1270,23 @@ Known Problems that when using 4 processors, a simple collective write will be hung sometimes. This can be verified with t_mpi test under testpar. * On IRIX6.5, when C compiler version >7.4, the complicate MPI derived data type - code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment - variable to some certian value in order to use collective irregular selection code. - For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to + code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment + variable to some certain value in order to use collective irregular selection code. + For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to 200,000 to make the test pass. -* The dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is - enabled. There was a bug in the calculating code of the Fletcher32 - checksum in the library before v1.6.3. The checksum value wasn't consistent - between big-endian and little-endian systems. This bug was fixed in - Release 1.6.3. However, after fixing the bug, the checksum value is no - longer the same as before on little-endian system. The library release +* The dataset created or rewritten with the v1.6.3 library or after can't + be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is + enabled. There was a bug in the calculating code of the Fletcher32 + checksum in the library before v1.6.3. The checksum value wasn't consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value is no + longer the same as before on little-endian system. The library release after 1.6.4 can still read the dataset created or rewritten with the library of v1.6.2 or before. SLU - 2005/6/30 * For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron processor, there's a bug in the compiler for optimization(-O2). The library - failed in several tests but all related to multi driver. The problem has - been reported to the vendor. + failed in several tests but all related to multi driver. The problem has + been reported to the vendor. * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command poe. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages @@ -1300,7 +1300,7 @@ Known Problems to provide a mean to run poe without the debug socket. * The C++ library's tests fails when compiling with PGI C++ compiler. The - workaround until the problem is correctly handled is to use the + workaround until the problem is correctly handled is to use the flag "--instantiate=local" prior to the configure and build steps, as: setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher @@ -1318,7 +1318,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. - + It is suggested that you don't use this option on these platforms during configuration. @@ -1327,7 +1327,7 @@ Known Problems able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' - + This warning is innocuous and can be safely ignored. @@ -1347,7 +1347,7 @@ Known Problems the different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from this site: @@ -1362,7 +1362,7 @@ Known Problems * On some platforms that use Intel and Absoft compilers to build HDF5 fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line + complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) * On IA32 and IA64 systems, if you use a compiler other than GCC (such as @@ -1386,28 +1386,28 @@ Known Problems INSTALL file sections 5.7 and 5.8 * On at least one system, (SDSC DataStar), the scheduler (in this case - LoadLeveler) sends job status updates to standard error when you run + LoadLeveler) sends job status updates to standard error when you run any executable that was compiled with the parallel compilers. - This causes problems when running "make check" on parallel builds, as + This causes problems when running "make check" on parallel builds, as many of the tool tests function by saving the output from test runs, - and comparing it to an exemplar. + and comparing it to an exemplar. The best solution is to reconfigure the target system so it no longer inserts the extra text. However, this may not be practical. - In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to - the configure and build. This will cause "make check" to continue after + In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to + the configure and build. This will cause "make check" to continue after detecting errors in the tool tests. However, in the case of SDSC DataStar, it also leaves you with some 150 "failed" tests to examine by hand. A second solution is to write a script to run serial tests and filter out the text added by the scheduler. A sample script used on SDSC - DataStar is given below, but you will probably have to customize it - for your installation. + DataStar is given below, but you will probably have to customize it + for your installation. - Observe that the basic idea is to insert the script as the first item - on the command line which executes the the test. The script then + Observe that the basic idea is to insert the script as the first item + on the command line which executes the the test. The script then executes the test and filters out the offending text before passing it on. @@ -1420,20 +1420,20 @@ Known Problems ($* > $STDOUT_FILE) >& $STDERR_FILE - set RETURN_VALUE=$status + set RETURN_VALUE=$status cat $STDOUT_FILE tail +3 $STDERR_FILE - exit $RETURN_VALUE + exit $RETURN_VALUE - You get the HDF make files and test scipts to execute your filter script - by setting the environment variable "RUNSERIAL" to the full path of the - script prior to running configure for parallel builds. Remember to + You get the HDF make files and test scripts to execute your filter script + by setting the environment variable "RUNSERIAL" to the full path of the + script prior to running configure for parallel builds. Remember to "unsetenv RUNSERIAL" before running configure for a serial build. - Note that the RUNSERIAL environment variable exists so that we can + Note that the RUNSERIAL environment variable exists so that we can can prefix serial runs as necessary on the target system. On DataStar, no prefix is necessary. However on an MPICH system, the prefix might have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to @@ -1453,16 +1453,16 @@ HDF5 version 1.6.7 released on Thu Jan 31 21:09:10 CST 2008 INTRODUCTION ============ -This document describes the differences between HDF5-1.6.6 and HDF5-1.6.7 +This document describes the differences between HDF5-1.6.6 and HDF5-1.6.7 It contains information on the platforms tested and known problems in HDF5-1.6.7. For more details, check the HISTORY.txt file in the HDF5 source. HDF5 documentation can be found in the distributed release source code -in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server: +in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server: ftp://ftp.hdfgroup.org/HDF5/docs/ -Documentation for the current release in the HDF5 Release 1.6.x series is +Documentation for the current release in the HDF5 Release 1.6.x series is also on the HDF web site: http://hdfgroup.org/HDF5/doc1.6/ @@ -1492,7 +1492,7 @@ New Features ============ Configuration: ------------------------- - '--enable-stream-vfd' and '--disable-stream-vfd' are no longer valid + '--enable-stream-vfd' and '--disable-stream-vfd' are no longer valid configure options because the stream I/O driver has ben removed from the distribution. @@ -1502,12 +1502,12 @@ New Features -------- The stream I/O driver is not included with the HDF5 Library in this release. The source code files hdf5/src/H5FDstream.c and - hdf5/src/H5FDstream.h and the driver ENUM value H5FD_STREAM have been + hdf5/src/H5FDstream.h and the driver ENUM value H5FD_STREAM have been removed. Parallel Library: ----------------- - None + None Tools: ------ @@ -1533,9 +1533,9 @@ Bug Fixes since HDF5-1.6.6 Release Library ------- - - H5Iget_name could not be used with an object identifier returned - by H5Rdereference; the function would not be able to determine - a valid object name. It has been fixed. SLU - 2008/1/30 + - H5Iget_name could not be used with an object identifier returned + by H5Rdereference; the function would not be able to determine + a valid object name. It has been fixed. SLU - 2008/1/30 - Changed library's behavior for reading files that might have corrupted object header information from a previous (buggy) version of the library. By default, the library now rebuilds the @@ -1557,15 +1557,15 @@ Bug Fixes since HDF5-1.6.6 Release Performance ------------- None - + Tools ----- None - Documentation - ------------- + Documentation + ------------- None @@ -1573,7 +1573,7 @@ Bug Fixes since HDF5-1.6.6 Release ------- None - + C++ API ------- None @@ -1581,13 +1581,13 @@ Bug Fixes since HDF5-1.6.6 Release Documentation ============= - HDF5 documentation can be found in the distributed release source - code in the subdirectory doc/html/ (start with index.html) or on the - THG (The HDF Group) FTP server: + HDF5 documentation can be found in the distributed release source + code in the subdirectory doc/html/ (start with index.html) or on the + THG (The HDF Group) FTP server: ftp://ftp.hdfgroup.org/HDF5/docs/ - Online documentation for the current release in the HDF5 Release 1.6.x + Online documentation for the current release in the HDF5 Release 1.6.x series can be found on the THG web site: http://hdfgroup.org/HDF5/doc1.6/ @@ -1596,9 +1596,9 @@ Documentation in the document "HDF5 Software Changes from Release to Release": http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html - - Since the stream I/O driver is not included in this release, the - functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream + + Since the stream I/O driver is not included in this release, the + functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream ENUM value H5FD_STREAM have been removed from the documentation. @@ -1622,20 +1622,20 @@ Platforms Tested Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) April 18 2007) - (kagiso) PGI C, Fortran, C++ 7.0-7 32-bit - Intel(R) C Compiler for 32-bit - applications, Version 9.1 - Intel(R) C++ Compiler for 32-bit + (kagiso) PGI C, Fortran, C++ 7.0-7 32-bit + Intel(R) C Compiler for 32-bit + applications, Version 9.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 9.1 + Intel(R) Fortran Compiler for 32-bit applications, Version 9.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 9.1 Absoft 32-bit Fortran 95 10.0.4 - MPICH mpich2-1.0.6p1 compiled with - gcc 4.2.1 and G95 (GCC 4.0.3 (g95 0.91!) + MPICH mpich2-1.0.6p1 compiled with + gcc 4.2.1 and G95 (GCC 4.0.3 (g95 0.91!) Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025 SMP ia64 GNU/Linux Intel(R) Fortran Itanium(R) Version 10.0.025 - (ucar hir1) + (ucar hir1) Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037 SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031 @@ -1654,7 +1654,7 @@ Platforms Tested SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 Sun WorkShop 6 update 2 C++ 5.8 - Patch 121019-06 + Patch 121019-06 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre (tungsten) Intel(R) C++ Version 9.0 @@ -1724,34 +1724,34 @@ SuSE Linux 2.4 ia64 C y y y y y y SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y -Platform Shared static- Thread- - libraries(4) exec safe -Solaris2.8 32- and 64-bit y n y -Solaris2.10 32- and 64-bit y n y -IRIX64_6.5 32-bit y n y -IRIX64_6.5 64-bit y n y -WinXP Visual Studio 6.0 y n n -WinXP CYGWIN y n n -WinXP 2005 y n n -WinXP .Net y n n -WinVista 2005 y n n -Mac OS X 10.4.10 y n n -AIX-5.2 & 5.3 32- and 64-bit n n n -FreeBSD 6.2 32- and 64-bit y n n -RedHat Linux 2.4.21 W y n n -SuSE Linux 2.6.9-42 i686 GNU (1) W y n y -SuSE Linux 2.6.9-42 i686 Intel W y n n -SuSE Linux 2.6.9-42 i686 PGI W n n n -SuSE Linux 2.6.16 x86_64 GNU (1) W y n y -SuSE Linux 2.6.16 x86_64 Intel W y n n -SuSE Linux 2.6.16 x86_64 PGI W n n n -RHEL 4 Linux 2.6.9 Xeon Lustre C y n n -RedHat Linux 2.4 Xeon Lustre C y n n -SuSE Linux 2.4 ia64 C y n n -SuSe Linux 2.6.5 SGI Altix ia64 n n n - -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, +Platform Shared static- Thread- + libraries(4) exec safe +Solaris2.8 32- and 64-bit y n y +Solaris2.10 32- and 64-bit y n y +IRIX64_6.5 32-bit y n y +IRIX64_6.5 64-bit y n y +WinXP Visual Studio 6.0 y n n +WinXP CYGWIN y n n +WinXP 2005 y n n +WinXP .Net y n n +WinVista 2005 y n n +Mac OS X 10.4.10 y n n +AIX-5.2 & 5.3 32- and 64-bit n n n +FreeBSD 6.2 32- and 64-bit y n n +RedHat Linux 2.4.21 W y n n +SuSE Linux 2.6.9-42 i686 GNU (1) W y n y +SuSE Linux 2.6.9-42 i686 Intel W y n n +SuSE Linux 2.6.9-42 i686 PGI W n n n +SuSE Linux 2.6.16 x86_64 GNU (1) W y n y +SuSE Linux 2.6.16 x86_64 Intel W y n n +SuSE Linux 2.6.16 x86_64 PGI W n n n +RHEL 4 Linux 2.6.9 Xeon Lustre C y n n +RedHat Linux 2.4 Xeon Lustre C y n n +SuSE Linux 2.4 ia64 C y n n +SuSe Linux 2.6.5 SGI Altix ia64 n n n + +Compiler versions for each platform are listed in the "Platforms Tested" +table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: @@ -1763,13 +1763,13 @@ Known Problems * We discovered two problems when running collective IO parallel HDF5 tests with chunking storage with the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. - Under some complex selection cases, + Under some complex selection cases, 1) MPI_Get_element returns the wrong value. - 2) MPI_Type_struct also generates the wrong derived datatype and corrupt + 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. This only happens when turning on collective IO with chunking storage - with some complex selections. We haven't found these problems on other - MPI-IO compilers. If you encounter these problems, you may use Independent + with some complex selections. We haven't found these problems on other + MPI-IO compilers. If you encounter these problems, you may use Independent IO instead. To avoid this problem, change the following line in your code: @@ -1777,7 +1777,7 @@ Known Problems to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); - + KY - 2007/08/24 * QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It @@ -1790,7 +1790,7 @@ Known Problems "523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname 'libh5test.so.1' under any of the filenames .......(bunch of directories) " - And the testing will fail. + And the testing will fail. We believe this is a libtool problem. One way to get rid of this is to add the paths of libh5test.so.1 and libh5.so.1 to the shared library path. @@ -1804,15 +1804,15 @@ Known Problems setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5 directory/test/.libs]:[full path of HDF5 directory/src/.libs] - NOTE: This problem ONLY affects the testing of the HDF5 library when you - build from source. It won't affect any applications that would like to link - with the HDF5 shared library since the shared library path needs to be set + NOTE: This problem ONLY affects the testing of the HDF5 library when you + build from source. It won't affect any applications that would like to link + with the HDF5 shared library since the shared library path needs to be set anyway. KY - 2007/8/2 * QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test - "calloc". All other tests passed. This indicates that a dataset using - chunked storage created by serial HDF5 may not work properly with parallel - HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x + "calloc". All other tests passed. This indicates that a dataset using + chunked storage created by serial HDF5 may not work properly with parallel + HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x calloc". AKC - 2007/7/12. * The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has @@ -1821,30 +1821,30 @@ Known Problems PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10. * When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX - 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for - example 120000, in order to pass the complicated collective IO tests inside - the parallel HDF5 library. This is not a problem inside the parallel HDF5 + 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for + example 120000, in order to pass the complicated collective IO tests inside + the parallel HDF5 library. This is not a problem inside the parallel HDF5 library. You can always set a bigger number on your system. KY - 2005/10/6 -* A contiguous or chunked dataset created by a sequential version of HDF5 - might not be able to be modified with a parallel version of the library. - Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the +* A contiguous or chunked dataset created by a sequential version of HDF5 + might not be able to be modified with a parallel version of the library. + Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the dataset creation property list to avoid the problem. EIP - 2005/09/09 -* A dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is - enabled. There was a bug in the calculating code of the Fletcher32 - checksum in the library before v1.6.3. The checksum value wasn't consistent - between big-endian and little-endian systems. This bug was fixed in - Release 1.6.3. However, after fixing the bug, the checksum value is no - longer the same as before on little-endian system. HDF5 library releases - after 1.6.4 can still read datasets created or rewritten with an HDF5 +* A dataset created or rewritten with the v1.6.3 library or after can't + be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is + enabled. There was a bug in the calculating code of the Fletcher32 + checksum in the library before v1.6.3. The checksum value wasn't consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value is no + longer the same as before on little-endian system. HDF5 library releases + after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/7/8 * For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron processor, there's a bug in the compiler for optimization(-O2). The library - failed in several tests, all related to the multi driver. The problem has - been reported to the vendor. + failed in several tests, all related to the multi driver. The problem has + been reported to the vendor. * test/big fails sometimes with the message "Possible overlap with another region." The test selects regions randomly, and this error occurs when @@ -1852,7 +1852,7 @@ Known Problems HDF5. Since the error is triggered by a random situation, it will usually disappear if the test is re-run. -* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but +* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but have a "guard" statement in stdint.h that will #error and skip the rest of the header file if the C99 option is not used explicitly. Hardsetting $CC to c99 will resolve the problem. AKC - 2004/12/13 @@ -1863,11 +1863,11 @@ Known Problems and run the tests again. The tests may also fail with messages like "The socket name is already - in use". HDF5 does not use sockets. This is due to problems of the - poe command trying to set up the debug socket. Check whether there are - many old /tmp/s.pedb.* files staying around. These are sockets used by - the poe command and left behind due to failed commands. Ask your system - administrator to clean them out. Lastly, request IBM to provide a means + in use". HDF5 does not use sockets. This is due to problems of the + poe command trying to set up the debug socket. Check whether there are + many old /tmp/s.pedb.* files staying around. These are sockets used by + the poe command and left behind due to failed commands. Ask your system + administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The h5dump tests may fail to match the expected output on some platforms @@ -1885,7 +1885,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on the HPUX 11.00. - + It is suggested that you don't use this option on these platforms during configuration. @@ -1899,9 +1899,9 @@ Known Problems long long (absolute values less than 1**-308) to double. This triggers the test/dtypes to report failure in the following test: Testing random sw long double -> double conversions - If -ieee is used, the converted doubles spread over the range 0.0 to - 10**-308. If -ieee is not used, the converted double values are mostly - 0.0, but occasionally appear as 10**-308. This has been reported to the + If -ieee is used, the converted doubles spread over the range 0.0 to + 10**-308. If -ieee is not used, the converted double values are mostly + 0.0, but occasionally appear as 10**-308. This has been reported to the system staff. All other tests have passed. @@ -1975,8 +1975,8 @@ HDF5-1.6.6 It contains information on the platforms tested and known problems in HDF5-1.6.6. For more details, check the HISTORY.txt file in the HDF5 source. -HDF5 documentation can be found in the distributed release source -code in the subdirectory doc/html/ or on the THG (The HDF Group) +HDF5 documentation can be found in the distributed release source +code in the subdirectory doc/html/ or on the THG (The HDF Group) ftp server (ftp.hdfgroup.org) in the directory: /HDF5/docs/ @@ -2020,28 +2020,28 @@ New Features Parallel Library: ----------------- - None - + Tools: ------ - h52gif and gif2h5: Both these tools were revised to include High Level Image API support. Tests were added to /hl/tools/gif2h5. PVN - 2007/04/13 - - h5dump: Added support for double long type H5T_NATIVE_LDOUBLE. + - h5dump: Added support for double long type H5T_NATIVE_LDOUBLE. PVN - 2007/03/13 - h5dump: Added support for binary output; see usage. PVN 2007/03/13 - h5repack: Added support for reading and writing by hyperslabs for large files. PVN - 2007/03/01 - h5repack: A new option allows the copy to use the source file type - (default) instead of the previous conversion to native type. + (default) instead of the previous conversion to native type. PVN - 2007/03/01 - - h5repack: Added output of the percentage of compression achieved. + - h5repack: Added output of the percentage of compression achieved. PVN - 2007/03/01 - h5diff: Added support for comparing dataset regions. PVN - 2007/02/20 - - h5diff: Added support for reading and comparing by hyperslabs for + - h5diff: Added support for reading and comparing by hyperslabs for large files. PVN - 2007/02/20 - h5diff: Added printing of dataset dimensions along with dataset - name. + name. PVN - 2007/02/19 F90 API: @@ -2057,7 +2057,7 @@ Support for New Platforms, Languages and Compilers ================================================== - Added support for MAC Intel (Darwin 8.8.2) (gcc 4.0.1 and g95 0.91) EIP - 2007/02/13 - - Added support for GNU C compiler version 4.2.1 for FreeBSD 6.2 + - Added support for GNU C compiler version 4.2.1 for FreeBSD 6.2 (32- and 64-bit) @@ -2068,10 +2068,10 @@ Bug Fixes since HDF5-1.6.5 Release ------- - Fixed several bugs with writing fill values for datasets that have a variable-length datatype or component datatype. QAK - -2007/06/19 + 2007/06/19 - STDIO driver didn't support files bigger than 2GB because the OFFSET - parameter of fseek is of type LONG INT, not big enough for big - files. Use fseeko instead for big files if it's available on the + parameter of fseek is of type LONG INT, not big enough for big + files. Use fseeko instead for big files if it's available on the system. SLU - 2007/4/5 - Relaxed restrictions on attribute operations to allow a file ID to be used as the "location ID". If a file ID is used, the attribute @@ -2083,7 +2083,7 @@ Bug Fixes since HDF5-1.6.5 Release - Fixed potential file corruption bug which could overwrite a portion of an object's header when an attribute was renamed. If the new name for the attribute was longer than the old name, it was -possible + possible that the attribute would grow enough to overwrite another message in the object's header. QAK - 2007/01/02 - Fixed file corruption bug which could write an incorrect number of @@ -2098,7 +2098,7 @@ possible - Re-open the file. - Delete one of the attributes on the object. - Add a smaller attribute to the object. - - Delete the smaller atttribute on the object. + - Delete the smaller attribute on the object. - Add a larger attribute on the object. After this, the number of header messages stored for the object @@ -2108,11 +2108,11 @@ possible resembles the following, the object has been affected by this bug: #007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry(): -unable to load entry + unable to load entry major(08): Meta data cache layer minor(40): Unable to load metadata into cache #008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load(): -corrupt object header - too few messages + corrupt object header - too few messages major(12): Object header layer minor(40): Unable to load metadata into cache @@ -2129,12 +2129,12 @@ corrupt object header - too few messages Configuration ------------- - - Changed to default to --disable-shared if parallel is enabled. + - Changed to default to --disable-shared if parallel is enabled. AKC - 2007/5/12 - Corrected a coding error in configure when it tries to locate the - needed MPI and MPI-IO library for the fortran interface. + needed MPI and MPI-IO library for the fortran interface. AKC - 007/5/9. - - Changed default fortran compiler to g95 when gcc is used. + - Changed default fortran compiler to g95 when gcc is used. AKC - 007/2/17. - Configure can now use any tr command. No more need for defining the variable TR, nor is it supported. AKC - 2006/05/20 @@ -2142,28 +2142,28 @@ corrupt object header - too few messages Performance ------------- - None - + Tools ----- - Fixed a bug in h5dump regarding the display of named datatypes attributes. PVN - 2007/03/13 - - Fixed a bug in h5dump regarding the display of group comments. + - Fixed a bug in h5dump regarding the display of group comments. PVN - 2007/03/13 - - Fixed a bug in h5dump regarding the display of hardlinks pointing + - Fixed a bug in h5dump regarding the display of hardlinks pointing to the root group. PVN - 2007/03/13 - Fixed a bug in the h5diff percentage option -p. PVN - 2007/03/05 - Fixed a bug in h5dump that caused array indices greater than 2^32-1 not to be printed correctly. PVN - 2007/2/19 - Documentation - ------------- - - Corrected errors and extended the descriptions in Reference Manual - entries for several functions. + Documentation + ------------- + - Corrected errors and extended the descriptions in Reference Manual + entries for several functions. F90 API ------- - None - + C++ API ------- - Changed @@ -2175,8 +2175,7 @@ corrupt object header - too few messages - Wrappers of H5Rcreate had incorrect prototypes. Added these overloaded functions: IdComponent::reference(void* ref, const char* name, -DataSpace& - dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) + DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) IdComponent::void reference(void* ref, const char* name) IdComponent::reference(void* ref, const H5std_string& name) and will remove these incorrect member functions: @@ -2193,13 +2192,13 @@ DataSpace& Documentation ============= - HDF5 documentation can be found in the distributed release source - code in the subdirectory doc/html/ (start with index.html) or on the + HDF5 documentation can be found in the distributed release source + code in the subdirectory doc/html/ (start with index.html) or on the THG (The HDF Group) ftp server (ftp.hdfgroup.org) in the directory: /HDF5/docs/ - Online documentation for the current release can be found on the THG + Online documentation for the current release can be found on the THG web site: http://hdfgroup.org/HDF5/doc/ @@ -2235,17 +2234,17 @@ Platforms Tested Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) - (kagiso) PGI C, Fortran, C++ 6.2-5 32-bit - icc (ICC) 9.1 - Intel(R) C++ Compiler for 32-bit + (kagiso) PGI C, Fortran, C++ 6.2-5 32-bit + icc (ICC) 9.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 9.1 + Intel(R) Fortran Compiler for 32-bit applications, Version 9.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 9.1 Absoft 32-bit Fortran 95 10.0.4 - MPICH mpich2-1.0.4p1 compiled with - gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.91!) + MPICH mpich2-1.0.4p1 compiled with + gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.91!) - Linux 2.6.16.46-0.12-debug #1 + Linux 2.6.16.46-0.12-debug #1 SMP ia64 GNU/Linux Intel(R) C++ Version 10.0.025 (ucar hir1) Intel(R) Fortran Itanium(R) Version 10.0.025 @@ -2255,14 +2254,14 @@ Platforms Tested for 64-bit target on x86-64 tested for both 32- and 64-bit binaries - Linux 2.6.5-7.283-rtgfx Altix + Linux 2.6.5-7.283-rtgfx Altix SMP ia64 Intel(R) C++ Version 9.0 (cobalt) Intel(R) Fortran Itanium(R) Version 9.0 SGI MPI - OSF1 V5.1 (QSC) Compaq C V6.5-011 + OSF1 V5.1 (QSC) Compaq C V6.5-011 (See "Known Problems.") HP Fortran V5.5A-3548 - Compaq C++ V6.5-036 + Compaq C++ V6.5-036 MPIX200_64_r13.4 SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3 @@ -2272,7 +2271,7 @@ Platforms Tested SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 Sun WorkShop 6 update 2 C++ 5.8 - Patch 121019-06 + Patch 121019-06 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre (tungsten) Intel(R) C++ Version 9.0 @@ -2371,13 +2370,13 @@ SuSe Linux 2.6.16 SGI Altix ia64 n n n y SuSe Linux 2.6.5 SGI Altix ia64 n n n y OSF1 v5.1 n n n y -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, +Compiler versions for each platform are listed in the "Platforms Tested" +table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: (1) Fortran compiled with g95. -(2) In most cases, shared libraries are provided only for the C library, +(2) In most cases, shared libraries are provided only for the C library, except on Windows where they are provided for C, C++, and Fortran. (3) C++ works only with static libraries. @@ -2394,28 +2393,28 @@ Known Problems "523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname 'libh5test.so.1' under any of the filenames .......(bunch of directories) " - And the testing will fail. + And the testing will fail. We believe this is a libtool problem. One way to get rid of this is to add the paths of libh5test.so.1 and libh5.so.1 to the shared library path. For 32-bit: You may do this, under csh: - setenv LD_LIBRARYN32_PATH .......(existing pathes):[full path of HDF5 + setenv LD_LIBRARYN32_PATH .......(existing paths):[full path of HDF5 directory/test/.libs]:[full path of HDF5 directory/src/.libs] For 64-bit: - setenv LD_LIBRARY64_PATH ......(existing pathes):[full path of HDF5 + setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5 directory/test/.libs]:[full path of HDF5 directory/src/.libs] - NOTE: This problem ONLY affects the testing of the HDF5 library when you - build from source. It won't affect any applications that would like to link - with the HDF5 shared library since the shared library path needs to be set + NOTE: This problem ONLY affects the testing of the HDF5 library when you + build from source. It won't affect any applications that would like to link + with the HDF5 shared library since the shared library path needs to be set anyway. KY - 2007/8/2 * QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test - "calloc". All other tests passed. This indicates that a dataset using - chunked storage created by serial HDF5 may not work properly with parallel - HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x + "calloc". All other tests passed. This indicates that a dataset using + chunked storage created by serial HDF5 may not work properly with parallel + HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x calloc". AKC - 2007/7/12. * The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has @@ -2424,30 +2423,30 @@ Known Problems PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10. * When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX - 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for - example 120000, in order to pass the complicated collective IO tests inside - the parallel HDF5 library. This is not a problem inside the parallel HDF5 + 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for + example 120000, in order to pass the complicated collective IO tests inside + the parallel HDF5 library. This is not a problem inside the parallel HDF5 library. You can always set a bigger number on your system. KY - 2005/10/6 -* A contiguous or chunked dataset created by a sequential version of HDF5 - might not be able to be modified with a parallel version of the library. - Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the +* A contiguous or chunked dataset created by a sequential version of HDF5 + might not be able to be modified with a parallel version of the library. + Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the dataset creation property list to avoid the problem. EIP - 2005/09/09 -* The dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is - enabled. There was a bug in the calculating code of the Fletcher32 - checksum in the library before v1.6.3. The checksum value wasn't consistent - between big-endian and little-endian systems. This bug was fixed in - Release 1.6.3. However, after fixing the bug, the checksum value is no - longer the same as before on little-endian system. The library release +* The dataset created or rewritten with the v1.6.3 library or after can't + be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is + enabled. There was a bug in the calculating code of the Fletcher32 + checksum in the library before v1.6.3. The checksum value wasn't consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value is no + longer the same as before on little-endian system. The library release after 1.6.4 can still read the dataset created or rewritten with the library of v1.6.2 or before. SLU - 2005/7/8 * For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron processor, there's a bug in the compiler for optimization(-O2). The library - failed in several tests, all related to the multi driver. The problem has - been reported to the vendor. + failed in several tests, all related to the multi driver. The problem has + been reported to the vendor. * test/big fails sometimes with the message "Possible overlap with another region." The test selects regions randomly, and this error occurs when @@ -2455,7 +2454,7 @@ Known Problems HDF5. Since the error is triggered by a random situation, it will usually disappear if the test is re-run. -* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but +* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but have a "guard" statement in stdint.h that will #error and skip the rest of the header file if the C99 option is not used explicitly. Hardsetting $CC to c99 will resolve the problem. AKC - 2004/12/13 @@ -2468,7 +2467,7 @@ Known Problems The tests may also fail with messages like "The socket name is already in use". HDF5 does not use sockets (except for stream-VFD). This is due to problems of the poe command trying to set up the debug socket. - Check whether there are many old /tmp/s.pedb.* files staying around. These + Check whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. Ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. @@ -2494,7 +2493,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on the HPUX 11.00. - + It is suggested that you don't use this option on these platforms during configuration. @@ -2510,9 +2509,9 @@ Known Problems long long (absolute values less than 1**-308) to double. This triggers the test/dtypes to report failure in the following test: Testing random sw long double -> double conversions - If -ieee is used, the converted doubles spread over the range 0.0 to - 10**-308. If -ieee is not used, the converted double values are mostly - 0.0, but occasionally appear as 10**-308. This has been reported to the + If -ieee is used, the converted doubles spread over the range 0.0 to + 10**-308. If -ieee is not used, the converted double values are mostly + 0.0, but occasionally appear as 10**-308. This has been reported to the system staff. All other tests have passed. @@ -2621,62 +2620,62 @@ New Features ============ Configuration: ------------------------- - - Added yodconfigure, a configure tool, that patches up the configure - file to allow configure to launch executable via the proper - launching command like "yod -sz 1". AKC - 2005/11/10 - - Configure now recognizes the TR variable as the location of the - tr utility. JML 2005/10/20 + - Added yodconfigure, a configure tool, that patches up the configure + file to allow configure to launch executable via the proper + launching command like "yod -sz 1". AKC - 2005/11/10 + - Configure now recognizes the TR variable as the location of the + tr utility. JML 2005/10/20 Source code distribution: ------------------------- - - Added g95 as a testing "platform" informally. AKC - 2005/10/04. + - Added g95 as a testing "platform" informally. AKC - 2005/10/04. - Added MD5 checksumming to snapshot releases. Releases will now - produce an .md5 file as well as a .tar archive. md5sum can be - used to verify the arvhice with the .md5 checksum. -JL 2005/09/06 + produce an .md5 file as well as a .tar archive. md5sum can be + used to verify the arvhice with the .md5 checksum. -JL 2005/09/06 Library: -------- - Added HSYS_ERROR which retrieves the system error message and pushes - it to the error stack. This provides more information regarding the - failed system call. AKC - 2005/08/04 + it to the error stack. This provides more information regarding the + failed system call. AKC - 2005/08/04 - Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to - allow querying for objects in a file that was opened with a particular - file ID, instead of all objects opened in the file with any file ID. - QAK - 2005/06/01 + allow querying for objects in a file that was opened with a particular + file ID, instead of all objects opened in the file with any file ID. + QAK - 2005/06/01 Parallel Library: ----------------- - - Added mpich2 as a testing "platform" informally. AKC - 2005/10/04. - - HDF5 supports collective MPI-IO for irregular selection with HDF5 - dataset. Irregular selection is when users use API H5Sselect_hyperslab - more than once for the same dataset. - Currently, not all MPI-IO packages support the complicated - MPI derived datatypes used in the implementation of irregular - selections INSIDE HDF5. - 1) DEC 5.x wdoes not support complicated derived datatypes. - 2) For AIX 5.1: - If your poe version number is 3.2.0.20 or lower, - please edit powerpc-ibm-aix5.x in the directory hdf5/config/. - Find the line with - << hdf5_mpi_complex_derived_datatype_works >> - and UNCOMMENT this line before the configure. - check poe version with the following command: - lpp -l all | grep ppe.poe - 3) For Linux cluster,: - If mpich version is 1.2.5 or lower, collective irregular selection - IO is not supported; internally independent IO is used. - 4) For IRIX 6.5: - if C compiler version is 7.3 or lower, collective irregular - selection IO is not supported; internally independent IO is used. - 5) For platforms which internally used mpich: - If the mpich version is 1.2.5 or lower, please find the - corresponding config (in hdf5/config) file and add - hdf5_mpi_complex_derived_datatype_works='no' - at the end of the configuration file. For example, on the - NCSA SGI Altix, the internal mpich library is 1.2.5. So - hdf5_mpi_complex_derived_datatype_works='no' - should be added at the end of the config file ia64-linux-gnu. - KY - 2005/09/12 + - Added mpich2 as a testing "platform" informally. AKC - 2005/10/04. + - HDF5 supports collective MPI-IO for irregular selection with HDF5 + dataset. Irregular selection is when users use API H5Sselect_hyperslab + more than once for the same dataset. + Currently, not all MPI-IO packages support the complicated + MPI derived datatypes used in the implementation of irregular + selections INSIDE HDF5. + 1) DEC 5.x wdoes not support complicated derived datatypes. + 2) For AIX 5.1: + If your poe version number is 3.2.0.20 or lower, + please edit powerpc-ibm-aix5.x in the directory hdf5/config/. + Find the line with + << hdf5_mpi_complex_derived_datatype_works >> + and UNCOMMENT this line before the configure. + check poe version with the following command: + lpp -l all | grep ppe.poe + 3) For Linux cluster,: + If mpich version is 1.2.5 or lower, collective irregular selection + IO is not supported; internally independent IO is used. + 4) For IRIX 6.5: + if C compiler version is 7.3 or lower, collective irregular + selection IO is not supported; internally independent IO is used. + 5) For platforms which internally used mpich: + If the mpich version is 1.2.5 or lower, please find the + corresponding config (in hdf5/config) file and add + hdf5_mpi_complex_derived_datatype_works='no' + at the end of the configuration file. For example, on the + NCSA SGI Altix, the internal mpich library is 1.2.5. So + hdf5_mpi_complex_derived_datatype_works='no' + should be added at the end of the config file ia64-linux-gnu. + KY - 2005/09/12 Tools: ------ @@ -2691,26 +2690,26 @@ New Features C++ API: -------- - Added missing member functions: - H5::CompType::getMemberArrayType - H5::CompType::getMemberVarLenType - H5::AbstractDs::getArrayType - H5::AbstractDs::getVarLenType - H5::CommonFG::openArrayType - H5::CommonFG::openVarLenType - H5::PropList::copyProp -- this will replace the current - H5::PropList::copyProp in later releases due - to incorrect prototype. - BMR - 2005/07/27 + H5::CompType::getMemberArrayType + H5::CompType::getMemberVarLenType + H5::AbstractDs::getArrayType + H5::AbstractDs::getVarLenType + H5::CommonFG::openArrayType + H5::CommonFG::openVarLenType + H5::PropList::copyProp -- this will replace the current + H5::PropList::copyProp in later releases due + to incorrect prototype. + BMR - 2005/07/27 Support for New Platforms, Languages and Compilers ================================================== - - Added support for RedStorm platform (serial only.) AKC 2005/11/10 - - Added support for BG/L platform (serial only.) LA 2005/11/10 - - Added support for HPUX 11.23 (IA64); only C and C++ are supported - with the +DD64 flag + - Added support for RedStorm platform (serial only.) AKC 2005/11/10 + - Added support for BG/L platform (serial only.) LA 2005/11/10 + - Added support for HPUX 11.23 (IA64); only C and C++ are supported + with the +DD64 flag EIP 2005/10/05 - + Configuration ------------- @@ -2722,9 +2721,9 @@ Bug Fixes since HDF5-1.6.4 Release Library ------- - - Fixed collective IO in chunking-storage. HDF5 may have called the - wrong routine when the shape of the dataspace in the file and in - the bufferred chunk were different. This bug was fixed to make sure + - Fixed collective IO in chunking-storage. HDF5 may have called the + wrong routine when the shape of the dataspace in the file and in + the buffered chunk were different. This bug was fixed to make sure the correct routine is called. KY - 2005/10/19 - Fixed core dump when closing root groups opened through two different file handles that operate on the same actual file. QAK - 2005/10/02 @@ -2745,7 +2744,7 @@ Bug Fixes since HDF5-1.6.4 Release together all have the same "file close degree". QAK - 2005/07/19 - More bug fixes on holding open files that are mounted and have IDs open. QAK - 2005/07/14 - - Dataset sieve buffer cache was inadvertantly disabled; it has been + - Dataset sieve buffer cache was inadvertently disabled; it has been re-enabled. QAK - 2005/07/08 - Don't unmount child files until the parent file actually closes. (Previously, if an object was holding open a file, the child files @@ -2769,57 +2768,57 @@ Bug Fixes since HDF5-1.6.4 Release Configuration ------------- - - Configure can recognize -lmpich as a form of MPI library. -AKC- - 2005/9/28. - - Changed default C++ compiler for the IA64 platform from icc to - icpc which is the preferred compiler for Intel Compiler version - 8. AKC - 2005/09/02 + - Configure can recognize -lmpich as a form of MPI library. -AKC- + 2005/9/28. + - Changed default C++ compiler for the IA64 platform from icc to + icpc which is the preferred compiler for Intel Compiler version + 8. AKC - 2005/09/02 Performance ------------- - - Optimized I/O for enumerated datatypes that are a superset of a + - Optimized I/O for enumerated datatypes that are a superset of a source enumerated datatype. QAK - 2005/03/19 - + Tools ----- - Documentation - ------------- + Documentation + ------------- F90 API ------- - h5pget_driver_f was returning information that could not be interpreted by a Fortran application program; fixed. EIP - 2005/04/10 - + C++ API ------- - - Several member functions' prototype changed due to the - "int -> unsigned" change in the main library. They are: - H5::CompType::getMemberDataType(unsigned member_num) - H5::CompType::getMemberCompType(unsigned member_num) - H5::CompType::getMemberEnumType(unsigned member_num) - H5::CompType::getMemberIntType(unsigned member_num) - H5::CompType::getMemberFloatType(unsigned member_num) - H5::CompType::getMemberStrType(unsigned member_num) - BMR - 2005/07/27 + - Several member functions' prototype changed due to the + "int -> unsigned" change in the main library. They are: + H5::CompType::getMemberDataType(unsigned member_num) + H5::CompType::getMemberCompType(unsigned member_num) + H5::CompType::getMemberEnumType(unsigned member_num) + H5::CompType::getMemberIntType(unsigned member_num) + H5::CompType::getMemberFloatType(unsigned member_num) + H5::CompType::getMemberStrType(unsigned member_num) + BMR - 2005/07/27 + - Platforms Tested ================ AIX 5.1 (32 and 64-bit) xlc 6.0.0.6 xlf 8.1.1.3 - xlC 6.0.0.6 - mpcc_r 6.0.0.6 + xlC 6.0.0.6 + mpcc_r 6.0.0.6 mpxlf_r 8.1.1.3 - xlc 5.0.2.5 - xlf 7.1.1.2 - xlC 5.0.2.5 - mpcc_r 5.0.2.5 - mpxlf_r 7.1.1.2 + xlc 5.0.2.5 + xlf 7.1.1.2 + xlC 5.0.2.5 + mpcc_r 5.0.2.5 + mpxlf_r 7.1.1.2 AIX 5.2 (32/64 bit) xlc 6.0.0.8 xlC 6.0.0.9 xlf 8.1.1.7 @@ -2839,7 +2838,7 @@ Platforms Tested FreeBSD 4.11 gcc 2.95.4 g++ 2.95.4 gcc 3.2.3, 3.3.6, 3.4.4, 4.0.0 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.00 @@ -2851,30 +2850,30 @@ Platforms Tested IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m F90 MIPSpro 7.3.1.3m (64 only) C++ MIPSpro cc 7.3.1.3m - mpt 1.6 + mpt 1.6 Linux 2.4.20-28.7 gcc 2.96 (eirene, verbena) gcc 3.3.2 - PGI compilers (pgcc, pgf90, pgCC) + PGI compilers (pgcc, pgf90, pgCC) version 5.2-1 Absoft Fortran compiler v9.0 - Intel(R) C++ 32-bit Version 8.1 - Intel(R) Fortran 32-bit Version 8.1 + Intel(R) C++ 32-bit Version 8.1 + Intel(R) Fortran 32-bit Version 8.1 MPIch 1.2.6 Linux 2.4.21-268-smp x86_64 gcc 3.3.1 (SuSE Linux, AMD) - (mir) PGI 5.2-1 C and F90 (with k3-32) - Intel(R) C++ 32-bit Version 8.1 - Intel(R) Fortran 32-bit Version 8.1 - Linux 2.4.21-sgi306rp21 Altix + (mir) PGI 5.2-1 C and F90 (with k3-32) + Intel(R) C++ 32-bit Version 8.1 + Intel(R) Fortran 32-bit Version 8.1 + Linux 2.4.21-sgi306rp21 Altix SMP ia64 Intel(R) C++ Version 8.1 (cobalt) Intel(R) Fortran Itanium(R) Version 8.1 SGI MPI - OSF1 V5.1 (QSC) Compaq C V6.5-011 + OSF1 V5.1 (QSC) Compaq C V6.5-011 HP Fortran V5.5A-3548 - Compaq C++ V6.5-036 - MPIX200_64_r13.4 - OSF1 V5.1 (PSC) Compaq C V6.5-303 + Compaq C++ V6.5-036 + MPIX200_64_r13.4 + OSF1 V5.1 (PSC) Compaq C V6.5-303 HP Fortran V5.5A-3548 - Compaq C++ V6.5-040 + Compaq C++ V6.5-040 SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 @@ -2884,21 +2883,21 @@ Platforms Tested SunOS 5.10 Sun WorkShop 6 update 2 C 5.3 Sun WorkShop 6 update 2 Fortran 95 6.2 Sun WorkShop 6 update 2 C++ 5.3 - Patch 111685-13 + Patch 111685-13 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre - (tungsten) Intel(R) C++ Version 9.0 + (tungsten) Intel(R) C++ Version 9.0 Intel(R) Fortran Compiler Version 9.0 IA-64 Linux 2.4.21.SuSE_292.til1 ia64 (NCSA tg-login) Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 - mpich-gm-1.2.5..10-intel-r2 + mpich-gm-1.2.5..10-intel-r2 Windows XP MSVC++.NET MSVC++ 6.0 Intel 8.1 C++ MAC OS X Darwin 7.5 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.3.2 - IBM XL Fortran version 8.1 + IBM XL Fortran version 8.1 Absoft Fortran compiler v8.2 @@ -2912,8 +2911,8 @@ Key: y = tested and supported ( ) = footnote appears below second table Platform C F90 F90 C++ zlib SZIP - parallel parallel -IBM BG/L (16) n n n n y y + parallel parallel +IBM BG/L (16) n n n n y y Solaris2.8 64-bit y y y(1) y y y Solaris2.8 32-bit y y y(1) y y y Solaris2.9 64-bit y(1) y y(1) y y y @@ -2936,7 +2935,7 @@ FreeBSD 4.11 n n n y y y RedHat 7.3 W (3) y(1) y(11) n y y y RedHat 7.3 W Intel (3) n y n y y y RedHat 7.3 W PGI (3) n y n y y y -RedStorm (16) n y n y y n +RedStorm (16) n y n y y n SuSe x86_64 gcc (3,13) n y(12) n y y y SuSe x86_64 icc (3,13) n y(14) n y y y Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y y @@ -2944,9 +2943,9 @@ Linux 2.4 SuSE ia64 C Intel (3,7) y y y y y y Linux 2.4 SGI Altix ia64 Intel (3) y y y y y y -Platform Shared static- Thread- STREAM- - libraries(4) exec safe VFD -IBM BG/L n y n n +Platform Shared static- Thread- STREAM- + libraries(4) exec safe VFD +IBM BG/L n y n n Solaris2.8 64-bit y x y y Solaris2.8 32-bit y x y y Solaris2.9 64-bit y x y y @@ -2968,7 +2967,7 @@ FreeBSD 4.11 y y y y RedHat 7.3 W (3) y y y y RedHat 7.3 W Intel (3) n y n y RedHat 7.3 W PGI (3) n y n y -RedStorm n y n y +RedStorm n y n y SuSe x86_64 gcc (3,13) n y n y SuSe x86_64 icc (3,13) y y(15) n y Linux 2.4 Xeon C Lustre Intel (3,6) y y n y @@ -2976,28 +2975,28 @@ Linux 2.4 SuSE ia64 C Intel (3,7) y y n n Linux 2.4 SGI Altix ia64 Intel (3) y y n y -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, +Compiler versions for each platform are listed in the "Platforms Tested" +table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: (1) Using mpich 1.2.6 (2) Using mpt and mpich 1.2.6. - (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. + (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. - (4) Shared libraries are provided only for the C library, + (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++. (5) Using mpt. - (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp-perfctr-lustre + (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp-perfctr-lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.til1. Ia64 cluster with Intel compilers (8) Intel 8.1 (9) One test of this release failed with Compaq Visual Fortran 6.6c. No binary fortran release will be provided. Users should build - the library by themselves and use it at their own risk. - We recommend that users use HDF5 1.7 instead + the library by themselves and use it at their own risk. + We recommend that users use HDF5 1.7 instead or use Compaq Visual Fortran 6.0. (10) IBM XLF and Absoft - (11) PGI, Absoft. No shared libraries with Absoft; + (11) PGI, Absoft. No shared libraries with Absoft; use '--disable-shared'. (12) PGI and Intel compilers for both C and Fortran (13) AMD Opteron x86_64 @@ -3014,43 +3013,43 @@ Known Problems configure, edit the file config/intel-flags by changing the setting of PROD_CFLAGS from -O3 to -O0, then run configure. AKC - 2005/11/10. -* Fortran testing and compiling failures on windows XP +* Fortran testing and compiling failures on windows XP 1. Compaq visual fortran 6.6c with VS 6.0 The Fortran tests failed for both release, release dll, debug and debug dll. The failure is a random one. We won't provide fortran libraries. The - same test passed with the 1.7.51 snapshot. You may find the 1.7.51 + same test passed with the 1.7.51 snapshot. You may find the 1.7.51 snapshot under ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots/. 2. Intel fortran 8.1 under .Net environment The fortran library cannot even be compiled. Some users have pointed this to intel forum. * When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 at IRIX - 6.5, set enviroment variable MPI_TYPE_MAX to be a bigger number, for example - 120000, in order to pass the complicated collective IO tests inside parallel - HDF5 library. This is not a problem inside parallel HDF5 library. You can + 6.5, set environment variable MPI_TYPE_MAX to be a bigger number, for example + 120000, in order to pass the complicated collective IO tests inside parallel + HDF5 library. This is not a problem inside parallel HDF5 library. You can always set a bigger number in your system. KY - 2005/10/6 * A contiguous or chunked dataset created by a sequential version may - not be modified with a parallel version of the library. - Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the + not be modified with a parallel version of the library. + Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the dataset creation property list to avoid the problem. EIP - 2005/09/09 -* The dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is - enabled. There was a bug in the calculating code of the Fletcher32 - checksum in the library before v1.6.3. The checksum value wasn't consistent - between big-endian and little-endian systems. This bug was fixed in - Release 1.6.3. However, after fixing the bug, the checksum value is no - longer the same as before on little-endian system. The library release +* The dataset created or rewritten with the v1.6.3 library or after can't + be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is + enabled. There was a bug in the calculating code of the Fletcher32 + checksum in the library before v1.6.3. The checksum value wasn't consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value is no + longer the same as before on little-endian system. The library release after 1.6.4 can still read the dataset created or rewritten with the library of v1.6.2 or before. SLU - 2005/7/8 * For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron processor, there's a bug in the compiler for optimization(-O2). The library - failed in several tests but all related to multi driver. The problem has - been reported to the vendor. + failed in several tests but all related to multi driver. The problem has + been reported to the vendor. * test/big fails sometimes with the message "Possible overlap with another region." The test selects regions randomly, and this error occurs when @@ -3075,9 +3074,9 @@ Known Problems Ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. -* Two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5) - failed on windows xp with .NET for debug and debug dll. Release and - Release dll work fine. +* Two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5) + failed on windows xp with .NET for debug and debug dll. Release and + Release dll work fine. * The h5dump tests may fail to match the expected output on some platforms (e.g. parallel jobs, Windows) where the error messages directed to @@ -3100,14 +3099,14 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on the HPUX 11.00. - + It is suggested that you don't use this option on these platforms during configuration. * The Stream VFD was not tested yet under Windows. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: @@ -3129,10 +3128,10 @@ Known Problems All other tests have passed. * Fortran release DLL randomly failed with Compaq Visual Fortran 6.6c on - Windows. + Windows. * Fortran DLL built with Intel 8.1 in .NET environment crushed the compiler, - Building Fortran static library with Intel 8.1 in .NET environment + Building Fortran static library with Intel 8.1 in .NET environment requires manually setting the project file. Please contact to hdfhelp@ncsa.uiuc.edu if you need to build Fortran static library with Intel 8.1 with .NET environment. @@ -3213,7 +3212,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -3241,19 +3240,19 @@ New Features For HL documentation, see http://hdf.ncsa.uiuc.edu/HDF5/hdf5_hl/doc/RM_hdf5hl.html. - The HL library, libhdf5_hl.a(so), is built and installed by default. + The HL library, libhdf5_hl.a(so), is built and installed by default. Use --disable-hl configure flag to disable the HL library. Library: -------- - - We recommend you to use SZIP v2.0 with this release. + - We recommend you to use SZIP v2.0 with this release. For more information see - http://hdf.ncsa.uiuc.edu/doc_resource/SZIP/ - - The compound datatype has been enhanced with a new feature of size + http://hdf.ncsa.uiuc.edu/doc_resource/SZIP/ + - The compound datatype has been enhanced with a new feature of size adjustment. The size can be increased and decreased (without - cutting the last member). No API change is involved. SLU - + cutting the last member). No API change is involved. SLU - 2004/10/1 - - Removed PABLO support. 2005/01/20 EIP + - Removed PABLO support. 2005/01/20 EIP Parallel Library: ----------------- @@ -3262,7 +3261,7 @@ New Features Tools: ------ - - New tool, h5jam. See HDF5 Reference Manual. 2004/10/08 + - New tool, h5jam. See HDF5 Reference Manual. 2004/10/08 F90 API: -------- @@ -3270,9 +3269,9 @@ New Features C++ API: -------- - - Started using C library's reference counting in place of the class - RefCounter, which existed before the C mechanism was available. - As a result, RefCounter has been removed. 2005/03/12 BMR + - Started using C library's reference counting in place of the class + RefCounter, which existed before the C mechanism was available. + As a result, RefCounter has been removed. 2005/03/12 BMR Support for new platforms, languages and compilers. @@ -3280,7 +3279,7 @@ Support for new platforms, languages and compilers. Configuration ------------- - - Upgraded from GNU autoconf 2.53 to autoconf 2.59. JML - 2005/01/31 + - Upgraded from GNU autoconf 2.53 to autoconf 2.59. JML - 2005/01/31 Bug Fixes since HDF5-1.6.3 release @@ -3289,57 +3288,57 @@ Bug Fixes since HDF5-1.6.3 release Library ------- - Fixed a racing condition in MPIPOSIX virtual file drive close - function. Now all processes must completed the close before any - of them is returned. This prevents some "faster" processes start - accessing the file for another purpose (e.g., open with truncate) - while other "slower" processes have not closed the same file with - the previous purpose. AKC - 2005/03/01 - - H5Tget_member_value calls for enum datatype didn't return correct - value if H5Tenum_valueof was called first. It's fixed. SLU - - 2005/02/08 + function. Now all processes must completed the close before any + of them is returned. This prevents some "faster" processes start + accessing the file for another purpose (e.g., open with truncate) + while other "slower" processes have not closed the same file with + the previous purpose. AKC - 2005/03/01 + - H5Tget_member_value calls for enum datatype didn't return correct + value if H5Tenum_valueof was called first. It's fixed. SLU - + 2005/02/08 - For variable-length string, H5Tget_class returned H5T_STRING as its - class. But H5Tdetect_class and H5Tget_member_class considered it - as H5T_VLEN. This is fixed to let all these 3 functions treat it - as H5T_STRING. SLU - 2005/02/08 + class. But H5Tdetect_class and H5Tget_member_class considered it + as H5T_VLEN. This is fixed to let all these 3 functions treat it + as H5T_STRING. SLU - 2005/02/08 - The byte order of all 1-byte integer types was fixed as - little-endian even on a big-endian machine. It's corrected. - SLU - 2005/02/07 + little-endian even on a big-endian machine. It's corrected. + SLU - 2005/02/07 - Fixed segmentation fault when calling H5Fflush with an attribute that - hasn't had a value written to it open. QAK - 2004/10/18 + hasn't had a value written to it open. QAK - 2004/10/18 - Backed out support for bitfield and time types in H5Tget_native_type. - Leave it to future support. The function simply returns error - message of "not support" for bitfield and time types. SLU - 2004/10/5 + Leave it to future support. The function simply returns error + message of "not support" for bitfield and time types. SLU - 2004/10/5 - Fixed address check in Core VFL driver to avoid spurious address/size - overflows for odd valued addresses and/or sizes. QAK - 2004/09/27 + overflows for odd valued addresses and/or sizes. QAK - 2004/09/27 - Fixed problem where chunked datasets were not able to be deleted - from a file under certain circumstances. QAK - 2004/09/27/ + from a file under certain circumstances. QAK - 2004/09/27/ Configuration ------------- - - IRIX64 MIPSpro compiler of 7.4.x supports C99 features. Default - to use the 'c99' compiler if available. AKC - 2004/12/13 - - Intel v8.0 compiler would infinite loop when compiling some test - code with -O3 option. Changed enable-production default compiler - option to -O2. AKC - 2004/12/06 - - Long double is assumed to be a supported C data type. It is a - standard C89 type. AKC - 2004/10/22 + - IRIX64 MIPSpro compiler of 7.4.x supports C99 features. Default + to use the 'c99' compiler if available. AKC - 2004/12/13 + - Intel v8.0 compiler would infinite loop when compiling some test + code with -O3 option. Changed enable-production default compiler + option to -O2. AKC - 2004/12/06 + - Long double is assumed to be a supported C data type. It is a + standard C89 type. AKC - 2004/10/22 Performance ------------- - Many changes were made to the library to improve performance, - especially for the variable-length datatypes and metadata cache. - + Many changes were made to the library to improve performance, + especially for the variable-length datatypes and metadata cache. + Tools ----- - h5fc and h5c++ work correctly when -c compiler flag - is used. EIP - 2005/03/14 - - Fixed h5dump to print attributes data in ASCII if -r option is used. - AKC - 2004/11/18 - - Fixed space utilization reported in h5ls to correct error - in formula used. QAK - 2004/10/22 + is used. EIP - 2005/03/14 + - Fixed h5dump to print attributes data in ASCII if -r option is used. + AKC - 2004/11/18 + - Fixed space utilization reported in h5ls to correct error + in formula used. QAK - 2004/10/22 - Documentation - ------------- + Documentation + ------------- F90 API ------- @@ -3356,7 +3355,7 @@ Documentation HDF5 Library documentation -------------------------- - No substantive changes to the structure or types of content in the + No substantive changes to the structure or types of content in the HDF5 Library documentation. Windows installation documentation @@ -3365,24 +3364,24 @@ Documentation either http://www.zlib.net/zlib122-dll.zip or ftp://hdf.ncsa.uiuc.edu/lib-external/zlib/bin/windows - 2. Only DLLs of external libraries (zlib and szip) are linked with the - HDF5 Library. We will no longer provide binary to link static library + 2. Only DLLs of external libraries (zlib and szip) are linked with the + HDF5 Library. We will no longer provide binary to link static library with HDF5. For details, please check INSTALL_Windows in this directory. - + Platforms Tested ================ AIX 5.1 (32 and 64-bit) xlc 6.0.0.6 xlf 8.1.1.3 - xlC 6.0.0.6 - mpcc_r 6.0.0.6 + xlC 6.0.0.6 + mpcc_r 6.0.0.6 mpxlf_r 8.1.1.3 - xlc 5.0.2.5 - xlf 7.1.1.2 - xlC 5.0.2.5 - mpcc_r 5.0.2.5 - mpxlf_r 7.1.1.2 + xlc 5.0.2.5 + xlf 7.1.1.2 + xlC 5.0.2.5 + mpcc_r 5.0.2.5 + mpxlf_r 7.1.1.2 AIX 5.2 (32/64 bit) xlc 6.0.0.8 xlC 6.0.0.9 xlf 8.1.1.7 @@ -3400,7 +3399,7 @@ Platforms Tested FreeBSD 4.9 gcc 2.95.4 g++ 2.95.4 gcc 3.2.3, 3.3.6, 3.4.4, 4.0.0 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 MPIch 1.2.4 @@ -3410,32 +3409,32 @@ Platforms Tested IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m F90 MIPSpro 7.3.1.3m (64 only) C++ MIPSpro cc 7.3.1.3m - mpt 1.6 + mpt 1.6 Linux 2.4.20-28.7 gcc 2.96 (eirene, verbena) gcc 3.3.2 - PGI compilers (pgcc, pgf90, pgCC) + PGI compilers (pgcc, pgf90, pgCC) version 5.2-1 Absoft Fortran compiler v9.0 - Intel(R) C++ 32-bit Version 8.1 - Intel(R) Fortran 32-bit Version 8.1 + Intel(R) C++ 32-bit Version 8.1 + Intel(R) Fortran 32-bit Version 8.1 MPIch 1.2.6 Linux 2.4.21-268-smp x86_64 gcc 3.3.1 (SuSE Linux, AMD) - (mir) PGI 5.2-1 C and F90 (with k3-32) - Intel(R) C++ 32-bit Version 8.1 - Intel(R) Fortran 32-bit Version 8.1 - Linux 2.4.21-sgi303r2 Altix + (mir) PGI 5.2-1 C and F90 (with k3-32) + Intel(R) C++ 32-bit Version 8.1 + Intel(R) Fortran 32-bit Version 8.1 + Linux 2.4.21-sgi303r2 Altix SMP ia64 Intel(R) C++ Version 8.1 (cobalt) Intel(R) Fortran Itanium(R) Version 8.1 SGI MPI - OSF1 V5.1 (QSC) Compaq C V6.5-011 + OSF1 V5.1 (QSC) Compaq C V6.5-011 HP Fortran V5.5A-3548 - Compaq C++ V6.5-036 - MPIX200_64_r13.4 - OSF1 V5.1 (PSC) Compaq C V6.5-303 + Compaq C++ V6.5-036 + MPIX200_64_r13.4 + OSF1 V5.1 (PSC) Compaq C V6.5-303 HP Fortran V5.5A-3548 - Compaq C++ V6.5-040 - MPIX200_64_r13.4 - FORTRAN 90 2.0 Patch 107356-04 + Compaq C++ V6.5-040 + MPIX200_64_r13.4 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 @@ -3445,20 +3444,20 @@ Platforms Tested TFLOPS r1.0.4 v4.5.2 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with local modifications Xeon Linux 2.4.20-31.9smp_perfctr_lustre - (tungsten) Intel(R) C++ Version 8.0 + (tungsten) Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 IA-64 Linux 2.4.21.SuSE_128.bef1 ia64 (NCSA tg-login) Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 - mpich-gm-1.2.5..intel + mpich-gm-1.2.5..intel Windows XP MSVC++.NET MSVC++ 6.0 Compaq Visual Fortran 6.6C Intel 8.1 C++ MAC OS X Darwin 7.5 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.3.2 - IBM XL Fortran version 8.1 + IBM XL Fortran version 8.1 Absoft Fortran compiler v8.2 @@ -3472,7 +3471,7 @@ Key: y = tested and supported ( ) = footnote appears below second table Platform C F90 F90 C++ zlib SZIP - parallel parallel + parallel parallel Solaris2.8 64-bit y y y(1) y y y Solaris2.8 32-bit y y y(1) y y y Solaris2.9 64-bit y(1) y y(1) y y y @@ -3500,8 +3499,8 @@ Linux 2.4 SuSE ia64 C Intel (3,7) y y y y y y Linux 2.4 SGI Altix ia64 Intel (3) y y y y y y -Platform Shared static- Thread- STREAM- - libraries(4) exec safe VFD +Platform Shared static- Thread- STREAM- + libraries(4) exec safe VFD Solaris2.8 64-bit y x y y Solaris2.8 32-bit y x y y Solaris2.9 64-bit y x y y @@ -3529,24 +3528,24 @@ Linux 2.4 SuSE ia64 C Intel (3,7) y y n n Linux 2.4 SGI Altix ia64 Intel (3) y y n y -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, +Compiler versions for each platform are listed in the "Platforms Tested" +table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: (1) Using mpich 1.2.6 (2) Using mpt and mpich 1.2.6. - (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. + (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. - (4) Shared libraries are provided only for the C library, + (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++. (5) Using mpt. - (6) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre + (6) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_128.befl. Ia64 cluster with Intel compilers (8) Intel 8.1 (9) Compaq Visual Fortran 6.6C (10) IBM XLF and Absoft - (11) PGI, Absoft. No shared libraries with Absoft; + (11) PGI, Absoft. No shared libraries with Absoft; use '--disable-shared'. (12) PGI and Intel compilers for both C and Fortran (13) AMD Opteron x86_64 @@ -3583,12 +3582,12 @@ Known Problems Ask your system administrator to clean them out. Lastly, request IBM to provide a mean to run poe without the debug socket. -* Fortran subroutine h5pget_driver_f doesn't return a correct driver +* Fortran subroutine h5pget_driver_f doesn't return a correct driver information. -* There are two h5dump xml tests(h5dump --xml thlink.h5 and - h5dump --xml tmany.h5) failed on windows xp with .NET for debug and - debug dll. Release and Release dll work fine. +* There are two h5dump xml tests(h5dump --xml thlink.h5 and + h5dump --xml tmany.h5) failed on windows xp with .NET for debug and + debug dll. Release and Release dll work fine. * The h5dump tests may fail to match the expected output on some platforms (e.g. parallel jobs, Windows) where the error messages directed to @@ -3608,7 +3607,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. - + It is suggested that you don't use this option on these platforms during configuration. @@ -3627,15 +3626,15 @@ Known Problems the different precision in the values displayed. h5ls appears to be dumping floating-point numbers correctly. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/ -* On some platforms that use Intel and Absoft compilers to build HDF5 fortran - library, compilation may fail for fortranlib_test.f90, fflush1.f90 and - fflush2.f90 complaining about exit subroutine. Comment out the line +* On some platforms that use Intel and Absoft compilers to build HDF5 fortran + library, compilation may fail for fortranlib_test.f90, fflush1.f90 and + fflush2.f90 complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) * Use --disable-shared configure flag if building with Absoft Fortran @@ -3660,10 +3659,10 @@ Known Problems setenv CXX "pgCC -tlocal" for others * Fortran release DLL randomly failed with compaq visual fortran 6.6c on - windows. + windows. * Fortran DLL built with Intel 8.1 in .NET environment crushed the compiler, - To build Fortran Static library with Intel 8.1 in .NET environment + To build Fortran Static library with Intel 8.1 in .NET environment needs manually setting the project file, please contact to hdfhelp@ncsa.uiuc.edu if you need to build fortran static library with Intel 8.1 with .NET environment. @@ -3745,7 +3744,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -3776,74 +3775,74 @@ New Features - WINDOWS building,testing and installing improvements - - On Windows, FORTRAN,C++ and C projects are merged into one zip file, - users can choose an option to build either FORTRAN or C++ or both + - On Windows, FORTRAN,C++ and C projects are merged into one zip file, + users can choose an option to build either FORTRAN or C++ or both with basic C library.For detailed information, please read INSTALL_Windows.txt. - On Windows, szip compression library with or without encoder can be easily turned off or on when building HDF5. For detailed information, - please read INSTALL_Windows.txt, especially section V. - + please read INSTALL_Windows.txt, especially section V. + - On Windows, an optional procedure for building,testing and installing HDF5 from command line is provided. This procedure is supposed to be - convenient for experienced users, please read + convenient for experienced users, please read INSTALL_windows_From_Command_Line.txt for details. - On Windows, an alternative short instruction document for building, testing and installing HDF5 is provided. This instruction is supposed to - be convenient for general users, please read + be convenient for general users, please read INSTALL_Windows_Short.txt for details. - On Windows, h5repack,h5diff,h5ls and h5import tool tests have been added. - KY - 2004/9/16 - + KY - 2004/9/16 + Library: -------- - Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for - SZIP compression. Now there is no restriction on the size and shape of the - chunk except that the total number of elements in the chunk cannot be - bigger than 'pixels_per_block' parameter provided by the user. - EIP - 2004/07/21 + SZIP compression. Now there is no restriction on the size and shape of the + chunk except that the total number of elements in the chunk cannot be + bigger than 'pixels_per_block' parameter provided by the user. + EIP - 2004/07/21 - HDF5 can now link to SZIP with or without szip's encoder. - The new API function H5Zget_filter_info can be used to check - szip's status. Attempting to assign szip to a dataset property - list or attempting to write with szip will generate an error if - szip's encoder is disabled. JL/NF - 2004/6/30 + The new API function H5Zget_filter_info can be used to check + szip's status. Attempting to assign szip to a dataset property + list or attempting to write with szip will generate an error if + szip's encoder is disabled. JL/NF - 2004/6/30 - SZIP always uses K13 compression. This flag no longer needs to - be set when calling H5Pset_szip. If the flag for CHIP - compression is set, it will be ignored (since the two are mutually - exclusive). JL/NF - 2004/6/30 + be set when calling H5Pset_szip. If the flag for CHIP + compression is set, it will be ignored (since the two are mutually + exclusive). JL/NF - 2004/6/30 - A new API function H5Fget_name was added. It returns the name - of the file by object(file, group, data set, named data type, - attribute) ID. SLU - 2004/06/29 + of the file by object(file, group, data set, named data type, + attribute) ID. SLU - 2004/06/29 - A new API function H5Fget_filesize was added. It returns the - actual file size of the opened file. SLU - 2004/06/24 - - Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2, - will suppress all library version mismatch warning messages. - AKC - 2004/4/14 + actual file size of the opened file. SLU - 2004/06/24 + - Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2, + will suppress all library version mismatch warning messages. + AKC - 2004/4/14 Parallel Library: ----------------- Tools: ------ - - h5repack was added to the tools suite. h5repack regenerates an HDF5 file - from another HDF5 file, optionally applying HDF5 filters (compression) - and/or chunking to the copied file. The filters options are read from - the command line. See /doc/html/Tools.html for more details. - PVN - 2004/9/13 + - h5repack was added to the tools suite. h5repack regenerates an HDF5 file + from another HDF5 file, optionally applying HDF5 filters (compression) + and/or chunking to the copied file. The filters options are read from + the command line. See /doc/html/Tools.html for more details. + PVN - 2004/9/13 - h5dump includes new features: - 1) Printing of dataset filters, storage layout and fill value information. - 2) Print a list of the file contents. - 3) Escape non printing characters. - 4) Print the content of the boot block. - 5) Print array indices with the data (the default). - These options are all switch controlled. See /doc/html/Tools.html for more details. - PVN - 2004/9/13 - + 1) Printing of dataset filters, storage layout and fill value information. + 2) Print a list of the file contents. + 3) Escape non printing characters. + 4) Print the content of the boot block. + 5) Print array indices with the data (the default). + These options are all switch controlled. See /doc/html/Tools.html for more details. + PVN - 2004/9/13 + F90 API: -------- @@ -3853,18 +3852,18 @@ New Features h5premove_filter_f h5zget_filter_info_f EIP 2004/9/21 - + - added new h5fget_name_f and h5fget_filesize_f subroutines EIP 2004/07/08 C++ API: -------- - - Added wrappers for array and variable length datatypes APIs - - Added wrappers for newly added APIs from H5T, H5F, and H5I - - Added many wrappers that were missing from the H5P API - - Added the ability to reference HDF5 objects to these classes: - DataSet, DataType, Group, and H5File (wrappers for H5R APIs) - BMR 2004/08/04 + - Added wrappers for array and variable length datatypes APIs + - Added wrappers for newly added APIs from H5T, H5F, and H5I + - Added many wrappers that were missing from the H5P API + - Added the ability to reference HDF5 objects to these classes: + DataSet, DataType, Group, and H5File (wrappers for H5R APIs) + BMR 2004/08/04 Support for new platforms, languages and compilers. @@ -3872,14 +3871,14 @@ Support for new platforms, languages and compilers. - Added PGI Fortran support for Linux64 (x86_64) systems EIP - 2004/08/19 - Absoft compiler f95 v9.0 is supported on Linux 2.4 32bit - EIP - 2004/07/29 + EIP - 2004/07/29 - HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran - compiler version 8.1. This is a default compiler. + compiler version 8.1. This is a default compiler. - HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler - version 8.2; set F9X environment variable to f95, for example - setenv F9X f95 - Use --disable-shared --enable-static configure flags when Absoft - compiler is used. + version 8.2; set F9X environment variable to f95, for example + setenv F9X f95 + Use --disable-shared --enable-static configure flags when Absoft + compiler is used. EIP - 2004/07/27 Bug Fixes since HDF5-1.6.2 release @@ -3887,72 +3886,72 @@ Bug Fixes since HDF5-1.6.2 release Library ------- - - Fixed parallel bug in which some processes attempted collective - I/O while others did independent I/O. Bug appeared when some - processes used point selections, and others didn't. JRM - 2004/9/15 + - Fixed parallel bug in which some processes attempted collective + I/O while others did independent I/O. Bug appeared when some + processes used point selections, and others didn't. JRM - 2004/9/15 - Corrected error where dataset region references were written in an - incorrect way on Cray machines. PVN & QAK - 2004/09/13 + incorrect way on Cray machines. PVN & QAK - 2004/09/13 - The H5Tget_native_type now determines the native type for integers - based on the precision. This is to avoid cases of wrongly converting - an int to a short in machines that have a short of 8 bytes but with - 32bit precision (e.g Cray SV1). PVN - 2004/09/07 + based on the precision. This is to avoid cases of wrongly converting + an int to a short in machines that have a short of 8 bytes but with + 32bit precision (e.g Cray SV1). PVN - 2004/09/07 - Changed H5Dread() to not overwrite data in an application's buffer - with garbage when accessing a chunked dataset with an undefined fill - value and an unwritten chunk is uncountered. QAK - 2004/08/25 + with garbage when accessing a chunked dataset with an undefined fill + value and an unwritten chunk is uncountered. QAK - 2004/08/25 - Fixed error which could cause a core dump when a type conversion - routine was registered after a compound datatype had been - converted and then an equivalent compound datatype was converted - again. QAK - 2004/08/07 + routine was registered after a compound datatype had been + converted and then an equivalent compound datatype was converted + again. QAK - 2004/08/07 - Fixed memory overwrite when encoding "multi" file driver information - for file's superblock. QAK - 2004/08/05 + for file's superblock. QAK - 2004/08/05 - Fixed obscure bug where a filter which failed during chunk allocation - could allow library to write uncompressed data to disk but think - the data was compressed. QAK - 2004/07/29 + could allow library to write uncompressed data to disk but think + the data was compressed. QAK - 2004/07/29 - Fixed bug where I/O to an extendible chunked dataset with zero-sized - dimensions would cause library to fail an assertion. - QAK - 2004/07/27 + dimensions would cause library to fail an assertion. + QAK - 2004/07/27 - Fixed bug where chunked datasets which have filters defined, - allocation time set to "late" and whose chunks don't align with - the dataspace bounds could have incorrect data stored when - overwriting the entire dataset on the first write. QAK - 2004/07/27 + allocation time set to "late" and whose chunks don't align with + the dataspace bounds could have incorrect data stored when + overwriting the entire dataset on the first write. QAK - 2004/07/27 - Added check to ensure that dataspaces have extents set. JML-2004/07/26 - Fixed bug on some Solaris systems where HDF5 would try to use - gettimeofday() when that function didn't work properly. - JML - 2004/07/23 + gettimeofday() when that function didn't work properly. + JML - 2004/07/23 - Fixed bug in H5Sset_extent_simple where setting maximum size to - non-zero, then to zero would cause an error. JML - 2004/07/20 + non-zero, then to zero would cause an error. JML - 2004/07/20 - Allow NULL pointer for buffer parameter to H5Dread & H5Dwrite - when not writing data ("none" selection or hyperslab or point - selection with no elements defined). QAK - 2004/07/20 + when not writing data ("none" selection or hyperslab or point + selection with no elements defined). QAK - 2004/07/20 - Calling H5Gcreate() on "/" or "." throws an error instead of - failing quietly. JML - 2004/07/19 + failing quietly. JML - 2004/07/19 - Fixed bug where setting file address size to be very small could - trigger an assert if the file grew to more than 64 KB. Now throws - an error and data can be recovered. JL/NF - 2004/07/14 + trigger an assert if the file grew to more than 64 KB. Now throws + an error and data can be recovered. JL/NF - 2004/07/14 - Fixed bug where "resurrecting" a dataset was failing. - QAK - 2004/07/14 + QAK - 2004/07/14 - Fixed bug where incorrect data could be read from a chunked dataset - after it was extended. QAK - 2004/07/12 + after it was extended. QAK - 2004/07/12 - After compound datatype with variable-length string in the fields - is committed to file, the size is messed up when it's read back. - Fixed. SLU - 2004/06/11 + is committed to file, the size is messed up when it's read back. + Fixed. SLU - 2004/06/11 - Fixed potential file corruption bug when a block of metadata could - overlap the end of the internal metadata accumulator buffer and - the buffer would be extended correctly, but would incorrectly - change it's starting address. QAK - 2004/06/09 + overlap the end of the internal metadata accumulator buffer and + the buffer would be extended correctly, but would incorrectly + change it's starting address. QAK - 2004/06/09 - Opaque datatype with no tag failed for some operations. Fixed. - SLU - 2004/6/3 + SLU - 2004/6/3 - Fixed potential file corruption bug where dimensions that were - too large (a value greater than could be represented in 32-bits) - could cause the incorrect amount of space to be allocated in a - file for the raw data for the dataset. QAK - 2004/06/01 - - Fixed dtypes "sw long double -> double" failure in QSC class - machines. AKC - 2004/4/16 + too large (a value greater than could be represented in 32-bits) + could cause the incorrect amount of space to be allocated in a + file for the raw data for the dataset. QAK - 2004/06/01 + - Fixed dtypes "sw long double -> double" failure in QSC class + machines. AKC - 2004/4/16 Configuration ------------- - Fixed the long compile time of H5detect.c when v7.x Intel Compiler - is used with optimization NOT off. AKC - 2004/05/20 + is used with optimization NOT off. AKC - 2004/05/20 Performance ------------- @@ -3960,83 +3959,82 @@ Bug Fixes since HDF5-1.6.2 release Tools ----- - On SGI h5dump displayed only part of the data due to the bug - in the system printf; fixed. - EIP - 2004/09/21 - Documentation - ------------- - - Several descriptive errors have been fixed throughout the - documentation, particularly in the reference manual (RM). - A selection particularly worthy of note would be these: + in the system printf; fixed. + EIP - 2004/09/21 + Documentation + ------------- + - Several descriptive errors have been fixed throughout the + documentation, particularly in the reference manual (RM). + A selection particularly worthy of note would be these: - The H5Pset_szip description in the RM has been expanded and - corrected to facilitate use of SZIP compression. + corrected to facilitate use of SZIP compression. - A note has been added to the H5Dcreate description that an - unexplained failure is likely to be due to a property list error - that is detected only at the time of dataset creation. - - - FMB - 2004/09/21 + unexplained failure is likely to be due to a property list error + that is detected only at the time of dataset creation. + FMB - 2004/09/21 F90 API ------- - - Fortran functions h5dwrite/read_f and h5awrite/read_f do not - accept dims parameter of INTEGER type anymore. Code was removed. + - Fortran functions h5dwrite/read_f and h5awrite/read_f do not + accept dims parameter of INTEGER type anymore. Code was removed. 2004/04/15 + C++ API ------- - - H5::Exception's and its subclasses' constructors that were - overloaded to take char pointers are removed and constructors - that passed in reference of 'string' are changed to pass - by value. In addition, the default value of the data member - H5::Exception::detailMessage is changed from 0/NULL to - DEFAULT_MSG ("No detailed information provided".) - - Prototype for DSetCreatPropList::setLayout is changed: 1st parameter - is removed because it was there only by mistake. - BMR 2004/08/04 + - H5::Exception's and its subclasses' constructors that were + overloaded to take char pointers are removed and constructors + that passed in reference of 'string' are changed to pass + by value. In addition, the default value of the data member + H5::Exception::detailMessage is changed from 0/NULL to + DEFAULT_MSG ("No detailed information provided".) + - Prototype for DSetCreatPropList::setLayout is changed: 1st parameter + is removed because it was there only by mistake. + BMR 2004/08/04 Documentation ============= HDF5 Library documentation -------------------------- - HDF5 C++ API Reference Manual - This document has been added to the HDF5 document set. - The predecessor document, "HDF5 C++ Interfaces," has been removed. + This document has been added to the HDF5 document set. + The predecessor document, "HDF5 C++ Interfaces," has been removed. - HDF5 C++ API Design Specification - A first draft of this document has been added to the HDF5 document - set. The draft has been posted on the HDF5 website and a link - has been added to the HDF5 documents index (index.html at the top - level of the document set). + A first draft of this document has been added to the HDF5 document + set. The draft has been posted on the HDF5 website and a link + has been added to the HDF5 documents index (index.html at the top + level of the document set). - Parallel HDF5 - In prior releases, the HDF5 document set included two parallel - HDF5 documents. Those documents have been deleted and the - HDF5 documents index (index.html) now links to a "Parallel HDF5" - page on the HDF5 website (http://hdf.ncsa.uiuc.edu/HDF5/PHDF5/). + In prior releases, the HDF5 document set included two parallel + HDF5 documents. Those documents have been deleted and the + HDF5 documents index (index.html) now links to a "Parallel HDF5" + page on the HDF5 website (http://hdf.ncsa.uiuc.edu/HDF5/PHDF5/). - HDF5 High Level APIs - Links to the HDF5 High Level APIs and to the HDF5 High Level - Reference Manual have been added to the HDF5 documents index - (index.html). + Links to the HDF5 High Level APIs and to the HDF5 High Level + Reference Manual have been added to the HDF5 documents index + (index.html). - HDF5 Reference Manual - Tools: h5repack -- A description of the new h5repack tool has been + Tools: h5repack -- A description of the new h5repack tool has been added to the Tools page. - Tools: h5dump -- Several new options have been added to h5dump. - New functions -- All new functions have been added to the RM. - API changes -- Relevant function descriptions have been updated in - instances where programming interfaces have changed. - FMB - 2004/09/21 + Tools: h5dump -- Several new options have been added to h5dump. + New functions -- All new functions have been added to the RM. + API changes -- Relevant function descriptions have been updated in + instances where programming interfaces have changed. + FMB - 2004/09/21 Windows installation documentation ---------------------------------- - - INSTALL_Windows.txt has been enhanced to include instructions building - HDF5 with FORTRAN and C++. + - INSTALL_Windows.txt has been enhanced to include instructions building + HDF5 with FORTRAN and C++. - Two optional installation documents have been added. They are - INSTALL_Windows_Short.txt and INSTALL_Windows_From_Command_Line.txt. - INSTALL_Windows_Short.txt is supposed to help general users who - only want to build,test and install HDF5 in a quick way. - INSTALL_Windows_From_Command_Line.txt is supposed to help users who - would like to compile,test and install HDF5 in command line environment. + INSTALL_Windows_Short.txt and INSTALL_Windows_From_Command_Line.txt. + INSTALL_Windows_Short.txt is supposed to help general users who + only want to build,test and install HDF5 in a quick way. + INSTALL_Windows_From_Command_Line.txt is supposed to help users who + would like to compile,test and install HDF5 in command line environment. - INSTALL_Windows_withcpp.txt and INSTALL_Windows_withF90.txt became - obsolete. Files are deleted from the release_docs directory. - KY 2004/09/16, EIP 2004/9/21 - + obsolete. Files are deleted from the release_docs directory. + KY 2004/09/16, EIP 2004/9/21 + Platforms Tested @@ -4044,14 +4042,14 @@ Platforms Tested AIX 5.1 (32 and 64-bit) xlc 6.0.0.6 xlf 8.1.1.3 - xlC 6.0.0.6 - mpcc_r 6.0.0.6 + xlC 6.0.0.6 + mpcc_r 6.0.0.6 mpxlf_r 8.1.1.3 - xlc 5.0.2.5 - xlf 7.1.1.2 - xlC 5.0.2.5 - mpcc_r 5.0.2.5 - mpxlf_r 7.1.1.2 + xlc 5.0.2.5 + xlf 7.1.1.2 + xlC 5.0.2.5 + mpcc_r 5.0.2.5 + mpxlf_r 7.1.1.2 AIX 5.2 xlc 6.0.0.8 xlC 6.0.0.8 xlf 8.1.1.6 @@ -4065,14 +4063,14 @@ Platforms Tested Cray Fortran Version 3.6.0.3.1 FreeBSD 4.9 gcc 2.95.4 g++ 2.95.4 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 MPIch 1.2.4 IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m F90 MIPSpro 7.3.1.3m (64 only) C++ MIPSpro cc 7.3.1.3m - mpt 1.6 + mpt 1.6 Linux 2.4.18 gcc 2.96, 3.3.2 g++ 3.3.2 Intel(R) C++ Version 7.1 @@ -4085,27 +4083,27 @@ Platforms Tested MPIch 1.2.4 Linux 2.4.21-2.9.5ws #3 gcc 3.2.3 (Red Hat Linux 3.2.3-16) SMP x86_64 g++ 3.2.3 - Linux 2.4.21-4.ELsmp Intel(R) C++ 32-bit Version 8.0 - Intel(R) Fortran 32-bit Version 8.0 - gcc 3.4.0 - MPICH 1..5.2 Inmel 8.0 + Linux 2.4.21-4.ELsmp Intel(R) C++ 32-bit Version 8.0 + Intel(R) Fortran 32-bit Version 8.0 + gcc 3.4.0 + MPICH 1..5.2 Inmel 8.0 Linux 2.4.19-SMP x86_64 gcc (GCC) 3.2.2 (SuSE Linux) g++ 3.2.2 Linux 2.6.4-52smp x86_64 gcc 3.3.3 (SuSE Linux 9.1 AMD64)) - PGI 5.2-1 C and F90 + PGI 5.2-1 C and F90 - Linux 2.4.21-sgi Altix + Linux 2.4.21-sgi Altix SMP ia64 Intel(R) C++ Version 8.0 Intel(R) Fortran Itanium(R) Version 8.0 SGI MPI - OSF1 V5.1 Compaq C V6.5-303 + OSF1 V5.1 Compaq C V6.5-303 HP Fortran V5.5A-3548 - Compaq C++ V6.5-040 - MPI_64bit_R13 + Compaq C++ V6.5-040 + MPI_64bit_R13 SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 - WorkShop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 + WorkShop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8(32 and 64 bit) Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 @@ -4116,9 +4114,9 @@ Platforms Tested Intel(R) Fortran Compiler Version 7.0 Xeon Linux 2.4.20-31.9smp_perfctr_lustre - Intel(R) C++ Version 8.0 + Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 - + IA-64 Linux 2.4.16 ia64 gcc version 3.0.4 Intel(R) C++ Version 7.1 Intel(R) Fortran Compiler Version 7.1 @@ -4126,23 +4124,23 @@ Platforms Tested IA-64 Linux 2.4.21.SuSE_128.bef1 ia64 Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 - mpich-gm-1.2.5..intel + mpich-gm-1.2.5..intel Windows 2000 (NT5.0) MSVC++ 6.0 MSVC++ .NET DEC Visual Fortran 6.0 Intel C and F90 compilers version 7.1 - Code Warrior 8.0 + Code Warrior 8.0 Windows XP MSVC++.NET MSVC++ 6.0 DEC Visual Fortran 6.0 MAC OS X Darwin 7.5 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.3.2 - IBM XL Fortran version 8.1 + IBM XL Fortran version 8.1 Absoft Fortran compiler v8.2 - + Supported Configuration Features Summary @@ -4155,7 +4153,7 @@ Key: y = tested and supported ( ) = footnote appears below second table Platform C F90 F90 C++ zlib SZIP - parallel parallel + parallel parallel Solaris2.7 64-bit y (1) y y (1) y y y Solaris2.7 32-bit y (1) y y (1) y y y Solaris2.8 64-bit y (1) y y (1) y y y @@ -4187,8 +4185,8 @@ Linux 2.4 SuSE ia64 C Intel (3,8) y y y y y y Linux 2.4 SGI Altix ia64 Intel (3) y y y y y y -Platform Shared static- Thread- STREAM- - libraries (4) exec safe VFD +Platform Shared static- Thread- STREAM- + libraries (4) exec safe VFD Solaris2.7 64-bit y x y y Solaris2.7 32-bit y x y y Solaris2.8 64-bit y x y y @@ -4221,19 +4219,19 @@ Linux 2.4 SGI Altix ia64 Intel (3) y y n y -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, +Compiler versions for each platform are listed in the "Platforms Tested" +table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: (1) Using mpich 1.2.4 (2) Using mpt and mpich 1.2.4 - (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated + (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated W or C indicates workstation or cluster, respectively - (4) Shared libraries are provided only for the C library, + (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++ (5) Using mpt (6) Intel 7.1 compilers in Visual Studio 6.0 environment - (7) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre + (7) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre and Intel compilers (8) Linux 2.4.21, SuSE_128.befl. Ia64 cluster with Intel compilers (9) DEC Visual Fortran 6.0 and Intel 7.1 @@ -4249,14 +4247,14 @@ Known Problems ============== * h5fc and h5c++ compilation scripts have a bug: object files (*.o) cannot be created when source code is compiled using h5fc or h5c++. We will provide - a fix. Please check ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/ + a fix. Please check ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/ for the patches. * Fortran subroutine h5pget_driver_f doesn't return a correct driver information. * There are two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5) failed on windows xp with .NET for debug and debug dll. Release and Release - dll work fine. + dll work fine. * The h5dump tests may fail to match the expected output on some platforms (e.g. parallel jobs, Windows) where the error messages directed to @@ -4276,7 +4274,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. - + It is suggested that you don't use this option on these platforms during configuration. @@ -4295,7 +4293,7 @@ Known Problems the different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: @@ -4303,7 +4301,7 @@ Known Problems * On some platforms that use Intel and Absoft compilers to build HDF5 fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line + complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) * On IA32 and IA64 systems, if you use a compiler other than GCC (such as @@ -4411,7 +4409,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -4435,31 +4433,31 @@ New Features Configuration: -------------- - Default of $prefix is changed to $PWD/hdf5 so that multiple - builds using --srcdir is possible in the same machine. - AKC - 2003/12/1 + builds using --srcdir is possible in the same machine. + AKC - 2003/12/1 Library: -------- - Added H5Iget_ref, H5Iinc_ref and H5Idec_ref routines to the C - library and the FORTRAN wrapper. See the reference manual for a - full description of these new routines. QAK - 2003/12/11 + library and the FORTRAN wrapper. See the reference manual for a + full description of these new routines. QAK - 2003/12/11 Parallel Library: ----------------- - - The parallel tests in testpar/ now provides different levels of - verbosity via the '-v' option. The default is less verbose - than before. AKC - 2004/01/23 + - The parallel tests in testpar/ now provides different levels of + verbosity via the '-v' option. The default is less verbose + than before. AKC - 2004/01/23 - Added parallel test, test_mpio_1wMr, which tests if the - underlaying parallel I/O system is conforming to the POSIX - write/read requirement. This version includes options of using - atomicity and file-sync. AKC - 2003/11/27 + underlying parallel I/O system is conforming to the POSIX + write/read requirement. This version includes options of using + atomicity and file-sync. AKC - 2003/11/27 Tools: ------ - Added option -showconfig to compiler tools (h5cc,h5fc,h5c++). - AKC - 2004/01/08 - - Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc" - respectively if library is built in parallel mode. AKC - 2004/01/07 + AKC - 2004/01/08 + - Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc" + respectively if library is built in parallel mode. AKC - 2004/01/07 - Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03 C++ API: @@ -4469,8 +4467,8 @@ New Features Support for new platforms, languages and compilers. ======================================= - HDF5 Fortran APIs are supported on MAC OSX with IBM XL Fortran compiler - version 8.1 Beta - Use --disbale-shared --enable-static flags with configure when + version 8.1 Beta + Use --disbale-shared --enable-static flags with configure when building HDF5 Fortran Library on MAC OSX. - C and C++ Libraries are available for Linux64 RH8 - C, C++ and Fortran sequential Libraries, and C and Fortran parallel @@ -4547,12 +4545,12 @@ Bug Fixes since HDF5-1.6.1 release Tools ----- - - Fixed h5redeploy which sometimes complain too many argument for the - test command. (The complain did not hinder the h5redploy to proceed - correctly.) AKC - 2003/11/03 + - Fixed h5redeploy which sometimes complain too many argument for the + test command. (The complain did not hinder the h5redploy to proceed + correctly.) AKC - 2003/11/03 - Documentation - ------------- + Documentation + ------------- Documentation @@ -4565,12 +4563,12 @@ Platforms Tested AIX 5.1 (32 and 64-bit) xlc 6.0.0.2 xlf 8.1.0.3 - xlC 6.0.0.4 - xlc 5.0.2.5 - xlf 7.1.1.2 - xlC 5.0.2.5 - mpcc_r 5.0.2.5 - mpxlf_r 7.1.1.2 + xlC 6.0.0.4 + xlc 5.0.2.5 + xlf 7.1.1.2 + xlC 5.0.2.5 + mpcc_r 5.0.2.5 + mpxlf_r 7.1.1.2 poe 3.2.0.10 Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2 Cray Fortran Version 3.6.0.2 @@ -4580,7 +4578,7 @@ Platforms Tested Cray Fortran Version 3.4.0.0 FreeBSD 4.9 gcc 2.95.4 g++ 2.95.4 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 MPIch 1.2.4 @@ -4601,20 +4599,20 @@ Platforms Tested Linux 2.4.19-SMP x86_64 gcc (GCC) 3.2.2 (SuSE Linux) g++ 3.2.2 - Linux 2.4.21-sgi Altix + Linux 2.4.21-sgi Altix SMP ia64 Intel(R) C++ Version 7.1 Intel(R) Fortran Itanium(R) Version 7.1 SGI MPI OSF1 V5.1 Compaq C V6.4-014 - Compaq Fortran V5.5-2602 - Compaq Fortran V5.5-1877 - Compaq C++ V6.5-033 - Compaq C++ V6.5-030 - MPI_64bit_R13 + Compaq Fortran V5.5-2602 + Compaq Fortran V5.5-1877 + Compaq C++ V6.5-033 + Compaq C++ V6.5-030 + MPI_64bit_R13 SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 - WorkShop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 + WorkShop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8(32 and 64 bit) Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 @@ -4623,7 +4621,7 @@ Platforms Tested IA-32 Linux 2.4.18 gcc 2.96 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 - + IA-64 Linux 2.4.16 ia64 gcc version 3.0.4 Intel(R) C++ Version 7.1 Intel(R) Fortran Compiler Version 7.1 @@ -4631,18 +4629,18 @@ Platforms Tested IA-64 Linux 2.4.21.SuSE_128.bef1 ia64 Intel(R) C++ Version 7.1 Intel(R) Fortran Compiler Version 7.1 - mpich-gm-1.2.5..intel + mpich-gm-1.2.5..intel Windows 2000 (NT5.0) MSVC++ 6.0 DEC Visual Fortran 6.0 Intel C and F90 compilers version 7.1 - Code Warrior 8.0 + Code Warrior 8.0 Windows XP MSVC++.NET MAC OS X Darwin 7.2 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.3.2 IBM XL Fortran version 8.1 Beta - + Supported Configuration Features Summary @@ -4686,10 +4684,10 @@ RedHat 7.1 ia64 C Intel (3) y n y n y n y RedHat 8 & SuSe x86_64 y n n n y n y gcc (3) Linux 2.4 SGI Altix ia64 y n y n y y y - Intel (3) + Intel (3) -Platform static- Thread- SZIP GASS STREAM- High- H4/H5 +Platform static- Thread- SZIP GASS STREAM- High- H4/H5 exec safe VFD level tools APIs (6) Solaris2.7 64-bit x y y n y y n @@ -4722,21 +4720,21 @@ RedHat 7.1 ia64 C Intel (3) y n y n y y y RedHat 8 & SuSe x86_64 y n y n y y y gcc (3) Linux 2.4 SGI Altix ia64 y n y n y y y - Intel (3) + Intel (3) -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, +Compiler versions for each platform are listed in the "Platforms Tested" +table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: (1) Using mpich 1.2.4. (2) Using mpt and mpich 1.2.4. - (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. + (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. - (4) Shared libraries are provided only for the C library, + (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++. (5) Using mpt. - (6) Includes the H4toH5 Library and the h4toh5 and h5toh4 + (6) Includes the H4toH5 Library and the h4toh5 and h5toh4 utilities. @@ -4746,7 +4744,7 @@ Known Problems * There are two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5) failed on windows xp with .NET for debug and debug dll. Release and Release - dll work fine. + dll work fine. * The h5dump tests may fail to match the expected output on some platforms (e.g. parallel jobs, Windows) where the error messages directed to @@ -4766,7 +4764,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. - + It is suggested that you don't use this option on these platforms during configuration. @@ -4786,7 +4784,7 @@ Known Problems the different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: @@ -4794,7 +4792,7 @@ Known Problems * On some platforms that use Intel compilers to build HDF5 fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line + complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) * On IA32 and IA64 systems, if you use a compiler other than GCC (such as @@ -4823,7 +4821,7 @@ Known Problems Testing random sw long double -> double conversions If -ieee is used, the converted doubles spread over the range 0.0 to 1**-308. If -ieee is not used, the converted double values are mostly 0.0 but - occassionaly as 1**-308. This has been reported to the system staff. + occasionally as 1**-308. This has been reported to the system staff. All other tests have passed. * On AIX 5.1 when 64-bit parallel C Library is built with zlib configured in, @@ -4848,7 +4846,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -4921,7 +4919,7 @@ New Features Support for new platforms, languages and compilers. ======================================= - gcc 3.3.1 is supported on Linux. - + Bug Fixes since HDF5-1.6.0 release ================================== @@ -5003,25 +5001,25 @@ Bug Fixes since HDF5-1.6.0 release Tools ----- - - Fixed a segmentation fault of h5diff when percentage option is used. + - Fixed a segmentation fault of h5diff when percentage option is used. AKC - 2003/08/27 - Switched away from tools using internal "fixtype" function(s) to use H5Tget_native_type() internally. QAK - 2003/08/25 - Documentation - ------------- - - Added two missing Fortran APIs (h5pget_fapl_mpiposix_f and + Documentation + ------------- + - Added two missing Fortran APIs (h5pget_fapl_mpiposix_f and h5pset_fapl_mpiposix_f) to the reference manual. FMB - 2003/10/15 - - Corrected the reference manual descriptions of H5open/h5open_f and - H5close/h5close_f to indicate that these calls are required in + - Corrected the reference manual descriptions of H5open/h5open_f and + H5close/h5close_f to indicate that these calls are required in Fortran90 applications. FMB - 2003/10/15 Documentation ============= - Fortran90 APIs are being integrated into the main body of the + Fortran90 APIs are being integrated into the main body of the HDF5 Reference Manual (RM). This process is complete in all RM sections except H5P. @@ -5035,12 +5033,12 @@ Platforms Tested AIX 5.1 (32 and 64-bit) xlc 6.0.0.2 xlf 8.1.0.3 - xlC 6.0.0.4 - xlc 5.0.2.5 - xlf 7.1.1.2 - xlC 5.0.2.5 - mpcc_r 5.0.2.5 - mpxlf_r 7.1.1.2 + xlC 6.0.0.4 + xlc 5.0.2.5 + xlf 7.1.1.2 + xlC 5.0.2.5 + mpcc_r 5.0.2.5 + mpxlf_r 7.1.1.2 poe 3.2.0.10 Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2 Cray Fortran Version 3.6.0.2 @@ -5050,7 +5048,7 @@ Platforms Tested Cray Fortran Version 3.4.0.3 FreeBSD 4.9 gcc 2.95.4 g++ 2.95.4 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 HP MPI 01.07.00.00 @@ -5067,14 +5065,14 @@ Platforms Tested Linux 2.4.20-8 gcc 3.2.2 OSF1 V5.1 Compaq C V6.4-014 Compaq C V6.3-027 - Compaq Fortran V5.5-2602 - Compaq C++ V6.5-030 - MPI_64bit_R5 + Compaq Fortran V5.5-2602 + Compaq C++ V6.5-030 + MPI_64bit_R5 g++ version 3.0 for C++ SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 - WorkShop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 + WorkShop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8(32 and 64 bit) Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 @@ -5083,19 +5081,19 @@ Platforms Tested IA-32 Linux 2.4.9 gcc 2.96 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 - + IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 Windows 2000 (NT5.0) MSVC++ 6.0 DEC Visual Fortran 6.0 Intel C and F90 compilers version 7.1 - Code Warrior 8.0 + Code Warrior 8.0 Windows XP MSVC++.NET MAC OS X Darwin 6.8 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.1 - + Supported Configuration Features Summary @@ -5114,7 +5112,7 @@ Solaris2.7 64-bit y y (1) y y (1) y y y Solaris2.7 32-bit y y (1) y y (1) y y y Solaris2.8 64-bit y y (1) y y (1) y y y Solaris2.8 32-bit y y y y (1) y y y -IRIX6.5 y y (1) n n n y y +IRIX6.5 y y (1) n n n y y IRIX64_6.5 64-bit y y (2) y y y y y IRIX64_6.5 32-bit y y (2) n n n y y HPUX11.00 y y (1) y y y y y @@ -5141,7 +5139,7 @@ Linux 2.4 IA64 Intel y n y n y n y ASCII Table 2 -- for RELEASE.txt -Platform static- Thread- SZIP GASS STREAM- High-level H4/H5 +Platform static- Thread- SZIP GASS STREAM- High-level H4/H5 exec safe VFD APIs tools (7) Solaris2.7 64-bit x y y n y y n Solaris2.7 32-bit x y y n y y y @@ -5174,12 +5172,12 @@ Linux 2.4 IA64 Intel y n y n y y y Notes: (1) Using mpich 1.2.4. (2) Using mpt and mpich 1.2.4. (3) Linux 2.4 with GNU, Intel, and PGI compilers, respectively. - (4) Shared libraries are provided only for the C library, except + (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++. (5) Using mpt. - (6) Binaries only; source code for this platform is not being + (6) Binaries only; source code for this platform is not being released at this time. - (7) Includes the H4toH5 Library and the h4toh5 and h5toh4 + (7) Includes the H4toH5 Library and the h4toh5 and h5toh4 utilities. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. @@ -5189,10 +5187,10 @@ Linux 2.4 IA64 Intel y n y n y y y Known Problems ============== * Fortran subroutine h5pget_driver_f doesn't return a correct driver information. - The fix willl be available in the 1.6.2 release. + The fix will be available in the 1.6.2 release. * There are two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5) failed on windows xp with .NET for debug and debug dll. Release and Release - dll work fine. + dll work fine. * The h5dump tests may fail to match the expected output on some platforms (e.g. parallel jobs, Windows) where the error messages directed to @@ -5212,7 +5210,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. - + It is suggested that you don't use this option on these platforms during configuration. @@ -5221,7 +5219,7 @@ Known Problems able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' - + This warning is innocuous and can be safely ignored. @@ -5241,14 +5239,14 @@ Known Problems the different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: * On some platforms that use Intel compilers to build HDF5 fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line + complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays @@ -5272,6 +5270,8 @@ Known Problems * Information about building with PGI and Intel compilers is available in INSTALL file sections 5.7 and 5.8 + + %%%%1.6.0%%%% Release Information for hdf5-1.6.0 (03/July/03) 14. Release information for HDF5 version 1.6.0 @@ -5291,7 +5291,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -5336,8 +5336,8 @@ Library: For more information see http://hdf.ncsa.uiuc.edu/HDF5/doc_resource/SZIP/index.html http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide.html - http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide/Changes.html - + http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide/Changes.html + Complete list of changes: * Changed dataset modification time to _not_ be updated when raw data is @@ -5365,16 +5365,16 @@ Library: I/O filters: H5Pmodify_filter, H5Pget_filter_by_id and H5Pall_filters_avail. Also changed H5Zregister to use new method of registering filters with library. QAK - 2003/04/08 - * The first version of szip compression support were implemented. + * The first version of szip compression support were implemented. User should have static szlib library installed. Using function H5Pset_szip to pass the szip parameters to the HDF5 library. - More detailed decription of the process will be followed. + More detailed description of the process will be followed. KY-2003/04/01 - * Added Fletcher32 checksum as a filter in pipeline. It only works in + * Added Fletcher32 checksum as a filter in pipeline. It only works in chunked dataset. SLU - 2003/2/11 * MPICH/MPE instrumentation feature added. Use --with-mpe[=DIR] to configure it. AKC - 2003/1/3 - * New functions H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx + * New functions H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx are added to the library. SLU - 2002/11/25 * H5Dget_offset is added to return the offset of a dataset's data relative to the beginning of the file. SLU - 2002/11/7 @@ -5399,7 +5399,7 @@ Library: H5D_SPACE_ALLOC_LATE for H5Dset_space_time(). This allows chunked datasets to be incrementally allocated as in the 1.4.x branch. QAK - 2002/08/27 - * Compact dataset is added to the library. The data will be stored in + * Compact dataset is added to the library. The data will be stored in the header message of dataset layout. Space allocation time has to be EARLY. No hyperslab is supported for parallel collective write. There is no API changes except activating H5Pset_layout and H5Pget_layout for @@ -5413,18 +5413,18 @@ Library: This can improve parallel I/O performance for chunked datasets. QAK - 2002/05/17 * New functions H5Glink2 and H5Gmove2 were added to allow link and move to - be in different locations in the same file. The old functions H5Glink - and H5Gmove remain valid. SLU - 2002/04/26 - * Fill-value's behaviors for contiguous dataset have been redefined. - Basicly, dataset won't allocate space until it's necessary. Full details + be in different locations in the same file. The old functions H5Glink + and H5Gmove remain valid. SLU - 2002/04/26 + * Fill-value's behaviors for contiguous dataset have been redefined. + Basically, dataset won't allocate space until it's necessary. Full details are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment. SLU - 2002/04/11 * Added new routine "H5Dfill" to fill a selection with a particular value in memory. QAK - 2002/04/09 * Improved performance of "regular" hyperslab I/O when using MPI-IO and the - datatype conversion is unneccessary. QAK - 2002/04/02 + datatype conversion is unnecessary. QAK - 2002/04/02 * Improved performance of single hyperslab I/O when datatype conversion is - unneccessary. QAK - 2002/04/02 + unnecessary. QAK - 2002/04/02 * Added new "H5Sget_select_type" API function to determine which type of selection is defined for a dataspace ("all", "none", "hyperslab" or "point"). QAK - 2002/02/07 @@ -5436,14 +5436,14 @@ Library: in order to correctly handle dataset region references. Moved H5Rget_object_type() to be only compiled into the library when v1.4 compatibility is enabled. - * Added a new file access property, file close degree, to control file + * Added a new file access property, file close degree, to control file close behavior. It has four values, H5F_CLOSE_WEAK, H5F_CLOSE_SEMI, - H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspont functions - H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two + H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspond functions + H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two new functions H5Fget_obj_count and H5Fget_obj_ids are offerted to assist - this new feature. For full details, please refer to the reference - manual under the description of H5Fcreate, H5Fopen, H5Fclose and the - functions mentioned above. + this new feature. For full details, please refer to the reference + manual under the description of H5Fcreate, H5Fopen, H5Fclose and the + functions mentioned above. * Removed H5P(get|set)_hyper_cache API function, since the property is no longer used. * Improved performance of non-contiguous hyperslabs (built up with @@ -5458,7 +5458,7 @@ Library: * Improved regular hyperslab I/O by about a factor of 6 or so. * Modified the Pablo build procedure to permit building of the instrumented library to link either with the Trace libraries as before or with the - Pablo Performance Caputure Facility. + Pablo Performance Capture Facility. * Added new F90 APIs for generic properties, new filters, and time/space allocation properties. * C++ API: @@ -5481,19 +5481,19 @@ Tools: QAK - 2003/06/06 * h5diff to compare two HDF5 files was added * h5import to import ascii and binary data to an HDF5 file was added. - Old h5import tool in the tools/misc directory was renamed to - h5createU8 to reflect its purpose. h5createU8 will be deleted in - 1.6.1 release. + Old h5import tool in the tools/misc directory was renamed to + h5createU8 to reflect its purpose. h5createU8 will be deleted in + 1.6.1 release. * Two new scripts h5fc and h5c++ were added to compile F90 and C++ HDF5 applications. Support for new platforms, languages and compilers. ======================================= * Added C++ API support on HPUX11.00. BMR - 2003/03/19 - * Absoft compiler is supported for Fortran HDF5 Library. + * Absoft compiler is supported for Fortran HDF5 Library. When building with Absoft compiler, add -DH5_ABSOFT to C compilation flags to get correct names of C functions - called by Fortran APIs. + called by Fortran APIs. Bug Fixes since HDF5-1.4.0 release @@ -5527,7 +5527,7 @@ Library for floating point data). This adds a new API function: H5Pset_shuffle. KY - 2002/11/13 * Allow scalar dataspaces to be used for parallel I/O. QAK - 2002/11/05 - * New functions H5Gget_comment(modification), H5Aget_storage_size, + * New functions H5Gget_comment(modification), H5Aget_storage_size, H5Arename. SLU - 2002/10/29 * Fixed an assertion of H5S_select_iterate that did not account for scalar type that has no dimension sizes. AKC - 2002/10/15 @@ -5536,10 +5536,10 @@ Library * Fixed data corruption problem which could occur when fill values were written to a contiguously stored dataset in parallel. QAK - 2002/08/27 * Fixed VL memory leak when data is overwritten. The heap objects holding - old data are freed. If the fill value writting time is set to + old data are freed. If the fill value writing time is set to H5D_FILL_TIME_NEVER, the library prohibits user to create VL type dataset. - The library free all the heap objects storing VL type if there is nested - VL type(a VL type contains another VL type). SLU - 2002/07/10 + The library free all the heap objects storing VL type if there is nested + VL type(a VL type contains another VL type). SLU - 2002/07/10 * Tweaked a few API functions to use 'size_t' instead of 'unsigned' or 'hsize_t', which may cause errors in some cases. @@ -5563,17 +5563,17 @@ Performance Tools ----- - * Added a -force option to h5redeploy. AKC - 2003/03/04 + * Added a -force option to h5redeploy. AKC - 2003/03/04 * The VL string bug(data and datatype cannot be shown) in h5dump is fixed. -SLU - 2002/11/18 - * Fixed segfault if h5dump was invoked with some options but no file + * Fixed segfault if h5dump was invoked with some options but no file (e.g., h5dump -H). -AKC, 2002/10/15 * Fixed so that the "-i" flag works correctly with the h5dumper. * Fixed segfault when "-v" flag was used with the h5dumper. -Documentation -------------- +Documentation +------------- @@ -5585,12 +5585,12 @@ Platforms Tested AIX 5.1 (32 and 64-bit) xlc 6.0.0.2 xlf 8.1.0.3 - xlC 6.0.0.4 - xlc 5.0.2.5 - xlf 7.1.1.2 - xlC 5.0.2.5 - mpcc_r 5.0.2.5 - mpxlf_r 7.1.1.2 + xlC 6.0.0.4 + xlc 5.0.2.5 + xlf 7.1.1.2 + xlC 5.0.2.5 + mpcc_r 5.0.2.5 + mpxlf_r 7.1.1.2 poe 3.2.0.10 Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2 Cray Fortran Version 3.6.0.0.2 @@ -5603,7 +5603,7 @@ Platforms Tested mpt 2.1.0.0 FreeBSD 4.7 gcc 2.95.4 g++ 2.95.5 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 MPIch 1.2.4 @@ -5619,14 +5619,14 @@ Platforms Tested MPIch 1.2.4 OSF1 V5.1 Compaq C V6.4-014 Compaq C V6.3-027 - Compaq Fortran V5.5-1877 - Compaq C++ V6.5-014 - MPI_64bit_R5 + Compaq Fortran V5.5-1877 + Compaq C++ V6.5-014 + MPI_64bit_R5 g++ version 3.0 for C++ SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 - WorkShop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 + WorkShop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8/32 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 @@ -5638,19 +5638,19 @@ Platforms Tested IA-32 Linux 2.4.9 gcc 2.96 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 - + IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 Windows 2000 (NT5.0) MSVC++ 6.0 DEC Visual Fortran 6.0 Intel C and F90 compilers version 7.1 - Code Warrior 8.0 + Code Warrior 8.0 Windows XP MSVC++.NET MAC OS X Darwin 6.5 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1161, based on gcc version 3.1 - + Supported Configuration Features Summary @@ -5669,7 +5669,7 @@ Solaris2.7 64-bit y y (1) y y (1) y y y Solaris2.7 32-bit y y (1) y y (1) y y y Solaris2.8 64-bit y y (1) y y (1) y y y Solaris2.8 32-bit y y y y (1) y y y -IRIX6.5 y y (1) n n n y y +IRIX6.5 y y (1) n n n y y IRIX64_6.5 64-bit y y (2) y y y y y IRIX64_6.5 32-bit y y (2) n n n y y HPUX11.00 y y (1) y y y y y @@ -5696,7 +5696,7 @@ Linux 2.4 IA64 Intel y n y n y n y ASCII Table 2 -- for RELEASE.txt -Platform static- Thread- SZIP GASS STREAM- High-level H4/H5 +Platform static- Thread- SZIP GASS STREAM- High-level H4/H5 exec safe VFD APIs tools (7) Solaris2.7 64-bit x y y n y y n Solaris2.7 32-bit x y y n y y y @@ -5729,12 +5729,12 @@ Linux 2.4 IA64 Intel y n y n y y y Notes: (1) Using mpich 1.2.4. (2) Using mpt and mpich 1.2.4. (3) Linux 2.4 with GNU, Intel, and PGI compilers, respectively. - (4) Shared libraries are provided only for the C library, except + (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++. (5) Using mpt. - (6) Binaries only; source code for this platform is not being + (6) Binaries only; source code for this platform is not being released at this time. - (7) Includes the H4toH5 Library and the h4toh5 and h5toh4 + (7) Includes the H4toH5 Library and the h4toh5 and h5toh4 utilities. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. @@ -5766,7 +5766,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. - + It is suggested that you don't use this option on these platforms during configuration. @@ -5775,7 +5775,7 @@ Known Problems able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' - + This warning is innocuous and can be safely ignored. @@ -5795,14 +5795,14 @@ Known Problems the different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. -* Before building HDF5 F90 Library from source on Crays +* Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: * On some platforms that use Intel compilers to build HDF5 fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line + complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays @@ -5838,7 +5838,7 @@ INTRODUCTION This document describes the differences between HDF5-1.4.4 and HDF5-1.4.5, and contains information on the platforms tested and -known problems in HDF5-1.4.5. For additional information check the +known problems in HDF5-1.4.5. For additional information check the HISTORY.txt file in the HDF5 source. The HDF5 documentation can be found on the NCSA ftp server @@ -5847,7 +5847,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information, see the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -5880,7 +5880,7 @@ New Features o Library ========= o General - --------- + --------- * Allow scalar dataspaces to be used for parallel I/O. QAK - 2002/11/05 * Added environment variable "HDF5_DISABLE_VERSION_CHECK", which disables the version checking between the header files and the library linked @@ -5893,8 +5893,8 @@ New Features output format; function call and return event times can be logged; total time spent in each function can be logged. The following HDF5_DEBUG environment variable words affect tracing: - trace -- turn on/off basic tracing - ttimes -- turn on tracing and report event times and + trace -- turn on/off basic tracing + ttimes -- turn on tracing and report event times and time spent in each API function. ttop -- turn on tracing but display only top-level API calls. @@ -5903,7 +5903,7 @@ New Features ------ * Several missing fortran APIs have been added to the library: - h5get_libversion_f h5tget_member_index_f h5dget_storage_size_f + h5get_libversion_f h5tget_member_index_f h5dget_storage_size_f h5check_version_f h5tvlen_create_f h5dvlen_get_max_len_f h5garbage_collect_f h5dwrite_vl_f h5dont_atexit_f h5dread_vl_f @@ -5937,11 +5937,11 @@ New Features ========================================= * C++ API now works on the Origin2000 (IRIX6.5.14.) BMR - 2002/11/14 - + o Misc. ========================================= - HDF5 1.4.5 works with Portland Group Compilers (pgcc, pgf90 and pgCC - version 4.0-2) on Linux 2.4 + HDF5 1.4.5 works with Portland Group Compilers (pgcc, pgf90 and pgCC + version 4.0-2) on Linux 2.4 Bug Fixes since HDF5-1.4.4 Release @@ -5955,8 +5955,8 @@ Bug Fixes since HDF5-1.4.4 Release QAK - 2003/01/21 * Added improved error assertion for nil VL strings. It return error stack instead of a simple assertion. SLU - 2002/12/16 - * Fixed h5dump bug(cannot dump data and datatype) for VL string. - SLU - 2002/11/18 + * Fixed h5dump bug(cannot dump data and datatype) for VL string. + SLU - 2002/11/18 * Fixed error condition where "none" selections were not being handled correctly in serial & parallel. QAK - 2002/10/29 * Fixed problem where optimized hyperslab routines were incorrectly @@ -5980,15 +5980,15 @@ Platforms Tested AIX 5.1 (32 and 64-bit) C for AIX Compiler, Version 6 xlf 8.1.0.2 poe 3.2.0.11 - Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.1.3 - Cray Fortran Version 3.6.0.0.12 + Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.1.3 + Cray Fortran Version 3.6.0.0.12 Cray SV1 10.0.1. 0 Cray Standard C Version 6.6.0.1.3 Cray Fortran Version 3.6.0.0.12 Cray T90IEEE 10.0.1.01u Cray Standard C Version 6.4.0.2.3 Cray Fortran Version 3.4.0.3 FreeBSD 4.7 gcc 2.95.4 g++ 2.95.5 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 IRIX 6.5 MIPSpro cc 7.30 IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m @@ -6003,16 +6003,16 @@ Platforms Tested Compaq Fortran X5.4A-1684 gcc version 3.0 for C++ SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 - WorkShop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 + WorkShop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 Patch 109503-07 2001/08/11 Sun WorkShop 6 update 1 C++ 5.2 Patch 109508-04 2001/07/11 SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 Patch 109503-07 2001/08/11 Sun WorkShop 6 update 1 C++ 5.2 Patch 109508-04 2001/07/11 @@ -6021,7 +6021,7 @@ Platforms Tested IA-32 Linux 2.4.9 gcc 2.96 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 - + IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 @@ -6030,9 +6030,9 @@ Platforms Tested Windows XP .NET Windows NT4.0 Code Warrior 6.0 MAC OS X Darwin 6.2 - gcc and g++ Apple Computer, Inc. GCC + gcc and g++ Apple Computer, Inc. GCC version 1161, based on gcc version 3.1 - + Supported Configuration Features Summary @@ -6053,7 +6053,7 @@ Supported Configuration Features Summary Solaris2.7 32-bit y y (1) y y (1) y y y Solaris2.8 64-bit y n y y (1) y y y Solaris2.8 32-bit y n y y (1) y y y - IRIX6.5 y y (1) n n n y y + IRIX6.5 y y (1) n n n y y IRIX64_6.5 64-bit y y (2) y y y y y IRIX64_6.5 32-bit y y (2) n n n y y HPUX11.00 y y (1) y n n y y @@ -6075,7 +6075,7 @@ Supported Configuration Features Summary Linux 2.4 PGI (3) y n y n y n y Linux 2.4 IA32 y n y n n n y Linux 2.4 IA64 y n y n n n y - + Platform static- Thread- SRB GASS STREAM- exec safe VFD @@ -6111,23 +6111,23 @@ Supported Configuration Features Summary (2) Using mpt and mpich 1.2.4. (3) Linux 2.4 with GNU, Intel, and PGI compilers. (4) No HDF4-related tools. - (5) Shared libraries are provided only for the C library, + (5) Shared libraries are provided only for the C library, except on Windows where they are provided for all languages. (6) Debug mode only. - (7) Binaries only; source code for this platform is not being + (7) Binaries only; source code for this platform is not being released at this time. Known Problems ============== - * On Linux 2.4 IA64, Fortran test fails for h5dwrite_vl_f + * On Linux 2.4 IA64, Fortran test fails for h5dwrite_vl_f for integer and real base datatypes. * When fortran library is built with Intel compilers, compilation - for fflush1.f90, fflush2.f90 and fortanlib_test.f90 will fail + for fflush1.f90, fflush2.f90 and fortanlib_test.f90 will fail complaining about EXEC function. Comment the call to EXEC subroutine - in each program, or get a patch for the HDF5 Fortran source code. + in each program, or get a patch for the HDF5 Fortran source code. * Fortran external dataset test fails on Linux 2.4 with pgf90 compiler. @@ -6137,11 +6137,11 @@ Known Problems * Datasets or attributes which have a variable-length string datatype are not printing correctly with h5dump and h5ls. - * When a dataset with the variable-length datatype is overwritten, - the library can develop memory leaks that cause the file to become + * When a dataset with the variable-length datatype is overwritten, + the library can develop memory leaks that cause the file to become unnecessarily large. This is planned to be fixed in the next release. - * On the SV1, the h5ls test fails due to a difference between the + * On the SV1, the h5ls test fails due to a difference between the SV1 printf precision and the printf precision on other platforms. * The h5dump tests may fail to match the expected output on some @@ -6152,17 +6152,17 @@ Known Problems * The --enable-static-exec configure flag fails to compile for HP-UX 11.00 platforms. - * The executables are always dynamic on IRIX64 6.5(64 and n32) and + * The executables are always dynamic on IRIX64 6.5(64 and n32) and IRIX 6.5 even if they are configured with --enable-static-exec. * IRIX 6.5 fails to compile if configured with --enable-static-exec. - * The executables are always dynamic on Solaris 2.7 ans 2.8(64 and n32) + * The executables are always dynamic on Solaris 2.7 and 2.8(64 and n32) even if they are configured with --enable-static-exec. - + * The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause a hang in some cases when chunked storage is used. This is now set to - be off by default. One may turn it on by setting the environment + be off by default. One may turn it on by setting the environment variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1. * On OSF1 v5.1 and IA32 h5dumpgentst program that generates test files @@ -6173,10 +6173,10 @@ Known Problems * On Cray T3E (sn6606 2.0.6.08 unicosmk CRAY T3E) with Cray Standard C Version 6.6.0.1.3 compiler optimization causes errors in many HDF5 Library tests. Use -g -h zero flags - to build HDF5 Library. + to build HDF5 Library. - * On Cray SV1 10.0.1. 0 datatype convertion test fails. Please check HDF FTP site - if patch is available. We will try to provide one in the nearest future. + * On Cray SV1 10.0.1. 0 datatype conversion test fails. Please check HDF FTP site + if patch is available. We will try to provide one in the nearest future. * For configuration, building and testing with Intel and PGI compilers see corresponding section in INSTALL file. @@ -6200,7 +6200,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information, see the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -6223,32 +6223,32 @@ New Features ============ o Configuration ================ - * The H4 to H5 tools have been removed from the main source and placed + * The H4 to H5 tools have been removed from the main source and placed in a separate package. You can get these tools from the HDF ftp site - (ftp://hdf.ncsa.uiuc.edu/). The "--with-hdf4" command-line option + (ftp://hdf.ncsa.uiuc.edu/). The "--with-hdf4" command-line option during configure is no longer valid. BW - 2002/06/25 o Library ========= o General - --------- + --------- * Fill-value forward-compatibility with release 1.5 was added. SLU - 2002/04/11 * A new query function H5Tget_member_index has been added for compound - and enumeration data types. This function retrieves a member's index + and enumeration data types. This function retrieves a member's index by name. SLU - 2002/04/05 * Added serial multi-gigabyte file size test. "test/big -h" shows the help page. AKC - 2002/03/29 - + o APIs ------ - * The F90 subroutines h5dwrite_f, h5dread_f, h5awrite_f, and h5aread_f - were overloaded with a "dims" argument of type INTEGER(HSIZE_T) to - specify the size of the array. We recommend using these subroutines + * The F90 subroutines h5dwrite_f, h5dread_f, h5awrite_f, and h5aread_f + were overloaded with a "dims" argument of type INTEGER(HSIZE_T) to + specify the size of the array. We recommend using these subroutines with the new type; module subroutines that accept "dims" as an i - INTEGER array of size 7 will be deprecated in release 1.6. + INTEGER array of size 7 will be deprecated in release 1.6. EIP - 2002/05/06 - + o Performance ------------- * Added internal "small data" aggregation, which can reduce the number of @@ -6305,15 +6305,15 @@ New Features * Intel C++ and F90 compilers Version 6.0 are supported on Linux 2.4. * Intel C++ compilers Version 6.0 are supported on Windows 2000. - + o Misc. ========================================= * zlib has been moved out of the Windows source release. Users should go to - the ZLIB homepage(http://www.zlib.org) to download the corresponding + the ZLIB homepage(http://www.zlib.org) to download the corresponding zlib library. - * The Windows binary release is built with the old version of the zlib - library. We expect users to use zlib 1.1.4 to build with the source - release. + * The Windows binary release is built with the old version of the zlib + library. We expect users to use zlib 1.1.4 to build with the source + release. * In the Windows-specific install document, we specify how to test backward compatibility. However, in this release, we are not testing the backward compatibility of HDF5. @@ -6337,7 +6337,7 @@ Bug Fixes since HDF5-1.4.3 Release library to go into infinite loop. QAK - 2002/06/10 * Fixed bug (#699, fix provided by a user) where a scalar dataspace was written to the file and then subsequently queried with the - H5Sget_simple_extent_type function; type was reported as H5S_SIMPLE + H5Sget_simple_extent_type function; type was reported as H5S_SIMPLE instead of H5S_SCALAR. EIP - 2002/06/04 * Clear symbol table node "dirty" flag when flushing symbol tables to disk, to reduce I/O calls made & improve performance. QAK - 2002/06/03 @@ -6369,32 +6369,32 @@ Bug Fixes since HDF5-1.4.3 Release Performance Improvements ======================== This release of the HDF5 library has been extensively tuned to improve -performance, especially to improve parallel I/O performance. + performance, especially to improve parallel I/O performance. Most of the specific information for particular performance improvements -is mentioned in the "New Features" and "Bug Fixes since HDF5-1.4.3" sections -of this document, but in general, the library should make fewer and larger -I/O requests when accessing a file. Additionally, improvements to the parallel -I/O portions of the library should have reduced the communications and barriers -used in various internal algorithms, improving the performance of the library. + is mentioned in the "New Features" and "Bug Fixes since HDF5-1.4.3" sections + of this document, but in general, the library should make fewer and larger + I/O requests when accessing a file. Additionally, improvements to the parallel + I/O portions of the library should have reduced the communications and barriers + used in various internal algorithms, improving the performance of the library. However, with the extensive changes to some portions of the library that -were required for these improvements, some errors or unanticipated results may -have been introduced also. Please report any problems encountered to our -support team at hdfhelp@ncsa.uiuc.edu. + were required for these improvements, some errors or unanticipated results may + have been introduced also. Please report any problems encountered to our + support team at hdfhelp@ncsa.uiuc.edu. Hopefully these improvements will benefit all HDF5 applications, but if -there are particular I/O patterns that appear to be slower than necessary, -please send e-mail to hdfhelp@ncsa.uiuc.edu with a sample program showing the -problem behavior; we will look into the issue to see if it is possible to -address it. + there are particular I/O patterns that appear to be slower than necessary, + please send e-mail to hdfhelp@ncsa.uiuc.edu with a sample program showing the + problem behavior; we will look into the issue to see if it is possible to + address it. Documentation ============= * Documentation was updated for the hdf5-1.4.4 release. - * A new "HDF5 User's Guide" is under development. See + * A new "HDF5 User's Guide" is under development. See http://hdf.ncsa.uiuc.edu/HDF5/doc_dev_snapshot/H5_NewUG/current/. - * A "Parallel HDF5 Tutorial" is available at + * A "Parallel HDF5 Tutorial" is available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/. - * The "HDF5 Tutorial" is not distributed with this release. It is + * The "HDF5 Tutorial" is not distributed with this release. It is available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/. @@ -6408,20 +6408,20 @@ Platforms Tested AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0 xlf 7.1.0.2 poe 3.1.0.12 (includes mpi) - AIX 5.1 xlc 5.0.2.0 + AIX 5.1 xlc 5.0.2.0 xlf 07.01.0000.0002 mpcc_r 5.0.2.0; mpxlf_r 07.01.0000.0002 Cray T3E sn6711 2.0.5.57 Cray Standard C Version 6.5.0.3 Cray Fortran Version 3.5.0.4 - Cray SV1 10.0.1.1 Cray Standard C Version 6.5.0.3 + Cray SV1 10.0.1.1 Cray Standard C Version 6.5.0.3 Cray Fortran Version 3.5.0.4 FreeBSD 4.6 gcc 2.95.4 g++ 2.95.4 HP-UX B.10.20 HP C HP92453-01 A.10.32.30 HP F90 v2.3 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 - HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP MPI [not a product] (03/24/2000) B6060BA IRIX 6.5 MIPSpro cc 7.30 @@ -6440,16 +6440,16 @@ Platforms Tested Compaq Fortran V5.5-1877-48BBF gcc version 3.0 for C++ SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 - WorkShop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 + WorkShop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 Patch 109503-07 2001/08/11 Sun WorkShop 6 update 1 C++ 5.2 Patch 109508-04 2001/07/11 SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 Patch 109503-07 2001/08/11 Sun WorkShop 6 update 1 C++ 5.2 Patch 109508-04 2001/07/11 @@ -6459,7 +6459,7 @@ Platforms Tested gcc 2.96 Intel(R) C++ Version 6.0 Intel(R) Fortran Compiler Version 6.0 - + IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731 Intel(R) C++ Version 6.0 Intel(R) Fortran Compiler Version 6.0 @@ -6540,10 +6540,10 @@ Supported Configuration Features Summary Footnotes: (1) Using mpich. (2) Using mpt and mpich. - (3) When configured with static-exec enabled, tests fail in + (3) When configured with static-exec enabled, tests fail in serial mode. (4) No HDF4-related tools. - (5) Shared libraries are provided only for the C library, + (5) Shared libraries are provided only for the C library, except on Windows where they are provided for all languages. (6) Linux 2.4 with Intel compilers. @@ -6554,11 +6554,11 @@ Known Problems * Datasets or attributes which have a variable-length string datatype are not printing correctly with h5dump and h5ls. - * When a dataset with the variable-length datatype is overwritten, - the library can develop memory leaks that cause the file to become + * When a dataset with the variable-length datatype is overwritten, + the library can develop memory leaks that cause the file to become unnecessarily large. This is planned to be fixed in the next release. - * On the SV1, the h5ls test fails due to a difference between the + * On the SV1, the h5ls test fails due to a difference between the SV1 printf precision and the printf precision on other platforms. * The h5dump tests may fail to match the expected output on some @@ -6569,14 +6569,14 @@ Known Problems * The --enable-static-exec configure flag fails to compile for HP-UX 11.00 platforms. - * The executables are always dynamic on IRIX64 6.5(64 and n32) and + * The executables are always dynamic on IRIX64 6.5(64 and n32) and IRIX 6.5 even if they are configured with --enable-static-exec. * IRIX 6.5 fails to compile if configured with --enable-static-exec. - + * The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause a hang in some cases when chunked storage is used. This is now set to - be off by default. One may turn it on by setting the environment + be off by default. One may turn it on by setting the environment variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1. * On IA32 and IA64 systems, if you use a compiler other than GCC (such as @@ -6592,7 +6592,7 @@ Known Problems # How to pass a linker flag through the compiler. wl="-Wl," - * To build the Fortran library using Intel compilers, one has to + * To build the Fortran library using Intel compilers, one has to x modify the source code in the fortran/src directory to remove the !DEC and !MS compiler directives. x The build will fail in the fortran/test directory and then in the @@ -6600,7 +6600,7 @@ Known Problems those directories to contain two lines work.pc - ../src/work.pc + ../src/work.pc * To build the Fortran library on IA64 use setenv CC "ecc -DIA64" @@ -6627,7 +6627,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -6655,7 +6655,7 @@ New Features o Library ========= o General - --------- + --------- * Added a new test to verify the information provided by the configure command. * Changed internal error handling macros to reduce code size of library by @@ -6756,7 +6756,7 @@ Bug Fixes since HDF5-1.4.2 Release Documentation ============= * Documentation was updated for the hdf5-1.4.3 release. - * A new "HDF5 User's Guide" is under development. See + * A new "HDF5 User's Guide" is under development. See http://hdf.ncsa.uiuc.edu/HDF5/doc_dev_snapshot/H5_NewUG/current/. * Parallel Tutorial is available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/ @@ -6773,15 +6773,15 @@ Platforms Tested poe 3.1.0.12 (includes mpi) Cray T3E sn6711 2.0.5.57 Cray Standard C Version 6.5.0.3 Cray Fortran Version 3.5.0.4 - Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.3 + Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.3 Cray Fortran Version 3.5.0.4 FreeBSD 4.5 gcc 2.95.3 g++ 2.95.3 HP-UX B.10.20 HP C HP92453-01 A.10.32.30 HP F90 v2.3 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 - HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP MPI [not a product] (03/24/2000) B6060BA IRIX 6.5 MIPSpro cc 7.30 @@ -6792,19 +6792,19 @@ Platforms Tested gcc 2.95.2 with mpich 1.2.1 g++ 2.95.2 pgf90 3.2-4 - OSF1 V5.1 Compaq C V6.3-028 + OSF1 V5.1 Compaq C V6.3-028 Compaq Fortran V5.4-1283 SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 - Workshop Compilers 5.0 98/10/25 - FORTRAN 90 2.0 Patch 107356-04 + (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 + Workshop Compilers 5.0 98/10/25 + FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 Patch 109503-07 2001/08/11 Sun WorkShop 6 update 1 C++ 5.2 Patch 109508-04 2001/07/11 SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 Patch 109503-07 2001/08/11 Sun WorkShop 6 update 1 C++ 5.2 Patch 109508-04 2001/07/11 @@ -6813,9 +6813,9 @@ Platforms Tested IA-32 Linux 2.2.10smpx cc Intel 5.0.1 egcs-2.91.66 IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731 - Intel(R) C++ Itanium(TM) Compiler + Intel(R) C++ Itanium(TM) Compiler for the Itanium(TM)-based applications, - Version 6.0 Beta, Build 20010905 + Version 6.0 Beta, Build 20010905 Windows 2000 (NT5.0) MSVC++ 6.0 DEC Visual Fortran 6.0 Windows NT4.0 MSVC++ 6.0 @@ -6841,7 +6841,7 @@ Supported Configuration Features Summary Solaris2.7 y y (1) y n y y y y Solaris2.8 64 y n y n y y y y Solaris2.8 32 y n y n y y y y - IA-64 y n n n n n y y + IA-64 y n n n n n y y IRIX6.5 y y (1) n n n y y y IRIX64_6.5 64 y y (2) y y n y y y IRIX64_6.5 32 y y (2) n n n y y y @@ -6863,12 +6863,12 @@ Supported Configuration Features Summary Linux 2.4 y y (1) n n y y y y - Platform 1.2 static- Thread- SRB GASS STREAM- + Platform 1.2 static- Thread- SRB GASS STREAM- compatibility exec safe VFD Solaris2.7 n x y n n y Solaris2.8 64 n y n n n y Solaris2.8 32 n x n n n y - IA-64 n n n n n y + IA-64 n n n n n y IRIX6.5 n x y n n y IRIX64_6.5 64 n x y n y y IRIX64_6.5 32 n x y n y y @@ -6892,11 +6892,11 @@ Supported Configuration Features Summary Footnotes: (1) Using mpich. (2) Using mpt and mpich. - (3) When configured with static-exec enabled, tests fail + (3) When configured with static-exec enabled, tests fail in serial mode. (4) No HDF4-related tools. (5) Shared libraries are provided only for the C library. - (6) Exception of (5): DLL is available for C++ API on Windows + (6) Exception of (5): DLL is available for C++ API on Windows Known Problems @@ -6905,11 +6905,11 @@ Known Problems * Datasets or attributes which have a variable-length string datatype are not printing correctly with h5dump and h5ls. - * When a dataset with the variable-legth datatype is overwritten, - the library can develop memory leaks that cause the file to become + * When a dataset with the variable-legth datatype is overwritten, + the library can develop memory leaks that cause the file to become unnecessarily large. This is planned to be fixed in the next release. - * On the SV1, the h5ls test fails due to a difference between the + * On the SV1, the h5ls test fails due to a difference between the SV1 printf precision and the printf precision on other platforms. @@ -6921,24 +6921,24 @@ Known Problems * The --enable-static-exec configure flag fails to compile for HP-UX 11.00 platforms. - * The executables are always dynamic on IRIX64 6.5(64 and n32) and + * The executables are always dynamic on IRIX64 6.5(64 and n32) and IRIX 6.5 even if they are configured with --enable-static-exec. * IRIX 6.5 fails to compile if configured with --enable-static-exec. - + * The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause a hang in some cases when chunked storage is used. This is now set to be off by default. One may turn it on by setting environment variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1. * On IA64 systems one has to use -DIA64 compilation flag to compile - h4toh5 and h5toh4 utilites. After configuration step manually modify - Makefile in the tools/h4toh4 and tools/h5toh4 directories to add + h4toh5 and h5toh4 utilities. After configuration step manually modify + Makefile in the tools/h4toh4 and tools/h5toh4 directories to add -DIA64 to the compilation flags. - * On IA32 ansd IA64 systems, if you use a compiler other than GCC + * On IA32 ansd IA64 systems, if you use a compiler other than GCC (such as Intel's ecc compiler), you will need to modify the generated - "libtool" program after configuration is finished. On or around line 102 + "libtool" program after configuration is finished. On or around line 102 of the libtool file, there are lines which look like: # How to pass a linker flag through the compiler. @@ -6952,7 +6952,7 @@ Known Problems %%%%1.4.2%%%% Release Information for hdf5-1.4.2 (31/July/01) -10. Release Information for hdf5-1.4.2 +10. Release Information for hdf5-1.4.2 ================================================================= @@ -6968,7 +6968,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -6998,34 +6998,34 @@ New Features and other version information in the source code. * Parallel HDF5 now runs on the HP V2500 and HP N4000 machines. * F90 API: - - Added aditional parameter "dims" to the h5dread_f/h5dwrite_f and - h5aread_f/h5awrite_f subroutines. This parameter is a 1-D array - of size 7 and contains the sizes of the data buffer dimensions. + - Added additional parameter "dims" to the h5dread_f/h5dwrite_f and + h5aread_f/h5awrite_f subroutines. This parameter is a 1-D array + of size 7 and contains the sizes of the data buffer dimensions. This change enables portability between Windows and UNIX platforms. - In previous versions of the F90 APIs, the data buffer parameters of - the above functions were declared as assumed-shape arrays, which - were passed to the C functions by a descriptor. There is no - portable means, however, of passing descriptors from F90 to C, + In previous versions of the F90 APIs, the data buffer parameters of + the above functions were declared as assumed-shape arrays, which + were passed to the C functions by a descriptor. There is no + portable means, however, of passing descriptors from F90 to C, causing portability problems between Windows and UNIX and among UNIX platforms. With this change, the data buffers are assumed- size arrays, which can be portably passed to the C functions. - * F90 static library is available on Windows platforms. + * F90 static library is available on Windows platforms. See INSTALL_Windows_withF90.txt for details. * F90 APIs are available on HPUX 11.00 and 10.20 and IBM SP platforms. - * H5 <-> GIF convertor has been added. This is available under - tools/gifconv. The convertor supports the ability to create animated + * H5 <-> GIF converter has been added. This is available under + tools/gifconv. The converter supports the ability to create animated gifs as well. * Verified correct operation of library on Solaris 2.8 in both 64-bit and 32-bit compilation modes. See INSTALL document for instructions on compiling the distribution with 64-bit support. - * Added support for the Metrowerks Code Warrior compiler for Windows. + * Added support for the Metrowerks Code Warrior compiler for Windows. * For H4->H5 converter utility, added a new option to choose not to convert HDF4 specified attributes(reference number, class) into HDF5 attributes. - * Added support chunking and compression in SDS and image in H4->H5 converter. - Currently HDF5 only supports gzip compression, so by default an HDF4 file - with any other compression method will be converted into an HDF5 file in - gzip compression. - * correct the order or reading HDF4 image array in H4->H5 conversion. + * Added support chunking and compression in SDS and image in H4->H5 converter. + Currently HDF5 only supports gzip compression, so by default an HDF4 file + with any other compression method will be converted into an HDF5 file in + gzip compression. + * correct the order or reading HDF4 image array in H4->H5 conversion. * Added new parallel hdf5 tests in t_mpi. The new test checks if the filesystem or the MPI-IO can really handle greater than 2GB files. If it fails, it prints information message only without failing the @@ -7040,8 +7040,8 @@ New Features * Added new checking in H5check_version() to verify the five HDF5 version information macros (H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE, H5_VERS_SUBRELEASE and H5_VERS_INFO) are consistent. - - + + Bug Fixes since HDF5-1.4.1 Release ================================== @@ -7050,21 +7050,21 @@ Bug Fixes since HDF5-1.4.1 Release * Fixed problems with Pablo build and linking with non-standard MPI I/O. * Fixed build on Linux systems with --enable-static-exec flag. It now works correctly. - * IMPORTANT: Fixed file metadata corruption bug which could cause + * IMPORTANT: Fixed file metadata corruption bug which could cause metadata data loss in certain situations. * The allocation by alignment (H5Pset_alignment) feature code somehow got dropped in some 1.3.x version. Re-implemented it with "new and improved" algorithm. It keeps track of "wasted" file-fragment in the free-list too. * Removed limitation that the data transfer buffer size needed to be - set for datasets whose dimensions were too large for the 'all' - selection code to handle. Any size dimensioned datasets should be + set for datasets whose dimensions were too large for the 'all' + selection code to handle. Any size dimensioned datasets should be handled correctly now. * Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x when --enable-hdf5v1_2 configure flag is enabled. - * Added --enable-linux-lfs flag to allow more control over whether to + * Added --enable-linux-lfs flag to allow more control over whether to enable or disable large file support on Linux. - * Fixed various bugs releated to SDS dimensional scale conversions in H4->H5 + * Fixed various bugs related to SDS dimensional scale conversions in H4->H5 converter. * Fixed a bug to correctly convert HDF4 objects with fill value into HDF5. * Fixed a bug of H5pubconf.h causing repeated definitions if it is included @@ -7082,18 +7082,18 @@ Documentation ============= * The H5T_conv_t and H5T_cdata_t structures are now properly defined - in the H5Tregister entry in the "H5T" section of the "HDF5 Reference - Manual" and described in detail in section 12, "Data Conversions," in + in the H5Tregister entry in the "H5T" section of the "HDF5 Reference + Manual" and described in detail in section 12, "Data Conversions," in the "Datatypes" chapter of the "HDF5 User's Guide." * The new tools h52gif and gif2h5 have been added to the "Tools" section of the Reference Manual. - * A "Freespace Management" section has been added to the "Performance" + * A "Freespace Management" section has been added to the "Performance" chapter of the User's Guide. * Several user-reported bugs have been fixed since Release 1.4.1. * The "HDF5 Image and Palette Specification" (in the "HDF5 Application - Developer's Guide") has been heavily revised. Based on extensive user - feedback and input from visualization software developers, Version 1.2 - of the image specification is substantially different from prior + Developer's Guide") has been heavily revised. Based on extensive user + feedback and input from visualization software developers, Version 1.2 + of the image specification is substantially different from prior versions. @@ -7108,15 +7108,15 @@ Platforms Tested xlf 7.1.0.2 poe 2.4.0.14 (includes mpi) Cray T3E sn6711 2.0.5.49a Cray Standard C Version 6.5.0.1 - Cray SV1 10.0.0.2 Cray Standard C Version 6.5.0.1 + Cray SV1 10.0.0.2 Cray Standard C Version 6.5.0.1 Cray Fortran Version 3.5.0.1 FreeBSD 4.3 gcc 2.95.3 g++ 2.95.3 HP-UX B.10.20 HP C HP92453-01 A.10.32.30 HP F90 v2.3 - HP-UX B.11.00 HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 - HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20 + HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20 HP F90 v2.4 IRIX 6.5 MIPSpro cc 7.30 IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.2m @@ -7128,19 +7128,19 @@ Platforms Tested pgf90 3.2-4 OSF1 V4.0 DEC-V5.2-040 on Digital UNIX V4.0 (Rev 564) Digital Fortran 90 V4.1-270 - SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.6) WorkShop Compilers 5.0 98/10/25 FORTRAN 90 + SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 + (Solaris 2.6) WorkShop Compilers 5.0 98/10/25 FORTRAN 90 2.0 Patch 107356-04 SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 + (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 Workshop Compilers 5.0 98/10/25 FORTRAN 90 - 2.0 Patch 107356-04 + 2.0 Patch 107356-04 SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 2000/09/11 Sun WorkShop 6 update 1 C++ 5.2 2000/09/11 SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11 - (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 + (Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1 2000/09/11 Sun WorkShop 6 update 1 C++ 5.2 2000/09/11 TFLOPS r1.0.4 v4.0.7 i386 pgcc Rel 3.1-4i with mpich-1.2.1 with @@ -7191,7 +7191,7 @@ Supported Configuration Features Summary Linux 2.4 y y (1) n n y y y y - Platform 1.2 static- Thread- SRB GASS STREAM- + Platform 1.2 static- Thread- SRB GASS STREAM- compatibility exec safe VFD Solaris2.6 y x n n n y Solaris2.7 y x y n n y @@ -7220,7 +7220,7 @@ Supported Configuration Features Summary Footnotes: (1) Using mpich. (2) Using mpt and mpich. - (3) When configured with static-exec enabled, tests fail + (3) When configured with static-exec enabled, tests fail in serial mode. (4) No HDF4-related tools. (5) Shared libraries are provided only for the C library. @@ -7229,11 +7229,11 @@ Supported Configuration Features Summary Known Problems ============== - * When a dataset with the variable-legth datatype is overwritten, - the library can develop memory leaks that cause the file to become + * When a dataset with the variable-legth datatype is overwritten, + the library can develop memory leaks that cause the file to become unnecessarily large. This is planned to be fixed in the next release. - * On the SV1, the h5ls test fails due to a difference between the + * On the SV1, the h5ls test fails due to a difference between the SV1 printf precision and the printf precision on other platforms. * The h5dump tests may fail to match the expected output in some @@ -7244,13 +7244,13 @@ Known Problems * The --enable-static-exec configure flag fails to compile for HP-UX 11.00 platforms. - * The executables are always dynamic on IRIX64 6.5(64 and n32) and + * The executables are always dynamic on IRIX64 6.5(64 and n32) and IRIX 6.5 even if they are configured with --enable-static-exec. * IRIX 6.5 fails to compile if configured with --enable-static-exec. - + * For 24-bit image conversion from H4->H5, the current conversion is - not consistent with HDF5 image specification. + not consistent with HDF5 image specification. * In some cases, and SDS with an UNLIMITED dimension that has not been written (current size = 0) is not converted correctly. @@ -7269,7 +7269,7 @@ Known Problems ===================================================================== - + HDF5 Release 1.4.1 @@ -7285,7 +7285,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -7307,10 +7307,10 @@ New Features ============ * XML output option for h5dump utility. - + A new option --xml to output data in XML format has been added. The XML output contains a complete description of the file, marked up in - XML. + XML. The XML conforms to the HDF5 Document Type Definition (DTD), which is available at: @@ -7345,7 +7345,7 @@ Bug Fixes since HDF5-1.4.0 Release causing errors during I/O * The RCSID string in H5public.h was causing the C++ compiling problem because when it was included multiple times, C++ did not like - multiple definitions of the same static variable. All occurance of + multiple definitions of the same static variable. All occurrence of RCSID definition are removed since we have not used it consistently before. @@ -7353,25 +7353,25 @@ Bug Fixes since HDF5-1.4.0 Release Documentation ============= - PDF and Postscript versions of the following documents are available + PDF and Postscript versions of the following documents are available for this release: Document Filename -------- -------- Introduction to HDF5 H5-R141-Introduction.pdf - HDF5 Reference Manual H5-R141-RefManual.pdf + HDF5 Reference Manual H5-R141-RefManual.pdf C++ APIs to HDF5 documents H5-R141-Cplusplus.pdf Fortran90 APIs to HDF5 documents H5-R141-Fortran90.pdf PDF and Postscript files containing H5-R141-DocSet.pdf all of the above H5-R141-DocSet.ps - These files are not included in this distribution, but are available + These files are not included in this distribution, but are available via the Web or FTP at the following locations: http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/ ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/docs/ - While these documents are labeled Release 1.4.1, they describe - Release 1.4.0 as well. + While these documents are labeled Release 1.4.1, they describe + Release 1.4.0 as well. Platforms Tested @@ -7392,8 +7392,8 @@ Due to the nature of this release only C, C++ libraries and tools were tested. g++ 2.95.2 OSF1 V4.0 DEC-V5.2-040 Digital Fortran 90 V4.1-270 - SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.6) + SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 + (Solaris 2.6) SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 @@ -7419,11 +7419,11 @@ Known Problems * The --enable-static-exec configure flag fails to compile for HP-UX 11.00 platforms. - * The executable are always dynamic on IRIX64 6.5(64 and n32) and + * The executable are always dynamic on IRIX64 6.5(64 and n32) and IRIX 6.5 even if they are configured with --enable-static-exec. * The shared library failed compilation on IRIX 6.5. - + * After "make install" or "make install-doc" one may need to reload the source from the tar file before doing another build. @@ -7434,7 +7434,7 @@ Known Problems 8. Release Information for hdf5-1.4.0 =================================================================== - + HDF5 Release 1.4.0 @@ -7451,7 +7451,7 @@ The HDF5 documentation can be found on the NCSA ftp server /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -7462,11 +7462,11 @@ If you have any questions or comments, please send them to: CONTENTS - New Features -- h4toh5 Utility +- h4toh5 Utility - F90 Support - C++ Support -- Pablo Support -- Bug Fixes since HDF5-1.2.0 +- Pablo Support +- Bug Fixes since HDF5-1.2.0 - Bug Fixes since HDF5-1.4.0-beta2 - Bug Fixes since HDF5-1.4.0 - Documentation @@ -7495,15 +7495,15 @@ New Features * Added new Virtual File Driver, Stream VFD, to send/receive entire HDF5 files via socket connections. * As parts of VFL, HDF-GASS and HDF-SRB are also added to this - release. To find out details, please read INSTALL_VFL file. + release. To find out details, please read INSTALL_VFL file. * Increased maximum number of dimensions for a dataset (H5S_MAX_RANK) from 31 to 32 to align with HDF4 & netCDF. * Added 'query' function to VFL drivers. Also added 'type' parameter to VFL 'read' & 'write' calls, so they are aware of the type of data being accessed in the file. Updated the VFL document also. * A new h4toh5 utility, to convert HDF4 files to analogous HDF5 files. - * Added a new array datatype to the datatypes which can be created. - Removed "array fields" from compound datatypes (use an array datatype + * Added a new array datatype to the datatypes which can be created. + Removed "array fields" from compound datatypes (use an array datatype instead). * Parallel HDF5 works correctly with mpich-1.2.1 on Solaris, SGI, Linux. * You can now install the HDF5 documentation using the @@ -7514,26 +7514,26 @@ New Features Check doc/html/TechNotes/openmp-hdf5.html for details. -h4toh5 Utility +h4toh5 Utility ============== - The h4toh5 utility is a new utility that converts an HDF4 file to an - HDF5 file. For details, see the document, "Mapping HDF4 Objects to + The h4toh5 utility is a new utility that converts an HDF4 file to an + HDF5 file. For details, see the document, "Mapping HDF4 Objects to HDF5 Objects": http://hdf.ncsa.uiuc.edu/HDF5/papers/H4-H5MappingGuidelines.pdf Known Bugs: The h4toh5 utility produces images that do not correctly conform - to the HDF5 Image and Palette Specification. + to the HDF5 Image and Palette Specification. http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html - Several required HDF5 attributes are omitted, and the dataspace - is reversed (i.e., the ht. and width of the image dataset is + Several required HDF5 attributes are omitted, and the dataspace + is reversed (i.e., the ht. and width of the image dataset is incorrectly described.) For more information, please see: http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.html - + This bug has been fixed for the snapshot of hdf5 1.4 release. March 12th,2001 Known Limitations of the h4toh5 release @@ -7555,7 +7555,7 @@ h4toh5 Utility be an H5T_INTEGER type. * For attributes of any HDF4 object, data of type 'DFNT_CHAR8' will be converted to an HDF5 'H5T_STRING' type. - * For an HDF4 Vdata, it is difficult to determine whether data + * For an HDF4 Vdata, it is difficult to determine whether data of type 'DFNT_CHAR8' is intended to be bytes or characters. The h4toh5 utility will consider them to be C characters, and will convert them to an HDF5 'H5T_STRING' type. @@ -7569,10 +7569,10 @@ h4toh5 Utility with analogous chunked storage. An HDF4 object that uses compression will be converted to an - uncompressed HDF5 object. + uncompressed HDF5 object. An HDF4 object that uses external storage will be converted to an - HDF5 object without external storage. + HDF5 object without external storage. 4. Memory Use @@ -7589,29 +7589,29 @@ h4toh5 Utility The h4toh5 utility requires HDF5-1.4.0 and HDF4r1.4 - h4toh5 utility has been tested on all platforms listed below (see + h4toh5 utility has been tested on all platforms listed below (see section "Platforms Tested") except TFLOPS. - + F90 Support =========== - This is the first release of the HDF5 Library with fully integrated - F90 API support. The Fortran Library is created when the + This is the first release of the HDF5 Library with fully integrated + F90 API support. The Fortran Library is created when the --enable-fortran flag is specified during configuration. - Not all F90 subroutines are implemented. Please refer to the HDF5 + Not all F90 subroutines are implemented. Please refer to the HDF5 Reference Manual for more details. - - F90 APIs are available for the Solaris 2.6 and 2.7, Linux, DEC UNIX, - T3E, SV1 and O2K (64 bit option only) platforms. The Parallel version of + + F90 APIs are available for the Solaris 2.6 and 2.7, Linux, DEC UNIX, + T3E, SV1 and O2K (64 bit option only) platforms. The Parallel version of the HDF5 F90 Library is supported on the O2K and T3E platforms. Changes since the last prototype release (July 2000) ---------------------------------------------------- - * h5open_f and h5close_f must be called instead of h5init_types and + * h5open_f and h5close_f must be called instead of h5init_types and h5close_types. - * The following subroutines are no longer available: + * The following subroutines are no longer available: h5pset_xfer_f h5pget_xfer_f @@ -7625,45 +7625,45 @@ F90 Support h5pget_core_f h5pset_family_f h5pget_family_f - + * The following functions have been added: h5pset_fapl_mpio_f h5pget_fapl_mpio_f h5pset_dxpl_mpio_f h5pget_dxpl_mpio_f - - * In the previous HDF5 F90 releases, the implementation of object - references and dataset region references was not portable. This - release introduces a portable implementation, but it also introduces - changes to the read/write APIs that handle references. If object or - dataset region references are written or read to/from an HDF5 file, - h5dwrite_f and h5dread_f must use the extra parameter, n, for the + + * In the previous HDF5 F90 releases, the implementation of object + references and dataset region references was not portable. This + release introduces a portable implementation, but it also introduces + changes to the read/write APIs that handle references. If object or + dataset region references are written or read to/from an HDF5 file, + h5dwrite_f and h5dread_f must use the extra parameter, n, for the buffer size: h5dwrite(read)_f(dset_id, mem_type_id, buf, n, hdferr, & - ^^^ + ^^^ mem_space_id, file_space_id, xfer_prp) - For other datatypes the APIs were not changed. - - + For other datatypes the APIs were not changed. + + C++ Support =========== - This is the first release of the HDF5 Library with fully integrated + This is the first release of the HDF5 Library with fully integrated C++ API support. The HDF5 C++ library is built when the --enable-cxx flag is specified during configuration. Check the HDF5 Reference Manual for available C++ documentation. - C++ APIs are available for Solaris 2.6 and 2.7, Linux, and FreeBSD. + C++ APIs are available for Solaris 2.6 and 2.7, Linux, and FreeBSD. Pablo Support ============= This version does not allow proper building of the Pablo-instrumented version of the library. A version supporting the pablo build is - available on the Pablo Website at + available on the Pablo Website at www-pablo.cs.uiuc.edu/pub/Pablo.Release.5/HDFLibrary/hdf5_v1.4.tar.gz @@ -7724,7 +7724,7 @@ Library Configuration ------------- * The hdf5.h include file was fixed to allow the HDF5 Library to be - compiled with other libraries/applications that use GNU autoconf. + compiled with other libraries/applications that use GNU autoconf. * Configuration for parallel HDF5 was improved. Configure now attempts to link with libmpi.a and/or libmpio.a as the MPI libraries by default. It also uses "mpirun" to launch MPI tests by default. It @@ -7774,14 +7774,14 @@ Tools * h5dump correctly displays the committed copy of predefined types correctly. * Added an option, -V, to show the version information of h5dump. - * Fixed a core dumping bug of h5toh4 when executed on platforms like + * Fixed a core dumping bug of h5toh4 when executed on platforms like TFLOPS. * The test script for h5toh4 used to not able to detect the hdp dumper command was not valid. It now detects and reports the failure of hdp execution. * Merged the tools with the 1.2.2 branch. Required adding new macros, VERSION12 and VERSION13, used in conditional compilation. - Updated the Windows project files for the tools. + Updated the Windows project files for the tools. * h5dump displays opaque and bitfield data correctly. * h5dump and h5ls can browse files created with the Stream VFD (eg. "h5ls <hostname>:<port>"). @@ -7794,10 +7794,10 @@ Tools Bug Fixes since HDF5-1.4.0-beta2 ================================ - * Fixed a bug in the conversion from a little endian double to a big + * Fixed a bug in the conversion from a little endian double to a big endian float in some special cases. - * Corrected configuration error which was not including compression - support correctly. + * Corrected configuration error which was not including compression + support correctly. * Cleaned up lots of warnings. * Changed a few h5dump command line switches and added long versions of the switches. @@ -7806,7 +7806,7 @@ Bug Fixes since HDF5-1.4.0-beta2 * Fixed fairly obscure bug in hyperslab I/O which could (in rare cases) not copy all the data during a transfer. * Removed ragged array code from library. - * F90 library and module files are installed properly now on all supported + * F90 library and module files are installed properly now on all supported platforms. @@ -7822,26 +7822,26 @@ Bug Fixes since HDF5-1.4.0 Release Documentation ============= - * A new document summarizing the changes in the library leading up to - the current release has been added: + * A new document summarizing the changes in the library leading up to + the current release has been added: HDF5 Software Changes from Release to Release - This document is in the Application Developer's Guide and is of - particular interest to developers who must keep an application + This document is in the Application Developer's Guide and is of + particular interest to developers who must keep an application synchronized with the library. * The documentation for the Fortran90 and C++ APIs is linked to the - opening page of the Reference Manual. Fortran90 functions are + opening page of the Reference Manual. Fortran90 functions are individually referenced from the corresponding C functions through- out the Reference Manual. - * User's Guide and Reference Manual were updated to reflect changed - function syntax and to fix reported bugs. - * Functions that are new at this release were added to the Reference - Manual. - * Functions that have been removed from the library were removed from + * User's Guide and Reference Manual were updated to reflect changed + function syntax and to fix reported bugs. + * Functions that are new at this release were added to the Reference + Manual. + * Functions that have been removed from the library were removed from the User's Guide and the Reference Manual. - * PostScript and PDF versions of the Release 1.4 document set are + * PostScript and PDF versions of the Release 1.4 document set are not available at the time of Release 1.4.0. - + Platforms Tested ================ AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 @@ -7865,7 +7865,7 @@ Platforms Tested mpich-1.2.1 OSF1 V4.0 DEC-V5.2-040 Digital Fortran 90 V4.1-270 - SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 + SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 (Solaris 2.6) WorkShop Compilers 5.0 99/10/25 Fortran 90 2.0 Patch 107356-04 Workshop Compilers 5.0 98/12/15 C++ 5.0 @@ -7874,7 +7874,7 @@ Platforms Tested 2.0 Patch 107356-04 Workshop Compilers 5.0 98/12/15 C++ 5.0 mpich-1.2.1 - SunOS 5.5.1 gcc-2.7.2 + SunOS 5.5.1 gcc-2.7.2 (Solaris 2.5.1 (x86)) TFLOPS r1.0.4 v4.0 mpich-1.2.1 with local changes Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0 @@ -7931,17 +7931,17 @@ Supported Configuration Features Summary Footnotes: (1) Using mpich. (2) Using mpt and mpich. - (3) When configured with static-exec enabled, tests fail + (3) When configured with static-exec enabled, tests fail in serial mode. (4) No HDF4-related tools. Known Problems ============== - * The stream-vfd test uses ip port 10007 for testing. If another - application is already using that port address, the test will hang - indefinitely and has to be terminated by the kill command. To try the - test again, change the port address in test/stream_test.c to one not + * The stream-vfd test uses ip port 10007 for testing. If another + application is already using that port address, the test will hang + indefinitely and has to be terminated by the kill command. To try the + test again, change the port address in test/stream_test.c to one not being used in the host. * The --enable-static-exec configure flag fails to compile for Solaris @@ -7950,7 +7950,7 @@ Known Problems The --enable-static-exec configure flag also fails to correctly compile on Linux platforms using the gcc-2.95.2 compiler. - + The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. @@ -7959,7 +7959,7 @@ Known Problems The executable files in hdf5/bin are dynamic-linked for IRIX64 6.5(64 and n32 modes) and IRIX 6.5, even though they are compiled with static library. - + It is suggested that you don't use this option on these platforms during configuration. @@ -7971,10 +7971,10 @@ Known Problems able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' - + This warning is innocuous and can be safely ignored. - * SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will + * SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will fail if library is compiled using optimization of any level. * When building hdf5 tools and applications on windows platform, a linking @@ -7982,8 +7982,8 @@ Known Problems on debug version when running VC++6.0. This warning doesn't affect building and testing hdf5 applications. We will continue investigating this. - * h5toh4 converter fails two cases(tstr.h5 and tmany.h5) for release dll - version on windows 2000 and NT. The reason is possibly due to Windows NT + * h5toh4 converter fails two cases(tstr.h5 and tmany.h5) for release dll + version on windows 2000 and NT. The reason is possibly due to Windows NT DLL convention on freeing memory. It seems that memory cannot be freed across library or DLL. It is still under investigation. @@ -7991,7 +7991,7 @@ Known Problems the configured with --with-gass. * HDF-SRB testing got segmentation error on Solaris 2.7. - + * The Stream VFD was not tested yet under Windows. It is not supported in the TFLOPS machine. @@ -8006,7 +8006,7 @@ Known Problems * Certain platforms give false negatives when testing h5ls: - Solaris x86 2.5.1, Cray T3E and Cray J90 give errors during testing - when displaying object references in certain files. These are benign + when displaying object references in certain files. These are benign differences due to the difference in sizes of the objects created on those platforms. h5ls appears to be dumping object references correctly. @@ -8015,18 +8015,18 @@ Known Problems different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. - * Before building HDF5 F90 Library from source on Crays (T3E and SV1) - replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src - subdirectory in the top level directory with the Cray-specific files from + * Before building HDF5 F90 Library from source on Crays (T3E and SV1) + replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src + subdirectory in the top level directory with the Cray-specific files from the ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/hdf5-1.4.0/src/crayf90/ directory. * The h4toh5 utility produces images that do not correctly conform - to the HDF5 Image and Palette Specification. + to the HDF5 Image and Palette Specification. http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html - Several required HDF5 attributes are omitted, and the dataspace - is reversed (i.e., the ht. and width of the image dataset is + Several required HDF5 attributes are omitted, and the dataspace + is reversed (i.e., the ht. and width of the image dataset is incorrectly described.) For more information, please see: http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.htm @@ -8037,17 +8037,17 @@ Known Problems ================================================================= INTRODUCTION -This document describes the differences between HDF5-1.2.1 and +This document describes the differences between HDF5-1.2.1 and HDF5-1.2.2, and contains information on the platforms where HDF5-1.2.2 -was tested and known problems in HDF5-1.2.2. +was tested and known problems in HDF5-1.2.2. -The HDF5 documentation can be found on the NCSA ftp server +The HDF5 documentation can be found on the NCSA ftp server (ftp.ncsa.uiuc.edu) in the directory: /HDF/HDF5/docs/ For more information look at the HDF5 home page at: - + http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: @@ -8057,7 +8057,7 @@ If you have any questions or comments, please send them to: CONTENTS -- Features Added since HDF5-1.2.1 +- Features Added since HDF5-1.2.1 - Bug Fixes since HDF5-1.2.1 - Known Problems - Platforms Tested @@ -8108,10 +8108,10 @@ Bug Fixes since HDF5-1.2.1 Known Problems ============== -o SunOS 5.6 with C WorkShop Compilers 4.2: hyperslab selections will +o SunOS 5.6 with C WorkShop Compilers 4.2: hyperslab selections will fail if library is compiled using optimization of any level. o TFLOPS: dsets test fails if compiled with optimization turned on. -o J90: tools fail to dispay data for the datasets with a compound datatype. +o J90: tools fail to display data for the datasets with a compound datatype. Platforms Tested ================ @@ -8125,13 +8125,13 @@ Platforms Tested mpt.1.3 FreeBSD 4.0 gcc 2.95.2 HP-UX B.10.20 HP C HP92453-01 A.10.32 - HP-UX B.11.00 HP92453-01 A.11.00.13 HP C Compiler - (static library only, h5toh4 tool is not available) + HP-UX B.11.00 HP92453-01 A.11.00.13 HP C Compiler + (static library only, h5toh4 tool is not available) IRIX 6.5 MIPSpro cc 7.30 IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m mpt.1.4 - Linux 2.2.10 SMP gcc 2.95.1 + Linux 2.2.10 SMP gcc 2.95.1 mpicc(gcc-2.95.1) gcc (egcs-2.91.66) mpicc (egcs-2.91.66) @@ -8162,7 +8162,7 @@ Configuration ------------- * The hdf5.h include file was fixed to allow the HDF5 Library to be compiled - with other libraries/applications that use GNU autoconf. + with other libraries/applications that use GNU autoconf. * Configuration for parallel HDF5 was improved. Configure now attempts to link with libmpi.a and/or libmpio.a as the MPI libraries by default. It also uses "mpirun" to launch MPI tests by default. It tests to @@ -8195,7 +8195,7 @@ Tools ------ * Added an option, -V, to show the version information of h5dump. - * Fixed a core dumping bug of h5toh4 when executed on platforms like + * Fixed a core dumping bug of h5toh4 when executed on platforms like TFLOPS. * The test script for h5toh4 used to not able to detect the hdp dumper command was not valid. It now detects and reports the @@ -8204,10 +8204,10 @@ Tools Documentation ------------- - * User's Guide and Reference Manual were updated. - See doc/html/PSandPDF/index.html for more details. + * User's Guide and Reference Manual were updated. + See doc/html/PSandPDF/index.html for more details. + - Platforms Tested: ================ Note: Due to the nature of bug fixes, only static versions of the library and tools were tested. @@ -8224,7 +8224,7 @@ Note: Due to the nature of bug fixes, only static versions of the library and to Linux 2.2.10 SuSE egcs-2.91.66 configured with (i686-pc-linux-gnu) --disable-hsizet - mpich-1.2.0 egcs-2.91.66 19990314/Linux + mpich-1.2.0 egcs-2.91.66 19990314/Linux OSF1 V4.0 DEC-V5.2-040 SunOS 5.6 cc WorkShop Compilers 4.2 no optimization @@ -8236,13 +8236,13 @@ Note: Due to the nature of bug fixes, only static versions of the library and to Known Problems: ============== -o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will +o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will fail if library is compiled using optimization of any level. %%%%1.2.0%%%% Release Information for hdf5-1.2.0 - + 5. Release Information for hdf5-1.2.0 =================================================================== @@ -8254,13 +8254,13 @@ applicable, are systems that HDF5 1.2.0 was tested on. Compiler & libraries Platform Information Comment - -------- ---------- -------- - + -------- ---------- -------- + AIX 4.3.2 (IBM SP) 3.6.6 Cray J90 10.0.0.6 cc 6.3.0.0 - Cray T3E 2.0.4.61 cc 6.2.1.0 + Cray T3E 2.0.4.61 cc 6.2.1.0 mpt.1.3 FreeBSD 3.2 gcc 2.95.1 @@ -8268,30 +8268,30 @@ applicable, are systems that HDF5 1.2.0 was tested on. HP-UX B.10.20 HP C HP92453-01 A.10.32 gcc 2.8.1 - IRIX 6.5 MIPSpro cc 7.30 + IRIX 6.5 MIPSpro cc 7.30 IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m - mpt.1.3 (SGI MPI 3.2.0.0) + mpt.1.3 (SGI MPI 3.2.0.0) Linux 2.2.10 egcs-2.91.66 configured with - --disable-hsizet + --disable-hsizet lbraries: glibc2 OSF1 V4.0 DEC-V5.2-040 - SunOS 5.6 cc WorkShop Compilers 4.2 + SunOS 5.6 cc WorkShop Compilers 4.2 no optimization - gcc 2.8.1 + gcc 2.8.1 SunOS 5.7 cc WorkShop Compilers 5.0 gcc 2.8.1 - + TFLOPS 2.7.1 cicc (pgcc Rel 3.0-4i) - mpich-1.1.2 with local changes + mpich-1.1.2 with local changes Windows NT4.0 intel MSVC++ 5.0 and 6.0 - Windows NT alpha 4.0 MSVC++ 5.0 + Windows NT alpha 4.0 MSVC++ 5.0 Windows 98 MSVC++ 5.0 @@ -8306,7 +8306,7 @@ B. Known Problems Hyperslab selections will fail if library is compiled using optimization of any level. - + C. Changes Since Version 1.0.1 --------------------------- @@ -8320,7 +8320,7 @@ C. Changes Since Version 1.0.1 * Self-contained documentation for installations isolated from the Internet. -* HDF5 Tutorial was added to the documentation +* HDF5 Tutorial was added to the documentation 2. Configuration ------------- @@ -8352,7 +8352,7 @@ C. Changes Since Version 1.0.1 * Optimizations to compound datatype conversions and I/O operations. -* Added nearly 100 optimized conversion functions for native datatypes +* Added nearly 100 optimized conversion functions for native datatypes including support for non-aligned data. * Added support for bitfield, opaque, and enumeration types. @@ -8379,7 +8379,7 @@ C. Changes Since Version 1.0.1 * New query functions for selections. * I/O operations bypass the stripmining loop and go directly to - storage for certain contiguous selections in the absense of type + storage for certain contiguous selections in the absence of type conversions. In other cases the stripmining buffers are used more effectively. @@ -8404,23 +8404,23 @@ C. Changes Since Version 1.0.1 * Improved the algorithm that translates an HDF5 hyperslab selection into an MPI type for better collective I/O performance. -8. New API functions +8. New API functions ----------------- a. Property List Interface: ------------------------ - H5Pset_xfer - set data transfer properties - H5Pset_preserve - set dataset transfer property list status + H5Pset_xfer - set data transfer properties + H5Pset_preserve - set dataset transfer property list status H5Pget_preserve - get dataset transfer property list status H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O - H5Pget_hyper_cache - returns information regarding the caching of + H5Pget_hyper_cache - returns information regarding the caching of hyperslab blocks during I/O - H5Pget_btree_ratios - sets B-tree split ratios for a dataset + H5Pget_btree_ratios - sets B-tree split ratios for a dataset transfer property list H5Pset_btree_ratios - gets B-tree split ratios for a dataset transfer property list - H5Pset_vlen_mem_manager - sets the memory manager for variable-length + H5Pset_vlen_mem_manager - sets the memory manager for variable-length datatype allocation H5Pget_vlen_mem_manager - sets the memory manager for variable-length datatype allocation @@ -8435,26 +8435,26 @@ C. Changes Since Version 1.0.1 c. Dataspace Interface: -------------------- H5Sget_select_hyper_nblocks - get number of hyperslab blocks - H5Sget_select_hyper_blocklist - get the list of hyperslab blocks + H5Sget_select_hyper_blocklist - get the list of hyperslab blocks currently selected - H5Sget_select_elem_npoints - get the number of element points + H5Sget_select_elem_npoints - get the number of element points in the current selection - H5Sget_select_elem_pointlist - get the list of element points + H5Sget_select_elem_pointlist - get the list of element points currently selected - H5Sget_select_bounds - gets the bounding box containing + H5Sget_select_bounds - gets the bounding box containing the current selection d. Datatype Interface: ------------------- - H5Tget_super - return the base datatype from which a + H5Tget_super - return the base datatype from which a datatype is derived H5Tvlen_create - creates a new variable-length dataype H5Tenum_create - creates a new enumeration datatype H5Tenum_insert - inserts a new enumeration datatype member - H5Tenum_nameof - returns the symbol name corresponding to a + H5Tenum_nameof - returns the symbol name corresponding to a + specified member of an enumeration datatype + H5Tvalueof - return the value corresponding to a specified member of an enumeration datatype - H5Tvalueof - return the value corresponding to a - specified member of an enumeration datatype H5Tget_member_value - return the value of an enumeration datatype member H5Tset_tag - tags an opaque datatype H5Tget_tag - gets the tag associated with an opaque datatype @@ -8468,16 +8468,16 @@ C. Changes Since Version 1.0.1 H5Rcreate - creates a reference H5Rdereference - open the HDF5 object referenced H5Rget_region - retrieve a dataspace with the specified region selected - H5Rget_object_type - retrieve the type of object that an + H5Rget_object_type - retrieve the type of object that an object reference points to g. Ragged Arrays (alpha) (names of those API functions were changed): ------------------------------------------------------------------ - H5RAcreate - create a new ragged array (old name was H5Rcreate) - H5RAopen - open an existing array (old name was H5Ropen) - H5RAclose - close a ragged array (old name was H5Rclose) - H5RAwrite - write to an array (old name was H5Rwrite) - H5RAread - read from an array (old name was H5Rread) + H5RAcreate - create a new ragged array (old name was H5Rcreate) + H5RAopen - open an existing array (old name was H5Ropen) + H5RAclose - close a ragged array (old name was H5Rclose) + H5RAwrite - write to an array (old name was H5Rwrite) + H5RAread - read from an array (old name was H5Rread) 9. Tools @@ -8486,7 +8486,7 @@ C. Changes Since Version 1.0.1 * Enhancements to the h5ls tool including the ability to list objects from more than one file, to display raw hexadecimal data, to show file addresses for raw data, to format output more reasonably, - to show object attributes, and to perform a recursive listing, + to show object attributes, and to perform a recursive listing, * Enhancements to h5dump: support new data types added since previous versions. @@ -8496,7 +8496,7 @@ C. Changes Since Version 1.0.1 %%%%1.0.1%%%% Release Information for hdf5-1.0.1 - + 4. Changes from Release 1.0.0 to Release 1.0.1 ===================================================================== @@ -8506,7 +8506,7 @@ C. Changes Since Version 1.0.1 * [Bug-Fix]: Configure failed for all IRIX versions other than 6.3. It now configures correctly for all IRIX 6.x version. -* Released Parallel HDF5 +* Released Parallel HDF5 Supported Features: ------------------ @@ -8526,7 +8526,7 @@ C. Changes Since Version 1.0.1 IBM SP2 SGI Origin 2000 - Changes In This Release: + Changes In This Release: ----------------------- o Support of Access to Extendable Dimension Datasets. @@ -8570,7 +8570,7 @@ C. Changes Since Version 1.0.1 ==================================================================== * Added fill values for datasets. For contiguous datasets fill value - performance may be quite poor since the fill value is written to the + performance may be quite poor since the fill value is written to the entire dataset when the dataset is created. This will be remedied in a future version. Chunked datasets using fill values do not incur any additional overhead. See H5Pset_fill_value(). @@ -8621,17 +8621,17 @@ C. Changes Since Version 1.0.1 %%%%1.0.0 Alpha 2%%%% Release Information for hdf5-1.0.0 Alpha 2 -1. Changes from the First Alpha 1.0.0 Release to +1. Changes from the First Alpha 1.0.0 Release to the Second Alpha 1.0.0 Release ===================================================================== * Two of the packages have been renamed. The data space API has been - renamed from `H5P' to `H5S' and the property list (template) API has + renamed from `H5P' to `H5S' and the property list (template) API has been renamed from `H5C' to `H5P'. -* The new attribute API `H5A' has been added. An attribute is a small +* The new attribute API `H5A' has been added. An attribute is a small dataset which can be attached to some other object (for instance, a - 4x4 transformation matrix attached to a 3-dimensional dataset, or an + 4x4 transformation matrix attached to a 3-dimensional dataset, or an English abstract attached to a group). * The error handling API `H5E' has been completed. By default, when an @@ -8643,7 +8643,7 @@ C. Changes Since Version 1.0.1 * Support for large files and datasets (>2GB) has been added. There is an html document that describes how it works. Some of the types for function arguments have changed to support this: all arguments - pertaining to sizes of memory objects are `size_t' and all arguments + pertaining to sizes of memory objects are `size_t' and all arguments pertaining to file sizes are `hsize_t'. * More data type conversions have been added although none of them are @@ -8669,7 +8669,7 @@ C. Changes Since Version 1.0.1 * Data types can be stored in the file as independent objects and multiple datasets can share a data type. -* The raw data I/O stream has been implemented and the application can +* The raw data I/O stream has been implemented and the application can control meta and raw data caches, so I/O performance should be improved from the first alpha release. @@ -8681,14 +8681,14 @@ C. Changes Since Version 1.0.1 applications or I/O libraries and described and accessed through HDF5. -* Hard and soft (symbolic) links are implemented which allow groups to +* Hard and soft (symbolic) links are implemented which allow groups to share objects. Dangling and recursive symbolic links are supported. * User-defined data compression is implemented although we may generalize the interface to allow arbitrary user-defined filters which can be used for compression, checksums, encryption, performance monitoring, etc. The publicly-available `deflate' - method is predefined if the GNU libz.a can be found at configuration + method is predefined if the GNU libz.a can be found at configuration time. * The configuration scripts have been modified to make it easier to @@ -8698,7 +8698,7 @@ C. Changes Since Version 1.0.1 with the correct version of header files. - Parallel HDF5 Changes + Parallel HDF5 Changes * Parallel support for fixed dimension datasets with contiguous or chunked storages. Also, support unlimited dimension datasets which @@ -8724,245 +8724,245 @@ C. Changes Since Version 1.0.1 sizes. - LIST OF API FUNCTIONS + LIST OF API FUNCTIONS The following functions are implemented. Errors are returned if an attempt is made to use some feature which is not implemented and printing the error stack will show `not implemented yet'. Library - H5check - check that lib version matches header version - H5open - initialize library (happens automatically) - H5close - shut down the library (happens automatically) - H5dont_atexit - don't call H5close on exit - H5get_libversion - retrieve library version info - H5check_version - check for specific library version + H5check - check that lib version matches header version + H5open - initialize library (happens automatically) + H5close - shut down the library (happens automatically) + H5dont_atexit - don't call H5close on exit + H5get_libversion - retrieve library version info + H5check_version - check for specific library version Property Lists - H5Pclose - release template resources - H5Pcopy - copy a template - H5Pcreate - create a new template - H5Pget_chunk - get chunked storage properties - H5Pset_chunk - set chunked storage properties - H5Pget_class - get template class - H5Pget_istore_k - get chunked storage properties - H5Pset_istore_k - set chunked storage properties - H5Pget_layout - get raw data layout class - H5Pset_layout - set raw data layout class - H5Pget_sizes - get address and size sizes - H5Pset_sizes - set address and size sizes - H5Pget_sym_k - get symbol table storage properties - H5Pset_sym_k - set symbol table storage properties - H5Pget_userblock - get user-block size - H5Pset_userblock - set user-block size - H5Pget_version - get file version numbers - H5Pget_alignment - get data alignment properties - H5Pset_alignment - set data alignment properties + H5Pclose - release template resources + H5Pcopy - copy a template + H5Pcreate - create a new template + H5Pget_chunk - get chunked storage properties + H5Pset_chunk - set chunked storage properties + H5Pget_class - get template class + H5Pget_istore_k - get chunked storage properties + H5Pset_istore_k - set chunked storage properties + H5Pget_layout - get raw data layout class + H5Pset_layout - set raw data layout class + H5Pget_sizes - get address and size sizes + H5Pset_sizes - set address and size sizes + H5Pget_sym_k - get symbol table storage properties + H5Pset_sym_k - set symbol table storage properties + H5Pget_userblock - get user-block size + H5Pset_userblock - set user-block size + H5Pget_version - get file version numbers + H5Pget_alignment - get data alignment properties + H5Pset_alignment - set data alignment properties H5Pget_external_count- get count of external data files - H5Pget_external - get information about an external data file - H5Pset_external - add a new external data file to the list - H5Pget_driver - get low-level file driver class - H5Pget_stdio - get properties for stdio low-level driver - H5Pset_stdio - set properties for stdio low-level driver - H5Pget_sec2 - get properties for sec2 low-level driver - H5Pset_sec2 - set properties for sec2 low-level driver - H5Pget_core - get properties for core low-level driver - H5Pset_core - set properties for core low-level driver - H5Pget_split - get properties for split low-level driver - H5Pset_split - set properties for split low-level driver - H5P_get_family - get properties for family low-level driver - H5P_set_family - set properties for family low-level driver - H5Pget_cache - get meta- and raw-data caching properties - H5Pset_cache - set meta- and raw-data caching properties - H5Pget_buffer - get raw-data I/O pipe buffer properties - H5Pset_buffer - set raw-data I/O pipe buffer properties - H5Pget_preserve - get type conversion preservation properties - H5Pset_preserve - set type conversion preservation properties - H5Pget_nfilters - get number of raw data filters - H5Pget_filter - get raw data filter properties - H5Pset_filter - set raw data filter properties - H5Pset_deflate - set deflate compression filter properties - H5Pget_mpi - get MPI-IO properties - H5Pset_mpi - set MPI-IO properties - H5Pget_xfer - get data transfer properties - + H5Pset_xfer - set data transfer properties - + H5Pset_preserve - set dataset transfer property list status + H5Pget_external - get information about an external data file + H5Pset_external - add a new external data file to the list + H5Pget_driver - get low-level file driver class + H5Pget_stdio - get properties for stdio low-level driver + H5Pset_stdio - set properties for stdio low-level driver + H5Pget_sec2 - get properties for sec2 low-level driver + H5Pset_sec2 - set properties for sec2 low-level driver + H5Pget_core - get properties for core low-level driver + H5Pset_core - set properties for core low-level driver + H5Pget_split - get properties for split low-level driver + H5Pset_split - set properties for split low-level driver + H5P_get_family - get properties for family low-level driver + H5P_set_family - set properties for family low-level driver + H5Pget_cache - get meta- and raw-data caching properties + H5Pset_cache - set meta- and raw-data caching properties + H5Pget_buffer - get raw-data I/O pipe buffer properties + H5Pset_buffer - set raw-data I/O pipe buffer properties + H5Pget_preserve - get type conversion preservation properties + H5Pset_preserve - set type conversion preservation properties + H5Pget_nfilters - get number of raw data filters + H5Pget_filter - get raw data filter properties + H5Pset_filter - set raw data filter properties + H5Pset_deflate - set deflate compression filter properties + H5Pget_mpi - get MPI-IO properties + H5Pset_mpi - set MPI-IO properties + H5Pget_xfer - get data transfer properties + + H5Pset_xfer - set data transfer properties + + H5Pset_preserve - set dataset transfer property list status + H5Pget_preserve - get dataset transfer property list status + H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O - + H5Pget_hyper_cache - returns information regarding the caching of + + H5Pget_hyper_cache - returns information regarding the caching of hyperslab blocks during I/O - + H5Pget_btree_ratios - sets B-tree split ratios for a dataset + + H5Pget_btree_ratios - sets B-tree split ratios for a dataset transfer property list + H5Pset_btree_ratios - gets B-tree split ratios for a dataset transfer property list - + H5Pset_vlen_mem_manager - sets the memory manager for variable-length + + H5Pset_vlen_mem_manager - sets the memory manager for variable-length datatype allocation + H5Pget_vlen_mem_manager - sets the memory manager for variable-length datatype allocation Datasets - H5Dclose - release dataset resources - H5Dcreate - create a new dataset - H5Dget_space - get data space - H5Dget_type - get data type - H5Dget_create_plist - get dataset creation properties - H5Dopen - open an existing dataset - H5Dread - read raw data - H5Dwrite - write raw data - H5Dextend - extend a dataset + H5Dclose - release dataset resources + H5Dcreate - create a new dataset + H5Dget_space - get data space + H5Dget_type - get data type + H5Dget_create_plist - get dataset creation properties + H5Dopen - open an existing dataset + H5Dread - read raw data + H5Dwrite - write raw data + H5Dextend - extend a dataset + H5Diterate - iterate over all selected elements in a dataspace + H5Dget_storage_size - return the amount of storage required for a dataset + H5Dvlen_reclaim - reclaim VL datatype memory buffers Attributes - H5Acreate - create a new attribute - H5Aopen_name - open an attribute by name - H5Aopen_idx - open an attribute by number - H5Awrite - write values into an attribute - H5Aread - read values from an attribute - H5Aget_space - get attribute data space - H5Aget_type - get attribute data type - H5Aget_name - get attribute name - H5Anum_attrs - return the number of attributes for an object - H5Aiterate - iterate over an object's attributes - H5Adelete - delete an attribute - H5Aclose - close an attribute + H5Acreate - create a new attribute + H5Aopen_name - open an attribute by name + H5Aopen_idx - open an attribute by number + H5Awrite - write values into an attribute + H5Aread - read values from an attribute + H5Aget_space - get attribute data space + H5Aget_type - get attribute data type + H5Aget_name - get attribute name + H5Anum_attrs - return the number of attributes for an object + H5Aiterate - iterate over an object's attributes + H5Adelete - delete an attribute + H5Aclose - close an attribute Errors - H5Eclear - clear the error stack - H5Eprint - print an error stack - H5Eget_auto - get automatic error reporting settings - H5Eset_auto - set automatic error reporting - H5Ewalk - iterate over the error stack - H5Ewalk_cb - the default error stack iterator function - H5Eget_major - get the message for the major error number - H5Eget_minor - get the message for the minor error number + H5Eclear - clear the error stack + H5Eprint - print an error stack + H5Eget_auto - get automatic error reporting settings + H5Eset_auto - set automatic error reporting + H5Ewalk - iterate over the error stack + H5Ewalk_cb - the default error stack iterator function + H5Eget_major - get the message for the major error number + H5Eget_minor - get the message for the minor error number Files - H5Fclose - close a file and release resources - H5Fcreate - create a new file - H5Fget_create_plist - get file creation property list - H5Fget_access_plist - get file access property list - H5Fis_hdf5 - determine if a file is an hdf5 file - H5Fopen - open an existing file + H5Fclose - close a file and release resources + H5Fcreate - create a new file + H5Fget_create_plist - get file creation property list + H5Fget_access_plist - get file access property list + H5Fis_hdf5 - determine if a file is an hdf5 file + H5Fopen - open an existing file H5Freopen - reopen an HDF5 file H5Fmount - mount a file H5Funmount - unmount a file H5Fflush - flush all buffers associated with a file to disk Groups - H5Gclose - close a group and release resources - H5Gcreate - create a new group - H5Gopen - open an existing group - H5Giterate - iterate over the contents of a group - H5Gmove - change the name of some object - H5Glink - create a hard or soft link to an object - H5Gunlink - break the link between a name and an object - H5Gget_objinfo - get information about a group entry - H5Gget_linkval - get the value of a soft link - H5Gget_comment - get the comment string for an object - H5Gset_comment - set the comment string for an object + H5Gclose - close a group and release resources + H5Gcreate - create a new group + H5Gopen - open an existing group + H5Giterate - iterate over the contents of a group + H5Gmove - change the name of some object + H5Glink - create a hard or soft link to an object + H5Gunlink - break the link between a name and an object + H5Gget_objinfo - get information about a group entry + H5Gget_linkval - get the value of a soft link + H5Gget_comment - get the comment string for an object + H5Gset_comment - set the comment string for an object Dataspaces - H5Screate - create a new data space - H5Scopy - copy a data space - H5Sclose - release data space - H5Screate_simple - create a new simple data space - H5Sset_space - set simple data space extents - H5Sis_simple - determine if data space is simple - H5Sset_extent_simple - set simple data space dimensionality and size - H5Sget_simple_extent_npoints - get number of points in simple extent + H5Screate - create a new data space + H5Scopy - copy a data space + H5Sclose - release data space + H5Screate_simple - create a new simple data space + H5Sset_space - set simple data space extents + H5Sis_simple - determine if data space is simple + H5Sset_extent_simple - set simple data space dimensionality and size + H5Sget_simple_extent_npoints - get number of points in simple extent H5Sget_simple_extent_ndims - get simple data space dimensionality H5Sget_simple_extent_dims - get simple data space size H5Sget_simple_extent_type - get type of simple extent - H5Sset_extent_none - reset extent to be empty - H5Sextent_copy - copy the extent from one data space to another + H5Sset_extent_none - reset extent to be empty + H5Sextent_copy - copy the extent from one data space to another H5Sget_select_npoints - get number of points selected for I/O - H5Sselect_hyperslab - set hyperslab dataspace selection + H5Sselect_hyperslab - set hyperslab dataspace selection H5Sselect_elements - set element sequence dataspace selection - H5Sselect_all - select entire extent for I/O - H5Sselect_none - deselect all elements of extent - H5Soffset_simple - set selection offset - H5Sselect_valid - determine if selection is valid for extent + H5Sselect_all - select entire extent for I/O + H5Sselect_none - deselect all elements of extent + H5Soffset_simple - set selection offset + H5Sselect_valid - determine if selection is valid for extent + H5Sget_select_hyper_nblocks - get number of hyperslab blocks - + H5Sget_select_hyper_blocklist - get the list of hyperslab blocks + + H5Sget_select_hyper_blocklist - get the list of hyperslab blocks currently selected - + H5Sget_select_elem_npoints - get the number of element points + + H5Sget_select_elem_npoints - get the number of element points in the current selection - + H5Sget_select_elem_pointlist - get the list of element points + + H5Sget_select_elem_pointlist - get the list of element points currently selected - + H5Sget_select_bounds - gets the bounding box containing + + H5Sget_select_bounds - gets the bounding box containing the current selection Datatypes - H5Tclose - release data type resources - H5Topen - open a named data type - H5Tcommit - name a data type - H5Tcommitted - determine if a type is named - H5Tcopy - copy a data type - H5Tcreate - create a new data type - H5Tequal - compare two data types - H5Tlock - lock type to prevent changes - H5Tfind - find a data type conversion function - H5Tconvert - convert data from one type to another - H5Tregister - register a conversion function - H5Tunregister - remove a conversion function - H5Tget_overflow - get function that handles overflow conv. cases - H5Tset_overflow - set function to handle overflow conversion cases - H5Tget_class - get data type class - H5Tget_cset - get character set - H5Tget_ebias - get exponent bias - H5Tget_fields - get floating point fields - H5Tget_inpad - get inter-field padding - H5Tget_member_dims - get struct member dimensions - H5Tget_member_name - get struct member name - H5Tget_member_offset - get struct member byte offset - H5Tget_member_type - get struct member type - H5Tget_nmembers - get number of struct members - H5Tget_norm - get floating point normalization - H5Tget_offset - get bit offset within type - H5Tget_order - get byte order - H5Tget_pad - get padding type - H5Tget_precision - get precision in bits - H5Tget_sign - get integer sign type - H5Tget_size - get size in bytes - H5Tget_strpad - get string padding - H5Tinsert - insert scalar struct member - H5Tinsert_array - insert array struct member - H5Tpack - pack struct members - H5Tset_cset - set character set - H5Tset_ebias - set exponent bias - H5Tset_fields - set floating point fields - H5Tset_inpad - set inter-field padding - H5Tset_norm - set floating point normalization - H5Tset_offset - set bit offset within type - H5Tset_order - set byte order - H5Tset_pad - set padding type - H5Tset_precision - set precision in bits - H5Tset_sign - set integer sign type - H5Tset_size - set size in bytes - H5Tset_strpad - set string padding - + H5Tget_super - return the base datatype from which a + H5Tclose - release data type resources + H5Topen - open a named data type + H5Tcommit - name a data type + H5Tcommitted - determine if a type is named + H5Tcopy - copy a data type + H5Tcreate - create a new data type + H5Tequal - compare two data types + H5Tlock - lock type to prevent changes + H5Tfind - find a data type conversion function + H5Tconvert - convert data from one type to another + H5Tregister - register a conversion function + H5Tunregister - remove a conversion function + H5Tget_overflow - get function that handles overflow conv. cases + H5Tset_overflow - set function to handle overflow conversion cases + H5Tget_class - get data type class + H5Tget_cset - get character set + H5Tget_ebias - get exponent bias + H5Tget_fields - get floating point fields + H5Tget_inpad - get inter-field padding + H5Tget_member_dims - get struct member dimensions + H5Tget_member_name - get struct member name + H5Tget_member_offset - get struct member byte offset + H5Tget_member_type - get struct member type + H5Tget_nmembers - get number of struct members + H5Tget_norm - get floating point normalization + H5Tget_offset - get bit offset within type + H5Tget_order - get byte order + H5Tget_pad - get padding type + H5Tget_precision - get precision in bits + H5Tget_sign - get integer sign type + H5Tget_size - get size in bytes + H5Tget_strpad - get string padding + H5Tinsert - insert scalar struct member + H5Tinsert_array - insert array struct member + H5Tpack - pack struct members + H5Tset_cset - set character set + H5Tset_ebias - set exponent bias + H5Tset_fields - set floating point fields + H5Tset_inpad - set inter-field padding + H5Tset_norm - set floating point normalization + H5Tset_offset - set bit offset within type + H5Tset_order - set byte order + H5Tset_pad - set padding type + H5Tset_precision - set precision in bits + H5Tset_sign - set integer sign type + H5Tset_size - set size in bytes + H5Tset_strpad - set string padding + + H5Tget_super - return the base datatype from which a datatype is derived + H5Tvlen_create - creates a new variable-length dataype + H5Tenum_create - creates a new enumeration datatype + H5Tenum_insert - inserts a new enumeration datatype member - + H5Tenum_nameof - returns the symbol name corresponding to a + + H5Tenum_nameof - returns the symbol name corresponding to a + specified member of an enumeration datatype + + H5Tvalueof - return the value corresponding to a specified member of an enumeration datatype - + H5Tvalueof - return the value corresponding to a - specified member of an enumeration datatype + H5Tget_member_value - return the value of an enumeration datatype member + H5Tset_tag - tags an opaque datatype + H5Tget_tag - gets the tag associated with an opaque datatype - - H5Tregister_hard - register specific type conversion function - - H5Tregister_soft - register general type conversion function + - H5Tregister_hard - register specific type conversion function + - H5Tregister_soft - register general type conversion function Filters - H5Tregister - register a conversion function + H5Tregister - register a conversion function Compression - H5Zregister - register new compression and uncompression + H5Zregister - register new compression and uncompression functions for a method specified by a method number Identifiers @@ -8972,14 +8972,14 @@ References + H5Rcreate - creates a reference + H5Rdereference - open the HDF5 object referenced + H5Rget_region - retrieve a dataspace with the specified region selected - + H5Rget_object_type - retrieve the type of object that an + + H5Rget_object_type - retrieve the type of object that an object reference points to Ragged Arrays (alpha) - H5RAcreate - create a new ragged array - H5RAopen - open an existing array - H5RAclose - close a ragged array - H5RAwrite - write to an array - H5RAread - read from an array + H5RAcreate - create a new ragged array + H5RAopen - open an existing array + H5RAclose - close a ragged array + H5RAwrite - write to an array + H5RAread - read from an array diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt new file mode 100644 index 0000000..1fc3c60 --- /dev/null +++ b/release_docs/HISTORY-1_10.txt @@ -0,0 +1,6562 @@ +HDF5 History +============ + +This file contains development history of the HDF5 1.10 branch + +09. Release Information for hdf5-1.10.7 +08. Release Information for hdf5-1.10.6 +07. Release Information for hdf5-1.10.5 +06. Release Information for hdf5-1.10.4 +05. Release Information for hdf5-1.10.3 +04. Release Information for hdf5-1.10.2 +03. Release Information for hdf5-1.10.1 +02. Release Information for hdf5-1.10.0-patch1 +01. Release Information for hdf5-1.10.0 + +[Search on the string '%%%%' for section breaks of each release.] + +%%%%1.10.7%%%% + +HDF5 version 1.10.7 released on 2020-09-11 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + + HDF5 binaries provided are fully tested with ZLIB and the free + Open Source SZIP successor Libaec (with BSD license). + The official ZLIB and SZIP/Libaec pages are at: + + ZLIB: http://www.zlib.net/ + http://www.zlib.net/zlib_license.html + SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec + https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.6 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Disable memory sanity checks in the Autotools in release branches + + The library can be configured to use internal memory sanity checking, + which replaces C API calls like malloc(3) and free(3) with our own calls + which add things like heap canaries. These canaries can cause problems + when external filter plugins reallocate canary-marked buffers. + + For this reason, the default will be to not use the memory allocation + sanity check feature in release branches (e.g., hdf5_1_10_7). + Debug builds in development branches (e.g., develop, hdf5_1_10) will + still use them by default. + + This change only affects Autotools debug builds. Non-debug autotools + builds and all CMake builds do not enable this feature by default. + + (DER - 2020/08/19) + + - Add file locking configure and CMake options + + HDF5 1.10.0 introduced a file locking scheme, primarily to help + enforce SWMR setup. Formerly, the only user-level control of the scheme + was via the HDF5_USE_FILE_LOCKING environment variable. + + This change introduces configure-time options that control whether + or not file locking will be used and whether or not the library + ignores errors when locking has been disabled on the file system + (useful on some HPC Lustre installations). + + In both the Autotools and CMake, the settings have the effect of changing + the default property list settings (see the H5Pset/get_file_locking() + entry, below). + + The yes/no/best-effort file locking configure setting has also been + added to the libhdf5.settings file. + + Autotools: + + An --enable-file-locking=(yes|no|best-effort) option has been added. + + yes: Use file locking. + no: Do not use file locking. + best-effort: Use file locking and ignore "disabled" errors. + + CMake: + + Two self-explanatory options have been added: + + HDF5_USE_FILE_LOCKING + HDF5_IGNORE_DISABLED_FILE_LOCKS + + Setting both of these to ON is the equivalent to the Autotools' + best-effort setting. + + NOTE: + The precedence order of the various file locking control mechanisms is: + + 1) HDF5_USE_FILE_LOCKING environment variable (highest) + + 2) H5Pset_file_locking() + + 3) configure/CMake options (which set the property list defaults) + + 4) library defaults (currently best-effort) + + (DER - 2020/07/30, HDFFV-11092) + + - CMake option to link the generated Fortran MOD files into the include + directory. + + The Fortran generation of MOD files by a Fortran compile can produce + different binary files between SHARED and STATIC compiles with different + compilers and/or different platforms. Note that it has been found that + different versions of Fortran compilers will produce incompatible MOD + files. Currently, CMake will locate these MOD files in subfolders of + the include directory and add that path to the Fortran library target + in the CMake config file, which can be used by the CMake find library + process. For other build systems using the binary from a CMake install, + a new CMake configuration can be used to copy the pre-chosen version + of the Fortran MOD files into the install include directory. + + The default will depend on the configuration of + BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: + YES YES Default to SHARED + YES NO Default to STATIC + NO YES Default to SHARED + NO NO Default to SHARED + The defaults can be overridden by setting the config option + HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC + + (ADB - 2020/07/09, HDFFV-11116) + + - CMake option to use AEC (open source SZip) library instead of SZip + + The open source AEC library is a replacement library for SZip. In + order to use it for hdf5, the libaec CMake source was changed to add + "-fPIC" and exclude test files. A new option USE_LIBAEC is required + to compensate for the different files produced by AEC build. + + Autotools does not build the compression libraries within hdf5 builds, + but will use an installed libaec when configured as before with the + option --with-libsz=<path to libaec directory>. + + (ADB - 2020/04/22, OESS-65) + + - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER + + Some handcrafted tests in HDFTests.c have been removed and the CMake + CHECK_STRUCT_HAS_MEMBER module has been used. + + (ADB - 2020/03/24, TRILAB-24) + + - Both build systems use same set of warnings flags + + GNU C, C++ and gfortran warnings flags were moved to files in a config + sub-folder named gnu-warnings. Flags that only are available for a specific + version of the compiler are in files named with that version. + Clang C warnings flags were moved to files in a config sub-folder + named clang-warnings. + Intel C, Fortran warnings flags were moved to files in a config sub-folder + named intel-warnings. + + There are flags in named "error-xxx" files with warnings that may + be promoted to errors. Some source files may still need fixes. + + There are also pairs of files named "developer-xxx" and "no-developer-xxx" + that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the + configure option:--enable-developer-warnings. + + In addition, CMake no longer applies these warnings for examples. + + (ADB - 2020/03/24, TRILAB-192) + + - Update CMake minimum version to 3.12 + + Updated CMake minimum version to 3.12 and added version checks + for Windows features. + + (ADB - 2020/02/05, TRILABS-142) + + - Fixed CMake include properties for Fortran libraries + + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. + + (ADB - 2020/02/04, HDFFV-11012) + + - Added common warnings files for gnu and intel + + Added warnings files to use one common set of flags + during configure for both autotools and CMake build + systems. The initial implementation only affects a + general set of flags for gnu and intel compilers. + + (ADB - 2020/01/17) + + - Added new options to CMake for control of testing + + Added CMake options (default ON); + HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL + combined with: + HDF5_TEST_TOOLS + HDF5_TEST_EXAMPLES + HDF5_TEST_SWMR + HDF5_TEST_FORTRAN + HDF5_TEST_CPP + HDF5_TEST_JAVA + + (ADB - 2020/01/15, HDFFV-11001) + + - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + + Added CMake code and files to execute the Clang sanitizers if + HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option + is set to one of the following: + Address + Memory + MemoryWithOrigins + Undefined + Thread + Leak + 'Address;Undefined' + + (ADB - 2019/12/12, TRILAB-135) + + + Library: + -------- + - Add metadata cache optimization to reduce skip list usage + + On file flush or close, the metadata cache attempts to write out + all dirty entries in increasing address order. To do this, it needs + an address sorted list of metadata entries. Further, since flushing + one metadata cache entry can dirty another, this list must support + efficient insertion and deletion. + + The metadata cache uses a skip list of all dirty entries for this + purpose. Before this release, this skip list was maintained at all + times. However, since profiling indicates that this imposes a + significant cost, we now construct and maintain the skip list only + when needed. Specifically, we enable the skip list and load it with + a list of all dirty entries in the metadata cache just before a flush, + and disable it after the flush. + + (JRM - 2020/08/17, HDFFV-11034) + + - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable + + This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that + were previously accepted. This option turns on file locking but + ignores locking errors when the library detects that file locking + has been disabled on a file system (useful on some HPC Lustre + installations). + + The capitalization of BEST_EFFORT is mandatory. + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + + - Add H5Pset/get_file_locking() API calls + + This change adds new API calls which can be used to set or get the + file locking parameters. The single API call sets both the "use file + locking" flag and the "ignore disabled file locking" flag. + + When opening a file multiple times without closing, the file MUST be + opened with the same file locking settings. Opening a file with different + file locking settings will fail (this is similar to the behavior of + H5Pset_fclose_degree()). + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + - Add Mirror VFD + + Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote + machine. Must be used in conjunction with the Splitter VFD. + + (JOS - 2020/03/13, TBD) + + - Add Splitter VFD + + Maintain separate R/W and W/O channels for "concurrent" file writes + to two files using a single HDF5 file handle. + + (JOS - 2020/03/13, TBD) + + - Fixed an assertion failure in the parallel library when collectively + filling chunks. As it is required that chunks be written in + monotonically non-decreasing order of offset in the file, this assertion + was being triggered when the list of chunk file space allocations being + passed to the collective chunk filling routine was not sorted according + to this particular requirement. + + The addition of a sort of the out of order chunks trades a bit of + performance for the elimination of this assertion and of any complaints + from MPI implementations about the file offsets used being out of order. + + (JTH - 2019/10/07) + + Fortran Library: + ---------------- + - Add wrappers for H5Pset/get_file_locking() API calls + + h5pget_file_locking_f() + h5pset_file_locking_f() + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + - Added new Fortran parameters: + + H5F_LIBVER_ERROR_F + H5F_LIBVER_NBOUNDS_F + H5F_LIBVER_V18_F + H5F_LIBVER_V110_F + + - Added new Fortran API: h5pget_libver_bounds_f + + (MSB - 2020/02/11, HDFFV-11018) + + C++ Library: + ------------ + - Add wrappers for H5Pset/get_file_locking() API calls + + FileAccPropList::setFileLocking() + FileAccPropList::getFileLocking() + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + Java Library: + ---------------- + - Add wrappers for H5Pset/get_file_locking() API calls + + H5Pset_file_locking() + H5Pget_use_file_locking() + H5Pget_ignore_disabled_file_locking() + + Unlike the C++ and Fortran wrappers, there are separate getters for the + two file locking settings, each of which returns a boolean value. + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + Tools: + ------ + - h5repack added options to control how external links are handled. + + Currently h5repack preserves external links and cannot copy and merge + data from the external files. Two options, merge and prune, were added to + control how to merge data from an external link into the resulting file. + --merge Follow external soft link recursively and merge data. + --prune Do not follow external soft links and remove link. + --merge --prune Follow external link, merge data and remove dangling link. + + (ADB - 2020/08/05, HDFFV-9984) + + High-Level APIs: + --------------- + - None + + C Packet Table API + ------------------ + - None + + Internal header file + -------------------- + - None + + Documentation + ------------- + - None + + +Support for new platforms, languages and compilers. +======================================= + - None + + +Bug Fixes since HDF5-1.10.6 release +================================== + + Library + ------- + - Fix bug and simplify collective metadata write operation when some ranks + have no entries to contribute. This fixes parallel regression test + failures with IBM SpectrumScale MPI on the Summit system at ORNL. + + (QAK - 2020/09/02) + + - Avoid setting up complex MPI types with 0-length vectors, which some + MPI implementations don't handle well. (In particular, IBM + SpectrumScale MPI on the Summit system at ORNL) + + (QAK - 2020/08/21) + + - Fixed use-of-uninitialized-value error + + Appropriate initialization of local structs was added to remove the + use-of-uninitialized-value errors reported by MemorySanitizer. + + (BMR - 2020/8/13, HDFFV-11101) + + - Creation of dataset with optional filter + + When the combination of type, space, etc doesn't work for filter + and the filter is optional, it was supposed to be skipped but it was + not skipped and the creation failed. + + A fix is applied to allow the creation of a dataset in such + situation, as specified in the user documentation. + + (BMR - 2020/8/13, HDFFV-10933) + + - Explicitly declared dlopen to use RTLD_LOCAL + + dlopen documentation states that if neither RTLD_GLOBAL nor + RTLD_LOCAL are specified, then the default behavior is unspecified. + The default on linux is usually RTLD_LOCAL while macos will default + to RTLD_GLOBAL. + + (ADB - 2020/08/12, HDFFV-11127) + + - Fixed issues CVE-2018-13870 and CVE-2018-13869 + + When a buffer overflow occurred because a name length was corrupted + and became very large, h5dump crashed on memory access violation. + + A check for reading past the end of the buffer was added to multiple + locations to prevent the crashes and h5dump now simply fails with an + error message when this error condition occurs. + + (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) + + - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which + causes asserts/errors when passed to other dataspace API calls. + + H5S_NO_CLASS is an internal class value that should not have been + exposed via a public API call. + + In debug builds of the library, this can cause asserts to trip. In + non-debug builds, it will produce normal library errors. + + The new library behavior is for H5Sset_extent_none() to convert + the dataspace into one of type H5S_NULL, which is better handled + by the library and easier for developers to reason about. + + (DER - 2020/07/27, HDFFV-11027) + + - Fixed the segmentation fault when reading attributes with multiple threads + + It was reported that the reading of attributes with variable length string + datatype will crash with segmentation fault particularly when the number + of threads is high (>16 threads). The problem was due to the file pointer + that was set in the variable length string datatype for the attribute. + That file pointer was already closed when the attribute was accessed. + + The problem was fixed by setting the file pointer to the current opened + file pointer when the attribute was accessed. Similar patch up was done + before when reading dataset with variable length string datatype. + + (VC - 2020/07/13, HDFFV-11080) + + - Fixed issue CVE-2018-17438 + + A division by zero was discovered in H5D__select_io() of H5Dselect.c. + https://security-tracker.debian.org/tracker/CVE-2018-17438 + + A check was added to protect against division by zero. When such + situation occurs again, the normal HDF5 error handling will be invoked, + instead of segmentation fault. + + (BMR, DER - 2020/07/09, HDFFV-10587) + + - Fixed CVE-2018-17435 + + The tool h52gif produced a segfault when the size of an attribute message + was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the attribute message's size against the + buffer size before accessing the buffer. h52gif was also fixed to display + the failure instead of silently exiting after the segfault was eliminated. + + (BMR - 2020/6/19, HDFFV-10591) + + - Don't allocate an empty (0-dimensioned) chunked dataset's chunk + index, until the dataset's dimensions are increased. + + (QAK - 2020/05/07) + + Configuration + ------------- + - Stopped addition of szip header and include directory path for + incompatible libsz + + szlib.h is the same for both 32-bit and 64-bit szip, and the header file + and its path were added to the HDF5 binary even though the configure + check of a function in libsz later failed and szip compression was not + enabled. The header file and include path are now added only when the + libsz function passes the configure check. + + (LRK - 2020/08/17, HDFFV-10830) + + - Added -fsanitize=address autotools configure option for Clang compiler + + Clang sanitizer options were also added for Clang compilers with CMake. + + (LRK, 2020/08/05, HDFFV-10836) + + - Updated testh5cc.sh.in for functions versioned in HDF5 1.10. + + testh5cc.sh previously tested that the correct version of a function + versioned in HDF5 1.6 or 1.8 was compiled when one of + H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This + test was extended for additional testing with H5_USE_18_API_DEFAULT. + + (LRK, 2020/06/22, HDFFV-11000) + + - Fixed CMake include properties for Fortran libraries + + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. + + (ADB - 2020/02/04, HDFFV-11012) + + Performance + ------------- + - None + + Java Library: + ---------------- + - None + + Fortran + -------- + - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + + (MSB - 2020/2/18, HDFFV-11029) + + - Fixed configure issue when building HDF5 with NAG Fortran 7.0. + + HDF5 now accounts for the addition of half-precision floating-point + in NAG 7.0 with a KIND=16. + + (MSB - 2020/02/28, HDFFV-11033) + + Tools + ----- + - The tools library was updated by standardizing the error stack process. + + General sequence is: + h5tools_setprogname(PROGRAMNAME); + h5tools_setstatus(EXIT_SUCCESS); + h5tools_init(); + ... process the command-line (check for error-stack enable) ... + h5tools_error_report(); + ... (do work) ... + h5diff_exit(ret); + + (ADB - 2020/07/20, HDFFV-11066) + + - h5diff fixed a command line parsing error. + + h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. + The macro H5_DBL_ABS_EQUAL was removed and a direct value comparison was used. + + (ADB - 2020/07/20, HDFFV-10897) + + - h5diff added a command line option to ignore attributes. + + h5diff would ignore all objects with a supplied path if the exclude-path argument is used. + Adding the exclude-attribute argument will only eclude attributes, with the supplied path, + from comparison. + + (ADB - 2020/07/20, HDFFV-5935) + + - h5diff added another level to the verbose argument to print filenames. + + Added verbose level 3 that is level 2 plus the filenames. The levels are: + 0 : Identical to '-v' or '--verbose' + 1 : All level 0 information plus one-line attribute status summary + 2 : All level 1 information plus extended attribute status report + 3 : All level 2 information plus file names + + (ADB - 2020/07/20, HDFFV-10005) + + - h5repack was fixed to repack the reference attributes properly. + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/10, HDFFV-11014) + + High-Level APIs: + ------ + - The H5DSis_scale function was updated to return "not a dimension scale" (0) + instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are + not written according to Dimension Scales Specification. + + (EIP - 2020/08/12, HDFFV-10436) + + Fortran High-Level APIs: + ------ + - None + + Documentation + ------------- + - None + + F90 APIs + -------- + - None + + C++ APIs + -------- + - None + + Testing + ------- + - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} + + Lib files needed are now copied to a subdirectory in the java/test + directory, and on Macs the loader path for libhdf5.xxxs.so is changed + in the temporary copy of libhdf5_java.dylib. + + (LRK, 2020/7/2, HDFFV-11063) + + +Supported Platforms +=================== + + Linux 3.10.0-1127.10.1.el7 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 2.6.32-754.31.1.el6 IBM XL C/C++ V13.1 + #1 SMP ppc64 GNU/Linux IBM XL Fortran V15.1 + (ostrich) + + Linux 3.10.0-327.18.2.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 4.0.0 compiled with GCC 7.2.0 + + SunOS 5.11 11.4.5.12.5.0 Sun C 5.15 SunOS_sparc 2017/05/30 + 32- and 64-bit Studio 12.6 Fortran 95 8.8 SunOS_sparc 2017/05/30 + (hedgehog) Sun C++ 5.15 SunOS_sparc 2017/05/30 + + Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (cmake) + + macOS Mojave 10.14.6 Apple LLVM version 10.0.1 (clang-1001.0.46.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (swallow) Intel icc/icpc/ifort version 19.0.4.233 20190416 + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 x64 y y/y y y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +MacOS Sierra 10.12.6 64-bit n y/y n y y y +MacOS High Sierra 10.13.6 64-bit n y/y n y y y +MacOS Mojave 10.14.6 64-bit n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-754.31.1.el6.ppc64 XL n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 x64 y y y y +Windows 10 y y y y +Windows 10 x64 y y y y +MacOS Sierra 10.12.6 64-bit y n y y +MacOS High Sierra 10.13.6 64-bit y n y y +MacOS Mojave 10.14.6 64-bit y n y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n +Linux 2.6.32-754.31.1.el6.ppc64 XL y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 19.10-0 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-754.31.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 2.1.6-GCC-7.2.0-2.29, + 3.1.3-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.1.4 compiled with GCC 4.9.3 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang/3.9.0, 8.0.1 + (quartz) gcc/7.3.0, 8.1.0 + intel/16.0.4 + + Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang/coral-2018.08.08 + (lassen) gcc/7.3.1 + xl/2019.02.07 + + Linux-4.12.14-150.52-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux gcc/7.3.0, 8.2.0 + (cori) intel/19.0.3 + + Linux-4.4.180-94.107-default cray-mpich/7.7.6 + # 1SMP x86_64 GNU/Linux gcc/7.2.0, 8.2.0 + (mutrino) intel/17.0.4, 18.0.2, 19.0.4 + + Fedora 32 5.7.15-200.fc32.x86_64 Clang version 10.0.0 (Fedora 10.0.0-2.fc32) + #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20200723 (Red Hat 10.2.1-1) + GNU Fortran (GCC) 10.2.1 20200723 (Red Hat 10.2.1) + (cmake and autotools) + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + SunOS 5.11 11.3 Sun C 5.15 SunOS_sparc + 32- and 64-bit Sun Fortran 95 8.8 SunOS_sparc + (emu) Sun C++ 5.15 SunOS_sparc + + +Known Problems +============== + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + + + +%%%%1.10.6%%%% + +HDF5 version 1.10.6 released on 2019-12-23 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.5 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Update CMake for VS2019 support + + CMake added support for VS2019 in version 3.15. Changes to the CMake + generator setting required changes to scripts. Also updated version + references in CMake files as necessary. + + (ADB - 2019/11/18, HDFFV-10962) + + - Update CMake options to match new autotools options + + Add configure options (autotools - CMake): + enable-asserts HDF5_ENABLE_ASSERTS + enable-symbols HDF5_ENABLE_SYMBOLS + enable-profiling HDF5_ENABLE_PROFILING + enable-optimization HDF5_ENABLE_OPTIMIZATION + In addition NDEBUG is no longer forced defined and relies on the CMake + process. + + (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) + + - Update CMake tests to use FIXTURES + + CMake test fixtures allow setup/cleanup tests and other dependency + requirements as properties for tests. This is more flexible for + modern CMake code. + + (ADB - 2019/07/23, HDFFV-10529) + + - Windows PDB files are always installed + + There are build configuration or flag settings for Windows that may not + generate PDB files. If those files are not generated then the install + utility will fail because those PDB files are not found. An optional + variable, DISABLE_PDB_FILES, was added to not install PDB files. + + (ADB - 2019/07/17, HDFFV-10424) + + - Add mingw CMake support with a toolchain file + + There have been a number of mingw issues that have been linked under + HDFFV-10845. It has been decided to implement the CMake cross-compiling + technique of toolchain files. We will use a linux platform with the mingw + compiler stack for testing. Only the C language is fully supported, and + the error tests are skipped. The C++ language works for static but shared + builds have a shared library issue with the mingw Standard Exception Handling + library, which is not available on Windows. Fortran has a common cross-compile + problem with the fortran configure tests. + + (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) + + - Windows PDB files are installed incorrectly + + For static builds, the PDB files for windows should be installed next + to the static libraries in the lib folder. Also the debug versions of + libraries and PDB files are now correctly built using the default + CMAKE_DEBUG_POSTFIX setting. + + (ADB - 2019/07/09, HDFFV-10581) + + - Add option to build only shared libs + + A request was made to prevent building static libraries and only build + shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will + skip building static libraries. Certain utility functions will build with + static libs but are not published. Tests are adjusted to use the correct + libraries depending on SHARED/STATIC settings. + + (ADB - 2019/06/12, HDFFV-10805) + + - Add options to enable or disable building tools and tests + + Configure options --enable-tests and --enable-tools were added for + autotools configure. These options are enabled by default, and can be + disabled with either --disable-tests (or tools) or --enable-tests=no + (or --enable-tools=no). Build time is reduced ~20% when tools are + disabled, 35% when tests are disabled, 45% when both are disabled. + Re-enabling them after the initial build requires running configure + again with the option(s) enabled. + + (LRK - 2019/06/12, HDFFV-9976) + + - Change tools tests to search the error stack + + There are some use cases which can cause the error stack of tools to be + different then the expected output. These tests now use grepTest.cmake; + this was changed to allow the error file to be searched for an expected string. + + (ADB - 2019/04/15, HDFFV-10741) + + + Library: + -------- + - Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5 + + These new VFDs have been introduced in HDF5-1.10.6. Instructions to + enable them when configuring HDF5 on Linux and Mac may be found at + https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS. + + Installing on Windows requires CMake 3.13 and the following additional setup. + Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + + PATH should have been updated with the installation dir. + set ENV variable OPENSSL_ROOT_DIR to the installation dir. + set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + Install libcurl library (with dev files); + download the latest released version using git: https://github.com/curl/curl.git + + Open a Visual Studio Command prompt + change to the libcurl root folder + run the "buildconf.bat" batch file + change to the winbuild directory + nmake /f Makefile.vc mode=dll MACHINE=x64 + copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + set ENV variable CURL_ROOT to C:\curl (installation dir) + update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + the aws credentials file should be in %USERPROFILE%\.aws folder + set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" + + (ADB - 2019/09/12, HDFFV-10854) + + C++ Library: + ------------ + - Added new wrappers for H5Pset/get_create_intermediate_group() + LinkCreatPropList::setCreateIntermediateGroup() + LinkCreatPropList::getCreateIntermediateGroup() + + (BMR - 2019/04/22, HDFFV-10622) + + + Java Library: + ---------------- + - Fixed a failure in JUnit-TestH5P on 32-bit architectures + + (JTH - 2019/04/30) + + +Support for new platforms, languages and compilers. +======================================= + - CMake added support for VS2019 in version 3.15. Updated scripts. + + - macOS 10.13.6 Darwin 17.7.0 with Apple clang LLVM version 10.0.0 + + - macOS 10.14.6 Darwin 18.7.0 with Apple clang LLVM version 10.0.1 + + +Bug Fixes since HDF5-1.10.5 release +================================== + + Library + ------- + - Improved performance when creating a large number of small datasets by + retrieving default property values from the API context instead of doing + skip list searches. More work is required to achieve parity with HDF5 1.8. + + (CJH - 2019/12/10, HDFFV-10658) + + - Fixed user-created data access properties not existing in the property list + returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a + reproducer and a patch. + + (CJH - 2019/12/9, HDFFV-10934) + + - Inappropriate linking with deprecated MPI C++ libraries + + HDF5 does not define *_SKIP_MPICXX in the public headers, so applications + can inadvertently wind up linking to the deprecated MPI C++ wrappers. + + MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h + so this should no longer be an issue. HDF5 makes no use of the deprecated + MPI C++ wrappers. + + (DER - 2019/09/17, HDFFV-10893) + + - fcntl(2)-based file locking incorrectly passed the lock argument struct + instead of a pointer to the struct, causing errors on systems where + flock(2) is not available. + + File locking is used when files are opened to enforce SWMR semantics. A + lock operation takes place on all file opens unless the + HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE". + flock(2) is preferentially used, with fcntl(2) locks as a backup if + flock(2) is unavailable on a system (if neither is available, the lock + operation fails). On these systems, the file lock will often fail, which + causes HDF5 to not open the file and report an error. + + This bug only affects POSIX systems. Win32 builds on Windows use a no-op + locking call which always succeeds. Systems which exhibit this bug will + have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output. + + This bug affects HDF5 1.10.0 through 1.10.5. + + fcntl(2)-based file locking now correctly passes the struct pointer. + + (DER - 2019/08/27, HDFFV-10892) + + - Fixed a bug caused by a bad tag value when condensing object header + messages + + There was an assertion failure when moving messages from running a + user test program with library release HDF5 1.10.4. It was because + the tag value (object header's address) was not set up when entering + the library routine H5O__chunk_update_idx(), which eventually + verifies the metadata tag value when protecting the object header. + + The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx() + with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag. + + (VC - 2019/08/23, HDFFV-10873) + + - Fixed the test failure from test_metadata_read_retry_info() in + test/swmr.c + + The test failure is due to an incorrect number of bins returned for + retry info (info.nbins). The # of bins expected for 101 read attempts + is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c + calculates the # of bins by first obtaining the log10 value for + (read attempts - 1). For PGI/19, the log10 value for 100 read attempts + is 1.9999999999999998 instead of 2.00000. When casting the log10 value + to unsigned later on, the decimal part is chopped off causing the test + failure. + + This was fixed by obtaining the rounded integer value (HDceil) for the + log10 value of read attempts first before casting the result to unsigned. + + (VC - 2019/8/14, HDFFV-10813) + + - Fixed an issue when creating a file with non-default file space info + together with library high bound setting to H5F_LIBVER_V18. + + When setting non-default file space info in fcpl via + H5Pset_file_space_strategy() and then creating a file with both high and + low library bounds set to H5F_LIBVER_V18 in fapl, the library succeeds in + creating the file. File creation should fail because the feature of + setting non-default file space info does not exist in library release 1.8 + or earlier. + + This was fixed by setting and checking the proper version in the file + space info message based on the library low and high bounds when creating + and opening the HDF5 file. + + (VC - 2019/6/25, HDFFV-10808) + + - Fixed an issue where copying a version 1.8 dataset between files using + H5Ocopy fails due to an incompatible fill version + + When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 + dataset to a file created with both high and low library bounds set to + H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating + that the fill value version is out of bounds. + + This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 + (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. + + (VC - 2019/6/14, HDFFV-10800) + + - Fixed a bug that would cause an error or cause fill values to be + incorrectly read from a chunked dataset using the "single chunk" index if + the data was held in cache and there was no data on disk. + + (NAF - 2019/03/06) + + - Fixed a bug that could cause an error or cause fill values to be + incorrectly read from a dataset that was written to using H5Dwrite_chunk + if the dataset was not closed after writing. + + (NAF - 2019/03/06, HDFFV-10716) + + - Fixed memory leak in scale offset filter + + In a special case where the MinBits is the same as the number of bits in + the datatype's precision, the filter's data buffer was not freed, causing + the memory usage to grow. In general the buffer was freed correctly. The + Minbits are the minimal number of bits to store the data values. Please + see the reference manual for H5Pset_scaleoffset for the details. + + (RL - 2019/3/4, HDFFV-10705) + + + Configuration + ------------- + - Correct option for default API version + + CMake options for default API version are not mutually exclusive. + Change the multiple BOOL options to a single STRING option with the + strings; v16, v18, v110. + + (ADB - 2019/08/12, HDFFV-10879) + + Tools + ----- + - h5repack was fixed to repack datasets with external storage + to other types of storage. + + New test added to repack files and verify the correct data using h5diff. + + (JS - 2019/09/25, HDFFV-10408) + (ADB - 2019/10/02, HDFFV-10918) + + +Supported Platforms +=================== + + Linux 2.6.32-696.20.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + + macOS 10.13.6, Darwin, Apple clang LLVM version 10.0.0 + 17.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4 + + macOS 10.14.6, Darwin Apple clang LLVM version 10.0.1 + 18.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0 + (bobcat) Intel icc/icpc/ifort version 19.0.4 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +MacOS High Sierra 10.13.6 64-bit n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Yosemite 10.10.5 64-bit y y y y +Mac OS X El Capitan 10.11.6 64-bit y y y y +MacOS High Sierra 10.13.6 64-bit y y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following configurations are not supported but have been tested for this release. + + Linux 2.6.32-754.11.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.2(Chiyoda) + GCC Version 7.1.0 + MPICH 3.2-GCC-4.9.3 + MPICH 3.2.1-GCC-7.2.0-2.29 + OpenMPI 2.1.5-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.2(Chiyoda) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Fedora30 5.3.11-200.fc30.x86_64 + #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) + GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) + (cmake and autotools) + + Mac OS X 10.11.6, Darwin, Apple clang version 7.3.0 from Xcode 7.3 + 15.6.0, x86-64 gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + macOS 10.12.6, Darwin, Apple clang LLVM version 8.1.0 from Xcode 8.3 + 16.6.0, x86_64 gfortran GNU Fortran (GCC) 7.1.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Windows 7 x64 Visual Studio 2008 + + +Known Problems +============== + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + t_pflush1/fails on exit + The first two tests fail attempting collective writes. + + Parallel builds using OpenMPI 3.03 or later and romio fail several tests + with collective writes or compression that will not fail when ompio is used + instead of romio. This can be done by adding "--mca io ompio" to the mpirun + command. For example, in autotools builds RUNPARALLEL can be set to + "mpirun --mca io ompio -n 6" provided ompio is installed. + + CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628. + This test will pass with VS2015 with Intel compiler. + + Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested + while attempting to resolve the Jira issue: HDFFV-10540. + The known problems of reading or writing > 2GBs when using MPI-2 was + partially resolved with the MPICH library. The proposed support recognizes + IO operations > 2GB and if the datatype is not a derived type, the library + breaks the IO into chunks which can be input or output with the existing + MPI 2 limitations, i.e. size reporting and function API size/count + arguments are restricted to be 32 bit integers. For derived types larger + than 2GB, MPICH 2.1.5 fails while attempting to read or write data. + OpenMPI in contrast, implements MPI-3 APIs even in the older releases + and thus does not suffer from the 32 bit size limitation described here. + OpenMPI releases prior to v3.1.3 appear to have other datatype issues however, + e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr) + report data verification errors before eventually aborting. + The most recent versions of OpenMPI (v3.1.3 or newer) have evidently + resolved these issues and parallel HDF5 testing does not currently report + errors though occasional hangs have been observed. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +%%%%1.10.5%%%% + +HDF5 version 1.10.5 released on 2019-02-25 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.4 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Cross compile on mutrino and other Cray XC40 systems. + + Added support for CMake options to use CrayLinuxEnvironment, craype-mic-knl + module for building with craype-haswell module for configuration, and + batch scripts in bin/batch for use with sbatch or bsub to run tests in + batch jobs on compute nodes. An instruction file README_HPC describing + the use of these options was added in release_docs. + + (LRK - 2019/02/18, TRILABS-34) + + - Rework CMake command files to fix MPI testing. + + Added setup fixture to remove any test generated files and added DEPENDS + to test properties to execute tests in order expected. + + (ADB - 2019/02/14, TRILABS-111) + + - Disable SZIP or ZLIB options if TGZ files are not available. + + Changed the TGZ option for SZip and ZLib to disable the options + if the source tar.gz files are not found. + + (ADB - 2019/02/05, HDFFV-10697) + + - Added a new option to enable/disable using pread/pwrite instead of + read/write in the sec2, log, and core VFDs. + + This option is enabled by default when pread/pwrite are detected. + + Autotools: --enable-preadwrite + CMake: HDF5_ENABLE_PREADWRITE + + (DER - 2019/02/03, HDFFV-10696) + + - Rework CMake versioning for OSX platforms. + + Changed the current_version and compatibility_version flags from optional + with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX. + + (ADB - 2019/01/22, HDFFV-10685) + + - Rework CMake command files to eliminate developer CMP005 warning + + Use variables without quotes in if () statements. + + (ADB - 2019/01/18, TILABS-105) + + - Rework CMake configure files to eliminate developer CMP0075 warning + + Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not + required for configuration. Also moved check includes calls to top of + files. + + (ADB - 2019/01/03, HDFFV-10546) + + - Keep stderr and stdout separate in tests + + Changed test handling of output capture. Tests now keep the stderr + output separate from the stdout output. It is up to the test to decide + which output to check against a reference. Also added the option + to grep for a string in either output. + + (ADB - 2018/12/12, HDFFV-10632) + + - Incorrectly installed private header files were removed from + CMake installs. + + The CMake build files incorrectly flagged the following header files + as public and installed them. They are private and will no longer be + installed. + + HDF5 library private package files (H5Xpkg.h) + H5Edefin.h + H5Einit.h + H5Eterm.h + H5LTparse.h + h5diff.h + h5tools_dump.h + h5tools.h + h5tools_ref.h + h5tools_str.h + h5tools_utils.h + h5trav.h + + (DER - 2018/10/26, HDFFV-10614, 10609) + + - Autotools installs now install H5FDwindows.h + + This is simply to align the installed header files between the + autotools and CMake. H5FDwindows.h has no functionality on + non-Windows systems. + + (DER - 2018/10/26, HDFFV-10614) + + + Library: + -------- + - The sec2, log, and core VFDs can now use pread/pwrite instead of + read/write. + + pread and pwrite do not change the file offset, a feature that was + requested by a user working with a multi-threaded application. + + The option to configure this feature is described above. + + (DER - 2019/02/03, HDFFV-10696) + + - Add ability to minimize dataset object headers. + + Creation of many, very small datasets resulted in extensive file bloat + due to extra space in the dataset object headers -- this space is + allocated by default to allow for the insertion of a small number of + attributes within the object header and not require a continuation + block, an unnecessary provision in the target use case. + + Inform the library to expect no attributes on created datasets, and to + allocate the least space possible for the object headers. + NOTE: A continuation block is created if attributes are added to a + 'minimized' dataset, which can reduce performance. + NOTE: Some extra space is allocated for attributes essential to the + correct behavior of the object header (store creation times, e.g.). This + does not violate the design principle, as the space is calculated and + allocated as needed at the time of dataset object header creation -- + unused space is not generated. + New API calls: + H5Fget_dset_no_attrs_hint + H5Fset_dset_no_attrs_hint + H5Pget_dset_no_attrs_hint + H5Pset_dset_no_attrs_hint + + (JOS - 2019/01/04, TRILAB-45) + + - Added new chunk query functions + + The following public functions were added to discover information about + the chunks in an HDF5 file. + herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) + herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) + herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) + + (BMR - 2018/11/07, HDFFV-10615) + + - Several empty public header files where removed from the distribution + + The following files were empty placeholders. They are for internal + packages that are unlikely to ever have public functionality and have + thus been removed. + + H5Bpublic.h + H5B2public.h + H5FSpublic.h + H5HFpublic.h + H5HGpublic.h + H5HLpublic.h + + They were only installed in CMake builds. + + (DER - 2018/10/26, HDFFV-10614) + + + Parallel Library: + ----------------- + - Changed the default behavior in parallel when reading the same dataset in its entirety + (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. + The dataset must be contiguous, less than 2GB, and of an atomic datatype. + The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from + the disk by the root process to the remain processes in the MPI communicator associated + with the HDF5 file. + + (MSB - 2019/01/02, HDFFV-10652) + + - All MPI-1 API calls have been replaced with MPI-2 equivalents. + + This was done to better support OpenMPI, as default builds no longer + include MPI-1 support (as of OpenMPI 4.0). + + (DER - 2018/12/30, HDFFV-10566) + + Fortran Library: + ---------------- + - Added wrappers for dataset object header minimization calls. + (see the note for TRILAB-45, above) + + New API calls: + + h5fget_dset_no_attrs_hint_f + h5fset_dset_no_attrs_hint_f + h5pget_dset_no_attrs_hint_f + h5pset_dset_no_attrs_hint_f + + (DER - 2019/01/09, TRILAB-45) + + - Added new Fortran derived type, c_h5o_info_t, which is interoperable with + C's h5o_info_t. This is needed for callback functions which + pass C's h5o_info_t data type definition. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure + to Fortran DATE AND TIME storage format. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, + h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. + + (MSB, 2019/01/08, HDFFV-10443) + + C++ Library: + ------------ + - Added new function to the C++ interface + + Added wrapper for H5Ovisit2: + H5Object::visit() + + (BMR - 2019/02/14, HDFFV-10532) + + + Java Library: + ---------------- + - Rewrote the JNI error handling to be much cleaner + + (JTH - 2019/02/12) + + - Add new functions to java interface + + Added wrappers for: + H5Fset_libver_bounds + H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint + H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint + + (ADB - 2019/01/07, HDFFV-10664) + + - Fix java unit tests when Time is a natural number + + Time substitution in java/test/junit.sh.in doesn't + handle the case when Time is a natural number. Fixed + the regular expression. + + (ADB - 2019/01/07, HDFFV-10674) + + - Duplicate the data read/write functions of Datasets for Attributes. + + Region references could not be displayed for attributes as they could + for datasets. Datasets had overloaded read and write functions for different + datatypes that were not available for attributes. After adding similar + functions, attribute region references work normally. + + (ADB - 2018/12/12, HDFVIEW-4) + + + Tools: + ------ + - The h5repart -family-to-sec2 argument was changed to -family-to-single + + In order to better support other single-file VFDs which could work with + h5repart, the -family-to-sec2 argument was renamed to -family-to-single. + This is just a name change and the functionality of the argument has not + changed. + + The -family-to-sec2 argument has been kept for backwards-compatibility. + This argument should be considered deprecated. + + (DER - 2018/11/14, HDFFV-10633) + + +Bug Fixes since HDF5-1.10.4 release +================================== + + Library + ------- + - Fix hangs with collective metadata reads during chunked dataset I/O + + In the parallel library, it was discovered that when a particular + sequence of operations following a pattern of: + + "write to chunked dataset" -> "flush file" -> "read from dataset" + + occurred with collective metadata reads enabled, hangs could be + observed due to certain MPI ranks not participating in the collective + metadata reads. + + To fix the issue, collective metadata reads are now disabled during + chunked dataset raw data I/O. + + (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) + + - Performance issue when closing an object + + The slow down is due to the search of the "tag_list" to find + out the "corked" status of an object and "uncork" it if so. + + Improve performance by skipping the search of the "tag_list" + if there are no "corked" objects when closing an object. + + (VC - 2019/02/06) + + - Uninitialized bytes from a type conversion buffer could be written + to disk in H5Dwrite calls where type conversion takes place + and the type conversion buffer was created by the HDF5 library. + + When H5Dwrite is called and datatype conversion must be performed, + the library will create a temporary buffer for type conversion if + one is not provided by the user via H5Pset_buffer. This internal + buffer is allocated via malloc and contains uninitialized data. In + some datatype conversions (float to long double, possibly others), + some of this uninitialized data could be written to disk. + + This was flagged by valgrind in the dtransform test and does not + appear to be a common occurrence (it is flagged in one test out + of the entire HDF5 test suite). + + Switching to calloc fixed the problem. + + (DER - 2019/02/03, HDFFV-10694) + + - There was missing protection against division by zero reported to + The HDF Group as issue #CVE-2018-17434. + + Protection against division by zero was added to address the issue + #CVE-2018-17434. + + (BMR - 2019/01/29, HDFFV-10586) + + - The issue CVE-2018-17437 was reported to The HDF Group + + Although CVE-2018-17437 reported a memory leak, the actual issue + was invalid read. It was found that the attribute name length + in an attribute message was corrupted, which caused the buffer + pointer to be advanced too far and later caused an invalid read. + + A check was added to detect when the attribute name or its length + was corrupted and report the potential of data corruption. + + (BMR - 2019/01/29, HDFFV-10588) + + - H5Ewalk did not stop when it was supposed to + + H5Ewalk was supposed to stop when the callback function stopped + even though the errors in the stack were not all visited, but it + did not. This problem is now fixed. + + (BMR - 2019/01/29, HDFFV-10684) + + - Revert H5Oget_info* and H5Ovisit* functions + + In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were + added for performance. Inadvertently, the original functions; + H5Oget_info, + H5Oget_info_by_name, + H5Oget_info_by_idx, + H5Ovisit, + H5Ovisit_by_name + were versioned to H5Oget_info*1 and H5Ovisit*1. This + broke the API compatibility for a maintenance release. The + original functions have been restored. + + (ADB - 2019/01/24, HDFFV-10686) + + - Fixed a potential invalid memory access and failure that could occur when + decoding an unknown object header message (from a future version of the + library). + + (NAF - 2019/01/07) + + - Deleting attributes in dense storage + + The library aborts with "infinite loop closing library" after + attributes in dense storage are created and then deleted. + + When deleting the attribute nodes from the name index v2 B-tree, + if an attribute is found in the intermediate B-tree nodes, + which may be merged/redistributed in the process, we need to + free the dynamically allocated spaces for the intermediate + decoded attribute. + + (VC - 2018/12/26, HDFFV-10659) + + - There was missing protection against division by zero reported to + The HDF Group as issue #CVE-2018-17233. + + Protection against division by zero was added to address the issue + #CVE-2018-17233. In addition, several similar occurrences in the same + file were fixed as well. + + (BMR - 2018/12/23, HDFFV-10577) + + - Fixed an issue where the parallel filters tests would fail + if zlib was not available on the system. Until support can + be added in the tests for filters beyond gzip/zlib, the tests + will be skipped if zlib is not available. + + (JTH - 2018/12/05) + + - A bug was discovered in the parallel library where an application + would eventually consume all of the available MPI communicators + when continually writing to a compressed dataset in parallel. This + was due to internal copies of an HDF5 File Access Property List, + which each contained a copy of the MPI communicator, not being + closed at the end of each write operation. This problem was + exacerbated by larger numbers of processors. + + (JTH - 2018/12/05, HDFFV-10629) + + + Fortran + -------- + - Fixed issue with Fortran not returning h5o_info_t field values + meta_size%attr%index_size and meta_size%attr%heap_size. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and + libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for + autotools installs. These were added to match the name of the files + installed by cmake and the general pattern of hl lib files. We will + change the names of the installed lib files to the matching name in + the next major release. + + (LRK - 2019/01/04, HDFFV-10596) + + - Made Fortran specific subroutines PRIVATE in generic procedures. + + Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. + + (MSB, 2018/12/04, HDFFV-10511) + + + Testing + ------- + - Fixed a test failure in testpar/t_dset.c caused by + the test trying to use the parallel filters feature + on MPI-2 implementations. + + (JTH, 2019/2/7) + + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2013 + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 8.3.0 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +MacOS High Sierra 10.13.6 64-bit n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Yosemite 10.10.5 64-bit y y y y +Mac OS X El Capitan 10.11.6 64-bit y y y y +MacOS High Sierra 10.13.6 64-bit y y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following configurations are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + MPICH 3.2-GCC-4.9.3 + MPICH 3.2.1-GCC-7.2.0-2.29 + OpenMPI 2.1.5-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Fedora 29 4.20.10-200.fc29.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 8.2.1 20181215 + (Red Hat 8.2.1-6) + GNU Fortran (GCC) 8.2.1 20181215 + (Red Hat 8.2.1-6) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 + + +Known Problems +============== + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + t_pflush1/fails on exit + The first two tests fail attempting collective writes. + + CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628. + This test will pass with VS2015 with Intel compiler. + + Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested + while attempting to resolve the Jira issue: HDFFV-10540. + The known problems of reading or writing > 2GBs when using MPI-2 was + partially resolved with the MPICH library. The proposed support recognizes + IO operations > 2GB and if the datatype is not a derived type, the library + breaks the IO into chunks which can be input or output with the existing + MPI 2 limitations, i.e. size reporting and function API size/count + arguments are restricted to be 32 bit integers. For derived types larger + than 2GB, MPICH 2.1.5 fails while attempting to read or write data. + OpenMPI in contrast, implements MPI-3 APIs even in the older releases + and thus does not suffer from the 32 bit size limitation described here. + OpenMPI releases prior to v3.1.3 appear to have other datatype issues however, + e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr) + report data verification errors before eventually aborting. + The most recent versions of OpenMPI (v3.1.3 or newer) have evidently + resolved these issues and parallel HDF5 testing does not currently report + errors though occasional hangs have been observed. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +%%%%1.10.4%%%% + +HDF5 version 1.10.4 released on 2018-10-05 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- Bug Fixes since HDF5-1.10.3 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Add toolchain and cross-compile support + + Added info on using a toolchain file to INSTALL_CMAKE.txt. A + toolchain file is also used in cross-compiling, which requires + CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling + the fortran configure process, the HDF5UseFortran.cmake file macros + were improved. Fixed a Fortran configure file issue that incorrectly + used #cmakedefine instead of #define. + + (ADB - 2018/10/04, HDFFV-10594) + + - Add warning flags for Intel compilers + + Identified Intel compiler specific warnings flags that should be used + instead of GNU flags. + + (ADB - 2018/10/04, TRILABS-21) + + - Add default rpath to targets + + Default rpaths should be set in shared executables and + libraries to allow the use of loading dependent libraries + without requiring LD_LIBRARY_PATH to be set. The default + path should be relative using @rpath on osx and $ORIGIN + on linux. Windows is not affected. + + (ADB - 2018/09/26, HDFFV-10594) + + Library: + -------- + - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + + Rather than always running H5detect and generating H5Tinit.c and + H5make_libsettings.c, supply a location for those files. + + (ADB - 2018/09/18, HDFFV-10332) + + +Bug Fixes since HDF5-1.10.3 release +================================== + + Library + ------- + - Allow H5detect and H5make_libsettings to take a file as an argument. + + Rather than only writing to stdout, add a command argument to name + the file that H5detect and H5make_libsettings will use for output. + Without an argument, stdout is still used, so backwards compatibility + is maintained. + + (ADB - 2018/09/05, HDFFV-9059) + + - A bug was discovered in the parallel library where an application + would hang if a collective read/write of a chunked dataset occurred + when collective metadata reads were enabled and some of the ranks + had no selection in the dataset's dataspace. The ranks which had no + selection in the dataset's dataspace called H5D__chunk_addrmap() to + retrieve the lowest chunk address in the dataset. This is because we + require reads/writes to be performed in strictly non-decreasing order + of chunk address in the file. + + When the chunk index used was a version 1 or 2 B-tree, these + non-participating ranks would issue a collective MPI_Bcast() call + that the participating ranks would not issue, causing the hang. Since + the non-participating ranks are not actually reading/writing anything, + the H5D__chunk_addrmap() call can be safely removed and the address used + for the read/write can be set to an arbitrary number (0 was chosen). + + (JTH - 2018/08/25, HDFFV-10501) + + Java Library: + ---------------- + - JNI native library dependencies + + The build for the hdf5_java native library used the wrong + hdf5 target library for CMake builds. Correcting the hdf5_java + library to build with the shared hdf5 library required testing + paths to change also. + + (ADB - 2018/08/31, HDFFV-10568) + + - Java iterator callbacks + + Change global callback object to a small stack structure in order + to fix a runtime crash. This crash was discovered when iterating + through a file with nested group members. The global variable + visit_callback is overwritten when recursion starts. When recursion + completes, visit_callback will be pointing to the wrong callback method. + + (ADB - 2018/08/15, HDFFV-10536) + + - Java HDFLibraryException class + + Change parent class from Exception to RuntimeException. + + (ADB - 2018/07/30, HDFFV-10534) + + - JNI Read and Write + + Refactored variable-length functions, H5DreadVL and H5AreadVL, + to correct dataset and attribute reads. New write functions, + H5DwriteVL and H5AwriteVL, are under construction. + + (ADB - 2018/06/02, HDFFV-10519) + + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +Mac OS Sierra 10.12.6 64-bit n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +Mac OS Sierra 10.12.6 64-bit y n y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29, + 3.1.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + (cmake and autotools) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + t_pflush1/fails on exit + The first two tests fail attempting collective writes. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +%%%%1.10.3%%%% + +HDF5 version 1.10.3 released on 2018-08-21 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Bug Fixes since HDF5-1.10.2 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Library + ------- + - Moved the H5DOread/write_chunk() API calls to H5Dread/write_chunk() + + The functionality of the direct chunk I/O calls in the high-level + library has been moved to the H5D package in the main library. This + will allow using those functions without building the high-level + library. The parameters and functionality of the H5D calls are + identical to the H5DO calls. + + The original H5DO high-level API calls have been retained, though + they are now just wrappers for the H5D calls. They are marked as + deprecated and are only available when the library is built with + deprecated functions. New code should use the H5D calls for this + reason. + + As a part of this work, the following symbols from H5Dpublic.h are no + longer used: + + H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME + H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME + H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME + H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME + H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME + H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME + H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME + + And properties with these names are no longer stored in the dataset + transfer property lists. The symbols are still defined in H5Dpublic.h, + but only when the library is built with deprecated symbols. + + (DER - 2018/05/04) + + Configuration: + ------------- + - Add missing USE_110_API_DEFAULT option. + + Option USE_110_API_DEFAULT sets the default version of + versioned APIs. The bin/makevers perl script did not set + the maxidx variable correctly when the 1.10 branch was + created. This caused the versioning process to always use + the latest version of any API. + + (ADB - 2018/08/17, HDFFV-10552) + + - Added configuration checks for the following MPI functions: + + MPI_Mprobe - Used for the Parallel Compression feature + MPI_Imrecv - Used for the Parallel Compression feature + + MPI_Get_elements_x - Used for the "big Parallel I/O" feature + MPI_Type_size_x - Used for the "big Parallel I/O" feature + + (JTH - 2018/08/02, HDFFV-10512) + + - Added section to the libhdf5.settings file to indicate + the status of the Parallel Compression and "big Parallel I/O" + features. + + (JTH - 2018/08/02, HDFFV-10512) + + - Add option to execute swmr shell scripts from CMake. + + Option TEST_SHELL_SCRIPTS redirects processing into a + separate ShellTests.cmake file for UNIX types. The tests + execute the shell scripts if a SH program is found. + + (ADB - 2018/07/16) + + + C++ Library: + ------------ + - New wrappers + + Added the following items: + + + Class DSetAccPropList for the dataset access property list. + + + Wrapper for H5Dget_access_plist to class DataSet + // Gets the access property list of this dataset. + DSetAccPropList getAccessPlist() const; + + + Wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class DSetAccPropList + // Sets the raw data chunk cache parameters. + void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0) + + // Retrieves the raw data chunk cache parameters. + void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0) + + + New operator!= to class DataType (HDFFV-10472) + // Determines whether two datatypes are not the same. + bool operator!=(const DataType& compared_type) + + + Wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2 + (HDFFV-10458) + + // Retrieves information about an HDF5 object. + void getObjinfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) const; + + // Retrieves information about an HDF5 object, given its name. + void getObjinfo(const char* name, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; + void getObjinfo(const H5std_string& name, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; + + // Retrieves information about an HDF5 object, given its index. + void getObjinfo(const char* grp_name, H5_index_t idx_type, + H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; + void getObjinfo(const H5std_string& grp_name, H5_index_t idx_type, + H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; + + (BMR - 2018/07/22, HDFFV-10150, HDFFV-10458, HDFFV-1047) + + + Java Library: + ---------------- + - Java HDFLibraryException class + + Change parent class from Exception to RuntimeException. + + (ADB - 2018/07/30, HDFFV-10534) + + - JNI Read and Write + + Refactored variable-length functions, H5DreadVL and H5AreadVL, + to correct dataset and attribute reads. New write functions, + H5DwriteVL and H5AwriteVL, are under construction. + + (ADB - 2018/06/02, HDFFV-10519) + + +Bug Fixes since HDF5-1.10.2 release +================================== + + Library + ------- + - Performance issue with H5Oget_info + + H5Oget_info family of routines retrieves information for an object such + as object type, access time, number of attributes, and storage space etc. + Retrieving all such information regardless is an overkill and causes + performance issue when doing so for many objects. + + Add an additional parameter "fields" to the the H5Oget_info family of routines + indicating the type of information to be retrieved. The same is done to + the H5Ovisit family of routines which recursively visits an object + returning object information in a callback function. Both sets of routines + are versioned and the corresponding compatibility macros are added. + + The version 2 names of the two sets of routines are: + (1) H5Oget_info2, H5Oget_info_by_idx2, H5Oget_info_by_name2 + (2) H5Ovisit2, H5Ovisit_by_name2 + + (VC - 2018/08/15, HDFFV-10180) + + - Test failure due to metadata size in test/vds.c + + The size of metadata from test_api_get_ex_dcpl() in test/vds.c is not as expected + because the latest format should be used when encoding the layout for VDS. + + Set the latest format in a temporary fapl and pass the setting to the routines that + encode the dataset selection for VDS. + + (VC - 2018/08/14 HDFFV-10469) + + - Java HDF5LibraryException class + + The error minor and major values would be lost after the + constructor executed. + + Created two local class variables to hold the values obtained during + execution of the constructor. Refactored the class functions to retrieve + the class values rather then calling the native functions. + The native functions were renamed and called only during execution + of the constructor. + Added error checking to calling class constructors in JNI classes. + + (ADB - 2018/08/06, HDFFV-10544) + + - Added checks of the defined MPI_VERSION to guard against usage of + MPI-3 functions in the Parallel Compression and "big Parallel I/O" + features when HDF5 is built with MPI-2. Previously, the configure + step would pass but the build itself would fail when it could not + locate the MPI-3 functions used. + + As a result of these new checks, HDF5 can again be built with MPI-2, + but the Parallel Compression feature will be disabled as it relies + on the MPI-3 functions used. + + (JTH - 2018/08/02, HDFFV-10512) + + - User's patches: CVEs + + The following patches have been applied: + + CVE-2018-11202 - NULL pointer dereference was discovered in + H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) + https://security-tracker.debian.org/tracker/CVE-2018-11202 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 + + CVE-2018-11203 - A division by zero was discovered in + H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) + https://security-tracker.debian.org/tracker/CVE-2018-11203 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 + + CVE-2018-11204 - A NULL pointer dereference was discovered in + H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) + https://security-tracker.debian.org/tracker/CVE-2018-11204 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 + + CVE-2018-11206 - An out of bound read was discovered in + H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c + (HDFFV-10480) + https://security-tracker.debian.org/tracker/CVE-2018-11206 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 + + CVE-2018-11207 - A division by zero was discovered in + H5D__chunk_init in H5Dchunk.c (HDFFV-10481) + https://security-tracker.debian.org/tracker/CVE-2018-11207 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 + + (BMR - 2018/7/22, PR#s: 1134 and 1139, + HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) + + - H5Adelete + + H5Adelete failed when deleting the last "large" attribute that + is stored densely via fractal heap/v2 b-tree. + + After removing the attribute, update the ainfo message. If the + number of attributes goes to zero, remove the message. + + (VC - 2018/07/20, HDFFV-9277) + + - A bug was discovered in the parallel library which caused partial + parallel reads of filtered datasets to return incorrect data. The + library used the incorrect dataspace for each chunk read, causing + the selection used in each chunk to be wrong. + + The bug was not caught during testing because all of the current + tests which do parallel reads of filtered data read all of the data + using an H5S_ALL selection. Several tests were added which exercise + partial parallel reads. + + (JTH - 2018/07/16, HDFFV-10467) + + - A bug was discovered in the parallel library which caused parallel + writes of filtered datasets to trigger an assertion failure in the + file free space manager. + + This occurred when the filter used caused chunks to repeatedly shrink + and grow over the course of several dataset writes. The previous chunk + information, such as the size of the chunk and the offset in the file, + was being cached and not updated after each write, causing the next write + to the chunk to retrieve the incorrect cached information and run into + issues when reallocating space in the file for the chunk. + + (JTH - 2018/07/16, HDFFV-10509) + + - A bug was discovered in the parallel library which caused the + H5D__mpio_array_gatherv() function to allocate too much memory. + + When the function is called with the 'allgather' parameter set + to a non-true value, the function will receive data from all MPI + ranks and gather it to the single rank specified by the 'root' + parameter. However, the bug in the function caused memory for + the received data to be allocated on all MPI ranks, not just the + singular rank specified as the receiver. In some circumstances, + this would cause an application to fail due to the large amounts + of memory being allocated. + + (JTH - 2018/07/16, HDFFV-10467) + + - Error checks in h5stat and when decoding messages + + h5stat exited with seg fault/core dumped when + errors are encountered in the internal library. + + Add error checks and --enable-error-stack option to h5stat. + Add range checks when decoding messages: old fill value, old + layout and refcount. + + (VC - 2018/07/11, HDFFV-10333) + + - If an HDF5 file contains a malformed compound datatype with a + suitably large offset, the type conversion code can run off + the end of the type conversion buffer, causing a segmentation + fault. + + This issue was reported to The HDF Group as issue #CVE-2017-17507. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME + + Fixing this problem would involve updating the publicly visible + H5T_conv_t function pointer typedef and versioning the API calls + which use it. We normally only modify the public API during + major releases, so this bug will not be fixed at this time. + + (DER - 2018/02/26, HDFFV-10356) + + + Configuration + ------------- + - Applied patches to address Cywin build issues + + There were three issues for Cygwin builds: + - Shared libs were not built. + - The -std=c99 flag caused a SIG_SETMASK undeclared error. + - Undefined errors when buildbing test shared libraries. + + Patches to address these issues were received and incorporated in this version. + + (LRK - 2018/07/18, HDFFV-10475) + + - The --enable-debug/production configure flags are listed as 'deprecated' + when they should really be listed as 'removed'. + + In the autotools overhaul several years ago, we removed these flags and + implemented a new --enable-build-mode= flag. This was done because we + changed the semantics of the modes and didn't want users to silently + be exposed to them. The newer system is also more flexible and us to + add other modes (like 'clean'). + + The --enable-debug/production flags are now listed as removed. + + (DER - 2018/05/31, HDFFV-10505) + + - Moved the location of gcc attribute. + + The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, + was located after the function name. Builds with GCC 7 did not + indicate any problem, but GCC 8 issued errors. Moved the + attribute before the function name, as required. + + (ADB - 2018/05/22, HDFFV-10473) + + - Reworked java test suite into individual JUnit tests. + + Testing the whole suite of java unit tests in a single JUnit run + made it difficult to determine actual failures when tests would fail. + Running each file set of tests individually, allows individual failures + to be diagnosed easier. A side benefit is that tests for optional components + of the library can be disabled if not configured. + + (ADB - 2018/05/16, HDFFV-9739) + + - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES + to use target_* type commands. This change modernizes the CMake usage + in the HDF5 library. + + In addition, there is the intention to convert to generator expressions, + where possible. The exception is Fortran FLAGS on Windows Visual Studio. + The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have + been removed with this change in usage. + + The additional language (C++ and Fortran) checks have also been localized + to only be checked when that language is enabled. + + (ADB - 2018/05/08) + + + Performance + ------------- + - Revamped internal use of DXPLs, improving performance + + (QAK - 2018/05/20) + + + Fortran + -------- + - Fixed issue with h5fget_obj_count_f and using a file id of H5F_OBJ_ALL_F not + returning the correct count. + + (MSB - 2018/5/15, HDFFV-10405) + + + C++ APIs + -------- + - Adding default arguments to existing functions + + Added the following items: + + Two more property list arguments are added to H5Location::createDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT + + + One more property list argument is added to H5Location::openDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + + (BMR - 2018/07/21, PR# 1146) + + - Improvement C++ documentation + + Replaced the table in main page of the C++ documentation from mht to htm format + for portability. + + (BMR - 2018/07/17, PR# 1141) + + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (swallow/kite) Intel icc/icpc/ifort version 17.0.2 + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +Mac OS Sierra 10.12.6 64-bit n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +Mac OS Sierra 10.12.6 64-bit y n y y +CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29, + 3.1.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + (cmake and autotools) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + t_pflush1/fails on exit + The first two tests fail attempting collective writes. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + + +%%%%1.10.2%%%% + +HDF5 version 1.10.2 released on 2018-03-29 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.1 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration and Build Systems: + -------------------------------- + - CMake builds + -------------- + + - Changed minimum CMake required version to 3.10. + + This change removed the need to support a copy of the FindMPI.cmake module, + which has been removed, along with its subfolder in the config/cmake_ext_mod + location. + + (ADB - 2018/03/09) + + - Added pkg-config file generation + + Added pkg-config file generation for the C, C++, HL, and HL C++ libraries. + In addition, builds on Linux will create h5cc, h5c++, h5hlcc, and h5hlc++ scripts in the bin + directory that use the pkg-config files. The scripts can be used to build HDF5 C and C++ + applications (i.e, similar to the compiler scripts produced by the Autotools builds). + + (ADB - 2018/03/08, HDFFV-4359) + + - Refactored use of CMAKE_BUILD_TYPE for new variable, which understands + the type of generator in use. + + Added new configuration macros to use new HDF_BUILD_TYPE variable. This + variable is set correctly for the type of generator being used for the build. + + (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296) + + - Autotools builds + ------------------ + + - Removed version-specific gcc/gfortran flags for version 4.0 (inclusive) + and earlier. + + The config/gnu-flags file, which is sourced as a part of the configure + process, adds version-specific flags for use when building HDF5. Most of + these flags control warnings and do not affect the final product. + + Flags for older versions of the compiler were consolidated into the + common flags section. Moving these flags simplifies maintenance of + the file. + + The upshot of this is that building with ancient versions of gcc + (<= 4.0) will possibly no longer work without hand-hacking the file + to remove the flags not understood by that version of the compiler. + Nothing should change when building with gcc >= 4.1. + + (DER - 2017/05/31, HDFFV-9937) + + - -fno-omit-frame-pointer was added when building with debugging symbols + enabled. + + Debugging symbols can be enabled independently of the overall build + mode in both the autotools and CMake. This allows (limited) debugging + of optimized code. Since many debuggers rely on the frame pointer, + we've disabled this optimization when debugging symbols are requested + (e.g.: via building with --enable-symbols). + + (DER - 2017/05/31, HDFFV-10226) + + + Library: + -------- + - Added an enumerated value to H5F_libver_t for H5Pset_libver_bounds(). + + Currently, the library defines two values for H5F_libver_t and supports + only two pairs of (low, high) combinations as derived from these values. + Thus the bounds setting via H5Pset_libver_bounds() is rather restricted. + + Added an enumerated value (H5F_LIBVER_V18) to H5F_libver_t and + H5Pset_libver_bounds() now supports five pairs of (low, high) combinations + as derived from these values. This addition provides the user more + flexibility in setting bounds for object creation. + + (VC - 2018/03/14) + + - Added prefix option to VDS files. + + Currently, VDS source files must be in the active directory to be + found by the virtual file. Adding the option of a prefix to be set + on the virtual file, using a data access property list (DAPL), + allows the source files to locate at an absolute or relative path + to the virtual file. + Private utility functions in H5D and H5L packages merged into single + function in H5F package. + + New public APIs: + herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix); + ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size); + The prefix can also be set with an environment variable, HDF5_VDS_PREFIX. + + (ADB - 2017/12/12, HDFFV-9724, HDFFV-10361) + + - H5FDdriver_query() API call added to the C library. + + This new library call allows the user to query a virtual file driver + (VFD) for the feature flags it supports (listed in H5FDpublic.h). + This can be useful to determine if a VFD supports SWMR, for example. + + Note that some VFDs have feature flags that may only be present + after a file has been created or opened (e.g.: the core VFD will + have the H5FD_FEAT_POSIX_COMPAT_HANDLE flag set if the backing + store is switched on). Since the new API call queries a generic VFD + unassociated with a file, these flags will never be returned. + + (DER - 2017/05/31, HDFFV-10215) + + - H5FD_FEAT_DEFAULT_VFD_COMPATIBLE VFD feature flag added to the C library. + + This new feature flag indicates that the VFD is compatible with the + default VFD. VFDs that set this flag create single files that follow + the canonical HDF5 file format. + + (DER - 2017/05/31, HDFFV-10214) + + - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h) + has been marked as deprecated. + + This ID type value is not used in the C library. i.e.: There are no + hid_t values that are of ID type H5I_REFERENCE. + + This enum value will be removed in a future major version of the library. + The code will remain unchanged in the HDF5 1.10.x releases and branches. + + (DER - 2017/04/05, HDFFV-10252) + + + Parallel Library: + ----------------- + - Enabled compression for parallel applications. + + With this release parallel applications can create and write compressed + datasets (or the datasets with the filters such as Fletcher32 applied). + + (EIP - 2018/03/29) + + - Addressed slow file close on some Lustre file systems. + + Slow file close has been reported on some Lustre file systems. + While the ultimate cause is not understood fully, the proximate + cause appears to be long delays in MPI_File_set_size() calls at + file close and flush. + + To minimize this problem pending a definitive diagnosis and fix, + PHDF5 has been modified to avoid MPI_File_set_size() calls when + possible. This is done by comparing the library's EOA (End of + Allocation) with the file systems EOF, and skipping the + MPI_File_set_size() call if the two match. + + (JRM - 2018/03/29) + + - Optimized parallel open/location of the HDF5 super-block. + + Previous releases of PHDF5 required all parallel ranks to + search for the HDF5 superblock signature when opening the + file. As this is accomplished more or less as a synchronous + operation, a large number of processes can experience a + slowdown in the file open due to filesystem contention. + + As a first step in improving the startup/file-open performance, + we allow MPI rank 0 of the associated MPI communicator to locate + the base offset of the super-block and then broadcast that result + to the remaining ranks in the parallel group. Note that this + approach is utilized ONLY during file opens which employ the MPIO + file driver in HDF5 by previously having called H5Pset_fapl_mpio(). + + HDF5 parallel file operations which do not employ multiple ranks + e.g. specifying MPI_COMM_SELF (whose MPI_Comm_size == 1) + as opposed to MPI_COMM_WORLD, will not be affected by this + optimization. Conversely, parallel file operations on subgroups + of MPI_COMM_WORLD are allowed to be run in parallel with each + subgroup operating as an independent collection of processes. + + (RAW - 2017/10/10, HDFFV-10294) + + - Added large (>2GB) MPI-IO transfers. + + Previous releases of PHDF5 would fail when attempting to + read or write greater than 2GB of data in a single IO operation. + This issue stems principally from an MPI API whose definitions + utilize 32 bit integers to describe the number of data elements + and datatype that MPI should use to effect a data transfer. + Historically, HDF5 has invoked MPI-IO with the number of + elements in a contiguous buffer represented as the length + of that buffer in bytes. + + Resolving the issue and thus enabling larger MPI-IO transfers + is accomplished first, by detecting when a user IO request would + exceed the 2GB limit as described above. Once a transfer request + is identified as requiring special handling, PHDF5 now creates a + derived datatype consisting of a vector of fixed sized blocks + which is in turn wrapped within a single MPI_Type_struct to + contain the vector and any remaining data. The newly created + datatype is then used in place of MPI_BYTE and can be used to + fulfill the original user request without encountering API + errors. + + (RAW - 2017/09/10, HDFFV-8839) + + + C++ Library: + ------------ + - The following C++ API wrappers have been added to the C++ Library: + + H5Lcreate_soft: + // Creates a soft link from link_name to target_name. + void link(const char *target_name, const char *link_name,...) + void link(const H5std_string& target_name,...) + + + H5Lcreate_hard: + // Creates a hard link from new_name to curr_name. + void link(const char *curr_name, const Group& new_loc,...) + void link(const H5std_string& curr_name, const Group& new_loc,...) + + // Creates a hard link from new_name to curr_name in same location. + void link(const char *curr_name, const hid_t same_loc,...) + void link(const H5std_string& curr_name, const hid_t same_loc,...) + + Note: previous version of H5Location::link will be deprecated. + + + H5Lcopy: + // Copy an object from a group of file to another. + void copyLink(const char *src_name, const Group& dst,...) + void copyLink(const H5std_string& src_name, const Group& dst,...) + + // Copy an object from a group of file to the same location. + void copyLink(const char *src_name, const char *dst_name,...) + void copyLink(const H5std_string& src_name,...) + + + H5Lmove: + // Rename an object in a group or file to a new location. + void moveLink(const char* src_name, const Group& dst,...) + void moveLink(const H5std_string& src_name, const Group& dst,...) + + // Rename an object in a group or file to the same location. + void moveLink(const char* src_name, const char* dst_name,...) + void moveLink(const H5std_string& src_name,...) + + Note: previous version H5Location::move will be deprecated. + + + H5Ldelete: + // Removes the specified link from this location. + void unlink(const char *link_name, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) + void unlink(const H5std_string& link_name, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) + + Note: additional parameter is added to previous H5Location::unlink. + + + H5Tencode and H5Tdecode: + // Creates a binary object description of this datatype. + void DataType::encode() - C API H5Tencode() + + // Returns the decoded type from the binary object description. + DataType::decode() - C API H5Tdecode() + ArrayType::decode() - C API H5Tdecode() + CompType::decode() - C API H5Tdecode() + DataType::decode() - C API H5Tdecode() + EnumType::decode() - C API H5Tdecode() + FloatType::decode() - C API H5Tdecode() + IntType::decode() - C API H5Tdecode() + StrType::decode() - C API H5Tdecode() + VarLenType::decode() - C API H5Tdecode() + + + H5Lget_info: + // Returns the information of the named link. + H5L_info_t getLinkInfo(const H5std_string& link_name,...) + + (BMR - 2018/03/11, HDFFV-10149) + + - Added class LinkCreatPropList for link create property list. + + (BMR - 2018/03/11, HDFFV-10149) + + - Added overloaded functions H5Location::createGroup to take a link + creation property list. + Group createGroup(const char* name, const LinkCreatPropList& lcpl) + Group createGroup(const H5std_string& name, const LinkCreatPropList& lcpl) + + (BMR - 2018/03/11, HDFFV-10149) + + - A document is added to the HDF5 C++ API Reference Manual to show the + mapping from a C API to C++ wrappers. It can be found from the main + page of the C++ API Reference Manual. + + (BMR - 2017/10/17, HDFFV-10151) + + + Java Library: + ---------------- + - Wrapper added for enabling the error stack. + + H5error_off would disable the error stack reporting. In order + to re-enable the reporting, the error stack info needs to be + saved so that H5error_on can revert state. + + (ADB - 2018/03/13, HDFFV-10412) + + - Wrappers were added for the following C APIs: + H5Pset_evict_on_close + H5Pget_evict_on_close + H5Pset_chunk_opts + H5Pget_chunk_opts + H5Pset_efile_prefix + H5Pget_efile_prefix + H5Pset_virtual_prefix + H5Pget_virtual_prefix + + (ADB - 2017/12/20) + + - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h) + has been marked as deprecated. + + JNI code which refers to this value will be removed in a future + major version of the library. The code will remain unchanged in the + 1.10.x releases and branches. + + See the C library section, above, for further information. + + (HDFFV-10252, DER, 2017/04/05) + + + Tools: + ------ + - h5diff has a new option to display error stack. + + Updated h5diff with the --enable-error-stack argument, which + enables the display of the hdf5 error stack. This completes the + improvement to the main tools: h5copy, h5diff, h5dump, h5ls and + h5repack. + + (ADB - 2017/08/30, HDFFV-9774) + + +Support for new platforms, languages and compilers. +======================================= + - None + +Bug Fixes since HDF5-1.10.1 release +================================== + + Library + ------- + - The data read after a direct chunk write to a chunked dataset with + one chunk was incorrect. + + The problem was due to the passing of a null dataset pointer to + the insert callback for the chunk index in the routine + H5D__chunk_direct_write() in H5Dchunk.c + The dataset was a single-chunked dataset which will use the + single chunk index when latest format was enabled on file creation. + The single chunk index was the only index that used this pointer + in the insert callback. + + Passed the dataset pointer to the insert callback for the chunk + index in H5D__chunk_direct_write(). + + (VC - 2018/03/20, HDFFV-10425) + + - Added public routine H5DOread_chunk to the high-level C library. + + The patch for H5DOwrite_chunk() to write an entire chunk to the file + directly was contributed by GE Healthcare and integrated by The HDF Group + developers. + + (VC - 2017/05/19, HDFFV-9934) + + - Freeing of object header after failed checksum verification. + + It was discovered that the object header (in H5Ocache.c) was not released properly + when the checksum verification failed and a re-load of the object + header was needed. + + Freed the object header that failed the chksum verification only + after the new object header is reloaded, deserialized and set up. + + (VC - 2018/03/14, HDFFV-10209) + + - Updated H5Pset_evict_on_close in H5Pfapl.c + + Changed the minor error number from H5E_CANTSET to H5E_UNSUPPORTED for + parallel library. + + (ADB - 2018/03/06, HDFFV-10414) + + - Fixed the problems with the utility function that could not handle lowercase + Windows drive letters. + + Added call to upper function for drive letter. + + (ADB - 2017/12/18, HDFFV-10307) + + - Fixed H5Sencode() bug when the number of elements selected was > 2^32. + + H5Sencode() incorrectly encodes dataspace selection with number of + elements exceeding 2^32. When decoding such selection via H5Sdecode(), + the number of elements in the decoded dataspace is not the same as + what is encoded. This problem exists for H5S_SEL_HYPER and + H5S_SEL_POINTS encoding. + + The cause of the problem is due to the fact that the library uses 32 bits to + encode counts and block offsets for the selection. + The solution is to use the original 32 bit encodings if possible, + but use a different way to encode selection if more that 32 bits is needed. + See details in the RFC: H5Sencode/H5Sdecode Format Change i + https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5_Library/H5SencodeFormatChange. + + (VC - 2017/11/28, HDFFV-9947) + + - Fixed filter plugin handling in H5PL.c and H5Z.c to not require i availability of + dependent libraries (e.g., szip or zlib). + + It was discovered that the dynamic loading process used by + filter plugins had issues with library dependencies. + + CMake build process changed to use LINK INTERFACE keywords, which + allowed HDF5 C library to make dependent libraries private. The + filter plugin libraries no longer require dependent libraries + (such as szip or zlib) to be available. + + (ADB - 2017/11/16, HDFFV-10328) + + - Fixed rare object header corruption bug. + + In certain cases, such as when converting large attributes to dense + storage, an error could occur which would either fail an assertion or + cause file corruption. Fixed and added test. + + (NAF - 2017/11/14, HDFFV-10274) + + - Updated H5Zfilter_avail in H5Z.c. + + The public function checked for plugins, while the private + function did not. + + Modified H5Zfilter_avail and private function, H5Z_filter_avail. + Moved check for plugin from public to private function. Updated + H5P__set_filter due to change in H5Z_filter_avail. Updated tests. + + (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) + + - h5dump produced SEGFAULT when dumping corrypted file. + + The behavior was due to the error in the internal function H5HL_offset_into(). + + (1) Fixed H5HL_offset_into() to return error when offset exceeds heap data + block size. + (2) Fixed other places in the library that call this routine to detect + error routine. + + (VC - 2017/08/30, HDFFV-10216) + + - Fixes for paged aggregation feature. + + Skip test in test/fheap.c when: + (1) multi/split drivers and + (2) persisting free-space or using paged aggregation strategy + + (VC, 2017/07/10) + + Changes made based on RFC review comments: + (1) Added maximum value for file space page size + (2) Dropped check for page end metadata threshold + (3) Removed "can_shrink" and "shrink" callbacks for small section class + + (VC - 2017/06/09) + + - Fixed for infinite loop in H5VM_power2up(). + + The function H5VM_power2up() returns the next power of 2 + for n. When n exceeds 2^63, it overflows and becomes 0 causing + the infinite looping. + + The fix ensures that the function checks for n >= 2^63 + and returns 0. + + (VC - 2017/07/10, HDFFV-10217) + + - Fixed for H5Ocopy doesn't work with open identifiers. + + Changes made so that raw data for dataset objects are copied from + cached info when possible instead of flushing objects to file and + read them back in again. + + (VC - 2017/07/05, HDFFV-7853) + + - An uninitialized struct could cause a memory access error when using + variable-length or reference types in a compressed, chunked dataset. + + A struct containing a callback function pointer and a pointer to some + associated data was used before initialization. This could cause a + memory access error and system crash. This could only occur under + unusual conditions when using variable-lenth and reference types in + a compressed, chunked dataset. + + On recent versions of Visual Studio, when built in debug mode, the + debug heap will complain and cause a crash if the code in question + is executed (this will cause the objcopy test to fail). + + (DER - 2017/11/21, HDFFV-10330) + + - Fixed collective metadata writes on file close. + + It was discovered that metadata was being written twice as part of + the parallel file close behavior, once independently and once + collectively. + + A fix for this error was included as part of the parallel compression + feature but remained undocumented here. + + (RAW - 2017/12/01, HDFFV-10272) + + - If an HDF5 file contains a filter pipeline message with a 'number of + filters' field that exceeds the maximum number of allowed filters, + the error handling code will attempt to dereference a NULL pointer. + + This issue was reported to The HDF Group as issue #CVE-2017-17505. + https://security-tracker.debian.org/tracker/CVE-2017-17505 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17505 + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + This problem arose because the error handling code assumed that + the 'number of filters' field implied that a dynamic array of that + size had already been created and that the cleanup code should + iterate over that array and clean up each element's resources. If + an error occurred before the array has been allocated, this will + not be true. + + This has been changed so that the number of filters is set to + zero on errors. Additionally, the filter array traversal in the + error handling code now requires that the filter array not be NULL. + + (DER - 2018/02/06, HDFFV-10354) + + - If an HDF5 file contains a filter pipeline message which contains + a 'number of filters' field that exceeds the actual number of + filters in the message, the HDF5 C library will read off the end of + the read buffer. + + This issue was reported to The HDF Group as issue #CVE-2017-17506. + https://security-tracker.debian.org/tracker/CVE-2017-17506 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506 + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + The problem was fixed by passing the buffer size with the buffer + and ensuring that the pointer cannot be incremented off the end + of the buffer. A mismatch between the number of filters declared + and the actual number of filters will now invoke normal HDF5 + error handling. + + (DER - 2018/02/26, HDFFV-10355) + + - If an HDF5 file contains a malformed compound datatype with a + suitably large offset, the type conversion code can run off + the end of the type conversion buffer, causing a segmentation + fault. + + This issue was reported to The HDF Group as issue #CVE-2017-17507. + https://security-tracker.debian.org/tracker/CVE-2017-17506 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506 + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME + + Fixing this problem would involve updating the publicly visible + H5T_conv_t function pointer typedef and versioning the API calls + which use it. We normally only modify the public API during + major releases, so this bug will not be fixed at this time. + + (DER - 2018/02/26, HDFFV-10356) + + - If an HDF5 file contains a malformed compound type which contains + a member of size zero, a division by zero error will occur while + processing the type. + + This issue was reported to The HDF Group as issue #CVE-2017-17508. + https://security-tracker.debian.org/tracker/CVE-2017-17508 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17508 + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + Checking for zero before dividing fixes the problem. Instead of the + division by zero, the normal HDF5 error handling is invoked. + + (DER - 2018/02/26, HDFFV-10357) + + - If an HDF5 file contains a malformed symbol table node that declares + it contains more symbols than it actually contains, the library + can run off the end of the metadata cache buffer while processing + the symbol table node. + + This issue was reported to The HDF Group as issue #CVE-2017-17509. + https://security-tracker.debian.org/tracker/CVE-2017-17509 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17509 + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + Performing bounds checks on the buffer while processing fixes the + problem. Instead of the segmentation fault, the normal HDF5 error + handling is invoked. + + (DER - 2018/03/12, HDFFV-10358) + + - Fixed permissions passed to open(2) on file create. + + On Windows, the POSIX permissions passed to open(2) when creating files + were only incidentally correct. They are now set to the correct value of + (_S_IREAD | _S_IWRITE). + + On other platforms, the permissions were set to a mix of 666, 644, and + 000. They are now set uniformly to 666. + + (DER - 2017/04/28, HDFFV-9877) + + - The H5FD_FEAT_POSIX_COMPAT_HANDLE flag is no longer used to determine + if a virtual file driver (VFD) is compatible with SWMR. + + Use of this VFD feature flag was not in line with the documentation in + the public H5FDpublic.h file. In particular, it was being used as a + proxy for determining if SWMR I/O is allowed. This is unnecessary as we + already have a feature flag for this (H5FD_SUPPORTS_SWMR_IO). + + (DER - 2017/05/31, HDFFV-10214) + + + Configuration + ------------- + - CMake changes + + - Updated CMake commands configuration. + + A number of improvements were made to the CMake commands. Most + changes simplify usage or eliminate unused constructs. Also, + some changes support better cross-platform support. + + (ADB - 2018/02/01, HDFFV-10398) + + - Corrected usage of CMAKE_BUILD_TYPE variable. + + The use of the CMAKE_BUILD_TYPE is incorrect for multi-config + generators (Visual Studio and XCode) and is optional for single + config generators. Created a new macro to check + GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG + Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE. + Defaults for these variables is "Release". + + (ADB - 2018/01/10, HDFFV-10385) + + - Added replacement of fortran flags if using static CRT. + + Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in + config/cmake_ext_mod folder. + + (ADB - 2018/01/08, HDFFV-10334) + + + - The hdf5 library used shared szip and zlib, which needlessly required + applications to link with the same szip and zlib libraries. + + Changed the target_link_libraries commands to use the static libs. + Removed improper link duplication of szip and zlib. + Adjusted the link dependencies and the link interface values of + the target_link_libraries commands. + + (ADB - 2017/11/14, HDFFV-10329) + + - CMake MPI + + CMake implementation for MPI was problematic and would create incorrect + MPI library references in the hdf5 libraries. + + Reworked the CMake MPI code to properly create CMake targets. Also merged + the latest CMake FindMPI.cmake changes to the local copy. This is necessary + until HDF changes the CMake minimum to 3.9 or greater. + + (ADB - 2017/11/02, HDFFV-10321) + + - Corrected FORTRAN_HAVE_C_LONG_DOUBLE processing in the autotools. + + A bug in the autotools Fortran processing code always set the + FORTRAN_HAVE_C_LONG_DOUBLE variable to be true regardless of + whether or not a C long double type was present. + + This would cause compilation failures on platforms where a C + long double type was not available and the Fortran wrappers + were being built. + + (DER - 2017/07/05, HDFFV-10247) + + - The deprecated --enable-production and --enable-debug configure options + failed to emit errors when passed an empty string + (e.g.: --enable-debug=""). + + Due to the way we checked for these options being set, it was possible + to avoid the error message and continue configuration if an empty string + was passed to the option. + + Any use of --enable-production or --enable-debug will now halt the + configuration step and emit a helpful error message + (use --enable-build-mode=debug|production instead). + + (DER - 2017/07/05, HDFFV-10248) + + - CMake + + Too many commands for POST_BUILD step caused command line to be + too big on windows. + + Changed foreach of copy command to use a custom command with the + use of the HDFTEST_COPY_FILE macro. + + (ADB - 2017/07/12, HDFFV-10254) + + - CMake test execution environment + + The parallel HDF5 test: 't_pread' assumed the use of autotools + and the directory structure associated with that testing approach. + Modified the test code to check whether the 'h5jam' utility can be + found in the same directory as the test executable (which is + preferred directory structure utilized by cmake) and if found + will invoke the tool directly rather than utilizing a relative path. + + (RAW - 2017/11/03, HDFFV-10318) + + - Fortran compilation fails for xlf and CMake builds. + + Fixed CMake shared library build for H5match_types and modules + + (MSB - 2017/12/19, HDFFV-10363) + + - Shared libraries fail test on OSX with Fortran enabled with CMake. + + Fixed by removing the F77 use of EQUIVALENCE and COMMON, replaced + using MODULES. Updated CMake. + + (MSB - 2017/12/07, HDFFV-10223) + + - The bin/trace script now emits an error code on problems and autogen.sh + will fail if bin/trace fails. + + The bin/trace script adds tracing functionality to public HDF5 API calls. + It is only of interest to developers who modify the HDF5 source code. + Previously, bin/trace just wrote an error message to stdout when it + encountered problems, so autogen.sh processing did not halt and a broken + version of the library could be built. The script will now return an + error code when it encounters problems, and autogen.sh will fail. + + This only affects users who run autogen.sh to rebuild the Autotools files, + which is not necessary to build HDF5 from source in official releases of the + library. CMake users are unaffected as bin/trace is not run via CMake + at this time. + + (DER - 2017/04/25, HDFFV-10178) + + - FC_BASENAME was changed from gfortran40 to gfortran in a few places. + + In the autotools, FC_BASENAME was set to gfortran40 in a few locations + (config/gnu-fflags and config/freebsd). This was probably a historical + artifact and did not seem to affect many users. + + The value is now correctly set to gfortran. + + (DER - 2017/05/26, HDFFV-10249) + + - The ar flags were changed to -cr (was: -cru) + + The autotools set the flags for ar to -cru by default. The -u flag, + which allows selective replacement of only the members which have + changed, raises warnings on some platforms, so the flags are now set to + -cr via AR_FLAGS in configure.ac. This causes the static library to + always be completely recreated from the object files on each build. + + (DER - 2017/11/15, HDFFV-10428) + + + Fortran + -------- + - Fixed compilation errors when using Intel 18 Fortran compilers + (MSB - 2017/11/3, HDFFV-10322) + + Tools + ----- + - h5clear + + An enhancement to the tool in setting a file's stored EOA. + + It was discovered that a crashed file's stored EOA in the superblock + was smaller than the actual file's EOF. When the file was reopened + and closed, the library truncated the file to the stored EOA. + + Added an option to the tool in setting the file's stored EOA in the + superblock to the maximum of (EOA, EOF) + increment. + An option was also added to print the file's EOA and EOF. + + (VC - 2018/03/14, HDFFV-10360) + + - h5repack + + h5repack changes the chunk parameters when a change of layout is not + specified and a filter is applied. + + HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code + in the tools library. The check for an existing layout was incorrectly + placed into an if block and not executed. The check was moved into + the normal path of the function. + + (ADB - 2018/02/21, HDFFV-10412) + + - h5dump + + The tools library will hide the error stack during file open. + + While this is preferable almost always, there are reasons to enable + display of the error stack when a tool will not open a file. Adding an + optional argument to the --enable-error-stack will provide this use case. + As an optional argument it will not affect the operation of the + --enable-error-stack. h5dump is the only tool to implement this change. + + (ADB - 2018/02/15, HDFFV-10384) + + - h5dump + + h5dump would output an indented blank line in the filters section. + + h5dump overused the h5tools_simple_prefix function, which is a + function intended to account for the data index (x,y,z) option. + Removed the function call for header information. + + (ADB - 2018/01/25, HDFFV-10396) + + - h5repack + + h5repack incorrectly searched internal object table for name. + + h5repack would search the table of objects for a name, if the + name did not match it tried to determine if the name without a + leading slash would match. The logic was flawed! The table + stored names(paths) without a leading slash and did a strstr + of the table path to the name. + The assumption was that if there was a difference of one then + it was a match, however "pressure" would match "/pressure" as + well as "/pressure1", "/pressure2", etc. Changed logic to remove + any leading slash and then do a full compare of the name. + + (ADB - 2018/01/18, HDFFV-10393) + + - h5repack + + h5repack failed to handle command line parameters for customer filters. + + User defined filter parameter conversions would fail when integers were + represented on the command line with character string + larger then 9 characters. Increased local variable array for storing + the current command line parameter to prevent buffer overflows. + + (ADB - 2018/01/17, HDFFV-10392) + + - h5diff + + h5diff seg faulted if comparing VL strings against fixed strings. + + Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check + for string objects of same type in the diff_can_type function by + adding an if(tclass1 == H5T_STRING) block. This "if block" moves the + same check that was added for attributes to this function, which is + used by all object types. This function handles complex type structures. + Also added a new test file in h5diffgenttest for testing this issue + and removed the temporary files used in the test scripts. + + (ADB - 2018/01/04, HDFFV-8745) + + - h5repack + + h5repack failed to copy a dataset with existing filter. + + Reworked code for h5repack and h5diff code in the tools library. Added + improved error handling, cleanup of resources and checks of calls. + Modified H5Zfilter_avail and private function, H5Z_filter_avail. + Moved check for plugin from public to private function. Updated + H5P__set_filter due to change in H5Z_filter_avail. Updated tests. + Note, h5repack output display has changed to clarify the individual + steps of the repack process. The output indicates if an operation + applies to all objects. Lines with notation and no information + have been removed. + + (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) + + - h5repack + + h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY. + + Added another parameter to the 'UD=' option to set the flag by default + to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL. + + (ADB - 2017/08/31, HDFFV-10269) + + - h5ls + + h5ls generated error on stack when it encountered a H5S_NULL + dataspace. + + Adding checks for H5S_NULL before calling H5Sis_simple (located + in the h5tools_dump_mem function) fixed the issue. + + (ADB - 2017/08/17, HDFFV-10188) + + - h5repack + + Added tests to h5repack.sh.in to verify options added for paged + aggregation work as expected. + + (VC - 2017/08/03) + + - h5dump + + h5dump segfaulted on output of XML file. + + Function that escape'd strings used the full buffer length + instead of just the length of the replacement string in a + strncpy call. Using the correct length fixed the issue. + + (ADB - 2017/08/01, HDFFV-10256) + + - h5diff + + h5diff segfaulted on compare of a NULL variable length string. + + Improved h5diff compare of strings by adding a check for + NULL strings and setting the lengths to zero. + + (ADB - 2017/07/25, HDFFV-10246) + + - h5import + + h5import crashed trying to import data from a subset of a dataset. + + Improved h5import by adding the SUBSET keyword. h5import understands + to use the Count times the Block as the size of the dimensions. + Added INPUT_B_ORDER keyword to old-style configuration files. + The import from h5dump function expects the binary files to use native + types (FILE '-b' option) in the binary file. + + (ADB - 2017/06/15, HDFFV-10219) + + - h5repack + + h5repack did not maintain the creation order flag of the root + group. + + Improved h5repack by reading the creation order and applying the + flag to the new root group. Also added arguments to set the + order and index direction, which applies to the traversing of the + original file, on the command line. + + (ADB - 2017/05/26, HDFFV-8611) + + - h5diff + + h5diff failed to account for strpad type and null terminators + of char strings. Also, h5diff failed to account for string length + differences and would give a different result depending on file + order in the command line. + + Improved h5diff compare of strings and arrays by adding a check for + string lengths and if the strpad was null filled. + + (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) + + High-Level APIs: + ------ + - H5DOwrite_chunk() problems when overwriting an existing chunk with + no filters enabled. + + When overwriting chunks and no filters were being used, the library would + fail (when asserts are enabled, e.g. debug builds) or incorrectly + insert additional chunks instead of overwriting (when asserts are not + enabled, e.g. production builds). + + This has been fixed and a test was added to the hl/test_dset_opt test. + + (DER - 2017/05/11, HDFFV-10187) + + C++ APIs + -------- + - Removal of memory leaks. + + A private function was inadvertently called, causing memory leaks. This + is now fixed. + + (BMR - 2018/03/12 - User's reported in email) + + Testing + ------- + - Memory for three variables in testphdf5's coll_write_test was malloced + but not freed, leaking memory when running the test. + + The variables' memory is now freed. + + (LRK - 2018/03/12, HDFFV-10397) + + - Refactored the testpar/t_bigio.c test to include ALARM macros + + Changed the test to include the ALARM_ON and ALARM_OFF macros which + are intended to prevent nightly test hangs that have been observed + with this particular parallel test example. The code was also modified to + simplify status reporting (only from MPI rank 0) and additional + status checking added. + + (RAW - 2017/11/08, HDFFV-10301) + + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0, + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (swallow/kite) Intel icc/icpc/ifort version 17.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + (cmake and autotools) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + t_pflush1/fails on exit + The first two tests fail attempting collective writes. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +%%%%1.10.1%%%% + +HDF5 version 1.10.1 released on 2017-04-27 +================================================================================ + +INTRODUCTION + +This document describes the differences between HDF5-1.10.0-patch1 and +HDF5 1.10.1, and contains information on the platforms tested and known +problems in HDF5-1.10.1. For more details check the HISTORY*.txt files +in the HDF5 source. + +Links to HDF5 1.10.1 source code, documentation, and additional materials can +be found on The HDF5 web page at: + + https://support.hdfgroup.org/HDF5/ + +The HDF5 1.10.1 release can be obtained from: + + https://support.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for the snapshot can be accessed directly at this location: + + https://support.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.10.x release series, including brief general +descriptions of some new and modified APIs, are described in the "New Features +in HDF5 Release 1.10" document: + + https://support.hdfgroup.org/HDF5/docNewFeatures/index.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 10.1 (current +release) versus Release 1.10.0 + + https://support.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- Major New Features Introduced in HDF5 1.10.1 +- Other New Features and Enhancements +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.10.0-patch1 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems + + +Major New Features Introduced in HDF5 1.10.1 +============================================ + +For links to the RFCs and documentation in this section please view +https://support.hdfgroup.org/HDF5/docNewFeatures in a web browser. + +________________________________________ +Metadata Cache Image +________________________________________ + + HDF5 metadata is typically small, and scattered throughout the HDF5 file. + This can affect performance, particularly on large HPC systems. The + Metadata Cache Image feature can improve performance by writing the + metadata cache in a single block on file close, and then populating the + cache with the contents of this block on file open, thus avoiding the many + small I/O operations that would otherwise be required on file open and + close. See the RFC for complete details regarding this feature. Also, + see the Fine Tuning the Metadata Cache documentation. + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + +________________________________________ +Metadata Cache Evict on Close +________________________________________ + + The HDF5 library's metadata cache is fairly conservative about holding on + to HDF5 object metadata (object headers, chunk index structures, etc.), + which can cause the cache size to grow, resulting in memory pressure on + an application or system. The "evict on close" property will cause all + metadata for an object to be evicted from the cache as long as metadata + is not referenced from any other open object. See the Fine Tuning the + Metadata Cache documentation for information on the APIs. + + At present, evict on close is disabled in parallel builds. + +________________________________________ +Paged Aggregation +________________________________________ + + The current HDF5 file space allocation accumulates small pieces of metadata + and raw data in aggregator blocks which are not page aligned and vary + widely in sizes. The paged aggregation feature was implemented to provide + efficient paged access of these small pieces of metadata and raw data. + See the RFC for details. Also, see the File Space Management documentation. + +________________________________________ +Page Buffering +________________________________________ + + Small and random I/O accesses on parallel file systems result in poor + performance for applications. Page buffering in conjunction with paged + aggregation can improve performance by giving an application control of + minimizing HDF5 I/O requests to a specific granularity and alignment. + See the RFC for details. Also, see the Page Buffering documentation. + + At present, page buffering is disabled in parallel builds. + + + +Other New Features and Enhancements +=================================== + + Library + ------- + - Added a mechanism for disabling the SWMR file locking scheme. + + The file locking calls used in HDF5 1.10.0 (including patch1) + will fail when the underlying file system does not support file + locking or where locks have been disabled. To disable all file + locking operations, an environment variable named + HDF5_USE_FILE_LOCKING can be set to the five-character string + 'FALSE'. This does not fundamentally change HDF5 library + operation (aside from initial file open/create, SWMR is lock-free), + but users will have to be more careful about opening files + to avoid problematic access patterns (i.e.: multiple writers) + that the file locking was designed to prevent. + + Additionally, the error message that is emitted when file lock + operations set errno to ENOSYS (typical when file locking has been + disabled) has been updated to describe the problem and potential + resolution better. + + (DER, 2016/10/26, HDFFV-9918) + + - The return type of H5Pget_driver_info() has been changed from void * + to const void *. + + The pointer returned by this function points to internal library + memory and should not be freed by the user. + + (DER, 2016/11/04, HDFFV-10017) + + - The direct I/O VFD has been removed from the list of VFDs that + support SWMR. + + This configuration was never officially tested and several SWMR + tests fail when this VFD is set. + + (DER, 2016/11/03, HDFFV-10169) + + Configuration: + -------------- + - The minimum version of CMake required to build HDF5 is now 3.2.2. + + (ADB, 2017/01/10) + + - An --enable/disable-developer-warnings option has been added to + configure. + + This disables warnings that do not indicate poor code quality such + as -Winline and gcc's -Wsuggest-attribute. Developer warnings are + disabled by default. + + (DER, 2017/01/10) + + - A bin/restore.sh script was added that reverts autogen.sh processing. + + (DER, 2016/11/08) + + - CMake: Added NAMESPACE hdf5:: to package configuration files to allow + projects using installed HDF5 binaries built with CMake to link with + them without specifying the HDF5 library location via IMPORTED_LOCATION. + + (ABD, 2016/10/17, HDFFV-10003) + + - CMake: Changed the CTEST_BUILD_CONFIGURATION option to + CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation. + + (ABD, 2016/10/17, HDFFV-9971) + + + Fortran Library: + ---------------- + + - The HDF5 Fortran library can now be compiled with the NAG compiler. + + (MSB, 2017/2/10, HDFFV-9973) + + + C++ Library: + ------------ + + - The following C++ API wrappers have been added to the C++ Library: + + // Sets/Gets the strategy and the threshold value that the library + // will employ in managing file space. + FileCreatPropList::setFileSpaceStrategy - H5Pset_file_space_strategy + FileCreatPropList::getFileSpaceStrategy - H5Pget_file_space_strategy + + // Sets/Gets the file space page size for paged aggregation. + FileCreatPropList::setFileSpacePagesize - H5Pset_file_space_page_size + FileCreatPropList::getFileSpacePagesize - H5Pget_file_space_page_size + + // Checks if the given ID is valid. + IdComponent::isValid - H5Iis_valid + + // Sets/Gets the number of soft or user-defined links that can be + // traversed before a failure occurs. + LinkAccPropList::setNumLinks - H5Pset_nlinks + LinkAccPropList::getNumLinks - H5Pget_nlinks + + // Returns a copy of the creation property list of a datatype. + DataType::getCreatePlist - H5Tget_create_plist + + // Opens/Closes an object within a group or a file, regardless of object + // type + Group::getObjId - H5Oopen + Group::closeObjId - H5Oclose + + // Maps elements of a virtual dataset to elements of the source dataset. + DSetCreatPropList::setVirtual - H5Pset_virtual + + // Gets general information about this file. + H5File::getFileInfo - H5Fget_info2 + + // Returns the number of members in a type. + IdComponent::getNumMembers - H5Inmembers + + // Determines if an element type exists. + IdComponent::typeExists - H5Itype_exists + + // Determines if an object exists. + H5Location::exists - H5Lexists. + + // Returns the header version of an HDF5 object. + H5Object::objVersion - H5Oget_info for version + + (BMR, 2017/03/20, HDFFV-10004, HDFFV-10139, HDFFV-10145) + + - New exception: ObjHeaderIException for H5O interface. + + (BMR, 2017/03/15, HDFFV-10145) + + - New class LinkAccPropList for link access property list, to be used by + wrappers of H5Lexists. + + (BMR, 2017/01/04, HDFFV-10145) + + - New constructors to open datatypes in ArrayType, CompType, DataType, + EnumType, FloatType, IntType, StrType, and VarLenType. + + (BMR, 2016/12/26, HDFFV-10056) + + - New member functions: + + DSetCreatPropList::setNbit() to setup N-bit compression for a dataset. + + ArrayType::getArrayNDims() const + ArrayType::getArrayDims() const + both to replace the non-const versions. + + (BMR, 2016/04/25, HDFFV-8623, HDFFV-9725) + + + Tools: + ------ + - The following options have been added to h5clear: + -s: clear the status_flags field in the file's superblock + -m: Remove the metadata cache image from the file + + (QAK, 2017/03/22, PR#361) + + + High-Level APIs: + --------------- + - Added New Fortran 2003 API for h5tbmake_table_f. + + (MSB, 2017/02/10, HDFFV-8486) + + + +Support for New Platforms, Languages, and Compilers +=================================================== + + - Added NAG compiler + + + +Bug Fixes since HDF5-1.10.0-patch1 release +================================== + + Library + ------- + - Outdated data structure was used in H5D_CHUNK_DEBUG blocks, causing + compilation errors when H5D_CHUNK_DEBUG was defined. This is fixed. + + (BMR, 2017/04/04, HDFFV-8089) + + - SWMR implementation in the HDF5 1.10.0 and 1.10.0-patch1 releases has a + broken metadata flush dependency that manifested itself with the following + error at the end of the HDF5 error stack: + + H5Dint.c line 846 in H5D__swmr_setup(): dataspace chunk index must be 0 + for SWMR access, chunkno = 1 + major: Dataset + minor: Bad value + + It was also reported at https://github.com/areaDetector/ADCore/issues/203 + + The flush dependency is fixed in this release. + + - Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY + + (ABD, 2016/12/12, PR#201) + + - A number of issues were fixed when reading/writing from/to corrupted + files to ensure that the library fails gracefully in these cases: + + * Writing to a corrupted file that has an object message which is + incorrectly marked as shareable on disk results in a buffer overflow / + invalid write instead of a clean error message. + + * Decoding data from a corrupted file with a dataset encoded with the + H5Z_NBIT decoding can result in a code execution vulnerability under + the context of the application using the HDF5 library. + + * When decoding an array datatype from a corrupted file, the HDF5 library + fails to return an error in production if the number of dimensions + decoded is greater than the maximum rank. + + * When decoding an "old style" array datatype from a corrupted file, the + HDF5 library fails to return an error in production if the number of + dimensions decoded is greater than the maximum rank. + + (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993) + + - Fixed an error that would occur when copying an object with an attribute + which is a compound datatype consisting of a variable length string. + + (VC, 2016/08/24, HDFFV-7991) + + - H5DOappend will no longer fail if a dataset has no append callback + registered. + + (VC, 2016/08/14, HDFFV-9960) + + - Fixed an issue where H5Pset_alignment could result in misaligned blocks + with some input combinations, causing an assertion failure in debug mode. + + (NAF, 2016/08/11, HDFFV-9948) + + - Fixed a problem where a plugin compiled into a DLL in the default plugin + directory could not be found by the HDF5 library at runtime on Windows + when the HDF5_PLUGIN_PATH environment variable was not set. + + (ABD, 2016/08/01, HDFFV-9706) + + - Fixed an error that would occur when calling H5Adelete on an attribute + which is attached to an externally linked object in the target file and + whose datatype is a committed datatype in the main file. + + (VC, 2016/07/06, HDFFV-9940) + + - (a) Throw an error instead of assertion when v1 btree level hits the 1 + byte limit. + (b) Modifications to better handle error recovery when conversion by + h5format_convert fails. + + (VC, 2016/05/29, HDFFV-9434) + + - Fixed a memory leak where an array used by the library to track SWMR + read retries was unfreed. + + The leaked memory was small (on the order of a few tens of ints) and + allocated per-file. The memory was allocated (and lost) only when a + file was opened for SWMR access. + + (DER, 2016/04/27, HDFFV-9786) + + - Fixed a memory leak that could occur when opening a file for the first + time (including creating) and the call fails. + + This occurred when the file-driver-specific info was not cleaned up. + The amount of memory leaked varied with the file driver, but would + normally be less than 1 kB. + + (DER, 2016/12/06, HDFFV-10168) + + - Fixed a failure in collective metadata writes. + + This failure only appeared when collective metadata writes + were enabled (via H5Pset_coll_metadata_write()). + + (JRM, 2017/04/10, HDFFV-10055) + + + Parallel Library + ---------------- + - Fixed a bug that could occur when allocating a chunked dataset in parallel + with an alignment set and an alignment threshold greater than the chunk + size but less than or equal to the raw data aggregator size. + + (NAF, 2016/08/11, HDFFV-9969) + + + Configuration + ------------- + - Configuration will check for the strtoll and strtoull functions + before using alternatives + + (ABD, 2017/03/17, PR#340) + + - CMake uses a Windows pdb directory variable if available and + will generate both static and shared pdb files. + + (ABD, 2017/02/06, HDFFV-9875) + + - CMake now builds shared versions of tools. + + (ABD, 2017/02/01, HDFFV-10123) + + - Makefiles and test scripts have been updated to correctly remove files + created when running "make check" and to avoid removing any files under + source control. In-source builds followed by "make clean" and "make + distclean" should result in the original source files. + (LRK, 2017/01/17, HDFFV-10099) + + - The tools directory has been divided into two separate source and test + directories. This resolves a build dependency and, as a result, + 'make check' will no longer fail in the tools directory if 'make' was + not executed first. + + (ABD, 2016/10/27, HDFFV-9719) + + - CMake: Fixed a timeout error that would occasionally occur when running + the virtual file driver tests simultaneously due to test directory + and file name collisions. + + (ABD, 2016/09/19, HDFFV-9431) + + - CMake: Fixed a command length overflow error by converting custom + commands inside CMakeTest.cmake files into regular dependencies and + targets. + + (ABD, 2016/07/12, HDFFV-9939) + + - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by + condensing cygwin configuration files into a single file and + removing outdated compiler settings. + + (ABD, 2016/07/12, HDFFV-9946) + + + Fortran + -------- + - Changed H5S_ALL_F from INTEGER to INTEGER(HID_T) + + (MSB, 2016/10/14, HDFFV-9987) + + + Tools + ----- + - h5diff now correctly ignores strpad in comparing strings. + + (ABD, 2017/03/03, HDFFV-10128) + + - h5repack now correctly parses the command line filter options. + + (ABD, 2017/01/24, HDFFV-10046) + + - h5diff now correctly returns an error when it cannot read data due + to an unavailable filter plugin. + + (ADB 2017/01/18, HDFFV-9994 ) + + - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.) + in which they would erroneously drop the file argument specified via + the -o flag when the -o flag was specified before the -c flag on the + command line, resulting in a failure to compile. + + (LRK, 2016/11/04, HDFFV-9938, HDFFV-9530) + + - h5repack User Defined (UD) filter parameters were not parsed correctly. + + The UD filter parameters were not being parsed correctly. Reworked coding + section to parse the correct values and verify number of parameters. + + (ABD, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039) + + - h5repack allows the --enable-error-stack option on the command line. + + (ADB, 2016/08/08, HDFFV-9775) + + + C++ APIs + -------- + - The member function H5Location::getNumObjs() is moved to + class Group because the objects are in a group or a file only, + and H5Object::getNumAttrs to H5Location to get the number of + attributes at a given location. + + (BMR, 2017/03/17, PR#466) + + - Due to the change in the C API, the overloaded functions of + PropList::setProperty now need const for some arguments. They are + planned for deprecation and are replaced by new versions with proper + consts. + + (BMR, 2017/03/17, PR#344) + + - The high-level API Packet Table (PT) did not write data correctly when + the datatype is a compound type that has string type as one of the + members. This problem started in 1.8.15, after the fix of HDFFV-9042 + was applied, which caused the Packet Table to use native type to access + the data. It should be up to the application to specify whether the + buffer to be read into memory is in the machine's native architecture. + Thus, the PT is fixed to not use native type but to make a copy of the + user's provided datatype during creation or the packet table's datatype + during opening. If an application wishes to use native type to read the + data, then the application will request that. However, the Packet Table + doesn't provide a way to specify memory datatype in this release. This + feature will be available in future releases. + + (BMR, 2016/10/27, HDFFV-9758) + + - The obsolete macros H5_NO_NAMESPACE and H5_NO_STD have been removed from + the HDF5 C++ API library. + + (BMR, 2016/10/23, HDFFV-9532) + + - The problem where a user-defined function cannot access both, attribute + and dataset, using only one argument is now fixed. + + (BMR, 2016/10/11, HDFFV-9920) + + - In-memory array information, ArrayType::rank and + ArrayType::dimensions, were removed. This is an implementation + detail and should not affect applications. + + (BMR, 2016/04/25, HDFFV-9725) + + + Testing + ------- + - Fixed a problem that caused tests using SWMR to occasionally fail when + running "make check" using parallel make. + + (LRK, 2016/03/22, PR#338, PR#346, PR#358) + + +Supported Platforms +=================== + + Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 + (Red Hat 4.4.7-4) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 16.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== + +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.8.4 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 16.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 (Build 20150407) + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) compilers + Version 15.0.3.187 (Build 20150407) + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + (cmake and autotools) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +%%%%1.10.0-patch1%%%% + + +HDF5 version 1.10.0-patch1 released on 2016-05-23 +================================================================================ + +INTRODUCTION + +This document describes the differences between HDF5-1.8 series and +HDF5 1.10.0 releases, and contains information on the platforms +tested. + +Links to HDF5 1.10.0 source code can be found on The HDF Group's +development FTP server at the following location: + + https://www.hdfgroup.org/HDF5/release/obtain5110.html + +User documentation can be accessed directly at this location: + + https://www.hdfgroup.org/HDF5/docNewFeatures/ + +For more information, see the HDF5 home page: + + https://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF +Help Desk: + + help@hdfgroup.org + + + +CONTENTS + +- New Features +- Issues Addressed in this Release +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems and Limitations + + + +New Features +============ +This release supports the following features: + + Configuration + ------------- + - API Compatibility with HDF5 1.8 Flag Was Added + + The 1.10 version of the HDF5 Library can be configured to operate + identically to the 1.8 library with the --with-default-api-version=v18 + configure flag. This allows existing code to be compiled with the 1.10 + library without requiring immediate changes to the application source + code. For additional configuration options and other details, see + "API Compatibility Macros in HDF5" at + https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html. + + - Autotools Configuration Has Been Extensively Reworked + + The autotools configuration options have been updated to allow more + fine-grained control of the build options and to correct some bugs. + See configure --help for comprehensive information on each option. + + Specific changes: + + * --enable-debug and --enable-production are no longer accepted. + Use --enable-build-mode=(debug | production) instead. These set + appropriate defaults for symbols, optimizations, and other + configuration options. These defaults can be overridden by the + user. + + * Extra debug output messages are no longer enabled with + --enable-debug=<package list>. Use --enable-internal-debug=<pkg list> + instead. + + * A new --enable-symbols option allows symbols to be generated + independently of the build mode. --disable-symbols can be used + to strip symbols from the binary. + + * A new --enable-asserts option sets/unsets NDEBUG. This is + independent of the build mode. This also enables some extra + low-overhead debug checks in the library. + + * A new --enable-profiling option sets profiling flags. This is + independent of the build mode. + + * A new --enable-optimization option sets the optimization level. + This is independent of the build mode. + + * Many of these options can take a flags string that will be used + to build the library. This can be useful for specifying custom + optimization flags such as -Os and -Ofast. + + * gnu C++ and Fortran use configure sub-files that update the + build flags and turn on warnings. The increase in warnings when + building these wrapper libraries is due to these flag changes + and not to a decrease in code quality. + + * The option to clear file buffers has been removed. Any buffer that + will eventually be written to disk will now always be memset + to zero. This prevents the previous contents of the buffer from + being written to the disk if the buffer contents are not + completely overwritten, which has security implications. + + - LFS Changes + + The way the autotools handle large file support (LFS) has been + overhauled in this release. + + * We assume ftello and fseeko exist + + * We no longer explicitly use the *64 I/O functions. Instead, we + rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent. + + * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS. + + + + Parallel Library + ----------------- + - Collective Metadata I/O + + Calls for HDF5 metadata can result in many small reads and writes. + On metadata reads, collective metadata I/O can improve performance + by allowing the library to perform optimizations when reading the + metadata by having one rank read the data and broadcasting it to + all other ranks. + + Collective metadata I/O improves metadata write performance through + the construction of an MPI derived datatype that is then written + collectively in a single call. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html. + + + + Library + -------- + - Concurrent Access to HDF5 Files - Single Writer/ Multiple Reader (SWMR) + + The Single Writer/ Multiple Reader or SWMR feature enables users to + read data concurrently while writing it. Communications between the + processes and file locking are not required. The processes can run + on the same or on different platforms as long as they share a common + file system that is POSIX compliant. For more information, see the + Single-Writer/Multiple-Reader (SWMR) documentation at + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html. + + - Virtual Dataset (VDS) + + The VDS feature enables data to be accessed across HDF5 files + using standard HDF5 objects such as groups and datasets without + rewriting or rearranging the data. An HDF5 virtual dataset (VDS) + is an HDF5 dataset that is composed of source HDF5 datasets in + a predefined mapping. VDS can be used with the SWMR feature. For + documentation, check + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html. + + - Persistent Free File Space Tracking + + Usage patterns when working with an HDF5 file sometimes result in + wasted space within the file. This can also impair access times + when working with the resulting files. The new file space management + feature provides strategies for managing space in a file to improve + performance in both of these areas. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html. + + - Version 3 Metadata Cache + + The version 3 metadata cache moves management of metadata I/O from + the clients to the metadata cache proper. This change is essential for + SWMR and other features that have yet to be released. + + + + C++ Library + ------------ + - New Member Function Added to H5::ArrayType + + The assignment operator ArrayType::operator= was added because + ArrayType has pointer data members. + + (BMR - 2016/03/07, HDFFV-9562) + + + + Tools + ------ + - h5watch + + The h5watch tool allows users to output new records appended to + a dataset under SWMR access as it grows. The functionality is + similar to the Unix user command "tail" with the follow option, + which outputs appended data as the file grows. For more + information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools. + + - h5format_convert + + The h5format_convert tool allows users to convert the indexing + type of a chunked dataset made with a 1.10.x version of the HDF5 + Library when the latest file format is used to the 1.8.x version 1 B-tree indexing + type. For example, datasets created using SWMR access, can be + converted to be accessed by the HDF5 1.18 library and tools. The + tool does not rewrite raw data, but it does rewrite HDF5 metadata. + + + + High-Level APIs + ---------------- + - H5DOappend + + The function appends data to a dataset along a specified dimension. + + + C Packet Table API + ------------------ + - Replacement of a Public Function with H5PTcreate + + The existing function H5PTcreate_fl limits applications so they + can use the deflate compression only. The public function + H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/04, HDFFV-8623) + + - New Public Functions: H5PTget_dataset and H5PTget_type + + Two accessor functions have been added. H5PTget_dataset returns + the identifier of the dataset associated with the packet table, + and H5PTget_type returns the identifier of the datatype used by + the packet table. + + (BMR, 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table (PT) library source except for the following functions: + + H5PTis_varlen() has been made available again + + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() + + (BMR - 2016/03/04, HDFFV-442) + + C++ Packet Table API + -------------------- + - New Constructor Added to FL_PacketTable + + An overloaded constructor has been added to FL_PacketTable and + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/08, HDFFV-8623) + + - New Public Functions + + Two accessor wrappers are added to class PacketTable. + PacketTable::GetDataset() returns the identifier of the dataset + associated with the packet table, and PacketTable::GetDatatype() + returns the identifier of the datatype that the packet table uses. + + (BMR - 2016/03/04, HDFFV-8623) + + - Member Functions with "char*" as an Argument + + Overloaded functions were added to provide the "const char*" + argument; the existing version will be deprecated in future + releases. + + (BMR - 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table library source code except for the following functions: + + VL_PacketTable::IsVariableLength() was moved to PacketTable + + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() + + (BMR - 2016/03/04, HDFFV-442) + + + + Java Wrapper Library + -------------------- + + The Java HDF5 JNI library has been integrated into the HDF5 repository. + The configure option is "--enable-java", and the CMake option is + HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the + HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10, + "hdf.hdflib.hdf5". + + A number of new APIs were added including some for VDS and SWMR. + + + + Other Important Changes + ----------------------- + + The hid_t type was changed from 32-bit to a 64-bit value. + + + +Issues Addressed in this Release Since 1.10.0 +============================================= + + - h5diff would return from a compare attributes abnormally if one of the datatypes + was a vlen. This resulted in a memory leak as well as an incorrect report of + attribute comparison. + + Fixed. + (ADB - 2016/04/26, HDFFV-9784) + + - The JUnit-interface test may fail on Solaris platforms. The result of + a test for verifying the content of the error stack to stdout is + in a different order on Solaris then other platforms. + + This test is skipped on Solaris + (ADB - 2016/04/21, HDFFV-9734) + + - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE, + there was a missing command argument for the tests of the examples. + + Fixed. + (ADB - 2016/04/21, HDFFV-9743) + + - Changed h5diff to print a warning when a dataset is virtual, enabling + the data to be compared. In addition h5repack failed to copy the data + of a virtual dataset to the new file. Function H5D__get_space_status changed + to correctly determine the H5D_space_status_t allocation value. + + CMake added the Fixed Array indexing tests that were only in the autotools + test scripts. + + Fixed and tests added for vds issues. + (ADB,NAF - 2016/04/21, HDFFV-9756) + + - CMake added the h5format_convert tool and tests that were only in the autotools + build and test scripts. The autotools test script was reworked to allow CMake + to execute the test suite in parallel. + + Also, h5clear tool and tests were added to the misc folder. + + Fixed. + (ADB - 2016/04/21, HDFFV-9766) + + - CMake added the h5watch tool and argument tests that were only in the autotools + build and test scripts. The POSIX only tests were not added to CMake. + + CMake HL tools files were refactored to move the CMake test scripts into each tool folder. + + Fixed. + (ADB - 2016/04/21, HDFFV-9770) + + - Configure fails to detect valid real KINDs on FreeBSD 9.3 (i386) with Fortran enabled. + + Fixed. Added the exponential option to SELECTED_REAL_KIND to distinguish + KINDs of same precision + (MSB - 2016/05/14,HDFFV-9912) + + + - Corrected the f90 H5AWRITE_F integer interface's buf to be INTENT(IN). + (MSB - 2016/05/14) + + - Configure fails in sed command on FreeBSD 9.3 (i386) with Fortran enabled. + + Fixed. + (MSB - 2016/05/14,HDFFV-9912) + + - Compile time error in H5f90global.F90 with IBM XL Fortran 14.1.0.13 on BG/Q with Fortran + enabled. + + Fixed. + (MSB - 2016/05/16,HDFFV-9917) + + - A cmake build with Fortran enabled does not install module h5fortkit + + Fixed. + (MSB - 2016/05/23,HDFFV-9923) + + +Issues Addressed in this Release Since alpha1 +============================================= + + - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix + + The correct access property list settings from the + H5Pget_virtual_printf_gap, H5Pget_virtual_view, and + H5Pget_efile_prefix function calls could not be retrieved + using H5Dget_access_plist(). + + Fixed. + + (DER and NAF - 2016/03/14, HDFFV-9716) + + - h5dump + + When h5dump was provided with the name of a non-existing file or + when optional arguments were the last option on the command line, + h5dump would segfault. + + Fixed. + + (ADB 2016/02/28 HDFFV-9639, HDFFV-9684) + + - No Error Message for Corrupt Metadata + + The HDF5 Library did not propagate an error when it encountered + corrupt metadata in an HDF5 file. The issue was fixed for a + specific file provided by a user. If you still see the problem, + please contact help@hdfgroup.org + + Fixed. + + (MC - 2016/02/18, HDFFV-9670) + + - Problem Reading Chunked Datasets with a String Datatype Larger + Than the Chunk Size in Bytes + + When the latest file format was used and when a chunked dataset + was created with a datatype with the size bigger than a chunk + size, the data could not be read back. The issue was reported + for chunked datasets with a string datatype and was confirmed + for other datatypes with the sizes bigger than the chunk size in + bytes. + + Fixed. + + (JM - 2016/02/13, HDFFV-9672) + + - Control over the Location of External Files + + Users were unable to specify the locations of external files. + + Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were + added so that users could specify the locations of external files. + + (DER - 2016/02/04, HDFFV-8740) + + + +Issues Addressed in this Release Since alpha0 +============================================= + - h5format_convert + + The h5format_convert tool did not downgrade the version of the + superblock. + + Fixed. The tool now will downgrade the version of the superblock. + + (EIP 2016/01/11) + + - Crashes with multiple threads: invalid pointers + + It was reported that alpha0 crashed when used with multiple + threads. The issue exists in the HDF5 Library versions 1.8 and + 1.9. The problem is related to a shared file pointer used in some + miscellaneous data structures. The thread-safe library exposed + paths in the library where a file pointer became invalid. + + The alpha1 release contains the fixes for the specific use case + as described in HDFFV-9643. We will keep working on identifying + and fixing other paths in the library with similar problems. + + (EIP - 2016/01/15, HDFFV-9643) + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16) + Version 4.9.3, Version 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Windows 7 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS + + Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + + +Known Problems and Limitations +============================== +This section contains the list of known problems and limitations introduced +in this release of HDF5. + +Note: this list is not exhaustive of all known issues discovered in HDF5 +software to date. For a list of significant problems and known workarounds +identified in past releases, please refer to: + +https://www.hdfgroup.org/HDF5/release/known_problems/ + +The HDF Group also maintains a JIRA issue-tracking database which is used to +capture all known issues which are too numerous to reasonably list in this +document. The HDF Group is taking steps to make our JIRA issue database +open to the public, and this section will refer to that database in a future +release. In the meantime, please contact help@hdfgroup.org if you come across +an issue not listed here or at the link above, and we will provide any +information about known workarounds that we have or add it to our list of +known issues if it is a new issue. + + - The flush/refresh test occasionally fails on OS X platforms. This is + being investigated but no fix or workaround is available at this time. + (DER - 2016/03/22, HDFFV-9731) + + - The VDS/SWMR test will fail with a segmentation fault if the library + is built with --enable-using-memchecker. The is due to a VDS shutdown + procedure freeing a shared resource too early when the memory + checker changes are built. This problem does not arise when the + memory checker changes are not used since the internal library free + lists behave differently. The memory checker configure option should + normally only be used under special circumstances so this should not + affect most users. Users should be aware that the --enable-using-memchecker + + VDS combination may cause a segfault, however, so Valgrind et al. may + have to be used with an HDF5 library built without the feature if this + proves to be a problem. + (DER - 2016/03/21, HDFFV-9732) + + - SWMR feature limitations + The SWMR feature will only work if an HDF5 file under SWMR access resides + on a file system that obeys POSIX write() ordering semantics. Because of + this, SWMR will not work on network file systems such as NFS or SMB/Windows + file shares since those systems do not guarantee write odering. SWMR + regression tests are likely to fail if run on a network file system. SWMR + is currently not tested on Windows though it can be tested manually + (some of the SWMR test programs are built by CMake), and there are no + obvious reasons for it to not work on NTFS or GPFS. + (EIP - 2016/03/20, HDFFV-9733) + + - VDS feature limitation + Currently, the path to a VDS source file is interpreted as relative to the + directory where the executable program runs and not to the HDF5 file with + the VDS dataset unless a full path to the source file is specified during + the mapping. + (EIP - 2016/03/20, HDFFV-9724) + + - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle + and root group name ("/"): + + H5Lexists(fileid, "/") + + In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). + The documentation will be updated with information regarding this change. + (LRK - 2016/03/30, HDFFV-8746) + + +%%%%1.10.0%%%% + +HDF5 version 1.10.0 released on 2016-03-30 +================================================================================ + + + +INTRODUCTION + +This document describes the differences between HDF5-1.8 series and +HDF5 1.10.0 releases, and contains information on the platforms +tested. + +Links to HDF5 1.10.0 source code can be found on The HDF Group's +development FTP server at the following location: + + https://www.hdfgroup.org/HDF5/release/obtain5110.html + +User documentation can be accessed directly at this location: + + https://www.hdfgroup.org/HDF5/docNewFeatures/ + +For more information, see the HDF5 home page: + + https://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF +Help Desk: + + help@hdfgroup.org + + + +CONTENTS + +- New Features +- Issues Addressed in this Release +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems and Limitations + + + +New Features +============ +This release supports the following features: + + Configuration + ------------- + - API Compatibility with HDF5 1.8 Flag Was Added + + The 1.10 version of the HDF5 Library can be configured to operate + identically to the 1.8 library with the --with-default-api-version=v18 + configure flag. This allows existing code to be compiled with the 1.10 + library without requiring immediate changes to the application source + code. For additional configuration options and other details, see + "API Compatibility Macros in HDF5" at + https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html. + + - Autotools Configuration Has Been Extensively Reworked + + The autotools configuration options have been updated to allow more + fine-grained control of the build options and to correct some bugs. + See configure --help for comprehensive information on each option. + + Specific changes: + + * --enable-debug and --enable-production are no longer accepted. + Use --enable-build-mode=(debug | production) instead. These set + appropriate defaults for symbols, optimizations, and other + configuration options. These defaults can be overridden by the + user. + + * Extra debug output messages are no longer enabled with + --enable-debug=<package list>. Use --enable-internal-debug=<pkg list> + instead. + + * A new --enable-symbols option allows symbols to be generated + independently of the build mode. --disable-symbols can be used + to strip symbols from the binary. + + * A new --enable-asserts option sets/unsets NDEBUG. This is + independent of the build mode. This also enables some extra + low-overhead debug checks in the library. + + * A new --enable-profiling option sets profiling flags. This is + independent of the build mode. + + * A new --enable-optimization option sets the optimization level. + This is independent of the build mode. + + * Many of these options can take a flags string that will be used + to build the library. This can be useful for specifying custom + optimization flags such as -Os and -Ofast. + + * gnu C++ and Fortran use configure sub-files that update the + build flags and turn on warnings. The increase in warnings when + building these wrapper libraries is due to these flag changes + and not to a decrease in code quality. + + * The option to clear file buffers has been removed. Any buffer that + will eventually be written to disk will now always be memset + to zero. This prevents the previous contents of the buffer from + being written to the disk if the buffer contents are not + completely overwritten, which has security implications. + + - LFS Changes + + The way the autotools handle large file support (LFS) has been + overhauled in this release. + + * We assume ftello and fseeko exist + + * We no longer explicitly use the *64 I/O functions. Instead, we + rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent. + + * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS. + + + + Parallel Library + ----------------- + - Collective Metadata I/O + + Calls for HDF5 metadata can result in many small reads and writes. + On metadata reads, collective metadata I/O can improve performance + by allowing the library to perform optimizations when reading the + metadata by having one rank read the data and broadcasting it to + all other ranks. + + Collective metadata I/O improves metadata write performance through + the construction of an MPI derived datatype that is then written + collectively in a single call. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html. + + + + Library + -------- + - Concurrent Access to HDF5 Files - Single Writer/ Multiple Reader (SWMR) + + The Single Writer/ Multiple Reader or SWMR feature enables users to + read data concurrently while writing it. Communications between the + processes and file locking are not required. The processes can run + on the same or on different platforms as long as they share a common + file system that is POSIX compliant. For more information, see the + Single-Writer/Multiple-Reader (SWMR) documentation at + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html. + + - Virtual Dataset (VDS) + + The VDS feature enables data to be accessed across HDF5 files + using standard HDF5 objects such as groups and datasets without + rewriting or rearranging the data. An HDF5 virtual dataset (VDS) + is an HDF5 dataset that is composed of source HDF5 datasets in + a predefined mapping. VDS can be used with the SWMR feature. For + documentation, check + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html. + + - Persistent Free File Space Tracking + + Usage patterns when working with an HDF5 file sometimes result in + wasted space within the file. This can also impair access times + when working with the resulting files. The new file space management + feature provides strategies for managing space in a file to improve + performance in both of these areas. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html. + + - Version 3 Metadata Cache + + The version 3 metadata cache moves management of metadata I/O from + the clients to the metadata cache proper. This change is essential for + SWMR and other features that have yet to be released. + + + + C++ Library + ------------ + - New Member Function Added to H5::ArrayType + + The assignment operator ArrayType::operator= was added because + ArrayType has pointer data members. + + (BMR - 2016/03/07, HDFFV-9562) + + + + Tools + ------ + - h5watch + + The h5watch tool allows users to output new records appended to + a dataset under SWMR access as it grows. The functionality is + similar to the Unix user command "tail" with the follow option, + which outputs appended data as the file grows. For more + information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools. + + - h5format_convert + + The h5format_convert tool allows users to convert the indexing + type of a chunked dataset made with a 1.10.x version of the HDF5 + Library when the latest file format is used to the 1.8.x version 1 B-tree indexing + type. For example, datasets created using SWMR access, can be + converted to be accessed by the HDF5 1.18 library and tools. The + tool does not rewrite raw data, but it does rewrite HDF5 metadata. + + + + High-Level APIs + ---------------- + - H5DOappend + + The function appends data to a dataset along a specified dimension. + + + C Packet Table API + ------------------ + - Replacement of a Public Function with H5PTcreate + + The existing function H5PTcreate_fl limits applications so they + can use the deflate compression only. The public function + H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/04, HDFFV-8623) + + - New Public Functions: H5PTget_dataset and H5PTget_type + + Two accessor functions have been added. H5PTget_dataset returns + the identifier of the dataset associated with the packet table, + and H5PTget_type returns the identifier of the datatype used by + the packet table. + + (BMR, 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table (PT) library source except for the following functions: + + H5PTis_varlen() has been made available again + + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() + + (BMR - 2016/03/04, HDFFV-442) + + C++ Packet Table API + -------------------- + - New Constructor Added to FL_PacketTable + + An overloaded constructor has been added to FL_PacketTable and + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/08, HDFFV-8623) + + - New Public Functions + + Two accessor wrappers are added to class PacketTable. + PacketTable::GetDataset() returns the identifier of the dataset + associated with the packet table, and PacketTable::GetDatatype() + returns the identifier of the datatype that the packet table uses. + + (BMR - 2016/03/04, HDFFV-8623) + + - Member Functions with "char*" as an Argument + + Overloaded functions were added to provide the "const char*" + argument; the existing version will be deprecated in future + releases. + + (BMR - 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table library source code except for the following functions: + + VL_PacketTable::IsVariableLength() was moved to PacketTable + + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() + + (BMR - 2016/03/04, HDFFV-442) + + + + Java Wrapper Library + -------------------- + + The Java HDF5 JNI library has been integrated into the HDF5 repository. + The configure option is "--enable-java", and the CMake option is + HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the + HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10, + "hdf.hdflib.hdf5". + + A number of new APIs were added including some for VDS and SWMR. + + + + Other Important Changes + ----------------------- + + The hid_t type was changed from 32-bit to a 64-bit value. + + + +Issues Addressed in this Release Since alpha1 +============================================= + + - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix + + The correct access property list settings from the + H5Pget_virtual_printf_gap, H5Pget_virtual_view, and + H5Pget_efile_prefix function calls could not be retrieved + using H5Dget_access_plist(). + + Fixed. + + (DER and NAF - 2016/03/14, HDFFV-9716) + + - h5dump + + When h5dump was provided with the name of a non-existing file or + when optional arguments were the last option on the command line, + h5dump would segfault. + + Fixed. + + (ADB 2016/02/28 HDFFV-9639, HDFFV-9684) + + - No Error Message for Corrupt Metadata + + The HDF5 Library did not propagate an error when it encountered + corrupt metadata in an HDF5 file. The issue was fixed for a + specific file provided by a user. If you still see the problem, + please contact help@hdfgroup.org + + Fixed. + + (MC - 2016/02/18, HDFFV-9670) + + - Problem Reading Chunked Datasets with a String Datatype Larger + Than the Chunk Size in Bytes + + When the latest file format was used and when a chunked dataset + was created with a datatype with the size bigger than a chunk + size, the data could not be read back. The issue was reported + for chunked datasets with a string datatype and was confirmed + for other datatypes with the sizes bigger than the chunk size in + bytes. + + Fixed. + + (JM - 2016/02/13, HDFFV-9672) + + - Control over the Location of External Files + + Users were unable to specify the locations of external files. + + Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were + added so that users could specify the locations of external files. + + (DER - 2016/02/04, HDFFV-8740) + + + +Issues Addressed in this Release Since alpha0 +============================================= + - h5format_convert + + The h5format_convert tool did not downgrade the version of the + superblock. + + Fixed. The tool now will downgrade the version of the superblock. + + (EIP 2016/01/11) + + - Crashes with multiple threads: invalid pointers + + It was reported that alpha0 crashed when used with multiple + threads. The issue exists in the HDF5 Library versions 1.8 and + 1.9. The problem is related to a shared file pointer used in some + miscellaneous data structures. The thread-safe library exposed + paths in the library where a file pointer became invalid. + + The alpha1 release contains the fixes for the specific use case + as described in HDFFV-9643. We will keep working on identifying + and fixing other paths in the library with similar problems. + + (EIP - 2016/01/15, HDFFV-9643) + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.32-573.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16) + Version 4.9.3, Version 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.3 Apple clang/clang++ version 7.0.2 from Xcode 7.0.2 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Windows 7 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS + + Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + + +Known Problems and Limitations +============================== +This section contains the list of known problems and limitations introduced +in this release of HDF5. + +Note: this list is not exhaustive of all known issues discovered in HDF5 +software to date. For a list of significant problems and known workarounds +identified in past releases, please refer to: + +https://www.hdfgroup.org/HDF5/release/known_problems/ + +The HDF Group also maintains a JIRA issue-tracking database which is used to +capture all known issues which are too numerous to reasonably list in this +document. The HDF Group is taking steps to make our JIRA issue database +open to the public, and this section will refer to that database in a future +release. In the meantime, please contact help@hdfgroup.org if you come across +an issue not listed here or at the link above, and we will provide any +information about known workarounds that we have or add it to our list of +known issues if it is a new issue. + + - The JUnit-interface test may fail on Solaris platforms. The result of + a test for verifying the content of the error stack to stdout is + in a different order on Solaris then other platforms. Use make -i option + to test beyond the java/test folder. + (ADB - 2016/03/22, HDFFV-9734) + + - The flush/refresh test occasionally fails on OS X platforms. This is + being investigated but no fix or workaround is available at this time. + (DER - 2016/03/22, HDFFV-9731) + + - The VDS/SWMR test will fail with a segmentation fault if the library + is built with --enable-using-memchecker. The is due to a VDS shutdown + procedure freeing a shared resource too early when the memory + checker changes are built. This problem does not arise when the + memory checker changes are not used since the internal library free + lists behave differently. The memory checker configure option should + normally only be used under special circumstances so this should not + affect most users. Users should be aware that the --enable-using-memchecker + + VDS combination may cause a segfault, however, so Valgrind et al. may + have to be used with an HDF5 library built without the feature if this + proves to be a problem. + (DER - 2016/03/21, HDFFV-9732) + + - SWMR feature limitations + The SWMR feature will only work if an HDF5 file under SWMR access resides + on a file system that obeys POSIX write() ordering semantics. Because of + this, SWMR will not work on network file systems such as NFS or SMB/Windows + file shares since those systems do not guarantee write odering. SWMR + regression tests are likely to fail if run on a network file system. SWMR + is currently not tested on Windows though it can be tested manually + (some of the SWMR test programs are built by CMake), and there are no + obvious reasons for it to not work on NTFS or GPFS. + (EIP - 2016/03/20, HDFFV-9733) + + - VDS feature limitation + Currently, the path to a VDS source file is interpreted as relative to the + directory where the executable program runs and not to the HDF5 file with + the VDS dataset unless a full path to the source file is specified during + the mapping. + (EIP - 2016/03/20, HDFFV-9724) + + - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE, + there is a missing command argument for the tests of the examples. + + This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF, + or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF. + (LRK - 2016/03/30, HDFFV-9743) + + - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle + and root group name ("/"): + + H5Lexists(fileid, "/") + + In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). + The documentation will be updated with information regarding this change. + (LRK - 2016/03/30, HDFFV-8746) + diff --git a/release_docs/HISTORY-1_10_0-1_12_0.txt b/release_docs/HISTORY-1_10_0-1_12_0.txt new file mode 100644 index 0000000..a83e58d --- /dev/null +++ b/release_docs/HISTORY-1_10_0-1_12_0.txt @@ -0,0 +1,1183 @@ +HDF5 HISTORY +============= + + +INTRODUCTION + +This document describes the differences between the HDF5-1.10.0 and +HDF5 1.12.0 releases. For more details check the HISTORY*.txt files in the +HDF5 source. + +Information about supported and tested platforms is provided for historical +reasons only and may not be accurate. + + +For more information, see the HDF5 home page: + + http://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.3 +- Bug Fixes since HDF5-1.10.2 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Update CMake tests to use FIXTURES + + CMake test fixtures allow setup/cleanup tests and other dependency + requirements as properties for tests. This is more flexible for + modern CMake code. + + (ADB - 2019/07/23, HDFFV-10529) + + - Windows PDB files are always installed + + There are build configuration or flag settings for Windows that may not + generate PDB files. If those files are not generated then the install + utility will fail because those PDB files are not found. An optional + variable, DISABLE_PDB_FILES, was added to not install PDB files. + + (ADB - 2019/07/17, HDFFV-10424) + + - Add mingw CMake support with a toolchain file + + There has been a number of mingw issues that has been linked under + HDFFV-10845. It has been decided to implement the CMake cross-compiling + technique of toolchain files. We will use a linux platform with the mingw + compiler stack for testing. Only the C language is fully supported, and + the error tests are skipped. The C++ language works for static but shared + builds has a shared library issue with the mingw Standard Exception Handling + library, which is not available on Windows. Fortran has a common cross-compile + problem with the fortran configure tests. + + (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) + + - Windows PDB files are installed incorrectly + + For static builds, the PDB files for windows should be installed next + to the static libraries in the lib folder. Also the debug versions of + libraries and PDB files are now correctly built using the default + CMAKE_DEBUG_POSTFIX setting. + + (ADB - 2019/07/09, HDFFV-10581) + + - Add option to build only shared libs + + A request was made to prevent building static libraries and only build + shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will + skip building static libraries. Certain utility functions will build with + static libs but are not published. Tests are adjusted to use the correct + libraries depending on SHARED/STATIC settings. + + (ADB - 2019/06/12, HDFFV-10805) + + - Add options to enable or disable building tools and tests + + Configure options --enable-tests and --enable-tools were added for + autotools configure. These options are enabled by default, and can be + disabled with either --disable-tests (or tools) or --enable-tests=no + (or --enable-tools=no). Build time is reduced ~20% when tools are + disabled, 35% when tests are disabled, 45% when both are disabled. + Reenabling them after the initial build requires running configure + again with the option(s) enabled. + + (LRK - 2019/06/12, HDFFV-9976) + + - Change tools test that test the error stack + + There are some use cases which can cause the error stack of tools to be + different then the expected output. These tests now use grepTest.cmake, + this was changed to allow the error file to be searched for an expected string. + + (ADB - 2019/04/15, HDFFV-10741) + + - Keep stderr and stdout separate in tests + + Changed test handling of output capture. Tests now keep the stderr + output separate from the stdout output. It is up to the test to decide + which output to check against a reference. Also added the option + to grep for a string in either output. + + (ADB - 2018/12/12, HDFFV-10632) + + - Add toolchain and cross-compile support + + Added info on using a toolchain file to INSTALL_CMAKE.txt. A + toolchain file is also used in cross-compiling, which requires + CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling + the fortran configure process, the HDF5UseFortran.cmake file macros + were improved. Fixed a Fortran configure file issue that incorrectly + used #cmakedefine instead of #define. + + (ADB - 2018/10/04, HDFFV-10594) + + - Add warning flags for Intel compilers + + Identified Intel compiler specific warnings flags that should be used + instead of GNU flags. + + (ADB - 2018/10/04, TRILABS-21) + + - Add default rpath to targets + + Default rpaths should be set in shared executables and + libraries to allow the use of loading dependent libraries + without requiring LD_LIBRARY_PATH to be set. The default + path should be relative using @rpath on osx and $ORIGIN + on linux. Windows is not affected. + + (ADB - 2018/09/26, HDFFV-10594) + + - Add missing USE_110_API_DEFAULT option. + + Option USE_110_API_DEFAULT sets the default version of + versioned APIs. The bin/makevers perl script did not set + the maxidx variable correctly when the 1.10 branch was + created. This caused the versioning process to always use + the latest version of any API. + + (ADB - 2018/08/17, HDFFV-10552) + + - Added configuration checks for the following MPI functions: + + MPI_Mprobe - Used for the Parallel Compression feature + MPI_Imrecv - Used for the Parallel Compression feature + + MPI_Get_elements_x - Used for the "big Parallel I/O" feature + MPI_Type_size_x - Used for the "big Parallel I/O" feature + + (JTH - 2018/08/02, HDFFV-10512) + + - Added section to the libhdf5.settings file to indicate + the status of the Parallel Compression and "big Parallel I/O" + features. + + (JTH - 2018/08/02, HDFFV-10512) + + - Add option to execute swmr shell scripts from CMake. + + Option TEST_SHELL_SCRIPTS redirects processing into a + separate ShellTests.cmake file for UNIX types. The tests + execute the shell scripts if a SH program is found. + + (ADB - 2018/07/16) + + + Library: + -------- + - Add new H5R_ref_t type for object, dataset region and _attribute_ + references. This new type will deprecate the current hobj_ref_t + and hdset_reg_ref_t types for references. Added H5T_REF datatype + to read and write new reference types. As opposed to previous + reference types, reference creation no longer modifies existing + files. New reference types also now support references to external + files. + + (JS - 2019/10/08) + + - Add S3 and HDFS VFDs to HDF5 maintenance + + Fix windows requirements and java tests. Windows requires CMake 3.13. + Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + + PATH should have been updated with the installation dir. + set ENV variable OPENSSL_ROOT_DIR to the installation dir. + set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + Install libcurl library (with dev files); + download the latest released version using git: https://github.com/curl/curl.git + + Open a Visual Studio Command prompt + change to the libcurl root folder + run the "buildconf.bat" batch file + change to the winbuild directory + nmake /f Makefile.vc mode=dll MACHINE=x64 + copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + set ENV variable CURL_ROOT to C:\curl (installation dir) + update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + the aws credentials file should be in %USERPROFILE%\.aws folder + set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" + + (ADB - 2019/09/12, HDFFV-10854) + + - Added new chunk query functions + + The following public functions were added to discover information about + the chunks in an HDF5 file. + herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) + herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) + herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) + + (BMR - 2019/06/11, HDFFV-10677) + + - Improved the performance of virtual dataset I/O + + Refactored the internal dataspace routines used by the virtual dataset + code to improve performance, especially when one of the selections + involved is very long and non-contiguous. + + (NAF - 2019/05/31, HDFFV-10693) + + - Added the ability to open files with UTF-8 file names on Windows. + + The POSIX open(2) API call on Windows is limited to ASCII + file names. The library has been updated to convert incoming file + names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use + _wopen() instead. + + (DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691) + + - Add new API H5M for map objects. Currently not supported by native + library, can be supported by VOL connectors. + + (NAF - 2019/03/01) + + - Remove H5I_REFERENCE from the library + + This ID class was never used by the library and has been removed. + + (DER - 2018/12/08, HDFFV-10252) + + - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + + Rather than always running H5detect and generating H5Tinit.c and + H5make_libsettings.c, supply a location for those files. + + (ADB - 2018/09/18, HDFFV-10332) + + + Parallel Library: + ----------------- + - Changed the default behavior in parallel when reading the same dataset in its entirely + (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. + The dataset mush be contiguous, less than 2GB, and of an atomic datatype. + The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from + the disk by the root process to the remain processes in the MPI communicator associated + with the HDF5 file. + + (MSB - 2019/01/02, HDFFV-10652) + + Fortran Library: + ---------------- + - Added new Fortran derived type, c_h5o_info_t, which is interoperable with + C's h5o_info_t. This is needed for callback functions which + pass C's h5o_info_t data type definition. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure + to Fortran DATE AND TIME storage format. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, + h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. + + (MSB, 2019/01/08, HDFFV-10443) + + C++ Library: + ------------ + - Added new wrappers for H5Pset/get_create_intermediate_group() + LinkCreatPropList::setCreateIntermediateGroup() + LinkCreatPropList::getCreateIntermediateGroup() + + (BMR - 2019/04/22, HDFFV-10622) + + - Added new wrapper for H5Ovisit2() + H5Object::visit() + + (BMR - 2019/02/14, HDFFV-10532) + + + Java Library: + ---------------- + - Fix a failure in JUnit-TestH5P on 32-bit architectures + + (JTH - 2019/04/30) + + - Duplicate the data read/write functions of Datasets for Attributes. + + Region references could not be displayed for attributes as they could + for datasets. Datasets had overloaded read and write functions for different + datatypes that were not available for attributes. After adding similar + functions, attribute region references work normally. + + (ADB - 2018/12/12, HDFVIEW-4) + + - Removed H5I_REFERENCE from the Java wrappers + + This ID class was never used by the library and has been removed + from the Java wrappers. + + (DER - 2018/12/08, HDFFV-10252) + + + Tools: + ------ + - h5repack was fixed to repack datasets with external storage + to other types of storage. + + New test added to repack files and verify the correct data using h5diff. + + (JS - 2019/09/25, HDFFV-10408) + (ADB - 2019/10/02, HDFFV-10918) + + - h5dump was fixed for 128-bit floats, but was missing a test. + + New test greps for the first 15 numbers of the 128-bit value. + + (ADB - 2019/06/23, HDFFV-9407) + + + High-Level APIs: + --------------- + - + + C Packet Table API + ------------------ + - + + Internal header file + -------------------- + - + + Documentation + ------------- + - + +Support for new platforms, languages and compilers. +======================================= + - + +Bug Fixes since HDF5-1.10.3 release +================================== + + Library + ------- + - Improved performance when creating a large number of small datasets by + retrieving default property values from the API context instead of doing + skip list searches. + + (CJH - 2019/12/10, HDFFV-10658) + + - Fixed user-created data access properties not existing in the property list + returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a + reproducer and a patch. + + (CJH - 2019/12/9, HDFFV-10934) + + - Fixed the iteration error in test_versionbounds() in test/dtypes.c + + The test was supposed to loop through all valid combinations of + low and high bounds in the array versions[], but they were set to + H5F_LIBVER_EARLIEST always without changing. + + The problem was fixed by indexing low and high into the array versions[]. + + (VC - 2019/09/30) + + - Fixed the slowness of regular hyperslab selection in a chunked dataset + + It was reported that the selection of every 10th element from a 20G + chunked dataset was extremely slow and sometimes could hang the system. + The problem was due to the iteration and the building of the span tree + for all the selected elements in file space. + + As the selected elements are going to a 1-d contiguous single block + memory space, the problem was fixed by building regular hyperslab selections + in memory space for the selected elements in file space. + + (VC - 2019/09/26, HDFFV-10585) + + - Fixed a bug caused by bad tag value when condensing object header + messages + + There was an assertion failure when moving meessages from running a + user test program with library release hdf5.1.10.4. It was because + the tag value (object header's address) was not set up when entering + the library routine H5O__chunk_update_idx(), which will eventually + verifies the metadata tag value when protecting the object header. + + The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx() + with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag. + + (VC - 2019/08/23, HDFFV-10873) + + - Fixed the test failure from test_metadata_read_retry_info() in + test/swmr.c + + The test failure is due to the incorrect number of bins returned for + retry info (info.nbins). The # of bins expected for 101 read attempts + is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c + calculates the # of bins by first obtaining the log10 value for + (read attempts - 1). For PGI/19, the log10 value for 100 read attempts + is 1.9999999999999998 instead of 2.00000. When casting the log10 value + to unsigned later on, the decimal part is chopped off causing the test + failure. + + This was fixed by obtaining the rounded integer value (HDceil) for the + log10 value of read attempts first before casting the result to unsigned. + + (VC - 2019/8/14, HDFFV-10813) + + - Fixed an issue where creating a file with non-default file space info + together with library high bound setting to H5F_LIBVER_V18. + + When setting non-default file space info in fcpl via + H5Pset_file_space_strategy() and then creating a file with + both high and low library bounds set to + H5F_LIBVER_V18 in fapl, the library succeeds in creating the file. + File creation should fail because the feature of setting non-default + file space info does not exist in library release 1.8 or earlier. + + This was fixed by setting and checking the proper version in the + file space info message based on the library low and high bounds + when creating and opening the HDF5 file. + + (VC - 2019/6/25, HDFFV-10808) + + - When iterating over an old-style group (i.e., when not using the latest + file format) of size 0, a NULL pointer representing the empty links + table would be sent to qsort(3) for sorting, which is undefined behavior. + + Iterating over an empty group is explicitly tested in the links test. + This has not caused any failures to date and was flagged by gcc's + -fsanitize=undefined. + + The library no longer attempts to sort an empty array. + + (DER - 2019/06/18, HDFFV-10829) + + - Fixed an issue where copying a version 1.8 dataset between files using + H5Ocopy fails due to an incompatible fill version + + When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 + dataset to a file created with both high and low library bounds set to + H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating + that the fill value version is out of bounds. + + This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 + (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. + + (VC - 2019/6/14, HDFFV-10800) + + - Some oversights in the index iterating area of the library caused + a callback function to continue iterating even though it's supposed + to stop. + + Added the returned value check to the for loop's conditions in + H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). The + iteration now stops when it should. + + (BMR - 2019/06/11, HDFFV-10661) + + - Fixed a bug that would cause an error or cause fill values to be + incorrectly read from a chunked dataset using the "single chunk" index if + the data was held in cache and there was no data on disk. + + (NAF - 2019/03/06) + + - Fixed a bug that could cause an error or cause fill values to be + incorrectly read from a dataset that was written to using H5Dwrite_chunk + if the dataset was not closed after writing. + + (NAF - 2019/03/06, HDFFV-10716) + + - Fixed memory leak in scale offset filter + + In a special case where the MinBits is the same as the number of bits in + the datatype's precision, the filter's data buffer was not freed, causing + the memory usage to grow. In general the buffer was freed correctly. The + Minbits are the minimal number of bits to store the data values. Please + see the reference manual for H5Pset_scaleoffset for the detail. + + (RL - 2019/3/4, HDFFV-10705) + + - Fix hangs with collective metadata reads during chunked dataset I/O + + In the parallel library, it was discovered that when a particular + sequence of operations following a pattern of: + + "write to chunked dataset" -> "flush file" -> "read from dataset" + + occurred with collective metadata reads enabled, hangs could be + observed due to certain MPI ranks not participating in the collective + metadata reads. + + To fix the issue, collective metadata reads are now disabled during + chunked dataset raw data I/O. + + (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) + + - Performance issue when closing an object + + The slow down is due to the search of the "tag_list" to find + out the "corked" status of an object and "uncork" it if so. + + Improve porformance by skipping the search of the "tag_list" + if there are no "corked" objects when closing an object. + + (VC - 2019/2/6) + + - Fixed a potential invalid memory access and failure that could occur when + decoding an unknown object header message (from a future version of the + library). + + (NAF - 2019/01/07) + + - Deleting attributes in dense storage + + The library aborts with "infinite loop closing library" after + attributes in dense storage are created and then deleted. + + When deleting the attribute nodes from the name index v2 B-tree, + if an attribute is found in the intermediate B-tree nodes, + which may be merged/redistributed in the process, we need to + free the dynamically allocated spaces for the intermediate + decoded attribute. + + (VC - 2018/12/26, HDFFV-10659) + + - Allow H5detect and H5make_libsettings to take a file as an argument. + + Rather than only writing to stdout, add a command argument to name + the file that H5detect and H5make_libsettings will use for output. + Without an argument, stdout is still used, so backwards compatibility + is maintained. + + (ADB - 2018/09/05, HDFFV-9059) + + - A bug was discovered in the parallel library where an application + would hang if a collective read/write of a chunked dataset occurred + when collective metadata reads were enabled and some of the ranks + had no selection in the dataset's dataspace. The ranks which had no + selection in the dataset's dataspace called H5D__chunk_addrmap() to + retrieve the lowest chunk address in the dataset. This is because we + require reads/writes to be performed in strictly non-decreasing order + of chunk address in the file. + + When the chunk index used was a version 1 or 2 B-tree, these + non-participating ranks would issue a collective MPI_Bcast() call + that the participating ranks would not issue, causing the hang. Since + the non-participating ranks are not actually reading/writing anything, + the H5D__chunk_addrmap() call can be safely removed and the address used + for the read/write can be set to an arbitrary number (0 was chosen). + + (JTH - 2018/08/25, HDFFV-10501) + + - fcntl(2)-based file locking incorrectly passed the lock argument struct + instead of a pointer to the struct, causing errors on systems where + flock(2) is not available. + + File locking is used when files are opened to enforce SWMR semantics. A + lock operation takes place on all file opens unless the + HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE". + flock(2) is preferentially used, with fcntl(2) locks as a backup if + flock(2) is unavailable on a system (if neither is available, the lock + operation fails). On these systems, the file lock will often fail, which + causes HDF5 to not open the file and report an error. + + This bug only affects POSIX systems. Win32 builds on Windows use a no-op + locking call which always succeeds. Systems which exhibit this bug will + have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output. + + This bug affects HDF5 1.10.0 through 1.10.5. + + fcntl(2)-based file locking now correctly passes the struct pointer. + + (DER - 2019/08/27, HDFFV-10892) + + + Java Library: + ---------------- + - JNI native library dependencies + + The build for the hdf5_java native library used the wrong + hdf5 target library for CMake builds. Correcting the hdf5_java + library to build with the shared hdf5 library required testing + paths to change also. + + (ADB - 2018/08/31, HDFFV-10568) + - Java iterator callbacks + + Change global callback object to a small stack structure in order + to fix a runtime crash. This crash was discovered when iterating + through a file with nested group members. The global variable + visit_callback is overwritten when recursion starts. When recursion + completes, visit_callback will be pointing to the wrong callback method. + + (ADB - 2018/08/15, HDFFV-10536) + + - Java HDFLibraryException class + + Change parent class from Exception to RuntimeException. + + (ADB - 2018/07/30, HDFFV-10534) + + - JNI Read and Write + + Refactored variable-length functions, H5DreadVL and H5AreadVL, + to correct dataset and attribute reads. New write functions, + H5DwriteVL and H5AwriteVL, are under construction. + + (ADB - 2018/06/02, HDFFV-10519) + + + Configuration + ------------- + - Correct option for default API version + + CMake options for default API version are not mutually exclusive. + Change the multiple BOOL options to a single STRING option with the + strings; v16, v18, v110, v112. + + (ADB - 2019/08/12, HDFFV-10879) + + + Fortran + -------- + - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and + libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for + autotools installs. These were added to match the name of the files + installed by cmake and the general pattern of hl lib files. We will + change the names of the installed lib files to the matching name in + the next major release. + + (LRK - 2019/01/04, HDFFV-10596) + + - Made Fortran specific subroutines PRIVATE in generic procedures. + + Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. + + (MSB, 2018/12/04, HDFFV-10511) + + - Fixed issue with Fortran not returning h5o_info_t field values + meta_size%attr%index_size and meta_size%attr%heap_size. + + (MSB, 2018/1/8, HDFFV-10443) + + + Tools + ----- + - + + High-Level APIs: + ------ + - + + Fortran High-Level APIs: + ------ + - + + Documentation + ------------- + - + + F90 APIs + -------- + - + + C++ APIs + -------- + - + + Testing + ------- + - Fixed a test failure in testpar/t_dset.c caused by + the test trying to use the parallel filters feature + on MPI-2 implementations. + + (JTH, 2019/2/7) + +Bug Fixes since HDF5-1.10.2 release +================================== + + Library + ------- + - Java HDF5LibraryException class + + The error minor and major values would be lost after the + constructor executed. + + Created two local class variables to hold the values obtained during + execution of the constructor. Refactored the class functions to retrieve + the class values rather then calling the native functions. + The native functions were renamed and called only during execution + of the constructor. + Added error checking to calling class constructors in JNI classes. + + (ADB - 2018/08/06, HDFFV-10544) + + - Added checks of the defined MPI_VERSION to guard against usage of + MPI-3 functions in the Parallel Compression and "big Parallel I/O" + features when HDF5 is built with MPI-2. Previously, the configure + step would pass but the build itself would fail when it could not + locate the MPI-3 functions used. + + As a result of these new checks, HDF5 can again be built with MPI-2, + but the Parallel Compression feature will be disabled as it relies + on the MPI-3 functions used. + + (JTH - 2018/08/02, HDFFV-10512) + + - User's patches: CVEs + + The following patches have been applied: + + CVE-2018-11202 - NULL pointer dereference was discovered in + H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) + https://security-tracker.debian.org/tracker/CVE-2018-11202 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 + + CVE-2018-11203 - A division by zero was discovered in + H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) + https://security-tracker.debian.org/tracker/CVE-2018-11203 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 + + CVE-2018-11204 - A NULL pointer dereference was discovered in + H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) + https://security-tracker.debian.org/tracker/CVE-2018-11204 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 + + CVE-2018-11206 - An out of bound read was discovered in + H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c + (HDFFV-10480) + https://security-tracker.debian.org/tracker/CVE-2018-11206 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 + + CVE-2018-11207 - A division by zero was discovered in + H5D__chunk_init in H5Dchunk.c (HDFFV-10481) + https://security-tracker.debian.org/tracker/CVE-2018-11207 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 + + (BMR - 2018/7/22, PR#s: 1134 and 1139, + HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) + + - H5Adelete + + H5Adelete failed when deleting the last "large" attribute that + is stored densely via fractal heap/v2 b-tree. + + After removing the attribute, update the ainfo message. If the + number of attributes goes to zero, remove the message. + + (VC - 2018/07/20, HDFFV-9277) + + - A bug was discovered in the parallel library which caused partial + parallel reads of filtered datasets to return incorrect data. The + library used the incorrect dataspace for each chunk read, causing + the selection used in each chunk to be wrong. + + The bug was not caught during testing because all of the current + tests which do parallel reads of filtered data read all of the data + using an H5S_ALL selection. Several tests were added which exercise + partial parallel reads. + + (JTH - 2018/07/16, HDFFV-10467) + + - A bug was discovered in the parallel library which caused parallel + writes of filtered datasets to trigger an assertion failure in the + file free space manager. + + This occurred when the filter used caused chunks to repeatedly shrink + and grow over the course of several dataset writes. The previous chunk + information, such as the size of the chunk and the offset in the file, + was being cached and not updated after each write, causing the next write + to the chunk to retrieve the incorrect cached information and run into + issues when reallocating space in the file for the chunk. + + (JTH - 2018/07/16, HDFFV-10509) + + - A bug was discovered in the parallel library which caused the + H5D__mpio_array_gatherv() function to allocate too much memory. + + When the function is called with the 'allgather' parameter set + to a non-true value, the function will receive data from all MPI + ranks and gather it to the single rank specified by the 'root' + parameter. However, the bug in the function caused memory for + the received data to be allocated on all MPI ranks, not just the + singular rank specified as the receiver. In some circumstances, + this would cause an application to fail due to the large amounts + of memory being allocated. + + (JTH - 2018/07/16, HDFFV-10467) + + - Error checks in h5stat and when decoding messages + + h5stat exited with seg fault/core dumped when + errors are encountered in the internal library. + + Add error checks and --enable-error-stack option to h5stat. + Add range checks when decoding messages: old fill value, old + layout and refcount. + + (VC - 2018/07/11, HDFFV-10333) + + - If an HDF5 file contains a malformed compound datatype with a + suitably large offset, the type conversion code can run off + the end of the type conversion buffer, causing a segmentation + fault. + + This issue was reported to The HDF Group as issue #CVE-2017-17507. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME + + Fixing this problem would involve updating the publicly visible + H5T_conv_t function pointer typedef and versioning the API calls + which use it. We normally only modify the public API during + major releases, so this bug will not be fixed at this time. + + (DER - 2018/02/26, HDFFV-10356) + + - Inappropriate linking with deprecated MPI C++ libraries + + HDF5 does not define *_SKIP_MPICXX in the public headers, so applications + can inadvertently wind up linking to the deprecated MPI C++ wrappers. + + MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h + so this should no longer be an issue. HDF5 makes no use of the deprecated + MPI C++ wrappers. + + (DER - 2019/09/17, HDFFV-10893) + + + + Configuration + ------------- + - Applied patches to address Cywin build issues + + There were three issues for Cygwin builds: + - Shared libs were not built. + - The -std=c99 flag caused a SIG_SETMASK undeclared error. + - Undefined errors when buildbing test shared libraries. + + Patches to address these issues were received and incorporated in this version. + + (LRK - 2018/07/18, HDFFV-10475) + + - Moved the location of gcc attribute. + + The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, + was located after the function name. Builds with GCC 7 did not + indicate any problem, but GCC 8 issued errors. Moved the + attribute before the function name, as required. + + (ADB - 2018/05/22, HDFFV-10473) + + - Reworked java test suite into individual JUnit tests. + + Testing the whole suite of java unit tests in a single JUnit run + made it difficult to determine actual failures when tests would fail. + Running each file set of tests individually, allows individual failures + to be diagnosed easier. A side benefit is that tests for optional components + of the library can be disabled if not configured. + + (ADB - 2018/05/16, HDFFV-9739) + + - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES + to use target_* type commands. This change modernizes the CMake usage + in the HDF5 library. + + In addition, there is the intention to convert to generator expressions, + where possible. The exception is Fortran FLAGS on Windows Visual Studio. + The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have + been removed with this change in usage. + + The additional language (C++ and Fortran) checks have also been localized + to only be checked when that language is enabled. + + (ADB - 2018/05/08) + + Performance + ------------- + - + + Fortran + -------- + - + + Tools + ----- + - + + High-Level APIs: + ------ + - + + Fortran High-Level APIs: + ------ + - + + Documentation + ------------- + - + + F90 APIs + -------- + - + + C++ APIs + -------- + - Adding default arguments to existing functions + + Added the following items: + + Two more property list arguments are added to H5Location::createDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT + + + One more property list argument is added to H5Location::openDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + + (BMR - 2018/07/21, PR# 1146) + + - Improvement C++ documentation + + Replaced the table in main page of the C++ documentation from mht to htm format + for portability. + + (BMR - 2018/07/17, PR# 1141) + + Testing + ------- + - The dt_arith test failed on IBM Power8 and Power9 machines when testing + conversions from or to long double types, especially when special values + such as infinity or NAN were involved. In some cases the results differed + by extremely small amounts from those on other machines, while some other + tests resulted in segmentation faults. These conversion tests with long + double types have been disabled for ppc64 machines until the problems are + better understood and can be properly addressed. + + (SRL - 2019/01/07, TRILAB-98) + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0, + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2013 + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (swallow/kite) Intel icc/icpc/ifort version 17.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ? +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y ? +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y ? +CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n +CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + (cmake and autotools) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + diff --git a/release_docs/HISTORY-1_12.txt b/release_docs/HISTORY-1_12.txt new file mode 100644 index 0000000..6d0c1e2 --- /dev/null +++ b/release_docs/HISTORY-1_12.txt @@ -0,0 +1,628 @@ +HDF5 History +============ + +This file contains development history of the HDF5 1.12 branch + +01. Release Information for hdf5-1.12.0 + +[Search on the string '%%%%' for section breaks of each release.] + +%%%%1.12.0%%%% + +HDF5 version 1.12.0 released on 2020-02-28 +================================================================================ + + +INTRODUCTION + +This document describes the new features introduced in the HDF5 1.12.0 release. +It contains information on the platforms tested and known problems in this +release. For more details check the HISTORY*.txt files in the HDF5 source. + +Note that documentation in the links below will be updated at the time of the +release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +More information about the new features can be found at: + + https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12 + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.12.0-alpha1 +- Major Bug Fixes since HDF5-1.10.0 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Added test script for file size compare + + If CMake minimum version is at least 3.14, the fileCompareTest.cmake + script will compare file sizes. + + (ADB - 2020/02/24, HDFFV-11036) + + - Update CMake minimum version to 3.12 + + Updated CMake minimum version to 3.12 and added version checks + for Windows features. + + (ADB - 2020/02/05, TRILABS-142) + + - Fixed CMake include properties for Fortran libraries + + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. + + (ADB - 2020/02/04, HDFFV-11012) + + - Added common warnings files for gnu and intel + + Added warnings files to use one common set of flags + during configure for both autotools and CMake build + systems. The initial implementation only affects a + general set of flags for gnu and intel compilers. + + (ADB - 2020/01/17) + + - Added new options to CMake for control of testing + + Added CMake options (default ON); + HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL + combined with: + HDF5_TEST_TOOLS + HDF5_TEST_EXAMPLES + HDF5_TEST_SWMR + HDF5_TEST_FORTRAN + HDF5_TEST_CPP + HDF5_TEST_JAVA + + (ADB - 2020/01/15, HDFFV-11001) + + - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + + Added CMake code and files to execute the Clang sanitizers if + HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option + is set to one of the following: + Address + Memory + MemoryWithOrigins + Undefined + Thread + Leak + 'Address;Undefined' + + (ADB - 2019/12/12, TRILAB-135) + + - Update CMake for VS2019 support + + CMake added support for VS2019 in version 3.15. Changes to the CMake + generator setting required changes to scripts. Also updated version + references in CMake files as necessary. + + (ADB - 2019/11/18, HDFFV-10962) + + + Library: + -------- + - Refactored public exposure of haddr_t type in favor of "object tokens" + + To better accommodate HDF5 VOL connectors where "object addresses in a file" + may not make much sense, the following changes were made to the library: + + * Introduced new H5O_token_t "object token" type, which represents a + unique and permanent identifier for referencing an HDF5 object within + a container; these "object tokens" are meant to replace object addresses. + Along with the new type, a new H5Oopen_by_token API call was introduced + to open an object by a token, similar to how object addresses were + previously used with H5Oopen_by_addr. + + * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, + H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t + struct and H5L_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The original functions have been + renamed to version 1 functions and are deprecated in favor of the new version 2 + functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 + types and are now deprecated in favor of their version 2 counterparts. For each of + the functions and types, compatibility macros take place of the original symbols. + + * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, + H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t + struct and H5O_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The version 2 functions are now + deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t + types have been renamed to version 1 types and are now deprecated in favor of their + version 2 counterparts. For each, compatibility macros take place of the original + symbols. + + * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and + H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t + struct, which are used to retrieve the native HDF5 file format-specific information + about an object. This information (such as object header info and B-tree/heap info) + has been removed from the new H5O_info2_t struct so that the more generic + H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native + VOL connectors. + + * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare + two object tokens, convert an object token into a nicely-readable string format and + to convert an object token string back into a real object token, respectively. + + (DER, QAK, JTH - 2020/01/16) + + - Virtual Object Layer (VOL) + + In this major HDF5 release we introduce HDF5 Virtual Object Layer (VOL). + VOL is an abstraction layer within the HDF5 library that enables different + methods for accessing data and objects that conform to the HDF5 data model. + The VOL layer intercepts all HDF5 API calls that potentially modify data + on disk and forwards those calls to a plugin "object driver". The data on + disk can be a different format than the HDF5 format. For more information + about VOL we refer the reader to the following documents (under review): + + VOL HDF5 APIs + https://portal.hdfgroup.org/display/HDF5/Virtual+Object++Layer + + VOL Documentation + https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5/VOL + + Repository with VOL plugins + https://bitbucket.hdfgroup.org/projects/HDF5VOL + + - Enhancements to HDF5 References + + HDF5 references were extended to support attributes, and object and dataset + selections that reside in another HDF5 file. For more information including + a list of new APIs, see + + https://portal.hdfgroup.org/display/HDF5/Update+to+References + + - Add new public function H5Sselect_adjust. + + This function shifts a dataspace selection by a specified logical offset + within the dataspace extent. This can be useful for VOL developers to + implement chunked datasets. + + (NAF - 2019/11/18) + + - Add new public function H5Sselect_project_intersection. + + This function computes the intersection between two dataspace selections + and projects that intersection into a third selection. This can be useful + for VOL developers to implement chunked or virtual datasets. + + (NAF - 2019/11/13, ID-148) + + - Add new public function H5VLget_file_type. + + This function returns a datatype equivalent to the supplied datatype but + with the location set to be in the file. This datatype can then be used + with H5Tconvert to convert data between file and in-memory representation. + This funcition is intended for use only by VOL connector developers. + + (NAF - 2019/11/08, ID-127) + + - New S3 and HDFS Virtual File Drivers (VFDs) + + This release has two new VFDs. The S3 VFD allows accessing HDF5 files on + AWS S3 buckets. HDFS VFD allows accessing HDF5 files stored on Apache HDFS. + See https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS + for information on enabling those drivers and using those APIs. + + Below are specific instructions for enabling S3 VFD on Windows: + + Fix windows requirements and java tests. Windows requires CMake 3.13. + - Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + - PATH should have been updated with the installation dir. + - set ENV variable OPENSSL_ROOT_DIR to the installation dir. + - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + - Install libcurl library (with dev files); + - download the latest released version using git: https://github.com/curl/curl.git + - Open a Visual Studio Command prompt + - change to the libcurl root folder + - run the "buildconf.bat" batch file + - change to the winbuild directory + - nmake /f Makefile.vc mode=dll MACHINE=x64 + - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + - set ENV variable CURL_ROOT to C:\curl (installation dir) + - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + - the aws credentials file should be in %USERPROFILE%\.aws folder + - set the ENV variable HDF5_ROS3_TEST_BUCKET_URL to the s3 url for the + s3 bucket containing the HDF5 files to be accessed. + + FORTRAN Library: + ---------------- + - Added new Fortran parameters: + + H5F_LIBVER_ERROR_F + H5F_LIBVER_NBOUNDS_F + H5F_LIBVER_V18_F + H5F_LIBVER_V110_F + H5F_LIBVER_V112_F + + - Added new Fortran API: h5pget_libver_bounds_f + + (MSB - 2020/02/11, HDFFV-11018) + + Java Library: + ---------------- + - Added ability to test java library with VOLs. + + Created new CMake script that combines the java and vol test scripts. + + (ADB - 2020/02/03, HDFFV-10996) + + - Tests fail for non-English locale. + + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. + + (ADB - 2020/01/09, HDFFV-10995) + + + Tools: + ------ + - h5diff was updated to use the new reference APIs. + + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. + + (ADB - 2019/12/19, HDFFV-10980) + + - h5dump and h5ls were updated to use the new reference APIs. + + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. + + + Other improvements and changes: + + - Hyperslab selection code was reworked to improve performance, getting more + than 10x speedup in some cases. + + - The HDF5 Library was enhanced to open files with Unicode names on Windows. + + - Deprecated H5Dvlen_reclaim() and replaced it with H5Treclaim(). + This routine is meant to be used when resources are internally allocated + when reading data, i.e. when using either vlen or new reference types. + This is applicable to both attribute and dataset reads. + + - h5repack was fixed to repack datasets with external storage + to other types of storage. + + +Support for new platforms, languages and compilers. +======================================= + - Added spectrum-mpi with clang, gcc and xl compilers on Linux 3.10.0 + - Added OpenMPI 3.1 and 4.0 with clang, gcc and Intel compilers on Linux 3.10.0 + - Added cray-mpich/PrgEnv with gcc and Intel compilers on Linux 4.14.180 + - Added spectrum mpi with clang, gcc and xl compilers on Linux 4.14.0 + + +Bug Fixes since HDF5-1.12.0-alpha1 release +========================================== + Library + ------- + - Improved performance when creating a large number of small datasets by + retrieving default property values from the API context instead of doing + skip list searches. + + (CJH - 2019/12/10, HDFFV-10658) + + - Fixed user-created data access properties not existing in the property list + returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a + reproducer and a patch. + + (CJH - 2019/12/09, HDFFV-10934) + + - Fixed an assertion failure in the parallel library when collectively + filling chunks. As it is required that chunks be written in + monotonically non-decreasing order of offset in the file, this assertion + was being triggered when the list of chunk file space allocations being + passed to the collective chunk filling routine was not sorted according + to this particular requirement. + + The addition of a sort of the out of order chunks trades a bit of + performance for the elimination of this assertion and of any complaints + from MPI implementations about the file offsets used being out of order. + + (JTH - 2019/10/07, HDFFV-10792) + + FORTRAN library: + ---------------- + + - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + + (MSB - 2020/2/18, HDFFV-11029) + + Java Library: + ---------------- + - Added ability to test java library with VOLs. + + Created new CMake script that combines the java and vol test scripts. + + (ADB - 2020/02/03, HDFFV-10996) + + - Tests fail for non-English locale. + + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. + + (ADB - 2020/01/09, HDFFV-10995) + + Tools: + ------ + - h5repack was fixed to repack the reference attributes properly. + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/10, HDFFV-11014) + + - h5diff was updated to use the new reference APIs. + + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. + + (ADB - 2019/12/19, HDFFV-10980) + + - h5dump and h5ls were updated to use the new reference APIs. + + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. + + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + + +Major Bug Fixes since HDF5-1.10.0 release +========================================= + + - For major bug fixes please see HISTORY-1_10_0-1_12_0.txt file + + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, 5.2.0, 7.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 + + Linux-3.10.0- spectrum-mpi/rolling-release with cmake>3.10 and + 862.14.4.1chaos.ch6.ppc64le clang/3.9,8.0 + #1 SMP ppc64le GNU/Linux gcc/7.3 + (ray) xl/2016,2019 + + Linux 3.10.0- openmpi/3.1,4.0 with cmake>3.10 and + 957.12.2.1chaos.ch6.x86_64 clang 5.0 + #1 SMP x86_64 GNU/Linux gcc/7.3,8.2 + (serrano) intel/17.0,18.0/19.0 + + Linux 3.10.0- openmpi/3.1/4.0 with cmake>3.10 and + 1062.1.1.1chaos.ch6.x86_64 clang/3.9,5.0,8.0 + #1 SMP x86_64 GNU/Linux gcc/7.3,8.1,8.2 + (chama,quartz) intel/16.0,18.0,19.0 + + Linux 4.4.180-94.100-default cray-mpich/7.7.6 with PrgEnv-*/6.0.5, cmake>3.10 and + #1 SMP x86_64 GNU/Linux gcc/7.2.0,8.2.0 + (mutrino) intel/17.0,18.0 + + Linux 4.14.0- spectrum-mpi/rolling-release with cmake>3.10 and + 49.18.1.bl6.ppc64le clang/6.0,8.0 + #1 SMP ppc64le GNU/Linux gcc/7.3 + (lassen) xl/2019 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) + Visual Studio 2015 w/ MSMPI 10 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + + macOS 10.13.6 High Sierra Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4 + + macOS 10.14.6 Mohave Apple LLVM version 10.0.1 (clang/clang++-1001.0.46.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bobcat) Intel icc/icpc/ifort version 19.0.4 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +macOS 10.13.6 64-bit n y/y n y y ? +macOS 10.14.6 64-bit n y/y n y y ? +CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +macOS 10.13.6 64-bit y n y y +macOS 10.14.6 64-bit y n y y +CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n +CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + PGI C (pgcc), C++ (pgc++), Fortran (pgf90) + compilers: + Version 18.4, 19.4 + MPICH 3.3 + OpenMPI 2.1.5, 3.1.3, 4.0.0 + + Fedora30 5.3.11-200.fc30.x86_64 + #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) + GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) + (cmake and autotools) + + Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang/clang++-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + macOS 10.12.6 Sierra Apple LLVM version 9.0.0 (clang/clang++-900.0.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.8 + + +Known Problems +============== + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source, and in the HDF5 Jira database, available at + https://jira.hdfgroup.org/. Please register at https://www.hdfgroup.org to + create a free account for accessing the Jira database. Please report any + new problems found to help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + diff --git a/release_docs/HISTORY-1_13.txt b/release_docs/HISTORY-1_13.txt new file mode 100644 index 0000000..73b7feb --- /dev/null +++ b/release_docs/HISTORY-1_13.txt @@ -0,0 +1,3194 @@ +HDF5 History +============ + +This file contains development history of the HDF5 1.13 releases from +the develop branch + +04. Release Information for hdf5-1.13.3 +03. Release Information for hdf5-1.13.2 +02. Release Information for hdf5-1.13.1 +01. Release Information for hdf5-1.13.0 + +[Search on the string '%%%%' for section breaks of each release.] + + +%%%%1.13.3%%%% + +HDF5 version 1.13.3 released on 2022-10-28 +================================================================================ + + +INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.13.2 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + +New features and bug fixes previously added in 1.13.0 - 1.13.2 releases can be +found in release_docs/HISTORY-1_13.txt in the HDF5 source code. + + +New Features +============ + + Configuration: + ------------- + - Add new CMake configuration variable HDF5_USE_GNU_DIRS + + HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install + directory variables by including the CMake module, GNUInstallDirs(see CMake + documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file + sets various PATH variables for use during the build, test and install processes. + By default, the historical settings for these variables will be used. + + (ADB - 2022/10/21, GH-2175, GH-1716) + + - Update CMake minimum version to 3.18 + + Updated CMake minimum version from 3.12 to 3.18 and removed version checks + which were added for Windows features not yet available in version 3.12. Also + removed configure macros and code checks for old style code compile checks. + + (ADB - 2022/08/29, HDFFV-11329) + + + Library: + -------- + - Added multi dataset I/O feature + + Added H5Dread_multi, H5Dread_multi_async, H5Dwrite_multi, and + H5Dwrite_multi_async API routines to allow I/O on multiple datasets with a + single API call. Added H5Dread_multi_f and H5Dwrite_multi_f Fortran + wrappers. Updated VOL callbacks for dataset I/O to support multi dataset + I/O. + + (NAF - 2022/10/19) + + + Parallel Library: + ----------------- + - + + + Fortran Library: + ---------------- + - Added pointer based H5Dfill_f API + + Added Fortran H5Dfill_f, which is fully equivalent to the C API. It accepts pointers, + fill value datatype and datatype of dataspace elements. + + (MSB - 2022/10/10, HDFFV-10734.) + + C++ Library: + ------------ + - + + + Java Library: + ------------- + - + + + Tools: + ------ + - + + + High-Level APIs: + ---------------- + - + + + C Packet Table API: + ------------------- + - + + + Internal header file: + --------------------- + - + + + Documentation: + -------------- + - Doxygen User Guide documentation is available when configured and generated. + The resulting documentation files will be in the share/html subdirectory + of the HDF5 install directory. + + (ADB - 2022/08/09) + + +Support for new platforms, languages and compilers +================================================== + - + + +Bug Fixes since HDF5-1.13.2 release +=================================== + Library + ------- + - Fixed an issue with variable length attributes + + Previously, if a variable length attribute was held open while its file + was opened through another handle, the same attribute was opened through + the second file handle, and the second file and attribute handles were + closed, attempting to write to the attribute through the first handle + would cause an error. + + (NAF - 2022/10/24) + + - Memory leak + + A memory leak was observed with variable-length fill value in + H5O_fill_convert() function in H5Ofill.c. The leak is + manifested by running valgrind on test/set_extent.c. + + Previously, fill->buf is used for datatype conversion + if it is large enough and the variable-length information + is therefore lost. A buffer is now allocated regardless + so that the element in fill->buf can later be reclaimed. + + (VC - 2022/10/10, HDFFV-10840) + + - Fixed an issue with hyperslab selections + + Previously, when combining hyperslab selections, it was possible for the + library to produce an incorrect combined selection. + + (NAF - 2022/09/25) + + - Fixed an issue with attribute type conversion with compound datatypes + + Previously, when performing type conversion for attribute I/O with a + compound datatype, the library would not fill the background buffer with + the contents of the destination, potentially causing data to be lost when + only writing to a subset of the compound fields. + + (NAF - 2022/08/22, GitHub #2016) + + + Java Library + ------------ + - Improve variable-length datatype handling in JNI. + + The existing JNI read-write functions could handle variable-length datatypes + that were simple variable-length datatype with an atomic sub-datatype. More + complex combinations could not be handled. Reworked the JNI read-write functions + to recursively inspect datatypes for variable-length sub-datatypes. + + (ADB - 2022/10/12, HDFFV-8701,10375) + + + Configuration + ------------- + - + + + Tools + ----- + - + + + Performance + ------------- + - + + + Fortran API + ----------- + - + + High-Level Library + ------------------ + - + + + Fortran High-Level APIs + ----------------------- + - + + + Documentation + ------------- + - + + + F90 APIs + -------- + - + + + C++ APIs + -------- + - + + + Testing + ------- + - + + +Platforms Tested +=================== + + Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16 + #1 SMP x86_64 GNU/Linux Cray clang 14.0.0 + (crusher) GCC 11.2.0 + (cmake) + + Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 + #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5) + (stria) GCC 7.2.0 (Spack GCC) + (cmake) + + Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1 + (vortex) GCC 8.3.1 + XL 16.1.1 + (cmake) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 + (lassen) GCC 8.3.1 + XL 16.1.1.2, 2021,09.22, 2022.08.05 + (cmake) + + Linux-4.12.14-197.99-default cray-mpich/7.7.14 + #1 SMP x86_64 GNU/Linux cce 12.0.3 + (theta) GCC 11.2.0 + llvm 9.0 + Intel 19.1.2 + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + (autotools and cmake) + + Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 19.0.4, 2022.2, oneapi.2022.2 + + Linux-3.10.0-1160.71.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (skybridge) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (attaway) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux Intel/19.1 + (chama) (cmake) + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2021 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + + +Known Problems +============== + + ************************************************************ + * _ * + * (_) * + * __ ____ _ _ __ _ __ _ _ __ __ _ * + * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | * + * \ V V / (_| | | | | | | | | | | (_| | * + * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | * + * __/ | * + * |___/ * + * * + * Please refrain from running any program (including * + * HDF5 tests) which uses the subfiling VFD on Perlmutter * + * at the National Energy Research Scientific Computing * + * Center, NERSC. * + * Doing so may cause a system disruption due to subfiling * + * crashing Lustre. The sytem's Lustre bug is expected * + * to be resolved by 2023. * + * * + ************************************************************ + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Several tests currently fail on certain platforms: + MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. + + MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with + cray-mpich on theta and with XL compilers on ppc64le platforms. + + MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and can be avoided by not building +the gif tool. Disable building the High-Level tools with these options: + autotools: --disable-hltools + cmake: HDF5_BUILD_HL_TOOLS=OFF + + +%%%%1.13.2%%%% + +HDF5 version 1.13.2 released on 2022-08-15 +================================================================================ + + +INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.13.1 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Correct the usage of CMAKE_Fortran_MODULE_DIRECTORY and where to + install Fortran mod files. + + The Fortran modules files, ending in .mod are files describing a + Fortran 90 (and above) module API and ABI. These are not like C + header files describing an API, they are compiler dependent and + arch dependent, and not easily readable by a human being. They are + nevertheless searched for in the includes directories by gfortran + (in directories specified with -I). + + Autotools configure uses the -fmoddir option to specify the folder. + CMake will use "mod" folder by default unless overridden by the CMake + variable; HDF5_INSTALL_MODULE_DIR. + + (ADB - 2022/07/21) + + - HDF5 memory allocation sanity checking is now off by default for + Autotools debug builds + + HDF5 can be configured to perform sanity checking on internal memory + allocations by adding heap canaries to these allocations. However, + enabling this option can cause issues with external filter plugins + when working with (reallocating/freeing/allocating and passing back) + buffers. + + Previously, this option was off by default for all CMake build types, + but only off by default for non-debug Autotools builds. Since debug + is the default build mode for HDF5 when built from source with + Autotools, this can result in surprising segfaults that don't occur + when an application is built against a release version of HDF5. + Therefore, this option is now off by default for all build types + across both CMake and Autotools. + + (JTH - 2022/03/01) + + + Library: + -------- + - Onion VFD + + The onion VFD allows creating "versioned" HDF5 files. File open/close + operations after initial file creation will add changes to an external + "onion" file (.onion extension by default) instead of the original file. + Each written revision can be opened independently. + + To open a file with the onion VFD, use the H5Pset_fapl_onion() API call + (does not need to be used for the initial creation of the file). The + options for the H5FD_onion_fapl_info_t struct are described in H5FDonion.h. + + The H5FDonion_get_revision_count() API call can be used to query a file + to find out how many revisions have been created. + + (DER - 2022/08/02) + + - Subfiling VFD + + The HDF5 Subfiling VFD is a new MPI-based file driver that allows an + HDF5 application to distribute an HDF5 file across a collection of + "sub-files" in equal-sized data segment "stripes". I/O to the logical + HDF5 file is then directed to the appropriate "sub-file" according to + the Subfiling configuration and a system of I/O concentrators, which + are MPI ranks operating worker threads. + + By allowing a configurable stripe size, number of I/O concentrators and + method for selecting MPI ranks as I/O concentrators, the Subfiling VFD + aims to enable an HDF5 application to find a middle ground between the + single shared file and file-per-process approaches to parallel file I/O + for the particular machine the application is running on. In general, the + goal is to avoid some of the complexity of the file-per-process approach + while also minimizing the locking issues of the single shared file approach + on a parallel file system. + + Also included with the Subfiling VFD is a new h5fuse.sh script which + reads a Subfiling configuration file and then combines the various + sub-files back into a single HDF5 file. By default, the h5fuse.sh script + looks in the current directory for the Subfiling configuration file, + but can also be pointed to the configuration file with a command-line + option. + + The Subfiling VFD can be used by calling H5Pset_fapl_subfiling() on a + File Access Property List and using that FAPL for file operations. Note + that the Subfiling VFD currently has the following limitations: + + * Does not currently support HDF5 collective I/O, other than collective + metadata writes and reads as set by H5Pset_coll_metadata_write() and + H5Pset_all_coll_metadata_ops() + + * The Subfiling VFD should not currently be used with an HDF5 library + that has been built with thread-safety enabled. This can cause deadlocks + when failures occur due to interactions between the VFD's internal + threads and HDF5's global lock. + + (JTH - 2022/07/22) + + + Parallel Library: + ----------------- + - + + + Fortran Library: + ---------------- + - + + + C++ Library: + ------------ + - Added two new constructors to H5::H5File class + + Two new constructors were added to allow opening a file with non-default + access property list. + + + Java Library: + ------------- + - Added version of H5Rget_name to return the name as a Java string. + + Other functions that get_name process the get_size then get the name + within the JNI implementation. Now H5Rget_name has a H5Rget_name_string. + + (ADB - 2022/07/12) + + - Added reference support to H5A and H5D read write vlen JNI functions. + + Added the implementation to handle VL references as an Array of Lists + of byte arrays. + + The JNI wrappers translate the Array of Lists to/from the hvl_t vlen + structures. The wrappers use the specified datatype arguments for the + List type translation, it is expected that the Java type is correct. + + (ADB - 2022/07/11, HDFFV-11318) + + - H5A and H5D read write vlen JNI functions were incorrect. + + Corrected the vlen function implementations for the basic primitive types. + The VLStrings functions now correctly use the implementation that had been + the VL functions. (VLStrings functions did not have an implementation.) + The new VL functions implementation now expect an Array of Lists between + Java and the JNI wrapper. + + The JNI wrappers translate the Array of Lists to/from the hvl_t vlen + structures. The wrappers use the specified datatype arguments for the + List type translation, it is expected that the Java type is correct. + + (ADB - 2022/07/07, HDFFV-11310) + + - H5A and H5D read write JNI functions had flawed vlen datatype check. + + Adapted tools function for JNI utils file. This reduced multiple calls + to a single check and variable. The variable can then be used to call + the H5Treclaim function. Adjusted existing test and added new test. + + (ADB - 2022/06/22) + + + Tools: + ------ + - Building h5perf/h5perf_serial in "standalone mode" has been removed + + Building h5perf separately from the library was added circa 2008 + in HDF5 1.6.8. It's unclear what purpose this serves and the current + implementation is currently broken. The existing files require + H5private.h and the symbols we use to determine how the copied + platform-independence scheme should be used come from H5pubconf.h, + which may not match the compiler being used to build standalone h5perf. + + Due to the maintenance overhead and lack of a clear use case, support + for building h5perf and h5perf_serial separately from the HDF5 library + has been removed. + + (DER - 2022/07/15) + + - The perf tool has been removed + + The small `perf` tool didn't really do anything special and the name + conflicts with gnu's perf tool. + + (DER - 2022/07/15, GitHub #1787) + + - 1.10 References in containers were not displayed properly by h5dump. + + Ported 1.10 tools display function to provide ability to inspect and + display 1.10 reference data. + + (ADB - 2022/06/22) + + + High-Level APIs: + ---------------- + - + + + C Packet Table API: + ------------------- + - + + + Internal header file: + --------------------- + - All the #defines named H5FD_CTL__* were renamed to H5FD_CTL_*, i.e. the double underscore was reduced to a single underscore. + + + Documentation: + -------------- + - + + +Support for new platforms, languages and compilers +================================================== + - + + +Bug Fixes since HDF5-1.13.1 release +=================================== + Library + ------- + - The offset parameter in H5Dchunk_iter() is now scaled properly + + In earlier HDF5 1.13.x versions, the chunk offset was not scaled by the + chunk dimensions. This offset parameter in the callback now matches + that of H5Dget_chunk_info(). + + (@mkitti - 2022/08/06, GitHub #1419) + + - Converted an assertion on (possibly corrupt) file contents to a normal + error check + + Previously, the library contained an assertion check that a read superblock + doesn't contain a superblock extension message when the superblock + version < 2. When a corrupt HDF5 file is read, this assertion can be triggered + in debug builds of HDF5. In production builds, this situation could cause + either a library error or a crash, depending on the platform. + + (JTH - 2022/07/08, HDFFV-11316/HDFFV-11317) + + + Java Library + ------------ + - + + + Configuration + ------------- + - + + + Tools + ----- + - + + + Performance + ------------- + - + + + Fortran API + ----------- + - h5open_f and h5close_f fixes + * Fixed it so both h5open_f and h5close_f can be called multiple times. + * Fixed an issue with open objects remaining after h5close_f was called. + * Added additional tests. + (MSB, 2022/04/19, HDFFV-11306) + + + High-Level Library + ------------------ + - + + + Fortran High-Level APIs + ----------------------- + - + + + Documentation + ------------- + - + + + F90 APIs + -------- + - + + + C++ APIs + -------- + - + + + Testing + ------- + - + + +Platforms Tested +=================== + + Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16 + #1 SMP x86_64 GNU/Linux Cray clang 14.0.0 + (crusher) GCC 11.2.0 + (cmake) + + Linux 5.3.18-24-cray_shasta_c cray-mpich/8.1.12 + #1 SMP x86_64 GNU/Linux Cray clang 13.0.0 + (spock) AMD clang 13.0.0 + GCC 8.2.0, 11.2.0 + (cmake) + + Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 + #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5) + (stria) GCC 7.2.0 (Spack GCC) + (cmake) + + Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1 + (vortex) GCC 8.3.1 + XL 16.1.1 + (cmake) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 + (lassen) GCC 7.3.1 + XL 16.1.1.2 + (cmake) + + Linux-4.12.14-150.75-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 + (cori) Intel (R) Version 19.0.3.199 + (cmake) + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + (autotools and cmake) + + Linux-3.10.0-1160.71.1.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 16.0.4, 18.0.2, 19.0.4 + (cmake) + + Linux-3.10.0-1160.71.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (skybridge) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (attaway) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux Intel/19.1 + (chama) (cmake) + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2021 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + + +Known Problems +============== + Setting a variable-length dataset fill value will leak the memory allocated + for the p field of the hvl_t struct. A fix is in progress for this. + HDFFV-10840 + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Several tests currently fail on certain platforms: + MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. + + MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with + cray-mpich on theta and with XL compilers on ppc64le platforms. + + MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and can be avoided by not building +the gif tool. Disable building the High-Level tools with these options: + autotools: --disable-hltools + cmake: HDF5_BUILD_HL_TOOLS=OFF + + +%%%%1.13.1%%%% + +HDF5 version 1.13.1 released on 2022-03-02 +================================================================================ + + +INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.13.0 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Reworked corrected path searched by CMake find_package command + + The install path for cmake find_package files had been changed to use + "share/cmake" + for all platforms. However setting the HDF5_ROOT variable failed to locate + the configuration files. The build variable HDF5_INSTALL_CMAKE_DIR is now + set to the <INSTALL_DIR>/cmake folder. The location of the configuration + files can still be specified by the "HDF5_DIR" variable. + + (ADB - 2022/02/02) + + - CPack will now generate RPM/DEB packages. + + Enabled the RPM and DEB CPack generators on linux. In addition to + generating STGZ and TGZ packages, CPack will try to package the + library for RPM and DEB packages. This is the initial attempt and + may change as issues are resolved. + + (ADB - 2022/01/27) + + - Added new option to the h5cc scripts produced by CMake. + + Add -showconfig option to h5cc scripts to cat the + libhdf5.settings file to the standard output. + + (ADB - 2022/01/25) + + - CMake will now run the PowerShell script tests in test/ by default + on Windows. + + The test directory includes several shell script tests that previously + were not run by CMake on Windows. These are now run by default. + If TEST_SHELL_SCRIPTS is ON and PWSH is found, the PowerShell scripts + will execute. Similar to the bash scripts on unix platforms. + + (ADB - 2021/11/23) + + + Library: + -------- + - Add a new public function, H5ESget_requests() + + This function allows the user to retrieve request pointers from an event + set. It is intended for use primarily by VOL plugin developers. + + (NAF - 2022/01/11) + + + Parallel Library: + ----------------- + - Several improvements to parallel compression feature, including: + + * Improved support for collective I/O (for both writes and reads) + + * Significant reduction of memory usage for the feature as a whole + + * Reduction of copying of application data buffers passed to H5Dwrite + + * Addition of support for incremental file space allocation for filtered + datasets created in parallel. Incremental file space allocation is the + default for these types of datasets (early file space allocation is + also still supported), while early file space allocation is still the + default (and only supported at allocation time) for unfiltered datasets + created in parallel. Incremental file space allocation should help with + parallel HDF5 applications that wish to use fill values on filtered + datasets, but would typically avoid doing so since dataset creation in + parallel would often take an excessive amount of time. Since these + datasets previously used early file space allocation, HDF5 would + allocate space for and write fill values to every chunk in the dataset + at creation time, leading to noticeable overhead. Instead, with + incremental file space allocation, allocation of file space for chunks + and writing of fill values to those chunks will be delayed until each + individual chunk is initially written to. + + * Addition of support for HDF5's "don't filter partial edge chunks" flag + (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS) + + * Addition of proper support for HDF5 fill values with the feature + + * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h + so HDF5 applications can determine at compile-time whether the feature + is available + + * Addition of simple examples (ph5_filtered_writes.c and + ph5_filtered_writes_no_sel.c) under examples directory to demonstrate + usage of the feature + + * Improved coverage of regression testing for the feature + + (JTH - 2022/2/23) + + +Support for new platforms, languages and compilers +================================================== + - None + + +Bug Fixes since HDF5-1.13.0 release +=================================== + Library + ------- + - Fixed a metadata cache bug when resizing a pinned/protected cache entry + + When resizing a pinned/protected cache entry, the metadata + cache code previously would wait until after resizing the + entry to attempt to log the newly-dirtied entry. This + caused H5C_resize_entry to mark the entry as dirty and made + H5AC_resize_entry think that it didn't need to add the + newly-dirtied entry to the dirty entries skiplist. + + Thus, a subsequent H5AC__log_moved_entry would think it + needed to allocate a new entry for insertion into the dirty + entry skip list, since the entry didGn't exist on that list. + This caused an assertion failure, as the code to allocate a + new entry assumes that the entry is not dirty. + + (JRM - 2022/02/28) + + - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the + H5check_version function. + + Investigating the original fix, #812, we discovered some inconsistencies + with a new block added to check H5_VERS_RELEASE for incompatibilities. + This new block was not using the new warning text dealing with the + H5_VERS_RELEASE check and would cause the warning to be duplicated. + + By removing the H5_VERS_RELEASE argument in the first check for + H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check + the H5_VERS_RELEASE for incompatible release versions. This adheres + to the statement that except for the develop branch, all release versions + in a major.minor maintenance branch should be compatible. The prerequisite + is that an application will not use any APIs not present in all release versions. + + (ADB - 2022/02/24, #1438) + + - Unified handling of collective metadata reads to correctly fix old bugs + + Due to MPI-related issues occurring in HDF5 from mismanagement of the + status of collective metadata reads, they were forced to be disabled + during chunked dataset raw data I/O in the HDF5 1.10.5 release. This + wouldn't generally have affected application performance because HDF5 + already disables collective metadata reads during chunk lookup, since + it is generally unlikely that the same chunks will be read by all MPI + ranks in the I/O operation. However, this was only a partial solution + that wasn't granular enough. + + This change now unifies the handling of the file-global flag and the + API context-level flag for collective metadata reads in order to + simplify querying of the true status of collective metadata reads. Thus, + collective metadata reads are once again enabled for chunked dataset + raw data I/O, but manually controlled at places where some processing + occurs on MPI rank 0 only and would cause issues when collective + metadata reads are enabled. + + (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562) + + - Fixed several potential MPI deadlocks in library failure conditions + + In the parallel library, there were several places where MPI rank 0 + could end up skipping past collective MPI operations when some failure + occurs in rank 0-specific processing. This would lead to deadlocks + where rank 0 completes an operation while other ranks wait in the + collective operation. These places have been rewritten to have rank 0 + push an error and try to cleanup after the failure, then continue to + participate in the collective operation to the best of its ability. + + (JTH - 2021/11/09) + + +Platforms Tested +=================== + + Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 + #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 + Ubuntu20.10 Ubuntu clang version 11.0.0-2 + (cmake and autotools) + + Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 + #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 + SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) + (cmake and autotools) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 + (lassen) GCC 7.3.1 + XL 16.1.1.2 + (cmake) + + Linux-3.10.0-1160.49.1 openmpi-intel/4.1 + #1 SMP x86_64 GNU/Linux Intel(R) Version 18.0.5, 19.1.2 + (chama) (cmake) + + Linux-4.12.14-150.75-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 + (cori) Intel (R) Version 19.0.3.199 + (cmake) + + Linux-4.12.14-197.86-default cray-mpich/7.7.6 + # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 + (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 + (cmake) + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 16.0.4, 18.0.2, 19.0.4 + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + + +Known Problems +============== + Setting a variable-length dataset fill value will leak the memory allocated + for the p field of the hvl_t struct. A fix is in progress for this. + HDFFV-10840 + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and can be avoided by not building +the gif tool. Disable building the High-Level tools with these options: + autotools: --disable-hltools + + +%%%%1.13.0%%%% + +HDF5 version 1.13.0 released on 2021-12-01 +================================================================================ + + +INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- New platforms, languages and compilers tested +- Bug Fixes since HDF5-1.12.0 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Added new configure option to support building parallel tools. + See Tools below (autotools - CMake): + --enable-parallel-tools HDF5_BUILD_PARALLEL_TOOLS + + (RAW - 2021/10/25) + + - Added new configure options to enable dimension scales APIs (H5DS*) to + use new object references with the native VOL connector (aka native HDF5 + library). New references are always used for non-native terminal VOL + connectors (e.g., DAOS). + + Autotools --enable-dimension-scales-with-new-ref + CMake HDF5_DIMENSION_SCALES_NEW_REF=ON + + (EIP - 2021/10/25, HDFFV-11180) + + - Refactored the utils folder. + + Added subfolder test and moved the 'swmr_check_compat_vfd.c file' + from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c + file in hl/tools/h5watch folder. Also fixed vfd check options. + + (ADB - 2021/10/18) + + - Changed autotools and CMake configurations to derive both + compilation warnings-as-errors and warnings-only-warn configurations + from the same files, 'config/*/*error*'. Removed redundant files + 'config/*/*noerror*'. + + (DCY - 2021/09/29) + + - Added new option to control the build of High-Level tools + that default ON/enabled. + + Add configure options (autotools - CMake): + --enable-hltools HDF5_BUILD_HL_TOOLS + + Disabling this option prevents building the gif tool which + contains the following CVEs: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 + + (ADB - 2021/09/16, HDFFV-11266) + + - Adds C++ Autotools configuration file for Intel + + * Checks for icpc as the compiler + * Sets std=c++11 + * Copies most non-warning flags from intel-flags + + (DER - 2021/06/02) + + - Adds C++ Autotools configuration file for PGI + + * Checks for pgc++ as the compiler name (was: pgCC) + * Sets -std=c++11 + * Other options basically match new C options (below) + + (DER - 2021/06/02) + + - Updates PGI C options + + * -Minform set to warn (was: inform) to suppress spurious messages + * Sets -gopt -O2 as debug options + * Sets -O4 as 'high optimization' option + * Sets -O0 as 'no optimization' option + * Removes specific settings for PGI 9 and 10 + + (DER - 2021/06/02) + + - A C++11-compliant compiler is now required to build the C++ wrappers + + CMAKE_CXX_STANDARD is now set to 11 when building with CMake and + -std=c++11 is added when building with clang/gcc via the Autotools. + + (DER - 2021/05/27) + + - CMake will now run the shell script tests in test/ by default + + The test directory includes several shell script tests that previously + were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS + has been set to ON and SH_PROGRAM has been set to bash (some test + scripts use bash-isms). Platforms without bash (e.g., Windows) will + ignore the script tests. + + (DER - 2021/05/23) + + - Removed unused HDF5_ENABLE_HSIZET option from CMake + + This has been unused for some time and has no effect. + + (DER - 2021/05/23) + + - CMake no longer builds the C++ library by default + + HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the + Autotools build defaults. + + (DER - 2021/04/20) + + - Removal of pre-VS2015 work-arounds + + HDF5 now requires Visual Studio 2015 or greater, so old work-around + code and definitions have been removed, including: + + * <inttypes.h> + * snprintf and vsnprintf + * llround, llroundf, lround, lroundf, round, roundf + * strtoll and strtoull + * va_copy + * struct timespec + + (DER - 2021/03/22) + + - Add CMake variable HDF5_LIB_INFIX + + This infix is added to all library names after 'hdf5'. + e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' + This name is used in packages on debian based systems. + (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) + + (barcode - 2021/03/22) + + - On macOS, Universal Binaries can now be built, allowing native execution on + both Intel and Apple Silicon (ARM) based Macs. + + To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64" + + (SAM - 2021/02/07, github-311) + + - Added a configure-time option to control certain compiler warnings + diagnostics + + A new configure-time option was added that allows some compiler warnings + diagnostics to have the default operation. This is mainly intended for + library developers and currently only works for gcc 10 and above. The + diagnostics flags apply to C, C++ and Fortran compilers and will appear + in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They + will NOT be exported to h5cc, etc. + + The default is OFF, which will disable the warnings URL and color attributes + for the warnings output. ON will not add the flags and allow default behavior. + + Autotools: --enable-diags + + CMake: HDF5_ENABLE_BUILD_DIAGS + + (ADB - 2021/02/05, HDFFV-11213) + + - CMake option to build the HDF filter plugins project as an external project + + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in a hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. + + The option was refactored to use the CMake FetchContent process. This allows + more control over the filter targets, but required external project command + options to be moved to a CMake include file, HDF5PluginCache.cmake. Also + enabled the filter examples to be used as tests for operation of the + filter plugins. + + (ADB - 2020/12/10, OESS-98) + + - FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers + + On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did + not process C++ options. Since FreeBSD 10, the default compiler has + been clang (via 'cc'). + + The default compilers have been set to 'cc' for C and 'c++' for C++, + which will pick up clang and clang++ respectively on FreeBSD 10+. + Additionally, clang options are now set correctly for both C and C++ + and g++ options will now be set if that compiler is being used (an + omission from the former functionality). + + (DER - 2020/11/28, HDFFV-11193) + + - Fixed POSIX problems when building w/ gcc on Solaris + + When building on Solaris using gcc, the POSIX symbols were not + being set correctly, which could lead to issues like clock_gettime() + not being found. + + The standard is now set to gnu99 when building with gcc on Solaris, + which allows POSIX things to be #defined and linked correctly. This + differs slightly from the gcc norm, where we set the standard to c99 + and manually set POSIX #define symbols. + + (DER - 2020/11/25, HDFFV-11191) + + - Added a configure-time option to consider certain compiler warnings + as errors + + A new configure-time option was added that converts some compiler warnings + to errors. This is mainly intended for library developers and currently + only works for gcc and clang. The warnings that are considered errors + will appear in the generated libhdf5.settings file. These warnings apply + to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags", + respectively. They will NOT be exported to h5cc, etc. + + The default is OFF. Building with this option may fail when compiling + on operating systems and with compiler versions not commonly used by + the library developers. Compilation may also fail when headers not + under the control of the library developers (e.g., mpi.h, hdfs.h) raise + warnings. + + Autotools: --enable-warnings-as-errors + + CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS + + (DER - 2020/11/23, HDFFV-11189) + + - Autotools and CMake target added to produce doxygen generated documentation + + The default is OFF or disabled. + Autoconf option is '--enable-doxygen' + autotools make target is 'doxygen' and will build all doxygen targets + CMake configure option is 'HDF5_BUILD_DOC'. + CMake target is 'doxygen' for all available doxygen targets + CMake target is 'hdf5lib_doc' for the src subdirectory + + (ADB - 2020/11/03) + + - CMake option to use MSVC naming conventions with MinGW + + HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions + when using a MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to statically link gcc libs with MinGW + + HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ + with the MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to build the HDF filter plugins project as an external project + + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in a hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. + + The necessary options are (see the INSTALL_CMake.txt file): + HDF5_ENABLE_PLUGIN_SUPPORT + PLUGIN_TGZ_NAME or PLUGIN_GIT_URL + There are more options necessary for various filters and the plugin project + documents should be referenced. + + (ADB - 2020/09/27, OESS-98) + + - Added CMake option to format source files + + HDF5_ENABLE_FORMATTERS option will enable creation of targets using the + pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder + or tool folder. All sources can be formatted by executing the format target; + make format + + (ADB - 2020/08/24) + + - Add file locking configure and CMake options + + HDF5 1.10.0 introduced a file locking scheme, primarily to help + enforce SWMR setup. Formerly, the only user-level control of the scheme + was via the HDF5_USE_FILE_LOCKING environment variable. + + This change introduces configure-time options that control whether + or not file locking will be used and whether or not the library + ignores errors when locking has been disabled on the file system + (useful on some HPC Lustre installations). + + In both the Autotools and CMake, the settings have the effect of changing + the default property list settings (see the H5Pset/get_file_locking() + entry, below). + + The yes/no/best-effort file locking configure setting has also been + added to the libhdf5.settings file. + + Autotools: + + An --enable-file-locking=(yes|no|best-effort) option has been added. + + yes: Use file locking. + no: Do not use file locking. + best-effort: Use file locking and ignore "disabled" errors. + + CMake: + + Two self-explanatory options have been added: + + HDF5_USE_FILE_LOCKING + HDF5_IGNORE_DISABLED_FILE_LOCKS + + Setting both of these to ON is the equivalent to the Autotools' + best-effort setting. + + NOTE: + The precedence order of the various file locking control mechanisms is: + + 1) HDF5_USE_FILE_LOCKING environment variable (highest) + + 2) H5Pset_file_locking() + + 3) configure/CMake options (which set the property list defaults) + + 4) library defaults (currently best-effort) + + (DER - 2020/07/30, HDFFV-11092) + + - CMake option to link the generated Fortran MOD files into the include + directory. + + The Fortran generation of MOD files by a Fortran compile can produce + different binary files between SHARED and STATIC compiles with different + compilers and/or different platforms. Note that it has been found that + different versions of Fortran compilers will produce incompatible MOD + files. Currently, CMake will locate these MOD files in subfolders of + the include directory and add that path to the Fortran library target + in the CMake config file, which can be used by the CMake find library + process. For other build systems using the binary from a CMake install, + a new CMake configuration can be used to copy the pre-chosen version + of the Fortran MOD files into the install include directory. + + The default will depend on the configuration of + BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: + YES YES Default to SHARED + YES NO Default to STATIC + NO YES Default to SHARED + NO NO Default to SHARED + The defaults can be overridden by setting the config option + HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC + + (ADB - 2020/07/09, HDFFV-11116) + + - CMake option to use AEC (open source SZip) library instead of SZip + + The open source AEC library is a replacement library for SZip. In + order to use it for hdf5 the libaec CMake source was changed to add + "-fPIC" and exclude test files. Autotools does not build the + compression libraries within hdf5 builds. New option USE_LIBAEC is + required to compensate for the different files produced by AEC build. + + (ADB - 2020/04/22, OESS-65) + + - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER + + Some handcrafted tests in HDFTests.c has been removed and the CMake + CHECK_STRUCT_HAS_MEMBER module has been used. + + (ADB - 2020/03/24, TRILAB-24) + + - Both build systems use same set of warnings flags + + GNU C, C++ and gfortran warnings flags were moved to files in a config + sub-folder named gnu-warnings. Flags that only are available for a specific + version of the compiler are in files named with that version. + Clang C warnings flags were moved to files in a config sub-folder + named clang-warnings. + Intel C, Fortran warnings flags were moved to files in a config sub-folder + named intel-warnings. + + There are flags in named "error-xxx" files with warnings that may + be promoted to errors. Some source files may still need fixes. + + There are also pairs of files named "developer-xxx" and "no-developer-xxx" + that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the + configure option:--enable-developer-warnings. + + In addition, CMake no longer applies these warnings for examples. + + (ADB - 2020/03/24, TRILAB-192) + + - Added test script for file size compare + + If CMake minimum version is at least 3.14, the fileCompareTest.cmake + script will compare file sizes. + + (ADB - 2020/02/24, HDFFV-11036) + + - Update CMake minimum version to 3.12 + + Updated CMake minimum version to 3.12 and added version checks + for Windows features. + + (ADB - 2020/02/05, TRILABS-142) + + - Fixed CMake include properties for Fortran libraries + + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. + + (ADB - 2020/02/04, HDFFV-11012) + + - Added common warnings files for gnu and intel + + Added warnings files to use one common set of flags + during configure for both autotools and CMake build + systems. The initial implementation only affects a + general set of flags for gnu and intel compilers. + + (ADB - 2020/01/17) + + - Added new options to CMake for control of testing + + Added CMake options (default ON); + HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL + combined with: + HDF5_TEST_TOOLS + HDF5_TEST_EXAMPLES + HDF5_TEST_SWMR + HDF5_TEST_FORTRAN + HDF5_TEST_CPP + HDF5_TEST_JAVA + + (ADB - 2020/01/15, HDFFV-11001) + + - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + + Added CMake code and files to execute the Clang sanitizers if + HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option + is set to one of the following: + Address + Memory + MemoryWithOrigins + Undefined + Thread + Leak + 'Address;Undefined' + + (ADB - 2019/12/12, TRILAB-135) + + - Update CMake for VS2019 support + + CMake added support for VS2019 in version 3.15. Changes to the CMake + generator setting required changes to scripts. Also updated version + references in CMake files as necessary. + + (ADB - 2019/11/18, HDFFV-10962) + + - Update CMake options to match new autotools options + + Add configure options (autotools - CMake): + enable-asserts HDF5_ENABLE_ASSERTS + enable-symbols HDF5_ENABLE_SYMBOLS + enable-profiling HDF5_ENABLE_PROFILING + enable-optimization HDF5_ENABLE_OPTIMIZATION + In addition NDEBUG is no longer forced defined and relies on the CMake + process. + + (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) + + + Library: + -------- + - Adds new file driver-level memory copy operation for + "ctl" callback and updates compact dataset I/O routines + to utilize it + + When accessing an HDF5 file with a file driver that uses + memory allocated in special ways (e.g., without standard + library's `malloc`), a crash could be observed when HDF5 + tries to perform `memcpy` operations on such a memory + region. + + These changes add a new H5FD_FEAT_MEMMANAGE VFD feature + flag, which, if specified as supported by a VFD, will + inform HDF5 that the VFD either uses special memory + management routines or wishes to perform memory management + in a specific way. Therefore, this flag instructs HDF5 to + ask the file driver to perform memory management for + certain operations. + + These changes also introduce a new "ctl" callback + operation identified by the H5FD_CTL__MEM_COPY op code. + This operation simply asks a VFD to perform a memory copy. + The arguments to this operation are passed to the "ctl" + callback's "input" parameter as a pointer to a struct + defined as: + + struct H5FD_ctl_memcpy_args_t { + void * dstbuf; /**< Destination buffer */ + hsize_t dst_off; /**< Offset within destination buffer */ + const void *srcbuf; /**< Source buffer */ + hsize_t src_off; /**< Offset within source buffer */ + size_t len; /**< Length of data to copy from source buffer */ + } H5FD_ctl_memcpy_args_t; + + Further, HDF5's compact dataset I/O routines were + identified as a problematic area that could cause a crash + for VFDs that make use of special memory management. Those + I/O routines were therefore updated to make use of this new + "ctl" callback operation in order to ask the underlying + file driver to correctly handle memory copies. + + (JTH - 2021/09/28) + + - Adds new "ctl" callback to VFD H5FD_class_t structure + with the following prototype: + + herr_t (*ctl)(H5FD_t *file, uint64_t op_code, + uint64_t flags, const void *input, + void **output); + + This newly-added "ctl" callback allows Virtual File + Drivers to intercept and handle arbitrary operations + identified by an operation code. Its parameters are + as follows: + + `file` [in] - A pointer to the file to be operated on + `op_code` [in] - The operation code identifying the + operation to be performed + `flags` [in] - Flags governing the behavior of the + operation performed (see H5FDpublic.h + for a list of valid flags) + `input` [in] - A pointer to arguments passed to the + VFD performing the operation + `output` [out] - A pointer for the receiving VFD to + use for output from the operation + + (JRM - 2021/08/16) + + - Change how the release part of version, in major.minor.release is checked + for compatibility + + The HDF5 library uses a function, H5check_version, to check that + the version defined in the header files, which is used to compile an + application is compatible with the version codified in the library, which + the application loads at runtime. This previously required an exact match + or the library would print a warning, dump the build settings and then + abort or continue. An environment variable controlled the logic. + + Now the function first checks that the library release version, in + major.minor.release, is not older than the version in the headers. + Secondly, if the release version is different, it checks if either + the library version or the header version is in the exception list, in + which case the release part of version, in major.minor.release, must + be exact. An environment variable still controls the logic. + + (ADB - 2021/07/27) + + - gcc warning suppression macros were moved out of H5public.h + + The HDF5 library uses a set of macros to suppress warnings on gcc. + These warnings were originally located in H5public.h so that the + multi VFD (which only uses public headers) could also make use of them + but internal macros should not be publicly exposed like this. + + These macros have now been moved to H5private.h. Pending future multi + VFD refactoring, the macros have been duplicated in H5FDmulti.c to + suppress the format string warnings there. + + (DER - 2021/06/03) + + - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX + + The size_hint value is ultimately stored in a uint32_t struct field, + so specifying a value larger than this on a 64-bit machine can cause + undefined behavior including crashing the system. + + The documentation for this API call was also incorrect, stating that + passing a negative value would cause the library to use a default + value. Instead, passing a "negative" value actually passes a very large + value, which is probably not what the user intends and can cause + crashes on 64-bit systems. + + The Doxygen documentation has been updated and passing values larger + than UINT32_MAX for size_hint will now produce a normal HDF5 error. + + (DER - 2021/04/29, HDFFV-11241) + + + - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID + + When passed an invalid fapl ID, H5Pset_fapl_log() would usually + segfault when attempting to free an uninitialized pointer in the error + handling code. This behavior is more common in release builds or + when the memory sanitization checks were not selected as a build + option. + + The pointer is now correctly initialized and the API call now + produces a normal HDF5 error when fed an invalid fapl ID. + + (DER - 2021/04/28, HDFFV-11240) + + - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times + + The call incorrectly attempts to free an internal copy of the previous + log location string, which causes a segfault. This only happens + when the call is invoked multiple times on the same property list. + On the first call to a given fapl, the log location is set to NULL so + the segfault does not occur. + + The string is now handled properly and the segfault no longer occurs. + + (DER - 2021/04/27, HDFFV-11239) + + - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows + + HSYS_GOTO_ERROR is an internal macro that is used to produce error + messages when system calls fail. These strings include errno and the + the associated strerror() value, which are not particularly useful + when a Win32 API call fails. + + On Windows, this macro has been updated to include the result of + GetLastError(). When a system call fails on Windows, usually only + one of errno and GetLastError() will be useful, however we emit both + for the user to parse. The Windows error message is not emitted as + it would be awkward to free the FormatMessage() buffer given the + existing HDF5 error framework. Users will have to look up the error + codes in MSDN. + + The format string on Windows has been changed from: + + "%s, errno = %d, error message = '%s'" + + to: + + "%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32"" + + for those inclined to parse it for error values. + + (DER - 2021/03/21) + + - File locking now works on Windows + + Since version 1.10.0, the HDF5 library has used a file locking scheme + to help enforce one reader at a time accessing an HDF5 file, which can + be helpful when setting up readers and writers to use the single- + writer/multiple-readers (SWMR) access pattern. + + In the past, this was only functional on POSIX systems where flock() or + fcntl() were present. Windows used a no-op stub that always succeeded. + + HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the + same scheme as POSIX systems. We lock the entire file when we set up the + locks (by passing DWORDMAX as both size parameters to LockFileEx()). + + (DER - 2021/03/19, HDFFV-10191) + + - H5Epush_ret() now requires a trailing semicolon + + H5Epush_ret() is a function-like macro that has been changed to + contain a `do {} while(0)` loop. Consequently, a trailing semicolon + is now required to end the `while` statement. Previously, a trailing + semi would work, but was not mandatory. This change was made to allow + clang-format to correctly format the source code. + + (SAM - 2021/03/03) + + - Improved performance of H5Sget_select_elem_pointlist + + Modified library to cache the point after the last block of points + retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the + same function to retrieve the next block of points from the list can + proceed immediately without needing to iterate over the point list. + + (NAF - 2021/01/19) + + - Replaced H5E_ATOM with H5E_ID in H5Epubgen.h + + The term "atom" is archaic and not in line with current HDF5 library + terminology, which uses "ID" instead. "Atom" has mostly been purged + from the library internals and this change removes H5E_ATOM from + the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with + H5E_ID. + + (DER - 2020/11/24, HDFFV-11190) + + - Add a new public function H5Ssel_iter_reset + + This function resets a dataspace selection iterator back to an + initial state so that it may be used for iteration once more. + This can be useful when needing to iterate over a selection + multiple times without having to repeatedly create/destroy + a selection iterator for that dataspace selection. + + (JTH - 2020/09/18) + + - Remove HDFS VFD stubs + + The original implementation of the HDFS VFD included non-functional + versions of the following public API calls when the HDFS VFD is + not built as a part of the HDF5 library: + + * H5FD_hdfs_init() + * H5Pget_fapl_hdfs() + * H5Pset_fapl_hdfs() + + They will remain present in HDF5 1.10 and HDF5 1.12 releases + for binary compatibility purposes but have been removed as of 1.14.0. + + Note that this has nothing to do with the real HDFS VFD API calls + that are fully functional when the HDFS VFD is configured and built. + + We simply changed: + + #ifdef LIBHDFS + <real API call> + #else + <useless stub> + #endif + + to: + + #ifdef LIBHDFS + <real API call> + #endif + + Which is how the other optional VFDs are handled. + + (DER - 2020/08/27) + + - Add Mirror VFD + + Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote + machine. Must be used in conjunction with the Splitter VFD. + + (JOS - 2020/03/13, TBD) + + - Add Splitter VFD + + Maintain separate R/W and W/O channels for "concurrent" file writes + to two files using a single HDF5 file handle. + + (JOS - 2020/03/13, TBD) + + - Refactored public exposure of haddr_t type in favor of "object tokens" + + To better accommodate HDF5 VOL connectors where "object addresses in a file" + may not make much sense, the following changes were made to the library: + + * Introduced new H5O_token_t "object token" type, which represents a + unique and permanent identifier for referencing an HDF5 object within + a container; these "object tokens" are meant to replace object addresses. + Along with the new type, a new H5Oopen_by_token API call was introduced + to open an object by a token, similar to how object addresses were + previously used with H5Oopen_by_addr. + + * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, + H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t + struct and H5L_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The original functions have been + renamed to version 1 functions and are deprecated in favor of the new version 2 + functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 + types and are now deprecated in favor of their version 2 counterparts. For each of + the functions and types, compatibility macros take place of the original symbols. + + * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, + H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t + struct and H5O_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The version 2 functions are now + deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t + types have been renamed to version 1 types and are now deprecated in favor of their + version 2 counterparts. For each, compatibility macros take place of the original + symbols. + + * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and + H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t + struct, which are used to retrieve the native HDF5 file format-specific information + about an object. This information (such as object header info and B-tree/heap info) + has been removed from the new H5O_info2_t struct so that the more generic + H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native + VOL connectors. + + * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare + two object tokens, convert an object token into a nicely-readable string format and + to convert an object token string back into a real object token, respectively. + + (DER, QAK, JTH - 2020/01/16) + + - Add new public function H5Sselect_adjust. + + This function shifts a dataspace selection by a specified logical offset + within the dataspace extent. This can be useful for VOL developers to + implement chunked datasets. + + (NAF - 2019/11/18) + + - Add new public function H5Sselect_project_intersection. + + This function computes the intersection between two dataspace selections + and projects that intersection into a third selection. This can be useful + for VOL developers to implement chunked or virtual datasets. + + (NAF - 2019/11/13, ID-148) + + - Add new public function H5VLget_file_type. + + This function returns a datatype equivalent to the supplied datatype but + with the location set to be in the file. This datatype can then be used + with H5Tconvert to convert data between file and in-memory representation. + This function is intended for use only by VOL connector developers. + + (NAF - 2019/11/08, ID-127) + + + Parallel Library: + ----------------- + - + + + Fortran Library: + ---------------- + - H5Fget_name_f fixed to handle correctly trailing whitespaces and + newly allocated buffers. + + (MSB - 2021/08/30, github-826,972) + + - Add wrappers for H5Pset/get_file_locking() API calls + + h5pget_file_locking_f() + h5pset_file_locking_f() + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + C++ Library: + ------------ + - Add wrappers for H5Pset/get_file_locking() API calls + + FileAccPropList::setFileLocking() + FileAccPropList::getFileLocking() + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + + Java Library: + ------------- + - Replaced HDF5AtomException with HDF5IdException + + Since H5E_ATOM changed to H5E_ID in the C library, the Java exception + that wraps the error category was also renamed. Its functionality + remains unchanged aside from the name. + + (See also the HDFFV-11190 note in the C library section) + + (DER - 2020/11/24, HDFFV-11190) + + - Added new H5S functions. + + H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, + H5Sselect_intersect_block, H5Sselect_project_intersection, + H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select + wrapper functions added. + + (ADB - 2020/10/27, HDFFV-10868) + + - Add wrappers for H5Pset/get_file_locking() API calls + + H5Pset_file_locking() + H5Pget_use_file_locking() + H5Pget_ignore_disabled_file_locking() + + Unlike the C++ and Fortran wrappers, there are separate getters for the + two file locking settings, each of which returns a boolean value. + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + - Added ability to test java library with VOLs. + + Created a new CMake script that combines the java and vol test scripts. + + (ADB - 2020/02/03, HDFFV-10996) + + - Tests fail for non-English locales. + + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. + + (ADB - 2020/01/09, HDFFV-10995) + + + Tools: + ------ + - h5repack added an optional verbose value for reporting R/W timing. + + In addition to adding timing capture around the read/write calls in + h5repack, added help text to indicate how to show timing for read/write; + -v N, --verbose=N Verbose mode, print object information. + N - is an integer greater than 1, 2 displays read/write timing + (ADB - 2021/11/08) + + - Added a new (unix ONLY) parallel meta tool 'h5dwalk', which utilizes the + mpifileutils (https://hpc.github.io/mpifileutils) open source utility + library to enable parallel execution of other HDF5 tools. + This approach can greatly enhance the serial hdf5 tool performance over large + collections of files by utilizing MPI parallelism to distribute an application + load over many independent MPI ranks and files. + + An introduction to the mpifileutils library and initial 'User Guide' for + the new 'h5dwalk" tool can be found at: + https://github.com/HDFGroup/hdf5doc/tree/master/RFCs/HDF5/tools/parallel_tools + + (RAW - 2021/10/25) + + - Refactored the perform tools and removed depends on test library. + + Moved the perf and h5perf tools from tools/test/perform to + tools/src/h5perf so that they can be installed. This required + that the test library dependency be removed by copying the + needed functions from h5test.c. + The standalone scripts and other perform tools remain in the + tools/test/perform folder. + + (ADB - 2021/08/10) + + - Removed partial long exceptions + + Some of the tools accepted shortened versions of the long options + (ex: --datas instead of --dataset). These were implemented inconsistently, + are difficult to maintian, and occasionally block useful long option + names. These partial long options have been removed from all the tools. + + (DER - 2021/08/03) + + - h5repack added help text for user-defined filters. + + Added help text line that states the valid values of the filter flag + for user-defined filters; + filter_flag: 1 is OPTIONAL or 0 is MANDATORY + + (ADB - 2021/01/14, HDFFV-11099) + + - Added h5delete tool + + Deleting HDF5 storage when using the VOL can be tricky when the VOL + does not create files. The h5delete tool is a simple wrapper around + the H5Fdelete() API call that uses the VOL specified in the + HDF5_VOL_CONNECTOR environment variable to delete a "file". If + the call to H5Fdelete() fails, the tool will attempt to use + the POSIX remove(3) call to remove the file. + + Note that the HDF5 library does currently have support for + H5Fdelete() in the native VOL connector. + + (DER - 2020/12/16) + + - h5repack added options to control how external links are handled. + + Currently h5repack preserves external links and cannot copy and merge + data from the external files. Two options, merge and prune, were added to + control how to merge data from an external link into the resulting file. + --merge Follow external soft link recursively and merge data. + --prune Do not follow external soft links and remove link. + --merge --prune Follow external link, merge data and remove dangling link. + + (ADB - 2020/08/05, HDFFV-9984) + + - h5repack was fixed to repack the reference attributes properly. + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/07, HDFFV-11014) + + - h5diff was updated to use the new reference APIs. + + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. + + (ADB - 2019/12/19, HDFFV-10980) + + - h5dump and h5ls were updated to use the new reference APIs. + + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. + + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + + + High-Level APIs: + ---------------- + - added set/get for unsigned long long attributes + + The attribute writing high-level API has been expanded to include + public set/get functions for ULL attributes, analogously to the + existing set/get for other types. + + (AF - 2021/09/08) + + C Packet Table API: + ------------------- + - + + Internal header file: + --------------------- + - + + Documentation: + -------------- + - + + +New platforms, languages and compilers tested +============================================= + - Linux 5.13.14-200.fc34 #1 SMP x86_64 GNU/Linux Fedora34 + - Linux 5.11.0-34-generic #36-Ubuntu SMP x86_64 GNU/Linux Ubuntu 20.04 + - Linux 5.3.18-22-default #1 SMP x86_64 GNU/Linux SUSE15sp2 + - Linux-4.14.0-115.21.2 #1 SMP ppc64le GNU/Linux + - Linux-4.12.14-150.75-default #1 SMP x86_64 GNU/Linux + - macOS Apple M1 11.6 Darwin 20.6.0 arm64 + - macOS Big Sur 11.3.1 Darwin 20.4.0 x86_64 + - clang versions 11.0.1, 12.0.5 + - Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line + + +Bug Fixes since HDF5-1.12.0 release +=================================== + Library + ------- + - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs + + Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which + could trip as assert in debug versions of the library. The library now + returns a normal HDF5 error when the filter ID is out of range. + + (DER - 2021/11/23, HDFFV-11286) + + - Fixed an issue with collective metadata reads being permanently disabled + after a dataset chunk lookup operation. This would usually cause a + mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for + simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate(). + + (JTH - 2021/11/08, HDFFV-11090) + + - Fixed cross platform incompatibility of references within variable length + types + + Reference types within variable length types previously could not be + read on a platform with different endianness from where they were + written. Fixed so cross platform portability is restored. + + (NAF - 2021/09/30) + + - Detection of simple data transform function "x" + + In the case of the simple data transform function "x" the (parallel) + library recognizes this is the same as not applying this data transform + function. This improves the I/O performance. In the case of the parallel + library, it also avoids breaking to independent I/O, which makes it + possible to apply a filter when writing or reading data to or from + the HDF5 file. + + (JWSB - 2021/09/13) + + - Fixed an invalid read and memory leak when parsing corrupt file space + info messages + + When the corrupt file from CVE-2020-10810 was parsed by the library, + the code that imports the version 0 file space info object header + message to the version 1 struct could read past the buffer read from + the disk, causing an invalid memory read. Not catching this error would + cause downstream errors that eventually resulted in a previously + allocated buffer to be unfreed when the library shut down. In builds + where the free lists are in use, this could result in an infinite loop + and SIGABRT when the library shuts down. + + We now track the buffer size and raise an error on attempts to read + past the end of it. + + (DER - 2021/08/12, HDFFV-11053) + + + - Fixed CVE-2018-14460 + + The tool h5repack produced a segfault when the rank in dataspace + message was corrupted, causing invalid read while decoding the + dimension sizes. + + The problem was fixed by ensuring that decoding the dimension sizes + and max values will not go beyond the end of the buffer. + + (BMR - 2021/05/12, HDFFV-11223) + + - Fixed CVE-2018-11206 + + The tool h5dump produced a segfault when the size of a fill value + message was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the fill value's size + against the buffer size before attempting to access the buffer. + + (BMR - 2021/03/15, HDFFV-10480) + + - Fixed CVE-2018-14033 (same issue as CVE-2020-10811) + + The tool h5dump produced a segfault when the storage size message + was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the storage size against the + buffer size before attempting to access the buffer. + + (BMR - 2021/03/15, HDFFV-11159/HDFFV-11049) + + - Remove underscores on header file guards + + Header file guards used a variety of underscores at the beginning of the define. + + Removed all leading (some trailing) underscores from header file guards. + + (ADB - 2021/03/03, #361) + + - Fixed a segmentation fault + + A segmentation fault occurred with a Mathworks corrupted file. + + A detection of accessing a null pointer was added to prevent the problem. + + (BMR - 2021/02/19, HDFFV-11150) + + - Fixed issue with MPI communicator and info object not being + copied into new FAPL retrieved from H5F_get_access_plist + + Added logic to copy the MPI communicator and info object into + the output FAPL. MPI communicator is retrieved from the VFD, while + the MPI info object is retrieved from the file's original FAPL. + + (JTH - 2021/02/15, HDFFV-11109) + + - Fixed problems with vlens and refs inside compound using + H5VLget_file_type() + + Modified library to properly ref count H5VL_object_t structs and only + consider file vlen and reference types to be equal if their files are + the same. + + (NAF - 2021/01/22) + + - Fixed CVE-2018-17432 + + The tool h5repack produced a segfault on a corrupted file which had + invalid rank for scalar or NULL datatype. + + The problem was fixed by modifying the dataspace encode and decode + functions to detect and report invalid rank. h5repack now fails + with an error message for the corrupted file. + + (BMR - 2020/10/26, HDFFV-10590) + + - Creation of dataset with optional filter + + When the combination of type, space, etc doesn't work for filter + and the filter is optional, it was supposed to be skipped but it was + not skipped and the creation failed. + + Allowed the creation of the dataset in such a situation. + + (BMR - 2020/08/13, HDFFV-10933) + + - Explicitly declared dlopen to use RTLD_LOCAL + + dlopen documentation states that if neither RTLD_GLOBAL nor + RTLD_LOCAL are specified, then the default behavior is unspecified. + The default on linux is usually RTLD_LOCAL while macos will default + to RTLD_GLOBAL. + + (ADB - 2020/08/12, HDFFV-11127) + + - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which + causes asserts/errors when passed to other dataspace API calls. + + H5S_NO_CLASS is an internal class value that should not have been + exposed via a public API call. + + In debug builds of the library, this can cause assert() function to + trip. In non-debug builds, it will produce normal library errors. + + The new library behavior is for H5Sset_extent_none() to convert + the dataspace into one of type H5S_NULL, which is better handled + by the library and easier for developers to reason about. + + (DER - 2020/07/27, HDFFV-11027) + + - Fixed issues CVE-2018-13870 and CVE-2018-13869 + + When a buffer overflow occurred because a name length was corrupted + and became very large, h5dump crashed on memory access violation. + + A check for reading pass the end of the buffer was added to multiple + locations to prevent the crashes and h5dump now simply fails with an + error message when this error condition occurs. + + (BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121) + + - Fixed the segmentation fault when reading attributes with multiple threads + + It was reported that the reading of attributes with variable length string + datatype will crash with segmentation fault particularly when the number of + threads is high (>16 threads). The problem was due to the file pointer that + was set in the variable length string datatype for the attribute. That file + pointer was already closed when the attribute was accessed. + + The problem was fixed by setting the file pointer to the current opened file pointer + when the attribute was accessed. Similar patch up was done before when reading + dataset with variable length string datatype. + + (VC - 2020/07/13, HDFFV-11080) + + - Fixed CVE-2020-10810 + + The tool h5clear produced a segfault during an error recovery in + the superblock decoding. An internal pointer was reset to prevent + further accessing when it is not assigned with a value. + + (BMR - 2020/06/29, HDFFV-11053) + + - Fixed CVE-2018-17435 + + The tool h52gif produced a segfault when the size of an attribute + message was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the attribute message's size + against the buffer size before accessing the buffer. h52gif was + also fixed to display the failure instead of silently exiting + after the segfault was eliminated. + + (BMR - 2020/06/19, HDFFV-10591) + + + Java Library + ------------ + - JNI utility function does not handle new references. + + The JNI utility function for converting reference data to string did + not use the new APIs. In addition to fixing that function, added new + java tests for using the new APIs. + + (ADB - 2021/02/16, HDFFV-11212) + + - The H5FArray.java class, in which virtually the entire execution time + is spent using the HDFNativeData method that converts from an array + of bytes to an array of the destination Java type. + + 1. Convert the entire byte array into a 1-d array of the desired type, + rather than performing 1 conversion per row; + 2. Use the Java Arrays method copyOfRange to grab the section of the + array from (1) that is desired to be inserted into the destination array. + + (PGT,ADB - 2020/12/13, HDFFV-10865) + + - Added ability to test java library with VOLs. + + Created a new CMake script that combines the java and vol test scripts. + + (ADB - 2020/02/03, HDFFV-10996) + + - Tests fail for non-English locales. + + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. + + (ADB - 2020/01/09, HDFFV-10995) + + + Configuration + ------------- + - Corrected path searched by CMake find_package command + + The install path for cmake find_package files had been changed to use + "share/cmake" + for all platforms. However the trailing "hdf5" directory was not removed. + This "hdf5" additional directory has been removed. + + (ADB - 2021/09/27) + + - Corrected pkg-config compile script + + It was discovered that the position of the "$@" argument for the command + in the compile script may fail on some platforms and configurations. The + position of the "$@"command argument was moved before the pkg-config sub command. + + (ADB - 2021/08/30) + + - Fixed CMake C++ compiler flags + + A recent refactoring of the C++ configure files accidentally removed the + file that executed the enable_language command for C++ needed by the + HDFCXXCompilerFlags.cmake file. Also updated the intel warnings files, + including adding support for windows platforms. + + (ADB - 2021/08/10) + + - Better support for libaec (open-source Szip library) in CMake + + Implemented better support for libaec 1.0.5 (or later) library. This version + of libaec contains improvements for better integration with HDF5. Furthermore, + the variable USE_LIBAEC_STATIC has been introduced to allow to make use of + static version of libaec library. Use libaec_DIR or libaec_ROOT to set + the location in which libaec can be found. + + Be aware, the Szip library of libaec 1.0.4 depends on another library within + libaec library. This dependency is not specified in the current CMake + configuration which means that one can not use the static Szip library of + libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5. + + (JWSB - 2021/06/22) + + - Refactor CMake configure for Fortran + + The Fortran configure tests for KINDs reused a single output file that was + read to form the Integer and Real Kinds defines. However, if config was run + more then once, the CMake completed variable prevented the tests from executing + again and the last value saved in the file was used to create the define. + Creating separate files for each KIND solved the issue. + + In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in + defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION + correctly for a zero value. This was fixed by supplying the required defines. + In addition it was moved from the Fortran specific HDF5UseFortran.camke file + to the C centric ConfigureChecks.cmake file. + + (ADB - 2021/06/03) + + - Move emscripten flag to compile flags + + The emscripten flag, -O0, was removed from target_link_libraries command + to the correct target_compile_options command. + + (ADB - 2021/04/26 HDFFV-11083) + + - Remove arbitrary warning flag groups from CMake builds + + The arbitrary groups were created to reduce the quantity of warnings being + reported that overwhelmed testing report systems. Considerable work has + been accomplished to reduce the warning count and these arbitrary groups + are no longer needed. + Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON. + + Visual Studio warnings C4100, C4706, and C4127 have been moved to + developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds. + + (ADB - 2021/03/22, HDFFV-11228) + + - Reclassify CMake messages, to allow new modes and --log-level option + + CMake message commands have a mode argument. By default, STATUS mode + was chosen for any non-error message. CMake version 3.15 added additional + modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode + of STATUS were reviewed and most were reclassified as VERBOSE. The new + mode was protected by a check for a CMake version of at least 3.15. If CMake + version 3.17 or above is used, the user can use the command line option + of "--log-level" to further restrict which message commands are displayed. + + (ADB - 2021/01/11, HDFFV-11144) + + - Fixes Autotools determination of the stat struct having an st_blocks field + + A missing parenthesis in an autoconf macro prevented building the test + code used to determine if the stat struct contains the st_blocks field. + Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define + found in H5pubconf.h will be defined correctly on both the Autotools and + CMake. This #define is only used in the tests and does not affect the + HDF5 C library. + + (DER - 2021/01/07, HDFFV-11201) + + - Add missing ENV variable line to hdfoptions.cmake file + + Using the build options to use system SZIP/ZLIB libraries need to also + specify the library root directory. Setting the {library}_ROOT ENV + variable was added to the hdfoptions.cmake file. + + (ADB - 2020/10/19 HDFFV-11108) + + + Tools + ----- + - Changed how h5dump and h5ls identify long double. + + Long double support is not consistent across platforms. Tools will always + identify long double as 128-bit [little/big]-endian float nn-bit precision. + New test file created for datasets with attributes for float, double and + long double. In addition any unknown integer or float datatype will now + also show the number of bits for precision. + These files are also used in the java tests. + + (ADB - 2021/03/24, HDFFV-11229,HDFFV-11113) + + - Fixed tools argument parsing. + + Tools parsing used the length of the option from the long array to match + the option from the command line. This incorrectly matched a shorter long + name option that happened to be a subset of another long option. + Changed to match whole names. + + (ADB - 2021/01/19, HDFFV-11106) + + - The tools library was updated by standardizing the error stack process. + + General sequence is: + h5tools_setprogname(PROGRAMNAME); + h5tools_setstatus(EXIT_SUCCESS); + h5tools_init(); + ... process the command-line (check for error-stack enable) ... + h5tools_error_report(); + ... (do work) ... + h5diff_exit(ret); + + (ADB - 2020/07/20, HDFFV-11066) + + - h5diff fixed a command line parsing error. + + h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. + The macro H5_DBL_ABS_EQUAL was removed and a direct value comparison was used. + + (ADB - 2020/07/20, HDFFV-10897) + + - h5diff added a command line option to ignore attributes. + + h5diff would ignore all objects with a supplied path if the exclude-path argument is used. + Adding the exclude-attribute argument will only exclude attributes, with the supplied path, + from comparison. + + (ADB - 2020/07/20, HDFFV-5935) + + - h5diff added another level to the verbose argument to print filenames. + + Added verbose level 3 that is level 2 plus the filenames. The levels are: + 0 : Identical to '-v' or '--verbose' + 1 : All level 0 information plus one-line attribute status summary + 2 : All level 1 information plus extended attribute status report + 3 : All level 2 information plus file names + + (ADB - 2020/07/20, HDFFV-1005) + + - h5repack was fixed to repack the reference attributes properly. + + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/10, HDFFV-11014) + + - h5diff was updated to use the new reference APIs. + + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. + + (ADB - 2019/12/19, HDFFV-10980) + + - h5dump and h5ls were updated to use the new reference APIs. + + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. + + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + + + Performance + ------------- + - + + + Fortran API + ----------- + - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + + (MSB - 2020/02/18, HDFFV-11029) + + + High-Level Library + ------------------ + - Fixed HL_test_packet, test for packet table vlen of vlen. + + Incorrect length assignment. + + (ADB - 2021/10/14) + + + Fortran High-Level APIs + ----------------------- + - + + + Documentation + ------------- + - + + + F90 APIs + -------- + - + + + C++ APIs + -------- + - Added DataSet::operator= + + Some compilers complain if the copy constructor is given explicitly + but the assignment operator is implicitly set to default. + + (2021/05/19) + + + Testing + ------- + - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} + + Lib files needed are now copied to a subdirectory in the java/test + directory, and on Macs the loader path for libhdf5.xxxs.so is changed + in the temporary copy of libhdf5_java.dylib. + + (LRK, 2020/07/02, HDFFV-11063) + + +Platforms Tested +=================== + + Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 + #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 + Ubuntu20.10 Ubuntu clang version 11.0.0-2 + (cmake and autotools) + + Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 + #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 + SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) + (cmake and autotools) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 + (lassen) GCC 7.3.1 + XL 16.1.1.2 + (cmake) + + Linux-4.12.14-150.75-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 + (cori) Intel (R) Version 19.0.3.199 + (cmake) + + Linux-4.12.14-197.86-default cray-mpich/7.7.6 + # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 + (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 + (cmake) + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 16.0.4, 18.0.2, 19.0.4 + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + + +Known Problems +============== + Setting a variable-length dataset fill value will leak the memory allocated + for the p field of the hvl_t struct. A fix is in progress for this. + HDFFV-10840 + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and can be avoided by not building +the gif tool. Disable building the High-Level tools with these options: + autotools: --disable-hltools + cmake: HDF5_BUILD_HL_TOOLS=OFF + cmake: HDF5_BUILD_HL_TOOLS=OFF diff --git a/release_docs/HISTORY-1_8.txt b/release_docs/HISTORY-1_8.txt new file mode 100644 index 0000000..461e0be --- /dev/null +++ b/release_docs/HISTORY-1_8.txt @@ -0,0 +1,14439 @@ +HDF5 History +============ + +This file contains development history of HDF5 1.8 branch + +23. Release Information for hdf5-1.8.21 +22. Release Information for hdf5-1.8.20 +21. Release Information for hdf5-1.8.19 +20. Release Information for hdf5-1.8.18 +19. Release Information for hdf5-1.8.17 +18. Release Information for hdf5-1.8.16 +17. Release Information for hdf5-1.8.15 +16. Release Information for hdf5-1.8.14 +15. Release Information for hdf5-1.8.13 +14. Release Information for hdf5-1.8.12 +13. Release Information for hdf5-1.8.11 +12. Release Information for hdf5-1.8.10-patch1 +11. Release Information for hdf5-1.8.10 +10. Release Information for hdf5-1.8.9 +09. Release Information for hdf5-1.8.8 +08. Release Information for hdf5-1.8.7 +07. Release Information for hdf5-1.8.6 +06. Release Information for hdf5-1.8.5 +05. Release Information for hdf5-1.8.4 +04. Release Information for hdf5-1.8.3 +03. Release Information for hdf5-1.8.2 +02. Release Information for hdf5-1.8.1 +01. Release Information for hdf5-1.8.0 + +[Search on the string '%%%%' for section breaks of each release.] + +%%%%1.8.21%%%% + + +HDF5 version 1.8.21 released on 2018-06-04 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.20 and +HDF5-1.8.21, and contains information on the platforms tested and +known problems in HDF5-1.8.21. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.21 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + https://support.hdfgroup.org/HDF5/ + +The HDF5 1.8.21 release can be obtained from: + + https://support.hdfgroup.org/HDF5/release/obtain518.html + +User documentation for 1.8.21 can be accessed directly at this location: + + https://support.hdfgroup.org/HDF5/doc1.8/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.21 (current +release) versus Release 1.8.20 + + https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.20 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - CMake + + Change minimum version to 3.10. + + This change removes the need to support a copy of the FindMPI.cmake module, + which has been removed, along with its subfolder in the config/cmake_ext_mod + location. + + (ADB - 2018/03/09) + + - CMake + + Add pkg-config file generation + + Added pkg-config file generation for the C, C++, HL, and HL C++ libraries. + In addition, builds on linux will create h5cXXX scripts that use the pkg-config + files. This is a limited implementation of a script like autotools h5cc. + + (ADB - 2018/03/08, HDFFV-4359) + + - CMake + + Refactor use of CMAKE_BUILD_TYPE for new variable, which understands + the type of generator in use. + + Added new configuration macros to use new HDF_BUILD_TYPE variable. This + variable is set correctly for the type of generator being used for the build. + + (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296) + + C++ API + ------- + - The following C++ API wrappers have been added to class H5Location + + H5Lcreate_soft: + // Creates a soft link from link_name to target_name. + void link(const char *target_name, const char *link_name,...) + void link(const H5std_string& target_name,...) + + + H5Lcreate_hard: + // Creates a hard link from new_name to curr_name. + void link(const char *curr_name, const Group& new_loc,...) + void link(const H5std_string& curr_name, const Group& new_loc,...) + + // Creates a hard link from new_name to curr_name in the same location. + void link(const char *curr_name, const hid_t same_loc,...) + void link(const H5std_string& curr_name, const hid_t same_loc,...) + + Note: previous version CommonFG::link will be deprecated. + + + H5Lcopy: + // Copy an object from a group of file to another. + void copyLink(const char *src_name, const Group& dst,...) + void copyLink(const H5std_string& src_name, const Group& dst,...) + + // Copy an object from a group of file to the same location. + void copyLink(const char *src_name, const char *dst_name,...) + void copyLink(const H5std_string& src_name,...) + + + H5Lmove: + // Rename an object in a group or file to a new location. + void moveLink(const char* src_name, const Group& dst,...) + void moveLink(const H5std_string& src_name, const Group& dst,...) + + // Rename an object in a group or file to the same location. + void moveLink(const char* src_name, const char* dst_name,...) + void moveLink(const H5std_string& src_name,...) + + Note: previous version CommonFG::move will be deprecated. + + + H5Ldelete: + // Removes the specified link from this location. + void unlink(const char *link_name, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) + void unlink(const H5std_string& link_name, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) + + Note: An additional parameter is added to CommonFG::unlink and it + is moved to H5Location. + + (BMR - 2018/05/11 - HDFFV-10445) + + - New property list subclasses + + Property list subclasses StrCreatPropList, LinkCreatPropList, and + AttrCreatPropList are added for the C property list classes + H5P_STRING_CREATE, H5P_LINK_CREATE, and H5P_ATTRIBUTE_CREATE. + + (BMR - 2018/05/11 - HDFFV-10445) + + - Another argument, LinkCreatPropList& lcpl, is added to the following + functions for the use of link creation property list. + Group createGroup(const char* name, size_t size_hint = 0, + const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT) + Group createGroup(const H5std_string& name, size_t size_hint = 0, + const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT) + + (BMR - 2018/05/11 - HDFFV-10445) + + + +Support for New Platforms, Languages, and Compilers +=================================================== + + - Added support for Visual Studio 2017 w/ Intel Fortran 18 on Windows 10 x64. + + +Bug Fixes since HDF5-1.8.20 +=========================== + + - If an HDF5 file contains a filter pipeline message with a 'number of + filters' field that exceeds the maximum number of allowed filters, + the error handling code will attempt to dereference a NULL pointer. + + This issue was reported to The HDF Group as issue #CVE-2017-17505. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + This problem arose because the error handling code assumed that + the 'number of filters' field implied that a dynamic array of that + size had already been created and that the cleanup code should + iterate over that array and clean up each element's resources. If + an error occurred before the array has been allocated, this will + not be true. + + This has been changed so that the number of filters is set to + zero on errors. Additionally, the filter array traversal in the + error handling code now requires that the filter array not be NULL. + + (DER - 2018/02/06, HDFFV-10354) + + - If an HDF5 file contains a filter pipeline message which contains + a 'number of filters' field that exceeds the actual number of + filters in the message, the HDF5 C library will read off the end of + the read buffer. + + This issue was reported to The HDF Group as issue #CVE-2017-17506. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + The problem was fixed by passing the buffer size with the buffer + and ensuring that the pointer cannot be incremented off the end + of the buffer. A mismatch between the number of filters declared + and the actual number of filters will now invoke normal HDF5 + error handling. + + (DER - 2018/02/26, HDFFV-10355) + + - If an HDF5 file contains a malformed compound datatype with a + suitably large offset, the type conversion code can run off + the end of the type conversion buffer, causing a segmentation + fault. + + This issue was reported to The HDF Group as issue #CVE-2017-17507. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME + + Fixing this problem would involve updating the publicly visible + H5T_conv_t function pointer typedef and versioning the API calls + which use it. We normally only modify the public API during + major releases, so this bug will not be fixed at this time. + + (DER - 2018/02/26, HDFFV-10356) + + - If an HDF5 file contains a malformed compound type which contains + a member of size zero, a division by zero error will occur while + processing the type. + + This issue was reported to The HDF Group as issue #CVE-2017-17508. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + Checking for zero before dividing fixes the problem. Instead of the + division by zero, the normal HDF5 error handling is invoked. + + (DER - 2018/02/26, HDFFV-10357) + + - If an HDF5 file contains a malformed symbol table node that declares + it contains more symbols than it actually contains, the library + can run off the end of the metadata cache buffer while processing + the symbol table node. + + This issue was reported to The HDF Group as issue #CVE-2017-17509. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + Performing bounds checks on the buffer while processing fixes the + problem. Instead of the segmentation fault, the normal HDF5 error + handling is invoked. + + (DER - 2018/03/12, HDFFV-10358) + + + Configuration + ------------- + - Library + + Moved the location of gcc attribute. + + The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, + was located after the function name. Builds with GCC 7 did not + indicate any problem, but GCC 8 issued errors. Moved the + attribute before the function name, as required. + + (ADB 2018/05/22, HDFFV-10473) + + - CMake + + Update CMake commands configuration. + + A number of improvements were made to the CMake commands. Most + changes simplify usage or eliminate unused constructs. Also, + some changes support better cross-platform support. + + (ADB - 2018/02/01, HDFFV-10398) + + - CMake + + Correct usage of CMAKE_BUILD_TYPE variable. + + The use of the CMAKE_BUILD_TYPE is incorrect for multi-config + generators (Visual Studio and XCode) and is optional for single + config generators. Created a new macro to check + GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG + Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE. + Defaults for these variables is "Release". + + (ADB - 2018/01/10, HDFFV-10385) + + - CMake + + Add replacement of fortran flags if using static CRT. + + Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in + config/cmake_ext_mod folder. + + (ADB - 2018/01/08, HDFFV-10334) + + + Library + ------- + - Utility function can not handle lowercase Windows drive letters + + Added call to toupper function for drive letter. + + (ADB - 2017/12/18, HDFFV-10307) + + + Tools + ----- + - h5repack + + h5repack changes the chunk parameters when a change of layout is not + specified and a filter is applied. + + HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code + in the tools library. The check for an existing layout was incorrectly + placed into an if block and not executed. The check was moved into + the normal path of the function. + + (ADB - 2018/02/21, HDFFV-10412) + + - h5dump + + the tools library will hide the error stack during file open. + + While this is preferable almost always, there are reasons to enable + display of the error stack when a tool will not open a file. Adding an + optional argument to the --enable-error-stack will provide this use case. + As an optional argument it will not affect the operation of the + --enable-error-stack. h5dump is the only tool to implement this change. + + (ADB - 2018/02/15, HDFFV-10384) + + - h5dump + + h5dump would output an indented blank line in the filters section. + + h5dump overused the h5tools_simple_prefix function, which is a + function intended to account for the data index (x,y,z) option. + Removed the function call for header information. + + (ADB - 2018/01/25, HDFFV-10396) + + - h5repack + + h5repack incorrectly searched internal object table for name. + + h5repack would search the table of objects for a name, if the + name did not match it tried to determine if the name without a + leading slash would match. The logic was flawed! The table + stored names(paths) without a leading slash and did a strstr + of the table path to the name. + The assumption was that if there was a difference of one then + it was a match, however "pressure" would match "/pressure" as + well as "/pressure1", "/pressure2", etc. Changed logic to remove + any leading slash and then do a full compare of the name. + + (ADB - 2018/01/18, HDFFV-10393) + + - h5repack + + h5repack failed to handle command line parameters for customer filters. + + User defined filter parameter conversions would fail when integers + were represented on the command line with character strings + larger than 9 characters. Increased local variable array for storing + the current command line parameter to prevent buffer overflows. + + (ADB - 2018/01/17, HDFFV-10392) + + - h5diff + + h5diff seg faulted if comparing VL strings against fixed strings. + + Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check + for string objects of same type in the diff_can_type function by + adding an if(tclass1 == H5T_STRING) block. This "if block" moves the + same check that was added for attributes to this function, which is + used by all object types. This function handles complex type structures. + Also added a new test file in h5diffgentest for testing this issue + and removed the temporary files used in the test scripts. + + (ADB - 2018/01/04, HDFFV-8745) + + + C++ API + ------- + - Removal of memory leaks + + A private function was inadvertently called, causing memory leaks. This + is now fixed. + + (BMR - 2018/04/12 - User reported in email) + + - Changes in exception classes + + Some exception classes are reorganized to reflect the HDF5 object + hierarchy and allow customization. + DataSetIException -> LocationException -> Exception + DataTypeIException -> LocationException -> Exception + GroupIException -> LocationException -> Exception + AttributeIException -> LocationException -> Exception + FileIException -> GroupIException -> LocationException -> Exception + Member functions in H5Location and H5Object now throw specific exceptions + associated with the invoking objects. + + (BMR - 2018/05/11) + + - H5Location::closeObjId is made static + (BMR - 2018/05/11) + + - H5A wrappers in H5Location are removed as they have been in H5Object. + (BMR - 2018/05/11) + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus/mayll) Version 4.4.7 20120313 + Versions 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + OpenMPI 2.0.1 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Versions 4.9.3, 5.3.0, 6.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + NAG Fortran Compiler Release 6.1(Tozai) Build 6116 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +Mac OS Sierra 10.12.6 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +Mac OS Sierra 10.12.6 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-573.18.1.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (mayll) + + Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + (cmake and autotools) + + CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + (cmake and autotools) + + Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + (cmake and autotools) + + +Known Problems +============== + + The dynamically loaded plugin test libraries require undefined references + to HDF5 functions to be resolved at runtime in order to function properly. + With autotools on CYGWIN this results in build errors, and we have not + found a solution that satisfies both. Therefore the dynamically loaded + plugin tests have been disabled on CYGWIN. + + Mac OS X 10.13 added additional subdirectory structure in .libs for shared + libraries. Consequently "make check" will fail testing java and dynamically + loaded plugin test libraries attempting to copy files from the previous + locations in .libs directories. This will be addressed in the next release + when support for the Mac OS X 10.13 platform is added. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +%%%%1.8.20%%%% + + +HDF5 version 1.8.20 released on 2017-11-28 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.19 and +HDF5-1.8.20, and contains information on the platforms tested and +known problems in HDF5-1.8.20. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.20 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + https://support.hdfgroup.org/HDF5/ + +The HDF5 1.8.20 release can be obtained from: + + https://support.hdfgroup.org/HDF5/release/obtain518.html + +User documentation for 1.8.20 can be accessed directly at this location: + + https://support.hdfgroup.org/HDF5/doc1.8/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.20 (current +release) versus Release 1.8.19 + + https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.20 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Tools + ----- + - h5diff + + h5diff has new option enable-error-stack. + + Updated h5diff with the --enable-error-stack argument, which + enables the display of the hdf5 error stack. This completes the + improvement to the main tools; h5copy, h5diff, h5dump, h5ls and + h5repack. + + (ADB - 2017/08/30, HDFFV-9774) + + + C++ API + ------- + - The following C++ API wrappers have been added to the C++ Library: + + // Creates a binary object description of this datatype. + void DataType::encode() - C API H5Tencode() + + // Returns the decoded type from the binary object description. + DataType::decode() - C API H5Tdecode() + ArrayType::decode() - C API H5Tdecode() + CompType::decode() - C API H5Tdecode() + DataType::decode() - C API H5Tdecode() + EnumType::decode() - C API H5Tdecode() + FloatType::decode() - C API H5Tdecode() + IntType::decode() - C API H5Tdecode() + StrType::decode() - C API H5Tdecode() + VarLenType::decode() - C API H5Tdecode() + + // Three overloaded functions to retrieve information about an object + H5Location::getObjectInfo() - H5Oget_info()/H5Oget_info_by_name() + + (BMR - 2017/10/17, HDFFV-10175) + + - New constructors to open existing datatypes added in ArrayType, + CompType, DataType, EnumType, FloatType, IntType, StrType, and + VarLenType. + + (BMR - 2017/10/17, HDFFV-10175) + + - A document is added to the HDF5 C++ API Reference Manual to show the + mapping from a C API to C++ wrappers. It can be found from the main + page of the C++ API Reference Manual. + + (BMR - 2017/10/17, HDFFV-10151) + + + High-Level APIs + --------------- + - H5DOread_chunk + + Users wanted to read compressed data directly from a file without any + processing by the HDF5 data transfer pipeline, just as they were able + to write it directly to a file with H5DOwrite_chunk. + + New API function, corresponding to existing function H5DOwrite_chunk. + H5DOread_chunk reads a raw data chunk directly from a chunked dataset + in the file into the application buffer, bypassing the library’s internal + data transfer pipeline, including filters. + + (VC - 2017/05/02, HDFFV-9934) + + +Support for New Platforms, Languages, and Compilers +=================================================== + + - Added NAG compiler + + +Bug Fixes since HDF5-1.8.19 +=========================== + + Configuration + ------------- + - cmake + + The hdf5 library used shared szip and zlib, which needlessly required + applications to link with the same szip and zlib libraries. + + Changed the target_link_libraries commands to use the static libs. + Removed improper link duplication of szip and zlib. + Adjusted the link dependencies and the link interface values of + the target_link_libraries commands. + + (ADB - 2017/11/14, HDFFV-10329) + + - cmake MPI + + CMake implementation for MPI was problematic and would create incorrect + MPI library references in the hdf5 libraries. + + Reworked the CMake MPI code to properly create CMake targets.Also merged + the latest CMake FindMPI.cmake changes to the local copy. This is necessary + until HDF changes the CMake minimum to 3.9 or greater. + + (ADB - 2017/11/02, HDFFV-10321) + + + - Fixed Fortran linker flags when using the NAG Fortran compiler (autotools). + + (HDFFV-10037, MSB, 2017/10/21) + + - cmake + + Too many commands for POST_BUILD step caused command line to be + too big on windows. + + Changed foreach of copy command to use a custom command with the + use of the HDFTEST_COPY_FILE macro. + + (ADB - 2017/07/12, HDFFV-10254) + + + Library + ------- + - filter plugin handling in H5PL.c and H5Z.c + + It was discovered that the dynamic loading process used by + filter plugins had issues with library dependencies. + + CMake build process changed to use LINK INTERFACE keywords, which + allowed HDF5 C library to make dependent libraries private. The + filter plugin libraries no longer require dependent libraries + (such as szip or zlib) to be available. + (ADB - 2017/11/16, HDFFV-10328) + + - Fix rare object header corruption bug + + In certain cases, such as when converting large attributes to dense + storage, an error could occur which would either fail an assertion or + cause file corruption. Fixed and added test. + + (NAF - 2017/11/14, HDFFV-10274) + + - H5Zfilter_avail in H5Z.c + + The public function checked for plugins, while the private + function did not. + + Modified H5Zfilter_avail and private function, H5Z_filter_avail. + Moved check for plugin from public to private function. Updated + H5P__set_filter due to change in H5Z_filter_avail. Updated tests. + + (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) + + - Fix H5Sencode bug when num points selected is >2^32 + + Modified to fail if the 32 bit limit is exceeded when encoding either + offsets or counts in the selection. + + (HDFFV-10323, VC, 2017/09/07) + + - Fix H5HL_offset_into() + + (1) Fix H5HL_offset_into() to return error when offset exceeds heap data + block size. + (2) Fix other places in the library that call this routine to detect + error routine. + + (HDFFV-10216, VC, 2017/09/05) + + + Tools + ----- + - h5repack + + h5repack failed to copy a dataset with existing filter. + + Reworked code for h5repack and h5diff code in tools library. Added + improved error handling, cleanup of resources and checks of calls. + Modified H5Zfilter_avail and private function, H5Z_filter_avail. + Moved check for plugin from public to private function. Updated + H5P__set_filter due to change in H5Z_filter_avail. Updated tests. + Note, h5repack output display has changed to clarify the individual + steps of the repack process. The output indicates if an operation + applies to all objects. Lines with notation and no information + have been removed. + + (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) + + - h5repack + + h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY. + + Added another parameter to the 'UD=' option to set the flag by default + to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL. + + (ADB - 2017/08/31, HDFFV-10269) + + - h5ls + + h5ls generated error on stack when it encountered a H5S_NULL + dataspace. + + Adding checks for H5S_NULL before calling H5Sis_simple (located + in the h5tools_dump_mem function) fixed the issue. + + (ADB - 2017/08/17, HDFFV-10188) + + - h5dump + + h5dump segfaulted on output of XML file. + + Function that escape'd strings used the full buffer length + instead of just the length of the replacement string in a + strncpy call. Using the correct length fixed the issue. + + (ADB - 2017/08/01, HDFFV-10256) + + - h5diff + + h5diff segfaulted on compare of a NULL variable length string. + + Improved h5diff compare of strings by adding a check for + NULL strings and setting the lengths to zero. + + (ADB - 2017/07/25, HDFFV-10246) + + - h5import + + h5import crashed trying to import data from a subset of a dataset. + + Improved h5import by adding the SUBSET keyword. h5import understands + to use the Count times the Block as the size of the dimensions. + Added INPUT_B_ORDER keyword to old-style configuration files. + The import from h5dump function expects the binary files to use native + types (FILE '-b' option) in the binary file. + + (ADB - 2017/06/15, HDFFV-10219) + + + C++ API + ------- + - Marked the following functions deprecated because they were moved to + class H5Object: + H5Location::createAttribute() + H5Location::openAttribute() + H5Location::attrExists() + H5Location::removeAttr() + H5Location::renameAttr() + H5Location::getNumAttrs() + + (BMR - 2017/10/17) + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus/mayll) Version 4.4.7 20120313 + Versions 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 16.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.196 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + OpenMPI 2.0.1 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Versions 4.9.3, 5.3.0, 6.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + NAG Fortran Compiler Release 6.1(Tozai) Build 6116 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +Mac OS Sierra 10.12.6 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +Mac OS Sierra 10.12.6 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (mayll) + + Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + (cmake and autotools) + + CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + (cmake and autotools) + + Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + (cmake and autotools) + + +Known Problems +============== + + The dynamically loaded plugin test libraries require undefined references + to HDF5 functions to be resolved at runtime in order to function properly. + With autotools on CYGWIN this results in build errors, and we have not + found a solution that satisfies both. Therefore the dynamically loaded + plugin tests have been disabled on CYGWIN. + + Mac OS X 10.13 added additional subdirectory structure in .libs for shared + libraries. Consequently "make check" will fail testing java and dynamically + loaded plugin test libraries attempting to copy files from the previous + locations in .libs directories. This will be addressed in the next release + when support for the Mac OS X 10.13 platform is added. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +%%%%1.8.19%%%% + + +HDF5 version 1.8.19 released on 2017-06-15 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.18 and +HDF5-1.8.19, and contains information on the platforms tested and +known problems in HDF5-1.8.19. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.19 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + https://support.hdfgroup.org/HDF5/ + +The HDF5 1.8.19 release can be obtained from: + + https://support.hdfgroup.org/HDF5/release/obtain518.html + +User documentation for 1.8.19 can be accessed directly at this location: + + https://support.hdfgroup.org/HDF5/doc1.8/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.19 (current +release) versus Release 1.8.18 + + https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.19 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + -------------- + - CMake in the Tools + + User-defined filters on Windows require that tools be built + with shared libraries. + + CMake command code added to build tools with + shared libraries as well as with static libraries. + + (ADB - 2017/02/07, HDFFV-10123) + + + Library + ------- + - H5PL package + + Users would like to be able to set the plugin path programmatically + instead of through the environment variable. + + H5PL package obtained new APIs for manipulating the entries of + the plugin path table. The new APIs are; + H5PLappend - Insert a plugin path at the end of the list. + H5PLprepend - Insert a plugin path at the beginning of the list. + H5PLreplace - Replace the path at the specified index. + H5PLinsert - Insert a plugin path at the specified index, moving + other paths after the index. + H5PLremove - Remove the plugin path at the specified index and + compacting the list. + H5PLget - Query the plugin path at the specified index. + H5PLsize - Query the size of the current list of plugin paths. + + (ADB - 2017/04/04, HDFFV-10143) + + - H5Dget_chunk_storage_size + + The storage size of a chunk in the file is needed to determine the size + of the buffer to be allocated for reading a chunk directly from a file. + + New API function gets the size in bytes currently allocated within a + file for a raw data chunk in a dataset. This function was added to get + the chunk size in support of the implementation of H5DOread_chunks, but + may also be useful for other purposes. + + (VC - 2017/05/02, HDFFV-9934) + + C++ API + ------- + - The following C++ API wrappers have been added to the C++ Library: + // Determines if a name exists. + H5Location::nameExists() - C API H5Lexists() + + // Checks if an ID is valid. + IdComponent::isValid() - C API H5Iis_valid() + + // Sets the number of soft or user-defined links that can be + // traversed before a failure occurs. + LinkAccPropList::setNumLinks() - C API H5Pset_nlinks() + + // Gets the number of soft or user-defined link traversals allowed + LinkAccPropList::getNumLinks() - C API H5Pget_nlinks() + + // Returns a copy of the creation property list of a datatype. + DataType::getCreatePlist() - C API H5Tget_create_plist() + + // Opens an object within a location, regardless its type. + H5Location::openObjId() - C API H5Oopen() + H5Location::openObjId() - C API H5Oopen() + + // Closes an object opened by openObjId(). + H5Location::closeObjId() - C API H5Oclose() + + // Gets general information about a file. + H5File::getFileInfo() - C API H5Fget_info() + + // Returns the header version of an HDF5 object. + H5Object::objVersion() - C API H5Oget_info() + + (BMR, 2017/05/13, HDFFV-10004, HDFFV-10156) + + - New class LinkAccPropList is added for link access property list + + (BMR, 2017/05/13, HDFFV-10156) + + High-Level APIs + --------------- + - H5DOread_chunk + + Users wanted to read compressed data directly from a file without any + processing by the HDF5 data transfer pipeline, just as they were able + to write it directly to a file with H5DOwrite_chunk. + + New API function, corresponding to existing function H5DOwrite_chunk. + H5DOread_chunk reads a raw data chunk directly from a chunked dataset + in the file into the application buffer, bypassing the library’s internal + data transfer pipeline, including filters. + + (VC - 2017/05/02, HDFFV-9934) + + +Support for New Platforms, Languages, and Compilers +=================================================== + + - Added OpenMPI 2.0.1 compiled with GCC 4.9.3 + + +Bug Fixes since HDF5-1.8.18 +=========================== + + Configuration + ------------- + - Support for Fortran shared libraries on OS X with autotools now + works. Cmake builds still disables Fortran shared libraries on OS X. + (MSB - 2017/04/30, HDFFV-2772) + + + Library + ------- + - bitfield datatypes + + bitfield datatypes did not fully support endianness of the data. + + Improved the endianness of bitfield datatypes by adding missing functional + code. This code used integer types as a template. + + (ADB - 2017/05/12, HDFFV-10186) + + - Newly created datasets with H5D_COMPACT layout failed to open after + several H5Dopen/H5Dclose cycles. + + The layout "dirty" flag for a compact dataset is now properly reset + before flushing the message. + + (VC - 2017/05/11, HDFFV-10051) + - Missing #ifdef __cplusplus macros were added to the generated H5Epubgen.h file. + + (DER - 2017/04/25, HDFFV-9638) + + + Tools + ----- + - h5repack + + h5repack did not maintain the creation order flag of the root + group. + + Improved h5repack by reading the creation order and applying the + flag to the new root group. Also added arguments to set the + order and index direction, which applies to the traversing of the + original file, on the command line. + + (ADB - 2017/05/26, HDFFV-8611) + + - h5diff + + h5diff failed to account for strpad type and null terminators + of char strings. Also, h5diff failed to account for string length + differences and would give a different result depending on file + order in the command line. + + Improved h5diff compare of strings and arrays by adding a check for + string lengths and if the strpad was null filled. + + (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) + + - h5diff + + h5diff help text about epsilon comparison was confusing. + + Changed h5diff help text to indicate that the 'a' refers to the + datapoint in file1 and 'b' refers to the datapoint value in file2. + + (ADB - 2017/05/16, HDFFV-9995) + + - h5diff + + h5diff did not report user-defined filter data differences correctly. + + Improved h5diff compare of user-defined filter data by reporting an + error if the user-defined filter plugin cannot be found. + + (ADB - 2017/01/18, HDFFV-9994) + C++ API + ------- + - The class hierarchy is revised to better reflect the HDF5 model. + Class H5File is now derived from class Group instead of H5Location. + Class Attribute is now derived from H5Location instead of IdComponent. + Wrappers of H5A APIs in H5Location are now duplicated in H5Object, + the original wrappers in H5Location will be deprecated in future + releases. + + (BMR - 2017/05/15, HDFFV-10156) + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus/mayll) Version 4.4.7 20120313 + Versions 4.9.3, 5.2.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 16.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + OpenMPI 2.0.1 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Versions 4.9.3, 5.3.0, 6.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (mayll) + + Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + (cmake and autotools) + + CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + (cmake and autotools) + + Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + (cmake and autotools) + + +Known Problems +============== + + The dynamically loaded plugin test libraries require undefined references + to HDF5 functions to be resolved at runtime in order to function properly. + With autotools on CYGWIN this results in build errors, and we have not + found a solution that satisfies both. Therefore the dynamically loaded + plugin tests have been disabled on CYGWIN. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +%%%%1.8.18%%%% + + +HDF5 version 1.8.18 released on 2016-11-14 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.17 and +HDF5-1.8.18, and contains information on the platforms tested and +known problems in HDF5-1.8.18. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.18 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + https://support.hdfgroup.org/HDF5/ + +The HDF5 1.8.18 release can be obtained from: + + https://support.hdfgroup.org/HDF5/release/obtain518.html + +User documentation for 1.8.18 can be accessed directly at this location: + + https://support.hdfgroup.org/HDF5/doc1.8/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.18 (current +release) versus Release 1.8.17 + + https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.17 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + + - CMake: Added NAMESPACE hdf5:: to package configuration files to allow + projects using installed HDF5 binaries built with CMake to link with + them without specifying the HDF5 library location via IMPORTED_LOCATION. + + (ADB, 2016/10/17, HDFFV-10003) + + + - CMake: Changed the CTEST_BUILD_CONFIGURATION option to + CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation. + + (ADB, 2016/10/17, HDFFV-9971) + + - CMake: Added support for GIT + + (ADB, 2016/07/12) + + + Library + ------- + - None + + + Parallel Library + ---------------- + - None + + + Tools + ----- + - None + + + High-Level APIs + --------------- + - None + + + Fortran API + ----------- + - None + + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + + + +Bug Fixes since HDF5-1.8.17 +=========================== + + Configuration + ------------- + + - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by + condensing cygwin configuration files into a single file and + removing outdated compiler settings. + + (ABD, 2016/07/12, HDFFV-9946) + + + - CMake: Fixed a command length overflow error by converting custom + commands inside CMakeTest.cmake files into regular dependencies and + targets. + + (ABD, 2016/07/12, HDFFV-9939) + + + - CMake: Fixed a timeout error that would occasionally occur when running + the virtual file driver tests simultaneously due to test directory and file + name collisions. + + (ABD, 2016/09/19, HDFFV-9431) + + + Library + ------- + + - Fixed a memory leak that would occur when the library allocated memory + for an external file prefix (H5Pset_efile_prefix) and failed to free it. + + (DER, 2016/04/29) + + + - Fixed an error that would occur when calling H5Adelete on an attribute + which is attached to an externally linked object in the target file and + whose datatype is a committed datatype in the main file. + + (VC, 2016-07-04, HDFFV-9940) + + + - Fixed a problem where a plugin compiled into a DLL in the default plugin + directory could not be found by the HDF5 library at runtime on Windows + when the HDF5_PLUGIN_PATH environment variable was not set. + + (ABD, 2016/08/01, HDFFV-9706) + + + - Fixed an issue where H5Pset_alignment could result in misaligned blocks + with some input combinations, causing an assertion failure in debug mode. + + (NAF, 2016/08/11, HDFFV-9948) + + + - A number of issues were fixed when reading/writing from/to corrupted + files to ensure that the library fails gracefully in these cases: + + * Writing to a corrupted file that has an object message which is + incorrectly marked as shareable on disk results in a buffer overflow / + invalid write instead of a clean error message. + + * Decoding data from a corrupted file with a dataset encoded with the + H5Z_NBIT decoding can result in a code execution vulnerability under + the context of the application using the HDF5 library. + + * When decoding an array datatype from a corrupted file, the HDF5 library + fails to return an error in production if the number of dimensions + decoded is greater than the maximum rank. + + * When decoding an "old style" array datatype from a corrupted file, the + HDF5 library fails to return an error in production if the number of + dimensions decoded is greater than the maximum rank. + + (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993) + + + - Fixed an error that would occur when copying an object with an attribute + which is a compound datatype consisting of a variable length string. + + (VC, 2016-10-17, HDFFV-7991) + + + Parallel Library + ---------------- + + - Fixed a bug that could occur when allocating a chunked dataset in parallel + with an alignment set and an alignment threshold greater than the chunk + size but less than or equal to the raw data aggregator size. + + (NAF, 2016/08/11, HDFFV-9969) + + + Performance + ------------- + - None + + + Tools + ----- + + - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.) + in which they would erroneously drop the file argument specified via + the -o flag when the -o flag was specified before the -c flag on the + command line, resulting in a failure to compile. + + (LRK, 2016/06/08, HDFFV-9938, HDFFV-9530) + + + - h5repack User Defined (UD) filter parameters were not parsed correctly. + + The UD filter parameters were not being parsed correctly. Reworked coding + section to parse the correct values and verify number of parameters. + + (ADB, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039) + + + Fortran API + ----------- + + - Fortran library fails to compile and fails tests with NAG compiler. + + * Removed the non-standard assumption that KIND=SIZEOF, in the HDF5 + configure programs. + * Removed Fortran 66 character/integer conversions from tests. + * Removed the use of C_SIZEOF in the test programs + * Changed to using STORAGE_SIZE in the test programs if available. Otherwise, + uses C_SIZEOF or SIZEOF. + + (MSB, 2016/9/22, HDFFV-9973) + + + - Fortran segfaults for F03 tests with NAG compiler + + * Removed INTENT(OUT) from 'fillvalue' in F2003 interface + for H5Pget_fill_value_f. + + (MSB, 2016/9/22, HDFFV-9980) + + + C++ API + ------- + + - The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library. + In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may + also be removed. + + (BMR, 2016/10/27, HDFFV-9532) + + + High-Level APIs: + --------------- + + - The high-level API Packet Table (PT) did not write data correctly when + the datatype is a compound type that has string type as one of the + members. This problem started in 1.8.15, after the fix of HDFFV-9042 + was applied, which caused the Packet Table to use native type to access + the data. It should be up to the application to specify whether the + buffer to be read into memory in the machine’s native architecture. + Thus, the PT is fixed to not use native type but to make a copy of the + user's provided datatype during creation or the packet table's datatype + during opening. If an application wishes to use native type to read the + data, then the application will request that. However, the Packet Table + doesn't provide a way to specify memory datatype in this release. This + feature will be available in future releases, HDFFV-10023. + + (BMR, 2016/10/27, HDFFV-9758) + + + Fortran High-Level APIs: + ------------------------ + - None + + + Testing + ------- + - None + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus/mayll) Version 4.4.7 20120313 + Versions 4.8.4, 4.9.3, 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Versions 4.9.3, 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 10 n y/y n y y y +Windows 10 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + (cmake and autotools) + + CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + (cmake and autotools) + + Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + (cmake and autotools) + + +Known Problems +============== +* On windows platforms in debug configurations, the VFD flush1 tests will fail + with the split and multi VFD drivers. These tests will display a modal debug + dialog which must be answered or wait for the test timeout to expire. + (ADB - 2014/06/23 - HDFFV-8851) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. the issue. HL and C++ shared libraries should now be + working as intended, however. + (MAM - 2011/04/20) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.17%%%% + + +HDF5 version 1.8.17 released on 2016-05-10 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.16 and +HDF5-1.8.17-*, and contains information on the platforms tested and +known problems in HDF5-1.8.17-*. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.17 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.17 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.17 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.17 (current +release) versus Release 1.8.16 + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.16 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + + +New Features +============ + + Configuration + ------------- + - Cmakehdf5: Added Ability to Run Multiple Make Commands + + Added option --njobs to specify up to how many jobs to launch during + build (cmake) and testing (ctest). + + (AKC - 2015/12/13, HDFFV-9612) + + - Cmakehdf5: Added Szip Support and Verbose Option + + Added --with-szlib to support the Szip library; and + --enable/disable-verbose to display all CMake process output. + + (AKC - 2015/11/16, HDFFV-8932 and DAILYTEST-195) + + - CMake minimum is now 3.1.0. (ADB - 2015/11/14) + + - Large File System (LFS) Support has Changed in the Autotools + + We assume that fseeko and ftello exist. + + The *64 I/O functions and types are no longer explicitly used. + We now rely on a mapping provided by _FILE_OFFSET_BITS (or its + equivalent). + + _LARGEFILE(64)_SOURCE is no longer exposed via AM_CPPFLAGS. + + (DER - 2016/03/29, HDFFV-9626 and HDFFV-9541) + + + + Library + ------- + - New API Calls for Searching for External Dataset Storage + + API calls that determine the search path for dataset external + storage were added. H5Pset/get_efile_prefix() API calls were added + to the library. These functions give control over the search path + for dataset external storage that has been configured with + H5Pset_external(). + + Additionally, the HDF5_EXTFILE_PREFIX environment variable can be + used to control the search path. + + (DER - 2016/04/20, HDFFV-8740) + + + + Parallel Library + ---------------- + - None + + + + Tools + ----- + - None + + + + High-Level APIs + --------------- + + C Packet Table API + ------------------ + - Replacement of a Public Function with H5PTcreate + + The existing function H5PTcreate_fl limits applications so they + can use the deflate compression only. The public function + H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate + takes a property list identifier to provide flexibility on + creation properties. This also removes the following warning: + "deprecated conversion from string constant to "char*" + [-Wwrite-strings]". + + (BMR - 2016/04/25, HDFFV-9708, HDFFV-8615) + + - New Public Functions: H5PTget_dataset and H5PTget_type + + Two accessor functions have been added. H5PTget_dataset returns + the identifier of the dataset associated with the packet table, + and H5PTget_type returns the identifier of the datatype used by + the packet table. + + (BMR - 2016/04/25, HDFFV-8623 patch 3) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table (PT) library source except for the following functions: + + H5PTis_varlen() has been made available again + + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() + + (BMR - 2016/04/25, HDFFV-442) + + C++ Packet Table API + -------------------- + - New Constructor in FL_PacketTable + + An overloaded constructor has been added to FL_PacketTable and + takes a property list identifier to provide flexibility on + creation properties such as compression. + + FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID, + hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT) + + (BMR - 2016/04/25, HDFFV-8623 patch 5) + + - New Member Functions in PacketTable + + Two accessor wrappers were added to class PacketTable. + + PacketTable::GetDataset() returns the identifier of the dataset + associated with the packet table, and PacketTable::GetDatatype() + returns the identifier of the datatype that the packet table uses. + + (BMR - 2016/04/25, HDFFV-8623 patch 4) + + - New Member Functions with "char*" as an Argument + + Overloaded functions were added to provide the "const char*" + argument; the existing version will be deprecated in future + releases. This also removes the following warning: + "deprecated conversion from string constant to "char*" + [-Wwrite-strings]". + + (BMR - 2016/04/25, HDFFV-8623 patch 1, HDFFV-8615) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table library source code except for the following functions: + + VL_PacketTable::IsVariableLength() was moved to PacketTable + + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() + + (BMR - 2016/04/25, HDFFV-442) + + + + Fortran API + ----------- + - None + + + + C++ API + ------- + - New Member Function in DSetCreatPropList + + DSetCreatPropList::setNbit() was added to setup N-bit compression for + a dataset. + + (BMR - 2016/04/25, HDFFV-8623 patch 7) + + - New Overloaded "const" Member Functions in ArrayType + + The two following functions were added: + ArrayType::getArrayNDims() const + ArrayType::getArrayDims() const + to provide const version, and the non-const version was marked + deprecated. In-memory array information, ArrayType::rank and + ArrayType::dimensions, were removed. This is an implementation + detail and should not affect applications. + + (BMR, 2016/04/25, HDFFV-9725) + + - New member function added + + The assignment operator ArrayType::operator= is added because ArrayType + has pointer data members. + + (BMR, 2016/03/07, HDFFV-9562) + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Mac OS X El Capitan 10.11.4 with compilers Apple clang/clang++ + version 7.3.0 from Xcode 7.3, gfortran GNU Fortran (GCC) 5.2.0 + and Intel icc/icpc/ifort version 16.0.2 + + + +Bug Fixes since HDF5-1.8.16 +=========================== + + Configuration + ------------- + - Updated Linux Language Level Flags to Match the Autotools. Removed + Linux-specific Flags from OS X. + + An addition to the flags simply being out of sync with the Autotools, + the Linux flags were used on OS X builds which led to symbols not being + found. Although this was non-fatal and compilation continued (implicit + definitions were used by the compiler and the symbols resolved at link + time), a large number of warnings were raised. + + Linux changes: + + * CHANGED: _POSIX_C_SOURCE (from 199605 to 200112L) + * ADDED: _GNU_SOURCE + * REMOVED: _BSD_SOURCE + * REMOVED: _DEFAULT_SOURCE + + (DER - 2015/12/08, HDFFV-9627) + + - The --enable-clear-file-buffers configure Option was Non-functional + so the Feature was Always Enabled (its default value). + + Regardless of the configure flag, the setting was always enabled when + the Autotools were used to configure HDF5. This was due to the "no" + option being processed after the "*" option in configure.ac so "*" + matched first. CMake was unaffected. + + The option now works correctly. + + NOTE that builders are always advised to leave this option enabled. + When disabled, buffers that are written to disk may contain the + memory's previous contents, which may include secure information. + The performance overhead of the feature (a single memset call per + allocation) is minimal. + + (DER - 2016/02/03, HDFFV-9676) + + - Added a patch to remove '"'s from arguments for MPI compilers that + were causing errors compiling H5lib_settings.c with SGI MPT. + + (LRK - 2016/04/20, HDFFV-9439) + + Library + ------- + - Fixed shared file pointer problem which caused a crash when running a + program provided by a user. + + (VC - 2016/04/01, HDFFV-9469) + + - Fixed some format string warnings that prevent compiling with + -Werror=format-security on gcc. + + These only appeared in error messages and would not cause problems + under normal operation. + + (DER - 2016/01/13, HDFFV-9640) + + - Fixed a library segmentation fault when accessing a corrupted + file provided by a user. + + (MSC - 2016/02/19, HDFFV-9670) + + + + Parallel Library + ---------------- + - None + + + + Performance + ------------- + - None + + + + Tools + ----- + - h5dump: Sub-setting Fixed for Dimensions Greater than Two + + When a dataset has more than two dimensions, sub-setting would + incorrectly calculate the data that needed to be displayed. + Added in block and stride calculations that account for dimensions + greater than two. NOTE: lines that have line breaks inserted + because of display length calculations may have index info that + is incorrect until the next dimension break. + + (ADB - 2016/03/07, HDFFV-9698) + + - h5dump: Issue with Argument Segmentation Fault + + When an argument with an optional value was at the end of the command + line with a value, h5dump would crash. Reworked check for remaining + arguments. + + (ADB - 2016/03/07, HDFFV-9570, HDFFV-9684) + + - h5dump: Issue with Default Fill Value + + Added all default cases of fill value to the display of fill value. + + (ADB -, 2016/03/07, HDFFV-9241) + + - h5dump: Clarified Help + + Clarified usage of -O F option in h5dump utility help. + + (ADB - 2016/03/07, HDFFV-9066) + + - h5dump: Issue with Double Free Fault + + Added a check for filename not null before calling free(). + + (ADB - 2016/01/27, HDFFV-9639) + + - VS2015 Release Changed how Timezone was Handled + + Created a function, HDget_timezone, in H5system.c. Replaced + timezone variable usage with function call. + + (ADB - 2015/11/02, HDFFV-9550) + + + + Fortran API + ----------- + - None + + + + C++ API + ------- + - Removal of Obsolete Methods + + The overloaded methods which had parameters that should be const + but were not have been removed. + + (BMR - 2016/01/13, HDFFV-9789) + + + + High-Level APIs: + --------------- + - Fixed Memory Leak in Packet Table API + + Applied user's patch to fix memory leak in the creation of a + packet table. + + (BMR - 2016/04/25, HDFFV-9700) + + + + Fortran High-Level APIs: + ------------------------ + - None + + + + Testing + ------- + - None + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.9.3, Version 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-229.14.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/ox1011test) Intel icc/icpc/ifort version 16.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Windows 7 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2008 (cmake) + + Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + +Known Problems +============== +* On windows platforms in debug configurations, the VFD flush1 tests will fail + with the split and multi VFD drivers. These tests will display a modal debug + dialog which must be answered or wait for the test timeout to expire. + (ADB - 2014/06/23 - HDFFV-8851) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. the issue. HL and C++ shared libraries should now be + working as intended, however. + (MAM - 2011/04/20) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.16%%%% + + +HDF5 version 1.8.16 released on 2015-11-10 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.15 and +HDF5-1.8.16, and contains information on the platforms tested and +known problems in HDF5-1.8.16. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.16 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.16 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.16 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.16 (current +release) versus Release 1.8.15": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.15 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + +New Features +============ + + Configuration and Build + ------------- + - The thread-safety + high-level library combination has been marked + as "unsupported" in the Autotools + + The global lock used by the thread-safety feature has never been + raised to the high-level library level, making it possible that + the library state could change if a context switch were to occur in + a high-level library call. Because of this, the combination of + thread-safety and high-level library is officially unsupported by + The HDF Group. + + In the past, although this combination has never been supported, this + was not enforced by the build systems. These changes will cause an + Autotools configure step to fail if --enable-threadsafe and + --enable-hl are combined unless additional options are specified. + Since the high-level library is built by default, this means that + these extra configuration options will need to be used any time + --enable-threadsafe is selected. + + To build with --enable-threadsafe, either: + + 1) Use --disable-hl to disable the high-level library (recommended) + + 2) Use --enable-unsupported to build the high-level library with + the thread-safety feature. + + (DER - 2015/09/10 HDFFV-8719) + + - Using CMake now builds both static and shared libraries. + + The CMake files have been updated to build both static and shared + libraries, with tools only built statically. The packaging of the + libraries and tools will include cmake-config files that allows + projects to choose either shared or static (default) libraries + to be found with the find_package command using the COMPONENTS + keyword and a list of components. The imported libraries will + include any interface specific settings and dependent libraries. + + The default setting for BUILD_SHARED_LIBS has changed from OFF + to ON, which builds both static and shared libraries. The static + libraries are always built because of tools requirements. + + (ADB - 2015/08/24 HDFFV-5881) + + - Inline functions now correctly annotated with Autotools builds. + + The method used to detect the appropriate inline markup scheme was + nonfunctional in Autotools builds. The Autotools have been modified + to correctly detect the compiler's inline markup symbol and apply it + to the source. Note that only a very small number of internal + functions are marked inline so this was not a very big change or + likely to significantly affect performance. + + As a part of this change, the H5_inline symbol no longer appears in + H5pubconf.h. + + (DER - 2015/08/13 HDFFV-9119, HDFFV-9421) + + - Removed obsolete/unmaintained files from config/ + + Several files were removed from the config directory. These files + represent old operating systems, were no longer necessary, and/or + were no longer maintained. configure.ac was updated to reflect the + removed files. + + Removed: + + craynv + dec-flags + hpux11.23 + ia64-linux-gnu + nec-superux14.1 + sv1-cray + x86_64-redstorm-linux-gnu + powerpc-ibm-aix5.x + + As a part of this work, a few lines that deal with locating the + sys/fpu.h header on SGI machines and some OSF/1 configure lines + were also removed. The Solaris config was also renamed to not have + a version number since the version number was ignored by configure + as it applies to all Solaris versions. + + (DER - 2015/09/04 HDFFV-9116) + + - Removed the FP_TO_INTEGER_OVERFLOW_WORKS macro/defines from the library + + This was for working around bugs in the Cray X1 compiler, which is no + longer supported. + + (DER - 2015/09/09 HDFFV-9191) + + - Removed the H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS and + H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS symbols and associated code. + + H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS was a work-around on old 64-bit + SGI and Solaris systems. + + H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS was a work-around for old PGI + compilers on Linux. + + Neither of these were used in any current library code and only appeared + in the dt_arith test. + + (DER - 2015/09/09 HDFFV-9187) + + - Removed CONVERT_DENORMAL_FLOAT symbol and associated code from the + library. + + This was only set in configure files for Cray and NEC computers. These + config files no longer exist so there is no effect on currently + supported platforms. + + (DER - 2015/09/09 HDFFV-9188) + + - Removed _BSD_SOURCE and _DEFAULT_SOURCE from configure.ac + + These are old BSD-compatibility symbols that are no longer needed by + the library. + + (DER - 2015/09/10 HDFFV-9079) + + - Removed HW_FP_TO_LLONG_NOT_WORKS symbol and associated code from the + library. + + This was part of a work-around for the VS.NET 2003 compiler, which is + no longer supported. + + (DER - 2015/09/10 HDFFV-9189) + + - Removed the BAD_LOG2_CODE_GENERATED symbol and associated code from the + library. + + This was an IRIX work-around. + + (DER - 2015/09/11 HDFFV-9195) + + - Decoupled shared object version numbers for wrapper libraries from the + shared object version number for the HDF5 library. These will be + maintained on an individual basis according to the interface changes + specific to these wrapper libraries. + + For HDF5 1.8.16 the shared object version numbers were changed from + 10.0.1 to 10.1.0 for the HDF5 library due to added APIs. For the C++ + wrapper library they were changed from 10.0.1 to 11.0.0 due to changes + in existing APIs. For all other wrapper libraries the versions were + changed from 10.0.1 to 10.0.2 because while the APIs had no changes + there have been changes in code that did not result in changes to their + interfaces. + + (LRK - 2015/10/28) + + Library + ------- + + - H5F_ACC_DEBUG flag for H5Fopen/create: functionality removed + + The symbol was used to emit some extra debugging information + for HDF Group developers in the multi VFD. The underlying + functionality has been removed due to disuse. The symbol + remains defined since it was visible in H5Fpublic.h but it + has been set to zero and has no effect anywhere in the library. + + (DER - 2015-05-02, HDFFV-1074) + + - New public API call: H5is_library_threadsafe() + + This API call indicates if the library was built with thread- + safety enabled. + + (DER - 2015-09-01, HDFFV-9496) + + Parallel Library + ---------------- + - None + + Tools + ----- + - None + + High-Level APIs + --------------- + - None + + Fortran API + ----------- + - None + + + C++ API + ------- + - Class H5::ObjCreatPropList is added for the object creation property + list class. + + Class H5::ObjCreatPropList is derived from H5::PropList and is a + baseclass of H5::DSetCreatPropList. Additional property list classes + will be derived from H5::ObjCreatPropList when they are added to the + library in future releases. + + (BMR, 2015/10/13, Part of HDFFV-9169) + + - New Wrappers for C Functions H5P[s/g]et_attr_phase_change and + H5P[s/g]et_attr_creation_order. + + Wrappers were added to class H5::ObjCreatPropList for the C Functions + H5Pset_attr_phase_change: H5::ObjCreatPropList::setAttrPhaseChange + H5Pget_attr_phase_change: H5::ObjCreatPropList::getAttrPhaseChange + H5Pset_attr_creation_order: H5::ObjCreatPropList::setAttrCrtOrder + H5Pget_attr_creation_order: H5::ObjCreatPropList::getAttrCrtOrder + + (BMR, 2015/10/13, Part of HDFFV-9167 and HDFFV-9169) + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Added VS2015 with Intel Fortran 16 to supported Windows 7 platforms + + +Bug Fixes since HDF5-1.8.15 +=========================== + + Configuration + ------------- + + - CMake test for long long printf format improved + + The CMake configuration test for determining the printf format string + for printing a long long integer was fixed. The test would crash + when executed with VS2015. + + (ADB - 2015-10-21 HDFFV-9488) + + Library + ------- + - VS2015 removed global variable timezone + + The usage of the global variable timezone was modified for VS2015 by + adding an alias to Windows builds. + + (ADB - 2015-10-23 HDFFV-9550) + + - Fix potential error in H5Iclear_type + + If the ID type's close callback could close another ID of the same type, + H5Iclear_type could occasionally run into problems due to the inner + workings of the skip list package. This could potentially cause an + error on library shutdown without calling H5Iclear_type directly. This + issue has been fixed. + + (NAF - 2015-08-12) + + - Fix uninitialized memory in dataspace selection code + + When creating a dataspace with H5Screate and setting the extent with + H5Sextent_copy, the selection offset was not initialized, potentially + causing invalid I/O. There may be other cases where this happened. + Modified the library to always initialize the offset. + + (NAF - 2015-09-08) + + - Truncate file in H5Fflush() if EOA != EOF to avoid file + corruption in certain scenarios + + In the following scenario, the resulting HDF5 file would be + incorrectly corrupted because the truncate operation + was at some point wrongly moved out of the flush operation: + - Create a new file with a single dataset. + - Write parts of the dataset (make sure that some values at + the end of the dataset are not initialized). + - Flush the file. + - Crash the program. + - Try to open the file with h5dump or h5debug, but the + resulting file is corrupted. + + (MSC - 2015-06-15 HDFFV-9418) + + + Parallel Library + ---------------- + - + (XYZ - YYYY/MM/DD HDFFV-####) + + Performance + ------------- + - None + + Tools + ----- + - VS2015 changed the default format for printing of exponents + + VS2015 default format for exponents changed with the elimination + of the leading '0'. CMake now tests for the VS2015 compiler and + adjusts which reference files are used by tests. + + (ADB - 2015-10-23 HDFFV-9550) + + - Fixed h5repack with user-defined filters + + h5repack would throw a buffer overrun exception on Windows when + parsing a user-defined filter ID of 5 digits. A local variable in + the parse routine was not of sufficient size. + + (ADB - 2015/09/01 HDFFV-9515) + + Fortran API + ------------ + - None + + + C++ API + ------ + - Removed memory leaks + + The static global constant objects were changed to constant references + referencing dynamically allocated objects. This ensures that the clean-up + process in the C++ library occurs before the termination of the C library + and prevents memory leaks because the previous global constants were not + properly deleted before the C library termination. + + (BMR, 2015/10/13, HDFFV-9529) + + - Fixed the problem about identifiers being closed prematurely. + + The C++ library needs to increment the ID's reference counter when it is + duplicated in the form of C++ objects, but not when the ID is obtained + from a C function. With this approach, both problems, prematurely + closing ID's and memory leaks due to ID's not being closed, should be + eliminated. + + (BMR, 2015/10/15, HDFFV-7947) + + + High-Level APIs: + ------ + - None + + + Fortran High-Level APIs: + ------------------------ + - None + + + Testing + ------- + - None + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.32-573.3.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.4, Version 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-229.14.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.3 20140911 (Red Hat 4.8.3-9) + Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Mac OS X El Capitan 10.11 Apple clang/clang++ version 7.0.0 from Xcode 7.0.1 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM) + + Windows 7 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2008 (cmake) + + Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + +Known Problems +============== +* On Windows platforms in debug configurations, the VFD flush1 tests will fail + with the split and multi VFD drivers. These tests will display a modal debug + dialog which must be answered or wait for the test timeout to expire. + (ADB - 2014/06/23 - HDFFV-8851) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the Fortran and HL/Fortran + tests fail. HL and C++ shared libraries should now be working as intended, + however. + (MAM - 2011/04/20) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All of the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian systems. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.15%%%% + + +HDF5 version 1.8.15 released on 2015-05-04 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.14 and +HDF5-1.8.15, and contains information on the platforms tested and +known problems in HDF5-1.8.15. + +Links to the HDF5 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for HDF5 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document at this location: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.14 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - CMake + + Improvements made to the CMake build system. + + The default options were changed to align with the Autotools configure + defaults. CMake configure files now support components when packaged + with CPack. Windows CPack supports WiX packaging, and will look for + WiX and NSIS in the standard locations. + + The CMake minimum has been changed to 3.1. + + (ADB - 2015/04/01 HDFFV-8074, 8968, 9006) + + - cmakehdf5 for Cmake building. + Added configure options to support the building of Fortran or CXX API, + to enable/disable testings. Use "cmakehdf5 --help" for details. + (AKC - 2014/12/09 HDFFV-8932) + + - Building Shared and Parallel Made Explicit + + When --enable-parallel is specified, configure used to disable + shared by default. + + Removed the restriction for building shared when parallel is + enabled. --disable-shared has to be used explicitly if user + wishes to disable shared libraries. + + (MSC - 2015/02/19 HDFFV-9069) + + - Inferring Parallel Compilers + + configure was trying to infer if a compiler is a parallel + compiler with MPI support and enable parallel even if the user + did not explicitly enable parallel. This should not happen. + + Disabled inferring parallel compilers to enable parallel HDF5 + build. --enable-parallel has to be used explicitly to build + parallel HDF5 regardless of the compiler type being used. + + (MSC - 2015/02/19 HDFFV-9068) + + - Large File Support Configuration Option + + Removed the option to enable or disable large file support. It will + always be enabled. + + (MSC - 2015/02/19 HDFFV-9097) + + - Removed Configuration Feature + + When configure detected that the CodeWarrior compiler was being used it + would define a symbol that caused a test in test/tfile.c to be skipped + due to a broken CodeWarrior open() command. + + Since this only masks the problem instead of fixing it and we don't + support CodeWarrior anyway, this functionality was removed. + + (DER - 2015/02/21, HDFFV-9080) + + - VMS Build/Test Files Have Been Removed + + HDF5 no longer supports VMS, and the files were getting out of date. + Since we have no access to a VMS machine, there is no way for us to + maintain them. + + A Subversion tag was created at: + + https://svn.hdfgroup.uiuc.edu/tags/vms_last_support_1_8 + + immediately before removing the files. + + (DER - 2015-02-26, HDFFV-9147) + + - Removal of --with-default-vfd configure Option + + In theory, this option was intended to allow setting a default + VFD that would be used by the library. In practice, the feature + only accepted the POSIX (SEC2) VFD (already the default) and + the stdio VFD (a demo VFD not intended for production use). The + inability to pass key VFD parameters at configure time limits the + full implementation of this feature, so it was retired. + + (DER - 2015-02-26, HDFFV-9081) + + - Direct VFD configure Behavior + + The configure options for Linux now allow the Direct VFD to build + without passing additional compiler options/defines like _GNU_SOURCE. + Passing --enable-direct-vfd is now all that is needed to enable + the feature. + + The Direct VFD is now disabled by default since it is intended for + specialized audiences. It was previously enabled by default, but the + configure script did not set correct POSIX levels, etc. making this + a moot point. + + Note that the Direct VFD can only be configured on Linux when + the O_DIRECT flag to open()/create() and posix_memalign() function + are available. This is unchanged from previous behavior. + + (DER - 2015-02-26, HDFFV-9057, 7567, 9088, 7566) + + - _POSIX_C_SOURCE, _GNU_SOURCE, and _BSD_SOURCE No Longer Exported + to h5cc and Other Compiler Wrappers + + The _POSIX_C_SOURCE, _GNU_SOURCE, and _BSD_SOURCE definitions are + not required for using API functions and may conflict with user + code requirements. + + (DER - 2015-03-08, HDFFV-9152) + + - Removed the --enable-filters Option from configure + + This option allowed the user to disable selected internal filters, + presumably to make the library smaller. It has been removed since + it saved little space (the internal filters are small with respect + to the overall library size) and was not generally extendible to + the library at large due to the large number of #ifdefs that would + be required. + + Note that this features applied to internal filters such as shuffle + and n-bit and not external filters like gzip or Szip. Those are still + enabled or disabled via their own configure options. + + (DER - 2015-03-08, HDFFV-9086) + + - Removed Obsolete Time Functionality from configure and the C Library + + The library contained some residual functionality from obsolete + time zone handling code. This has been removed, and the configure + checks for the time functions have been cleaned up. + + * Lumped all the time functionality together in configure.ac. + This was previously more spread out due to Solaris issues + with the ordering of certain checks. + + * Removed processing that handles __tm_gmtoff members of struct + tm. (libc-4) + + * Removed BSDgettimeofday(). (IRIX 5.3) + + * Removed timezone struct handling in gettimeofday() (considered + harmful). + + Note that the HDF5 Library stores timestamps in a platform-independent + manner, so old files can still be read. This only affects converting + system time to HDF5 timestamps. + + The library currently uses the tm_gmtoff member of the tm struct + (preferred, if available) or the timezone global variable to + construct HDF5 timestamps. + + (DER - 2015-03-09, HDFFV-9083 and 9085) + + - Added -D_DEFAULT_SOURCE to CPPFLAGS on Linux Systems + + This is the replacement for -D_BSD_SOURCE in versions of glibc since 2.19. + Since both are defined, it should work for all versions of glibc. Defining + both suppresses the warning about defining _BSD_SOURCE. + + (NAF - 2015-04-02, HDFFV-9079) + + Library + ------- + - Added Memory Allocation Functions that Use the Library's Allocator + + HDF5 filters may need to allocate or resize the buffer that is passed + to them from the library. If the filter has been compiled separately + from the library, it and the library may use different memory + allocation libraries for the (re)allocation and free calls. This can + cause heap corruption and crashes. This is particularly a problem on + Windows since each C run-time library is implemented as a separate + shared library, but can also show up on POSIX systems when debug or + high-performance allocation libraries are in use. + + Two new functions (H5allocate_memory() and H5resize_memory()) were + added to the HDF5 C library. These functions have the same semantics as + malloc/calloc and realloc, respectively. Their primary purpose is to + allow filter authors to allocate or resize memory using the same + memory allocation library as the HDF5 library. Filter authors are + highly encouraged to use these new functions in place of malloc, + calloc, and realloc. They should also use the H5free_memory() call when + freeing memory. + + Note that the filters provided with the library (zlib, szip, etc.) do + not experience the problems that these new functions are intended to + fix. This work only applies to third-party filters that are compiled + separately from the library. + + (DER - 2015-04-01, HDFFV-9100) + + - H5Pset_istore_k and H5Pset_sym_k + + These two functions didn't check the value of the input parameter "ik". + When 2*ik exceeded 2 bytes of storage, data was lost in the file; + for example, some chunks would be overwritten. + + Added validation of "ik" to not exceed the max v1 btree entries (2 bytes) + to these two routines. + + (VC - 2015-03-24, HDFFV-9173) + + - Added Functions to Control the Value of H5PL_no_plugin_g without + Using an Environment Variable + + Sometimes it is necessary for an application to disable the use of + dynamically loaded plugin libraries without requiring the library to + be built with plugin support disabled or to set an environment + variable to disable plugin support globally. + + Two new functions (H5PLset_loading_state() and H5PLget_loading_state()) + were added to the HDF5 C Library. These functions require a parameter + that indicates which type of dynamically loaded plugin is enabled or + disabled. + + (ADB - 2015-03-17, HDFFV-8520) + + Parallel Library + ---------------- + - MPI_Finalize and HDF5 Library Shutdown + + Calling HDF5 routines after MPI_Finalize has been closed should + not be done, since those routines might call MPI functions that + would not be possible to do after finalizing the MPI library. + + Attached an attribute destroy callback to MPI_COMM_SELF that + shuts down the HDF5 library when MPI_COMM_SELF is destroyed, + in other words, on MPI_Finalize. This should fix several issues + that users see when they forget to close HDF5 objects before + calling MPI_Finalize(). + + (MSC - 2015/02/25, HDFFV-883) + + Tools + ----- + - None + + High-Level APIs + --------------- + - None + + Fortran API + ----------- + - Added Global Variables + + These new global variables are equivalent to the C definitions + without the '_F': + + H5G_UDLINK_F + H5G_SAME_LOC_F + H5O_TYPE_UNKNOWN_F + H5O_TYPE_GROUP_F + H5O_TYPE_DATASET_F + H5O_NAMED_DATATYPE_F + H5O_TYPE_NTYPES_F + + (MSB - 2015/02/03, HDFFV-9040) + + + C++ API + ------- + - New Wrappers for C Functions H5P[s/g]et_libver_bounds + + Wrappers were added to class H5::FileAccPropList for the + C Functions H5Pget_libver_bounds and H5Pset_libver_bounds. + + (BMR, 2015/04/06, Part of HDFFV-9167) + + - New Wrappers to Get the Object Header's Version + + The following wrappers are added to class H5::CommonFG + Returns the object header version of an object in a file or group, + given the object's name. + + unsigned childObjVersion(const char* objname) const; + unsigned childObjVersion(const H5std_string& objname) const; + + (BMR, 2015/04/06) + + - New DataType Constructor + + Added a DataType constructor that takes a PredType object, and this + constructor will invoke H5Tcopy to generate another datatype id + from a predefined datatype. + + (BMR, 2015/04/06) + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Support for Linux 3.10.0-123.20.1.el7 added (LK - 2015/04/01) + - Support for Mac OS X Yosemite 10.10 added (AKC - 2015/03/04, HDFFV-9007) + - Support for AIX 6.1 added and AIX 5.3 is retired. (AKC - 2015/01/09) + +Bug Fixes since HDF5-1.8.14 +=========================== + + Configuration + ------------- + - Make uninstall generated "test: argument expected". + The error is due to $EXAMPLETOPDIR is used without setting a value first. + + Fixed by assign it with the proper value. + + (AKC - 2015/04/29, HDFFV-9298) + + - Windows Installer Incorrect Display of PATH Environment Variable + + In the Windows installer, the dialog box where the user can elect to + add the product's bin path to the %PATH% environment variable displayed + an incorrect path. This path was missing the C:\Program Files part + and used the POSIX file separator '/' before the bin (<path>/bin, + instead of <path>\bin). + + The dialog box text was changed to simply say that the product's bin + path would be added instead of explicitly displaying the path. + This is in line with most installers. The reason for not fixing the + displayed path instead is that it is difficult to pass the correct + path from CPack to the NSIS installer for display. + + Note that this was never a code issue - it was just a display + problem. The installer always did the right thing when updating the + environment variable. + + (DER - 2014/11/14, HDFFV-9016) + + Library + ------- + - Incorrect Usage of List in CMake COMPILE_DEFINITIONS set_property + + The CMake command set_property with COMPILE_DEFINITIONS property + needs a quoted semi-colon separated list of values. CMake will + transform the list to a series of -D{value} for the compile. + + (ADB - 2014/12/09, HDFV-9041) + + - Fixed Compile Errors on Windows w/ Visual Studio and CMake When + UNICODE is Defined + + The HDF5 Library could not be built on Windows with Visual Studio when + UNICODE was defined. This was due to the incorrect use of the TEXT() + macro and some Win32 API functions that take TCHAR parameters. The faulty + code was a part of the filter plugin functionality. This was a + compile-time error that only affected users who build HDF5 from source + and define UNICODE, usually when HDF5 is being built as a part of a + larger product. There were no run-time effects. + + These errors caused no problems when UNICODE was not defined. HDF5 is + normally not built with UNICODE defined and the binaries were + unaffected. + + The fix was to remove the TEXT() macro and explicitly use the + 'A' form of the Win32 API calls, which expect char strings instead of + wchar_t strings. + + Note that HDF5 currently does not support Unicode file paths on Windows. + + (DER - 2015/02/22, HDFFV-8927) + + - Addition of Error Tracing Functionality to Several C API Calls + + A bug in a text processing script caused API calls that return a + pointer to not receive error tracing macros/functionality. + + The bug has been corrected and error tracing functionality has been + added to the affected API calls. These functions will now correctly + print trace information when library errors are encountered. + + (DER - 2015/02/26, HDFFV-9141) + + - H5Rdereference Now Checks for HADDR_UNDEF or Uninitialized References + + When passed HADDR_UNDEF or uninitialized references, the previous + behavior of H5Rdereference was to continue to process the reference + as a valid address. + + H5Rdereference was changed to return immediately (with an error + message) if the references are HADDR_UNDEF or uninitialized. + + (MSB - 2015/3/10, HDFFV-7959) + + - Fixed Bugs in H5Sextent_copy + + H5Sextent_copy would not free the previous extent, resulting in a memory + leak. Also, H5Sextent_copy would not update the number of elements + selected if the selection was "all", causing various problems. These + issues have been fixed. + + (NAF - 2015/04/02) + + + Parallel Library + ---------------- + - Fixed a Potential Memory Error + + Fixed a potential memory error when performing parallel I/O on a + dataset with a single chunk, and at least one process has nothing + to do. + + (NAF - 2015/02/16) + + - Parallel Test Problem Fixed + + Fixed problem with parallel tests where they failed beyond a + certain number of ranks. All tests should work for any arbitrary + number of ranks. + + (MSC - 2014/11/06, HDFFV-1027,8962,8963) + + - MPE Support + + Enabling MPE was causing HDF5 build to fail. Support for it was + dropped at some point in time. + + Fixed problem with enabling MPE. Users should use the community + maintained MPE on github (http://git.mpich.org/mpe.git/). + + (MSC - 2015/02/20, HDFFV-9135) + + Performance + ------------- + - None + + Tools + ----- + - h5repack crashed on enumerated 8-bit type. + + Previous version 1.8.14 introduced an error that caused the reading + of enumerated 8-bit type nested in compound type to fail. + + Fixed library code responsible for reading the particular type. + (AKC - 2015.03/31, HDFFV-8667) + + - h52gif crashed non-8bit images. + + h52gif crashed if instructed to convert images other than 8bit images. + + h52gif could handle only 8bit images. Added code to detect non-8bit + images and flag them as failure. Update tool document page to reflect + the limit. + (AKC - 2015/03/31, HDFFV-8957) + + - perform/benchpar.c retired. + + benchpar.c has not been built for a long time and its original purpose + is not needed any more. + (AKC - 2014/12/19, HDFFV-8156) + + - Source perform/ directory moved to tools/perform. + The perform directory is moved to tools/perform for easier maintenance. + (AKC - 2014/12/17, HDFFV-9046) + + Fortran API + ------------ + - Fortran Fails with --enable-fortran2003 and Intel 15.x Compilers + + Added BIND(C) to the offending APIs. + + The Fortran Library (--enable-fortran2003) now works using Intel 15.x + without the need for any additional compilers flags. + + (MSB - 2015/1/26, HDFFV-9049) + + - h5tenum_insert_f Does Not Work with Default 8 Byte Integers + (xlf compiler) + + In the Fortran 90 API, 'value' is no longer cast into the C int type. + Therefore, if h5tenum_insert_f is passed an 8 byte integer (via -i8) + then 'value' is written as the same type as the default Fortran + integer type (which can be 8 bytes). + + A new Fortran 2003 API was added which is more in line with the C + API and users are strongly encouraged to use the Fortran 2003 API + instead of the Fortran 90 API. + + SUBROUTINE h5tenum_insert_f(type_id, name, value, hdferr) + INTEGER(HID_T) , INTENT(IN) :: type_id + CHARACTER(LEN=*), INTENT(IN) :: name + TYPE(C_PTR) , INTENT(IN) :: value + INTEGER, INTENT(OUT) :: hdferr + + (MSB - 2015/2/19, HDFFV-8908) + + - Some Fortran APIs Never Returned the Error State + + Some Fortran APIs never returned the error state: they + would always return a positive number. The APIs include + the following: + + h5fget_file_image_f + h5lget_name_by_idx_f + h5oget_comment_by_name_f + + They were corrected to return a negative number as described in + the Reference Manual if an error occurred. + + (MSB - 2015/3/19, HDF5-239) + + - Fixed h5pget_class_f + + h5pget_class_f never correlated the class identifier to the property + list class name as indicated in the HDF5 Reference Manual; it instead + returned a property list class identifier as an INTEGER. The INTEGER + needed to be of type INTEGER(HID_T) to be correct. + + The h5pget_class_f API was changed to return an INTEGER(HID_T) + property list class identifier instead of an INTEGER. This mimics the + intended behavior of the C API. + + (MSB - 2015/3/16, HDFFV5-9162) + + C++ API + ------ + - Combined Two H5File::getObjCount Overloaded Methods + + The following two methods + + ssize_t getObjCount(unsigned types) const; + ssize_t getObjCount() const; + + were combined into one: + + ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const; + + (BMR - 2015/04/06) + + - Many Warnings Were Removed + + Many warnings such as conversion, unused variables, missing base + class initialization, and initializing base classes in wrong order + were removed. + + (BMR, 2015/04/06) + + - Functionality Deprecation + + The following two constructors of classes AbstractDs, IdComponent, + H5Location, and H5Object are no longer appropriate after the data member + "id" had been moved from IdComponent to the sub-classes in previous + releases. + + <Classname>(const hid_t h5_id); + <Classname>(const <Classname>& original); + + The copy constructors were no-op and removed in 1.8.15. The other + constructors will be removed from 1.10 release, and then from 1.8.17 + if their removal does not cause any problems. + + (BMR, 2015-04-06) + + + High-Level APIs: + ------ + - Suppress Warnings from Flex/Bison-generated Code + + Warning suppression #pragmas, etc. have been added to H5LTparse.c and + H5LTanalyze.c. We have no control over this code since it's created by + a generator. + + (DER - 2015/03/08 - HDFFV-9149) + + - Changed hdf5_hl.h to Include the HDF5 Main Library "hdf5.h" + + User's no longer need to include both hdf5_hl.h and hdf5.h + + (MSB - 2015/2/14, HDFFV-8685) + + + - H5PTcreate_fl Does Not Convert to Memory Datatype + + H5PTcreate_fl now converts to the table's native memory datatype + to fix the problem of handling BE and LE packet tables. + + (MSB - 2015/2/26 - HDFFV-9042) + + - Fix for H5LT Attribute Functions + + H5LT attribute functions fail to create attributes whose name + is a substring of an existing attribute. + + H5LT attribute functions can now create attributes whose name + is a substring of an existing attribute. + + (MSB - 2015/2/24, HDFFV-9132) + + + Fortran High-Level APIs: + ------------------------ + + - Internal Library Fix for Missing Argument Declaration + + In Interface block for h5tbmake_table_c, "max_char_size_field_names" + is listed as an input, but in the argument definitions it is + "INTEGER :: max_char_size". This caused no known problems with the + Fortran HL API. + + Fixed missing argument definition. + + (MSB - 2015/2/18, HDFFV-8559) + + + Testing + ------- + - None + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-55) + Version 4.8.4, 4.9.2 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 14.10-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 15.0.1.133 (Build 20141023) + + Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-55) + Version 4.8.4, 4.9.2 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 15.0.1.133 Build 20141023 + + Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.2, Version 4.9.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 14.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.1.133 Build 20141023 + + Linux 3.10.0-123.20.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (moohan) Version 4.8.2 20140120 (Red Hat 4.8.2-16) + Intel(R) C Intel(R) 64 Compiler XE for + applications running on Intel(R) 64, + Version 15.0.1.133 Build 20141023 + + Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 14.0.2 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.1.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (wren/quail) Intel icc/icpc/ifort version 14.0.2 + + Mac OS X Yosemite 10.10.2 Apple clang/clang++ version 6.0 from Xcode 6.1.1 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.1 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.2 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.0 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.0 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.2 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.0 Linux 3.10.0 x86_64 GNU y y y n +CentOS 7.0 Linux 3.10.0 x86_64 Intel y y y n +Linux 2.6.32-431.11.2.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.3 compiled with + #1 SMP i686 i686 i386 gcc 4.9.2 and gfortran 4.9.2 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.3 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.9.2 and gfortran 4.9.2 + (platypus) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 + (loyalty) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 + (freedom) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + +Known Problems +============== +* On Windows platforms in debug configurations, the VFD flush1 tests will fail + with the split and multi VFD drivers. These tests will display a modal debug + dialog which must be answered or wait for the test timeout to expire. + (ADB - 2014/06/23 - HDFFV-8851) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. the issue. HL and C++ shared libraries should now be + working as intended, however. + (MAM - 2011/04/20) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.14%%%% + + +HDF5 version 1.8.14 released on 2014-11-12 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.13 and +HDF5-1.8.14, and contains information on the platforms tested and +known problems in HDF5-1.8.14. + +All new and modified APIs are listed in the "HDF5 Software Changes +from Release to Release" document along with details about previous +releases at: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +Links to the HDF5 1.8.14 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.14 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.14 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.13 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - bin/cmakehdf5 configures, builds and installs C, C++, Fortran and High + level API's. (It used to build the C API only). + (AKC 2014/10/17 HDFFV-8932). + + Library + ------- + - None + + Parallel Library + ---------------- + - Chunk Fill Writes Changed to Collective + + Slow performance in chunk fill writes. Chunk fills + in the past were written independently by rank 0 one block + at a time. + + Optimized the chunk fill write algorithm so that all + chunk fill values will be written collectively in a single MPI-IO + call. This should show a great performance improvement when + creating chunked datasets in parallel when the chunk dimensions + are fairly small. + + (MSC - 2014/08/22, HDFFV-8878) + + Tools + ----- + - None + + High-level APIs + --------------- + - None + + Fortran API + ----------- + - None + + C++ API + ------- + - Initialization of Object IDs + + The data member "id" in classes that represent HDF5 objects were + initialized to 0, which caused problem for some users. + + Replaced 0 with H5I_INVALID_HID to initialize these "id"s. For the + PropList class, H5P_DEFAULT is used instead of H5I_INVALID_HID. + + (BMR - 2014/09/30, HDFFV-4259) + + + +Support for New Platforms, Languages, and Compilers +=================================================== + - None + +Bug Fixes since HDF5-1.8.13 +=========================== + + Configuration + ------------- + - CMake and SVN URLs + + The SVN URLs will be different when the HDF Group domain name changes. + + Removed the SVN URL references in the cacheinit.cmake and release_docs files. + + (ADB - 2014/10/27, HDFFV-8953) + + - CMake Packaging + + A Fortran module was not generated if the compiler was not F2003 + compliant. + + Removed the module name from the package list of Fortran modules because + that module was never generated. This was only an issue for Fortran + compilers that are not F2003 compatible. + + (ADB - 2014/10/16, HDFFV-8932) + + - Shared Library Interface Version Number (soname) + + In order to increase the maintainability of HDF5, an architectural + change was made which required the renaming of several public symbols in + H5Ppublic.h. + + The shared library interface version number ("soname") has been increased + on account of these changes. For a full list of the changed symbols, see + the interface compatibility report, which is available as a link off of + the 'HDF5 Software Changes from Release to Release' document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + + (AKC - 2014/10/03, HDFFV-8937) + + - Configure Settings for Mac OSX Need Defaults for PROD_XXX, DEBUG_XXX, + and PROFILE_XXX + + The configure setting files for Mac OSX (config/apple) did not + have the default settings of PROD_XXX, DEBUG_XXX, PROFILE_XXX. + + Added the default settings. Mac platforms now builds library with + "-O3" optimization when the default clang compiler is used. + + (AKC - 2014/10/01, HDFFV-8933) + + - CMake ConfigureChecks + + Two include files were missing from two C tests. + + Propagated the configure test changes to H5_LDOUBLE_TO_INTEGER_WORKS_TEST + and H5_ULLONG_TO_LDOUBLE_PRECISION_TEST to ConfigureChecks.cmake (added + stdlib.h and string.h in the HDFTests.c file). + + (ADB - 2014/09/02 HDFFV-8845) + + - CMake Parallel Test Missing + + The source file was removed in the previous release but the parallel + test t_posix_compliant was not. + + Removed the t_posix_compliant parallel test from the library. + + (ADB - 2014/8/14 HDFFV-8880) + + - Autotools Reconfigure. Bison. Flex. + + The Bison and Flex files were out of date. + + Bison was upgraded to 2.7, and Flex was upgraded to 2.5.37. The + bin/reconfigure script now will execute Bison and Flex and update + the hl/src files. + + (ADB - 2014/06/16 HDFFV-8709) + + - Autotools Reconfigure. m4. + + The m4 macro processor was out of date. + + Reconfigured Autotools with m4 upgraded to 1.4.17. + + (ADB - 2014/06/12 HDFFV-8743) + + - Autotools: Modified configure to add an entry at the beginning of AM_LDFLAGS + for the hdf5 install directory. Without this entry the relink commands + invoked by "make install" to create libraries dependent on libhdf5.so added + a dependency on the first libhdf5.so found in any directory in AM_LDFLAGS + regardless of its version. (LRK - 2014/10/17 HDFFV-8944) + + - Changed Autotools Build Behavior. Fortran High-level Library. + + The Fortran high-level (HL) library did not compile if the default + size of a REAL is DOUBLE PRECISION; the build would fail during + compilation. + + Configure now checks to see if REAL is DOUBLE PRECISION, Fortran is + enabled, and HL library is enabled. If this is true, then configure + will stop with an error message. + + (MSB - 2014/8/11, HDFFV-8883/HDFFV-889) + + + + Library + ------- + - Fixed Identifier Management Code + + Opening an object returns an identifier; closing the object should + free up the identifier. A problem was found where the identifiers + were not being freed up correctly. + + Fixed the problem so that identifiers that have been used can be + used again after their object has been closed. + + (QAK - 2014/10/16, HDFFV-8930) + + - Removal of DllMain() from Static Windows Builds + + A DllMain() function was added in HDF5 1.8.13 in order to handle + win32 thread cleanup. The preprocessor #ifdefs around the DllMain + function allowed it to be compiled when the static library is built, + which is incorrect behavior that can cause linkage problems in + clients. + + The fix was to change the preprocessor #ifdefs to exclude compiling + DllMain() in static builds. Our DllMain function is now only + compiled when the shared, thread-safe library is built on Windows. + + (DER - 2014/06/13, HDFFV-8837) + + - Enforce Constraint on page_size Parameter in H5Pset_core_write_tracking() + + The reference manual states that the page_size parameter cannot be + zero. + + This change checks the page_size parameter to see it is zero and + returns an error code if it is. + + (DER - 2014/08/11, HDFFV-8891) + + - H5Ldelete_by_idx() fails on non-existent group name. + (MSC - 2014/07/31, HDFFV-8888) + + - H5Ldelete_by_idx() Seg Fault on Non-existent Group Name + + If a non-existent group name was used by H5Ldelete_by_idx(), a + segmentation fault would result. + + Bug was fixed. + + (MSC - 2014/07/31, HDFFV-8888) + + - Bug in Test When Building Parallel HDF5 on PVFS2 + + There was a bug in a test when building Parallel HDF5 on PVFS2. + + The build now uses MPI_File_get_size() instead of stat(). + + (MSC - 2014/07/14, HDFFV-8856) + + - MPI-IO Driver Tried to Allocate Space for Zero-length Dataset + + MPI-IO driver tried to allocate space for zero-length dataset + and asserts. + + Fixed driver and added a regression test. + + (MSC - 2014/07/03, HDFFV-8761) + + + Parallel Library + ---------------- + - None + + Performance + ------------- + - None + + Tools + ----- + - None + + Fortran API + ------- + - SIZEOF Replaced by C_SIZEOF and STORAGE_SIZE. + + The intrinsic function SIZEOF is non-standard and should be replaced with a + standard intrinsic function. + + If the F2008 intrinsic C_SIZEOF and STORAGE_SIZE are available, then they will + be used instead of the non-standard SIZEOF intrinsic, even when the SIZEOF + function is available. + + (MSB - 2014/6/16, HDFFV-8653) + + - Non-functional API: h5pget_fill_value_f + + The Fortran wrapper h5pget_fill_value_f was calling the wrong C API. + + The correct C API, H5Pget_fill_value, is now called by the Fortran + wrapper. + + (MSB - 2014/9/25, HDFFV-8879) + + - Interoperability with C HDF5: H5Literate and h5literate_f + + h5literate_f assumes the return value for the callback function to + be of type int (or int_f in C). However, in the C wrapper the return + value of H5Literate is type herr_t, and this could cause + interoperability issues. + + The callback function should be declared INTEGER(C_INT) for + portability. The tests were updated accordingly. + + (MSB - 2014/9/26, HDFFV-8909) + + - Interoperability with C HDF5: Constant INTEGER Parameters with the + H5FD Interface + + Wrong type cast of constant Fortran INTEGER parameters was used. + + The following parameter constant types were changed from INTEGER to + INTEGER(HID_T) to match the C types: H5FD_CORE, H5FD_FAMILY, H5FD_LOG, + H5FD_MPIO, H5FD_MULTI, H5FD_SEC2, and H5FD_STDIO. + + Other internal 'int' types where changed to 'hid_t'; these are + transparent to the user. + + (MSB - 2014/7/18, HDFFV-8748) + + C++ API + ------ + - Memory Leaks + + There were several potential memory leaks in the library due to + dynamically allocated strings not being freed when failure occurs. + + Applied user's patches to remove these potential memory leaks. + + (BMR - 2014/09/30, HDFFV-8928) + + - Disallow H5F_ACC_CREAT + + H5F_ACC_CREAT was included in the C++ API but the C library does not + allow it at this time. + + Removed this flag from the functions in H5File class. + + (BMR - 2014/09/29, HDFFV-8852) + + - Missing Flags in Documentation: H5F_ACC_RDONLY and H5F_ACC_RDWR + + The H5F_ACC_RDONLY and H5F_ACC_RDWR flags were missing from the + documentation of the H5File constructors. + + These two flags are now included in the documentation for opening + files. + + (BMR - 2014/09/29, HDFFV-8852) + + High-level APIs: + ------ + - Seg Faults in H5TBread_field_name and H5TBread_field_name_f + + When H5TBread_field_name or H5TBread_field_name_f were used to read a + field and if the name of the field was wrong, a segmentation fault + would result. + + Both C and Fortran APIs were fixed so they no longer seg fault if + the name of the field is wrong, and both APIs return a negative + value if the name of the field is wrong. + + (MSB - 2014/09/29, HDFFV-8912) + + - Possible Buffer Overflow in High-level (HL) APIs + + Multiple HL APIs (H5DSis_scale is one example) had issues: + (1) The datatype from the file was re-used as the memory datatype, + and + (2) No effort was made to ensure that strings were actually + null-terminated. + + All of the HL routines now check for NULL pointers, for null-terminated + strings, and to see if string buffers are short enough not to overflow + the buffer. The minimum length of the buffers is now used in strncmp + to avoid overflow. + + (MSB - 2014/9/29, HDFFV-8670) + + - Behavior Change of H5LTdtype_to_text + + If a user buffer was passed in to H5LTdtype_to_text along with the + length, then the function would not truncate at the end of the + buffer, but would exceed the end of the user buffer. + + H5LTdtype_to_text was changed to truncate the string if the user + buffer is too small. + + (MSB - 2014/9/29, HDFFV-8855) + + Fortran High-level APIs: + ------ + - See entry for HDFFV-8912 above. + + Testing + ------- + - A subtest in parallel h5diff (ph5diff) testing was bypassed for the + local Linux 32 machine due to unknown issue in the previous version of + Mpich. The failure no long exists in the current Mpich. Therefore the + bypass is removed. (AKC - 2014/11/03 HDFFV-8954) + + - Fixed incorrect exit code values (was -1) in testframe which is commonly + used by several test programs. (AKC - 2014/07/22 HDFFV-8881) + + - Fixed Incorrect Exit Code Values in Testframe + The testframe which is commonly used by several test programs + had some incorrect exit code values. Fixed the incorrect exit code + values. (AKC - 2014/07/22, HDFFV-8881) + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 13.7-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 14.0.2 (Build 20140120) + + Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 14 (cmake) + Visual Studio 2013 w/ Intel Fortran 14 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.32(0.274/5/3) gcc(4.8.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 14 (cmake) + Visual Studio 2013 w/ Intel Fortran 14 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake) + Visual Studio 2013 w/ Intel Fortran 14 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake) + Visual Studio 2013 w/ Intel Fortran 14 (cmake) + + Mac OS X Lion 10.7.5 Apple clang/clang++ version 3.0 from Xcode 4.6.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (duck) Intel icc/icpc/ifort version 13.0.3 + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 14.0.2 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.0.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (wren) Intel icc/icpc/ifort version 14.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Lion 10.7.5 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ? +AIX 5.3 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Lion 10.7.5 64-bit y n y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +AIX 5.3 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n +Linux 2.6.32-431.11.2.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with + #1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1 + (platypus) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 + (loyalty) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 + (freedom) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.2.34 + hopper.nersc.gov pgcc 13.6-0 64-bit target on x86-64 Linux -tp istanbul + pgf90 13.6-0 64-bit target on x86-64 Linux -tp istanbul + pgCC 13.6-0 64-bit target on x86-64 Linux -tp istanbul + + +Known Problems +============== +* On cygwin platforms the feature to load dynamic filter libraries only looks + for libraries with the a so extension. Support for cygwin cygxxx.dll libraries + is planned for the next release. + (ADB - 2014/11/04 - HDFFV-8736) + +* On windows platforms in debug configurations, the VFD flush1 tests will fail + with the split and multi VFD drivers. These tests will display a modal debug + dialog which must be answered or wait for the test timeout to expire. + The flush1 and flush2 tests will be skipped under debug for this release. + (ADB - 2014/06/23 - HDFFV-8851) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* The h5dump and h5diff utilities occasionally produce different output + between Linux and Windows systems. This is caused by lower-level library + routines that fail to write fill values to the user's buffer when reading + unallocated chunks from datasets that have a fill value set to + H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of + spurious data values has only been encountered on Windows 32-bit systems. + (Issue HDFFV-8247; JP - 2013/03/27) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.13%%%% + + +HDF5 version 1.8.13 released on 2014-05-05 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.12 and +HDF5-1.8.13, and contains information on the platforms tested and +known problems in HDF5-1.8.13. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.13 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.13 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.13 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.13 (current +release) versus Release 1.8.12": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.12 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08) + + - CMake: Moved minimum CMake version to 2.8.11 which enables better library + include processing. (ADB - 2014/03/26) + + - When configuring a thread-safe HDF5 Library it is no longer necessary + to specify --enable-threadsafe with --with-pthreads if the Pthreads + library is in a standard location. (DER - 2014/04/11 HDFFV-8693) + + Library + ------- + - Added an H5free_memory API call. This should be used to free memory + that has been allocated by HDF5 API calls. H5Tget_member_name and + H5Pget_class_name are two examples. The main motivation for this call + is Windows, where it is common for application code and the HDF5 Library + to be using different C run-time libraries (CRT). Using the new call + ensures that the same CRT handles both the allocation and free. This + new function can also be useful in any case where the library uses a + different memory manager than the application, such as when a debug + memory manager is in use or when the HDF5 Library is wrapped for use + in a managed language like Python or Java. Fixes HDFFV-7710, 8519, + and 8851. (DER - 2014/04/11) + + - The Core VFD (aka Memory VFD) can now be configured to track dirty + regions in the file and only write out the changed regions on + flush/close. Additionally, a "page aggregation" size can be set that + will aggregate small writes into larger writes. For example, setting + a 1 MiB page aggregation size will logically partition the the + in-memory file into 1 MiB pages that will be written out in their + entirety if even a single byte is dirtied. The feature is controlled + via the new H5Pset/get_core_write_tracking() API call. A new + "core_paged" target has been added to the check-vfd target in + test/Makefile.am that exercises the feature over all HDF5 VFD-aware + tests. (DER - 2014/04/12) + + Parallel Library + ---------------- + - Removed MPI-POSIX VFD, as it wasn't helping anyone and was just + generating support questions. Application developers performing + parallel I/O should always use the MPI-IO VFD. + (QAK - 2014/03/28 HDFFV-8659) + + - Improved parallel I/O support to allow collective I/O on point + selections. (QAK - 2014/03/15) + + Tools + ----- + - None + + High-Level APIs + --------------- + - None + + Fortran API + ----------- + - Wrappers h5pset_file_image_f and h5pget_file_image_f were added to the + library. (MSB - 2014/1/2014) + + C++ API + ------- + - The following new features are added: + + Wrappers to class H5Object to get an object's name (HDFFV-8548). + ssize_t getObjName(char *obj_name, size_t buf_size = 0) + ssize_t getObjName(H5std_string& obj_name, size_t len = 0) + H5std_string getObjName() + + Wrappers to class H5CommonFG to get a child object's type from a + group or file (HDFFV-8367). + H5O_type_t childObjType(const H5std_string& objname) + H5O_type_t childObjType(const char* objname) + H5O_type_t childObjType(hsize_t index, + H5_index_t index_type=H5_INDEX_NAME, + H5_iter_order_t order=H5_ITER_INC, const char* objname=".") + + Wrappers to class DSetMemXferPropList for setting/getting a transform + property list (HDFFV-7907). + DSetMemXferPropList(const char* expression); + void setDataTransform(const char* expression) + void setDataTransform(const H5std_string& expression) + ssize_t getDataTransform(char* exp, size_t buf_size=0) + H5std_string getDataTransform() + + Wrapper to CompType for setting size to compound datatype (HDFFV-8642). + void setSize(size_t size) + + Overloaded functions to provide prototypes that declare constant + arguments const (HDFFV-3384). These include: + DataSet::fillMemBuf + DataSet::getVlenBufSize + DataSpace::extentCopy + DataType::commit + FileAccPropList::setSplit + H5File::getVFDHandle + + Additional overload to class H5Location to get a comment as a char* + ssize_t getComment(const char* name, size_t buf_size, char* comment) + + Additional overloads to class Attribute to get an attribute's name for + convenience: + ssize_t getName(char* attr_name, size_t buf_size=0) + ssize_t getName(H5std_string& attr_name, size_t buf_size=0) + (BMR, 2014/04/15) + + A static wrapper to Exception for printing the error stack without an + instance of Exception + static void printErrorStack(FILE* stream = stderr, + hid_t err_stack = H5E_DEFAULT); + (BMR, 2014/04/25) + + +Support for New Platforms, Languages, and Compilers +=================================================== + Mac OS X 10.6 Snow Leopard is not supported by Apple any more. In view of + the added support of Mac OS X 10.9, Mac OS X 10.6 is retired from HDF5 + supported platforms. (AKC - 2014/03/14 HDFFV-8704) + + Mac OS X 10.9 Mavericks is supported. (AKC - 2014/03/04 HDFFV-8694) + + +Bug Fixes since HDF5-1.8.12 +=========================== + + Configuration + ------------- + - CMake: When CMake commands are executed individually on the command line + and the external filters are being built, the CMAKE_BUILD_TYPE define + must be set to the same value as the configuration + (-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed + by the the szip and zlib filter build commands. (ADB - HDFFV-8695) + + - CMake: Removed use of the XLATE_UTILITY program. + (ADB - 2014/03/28 HDFFV-8640) + + - CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the + MPI option. (ADB - 2014/02/27 HDFFV-8674) + + - CMake: Configuration of the HDF5 C++ or Fortran libraries with the + thread-safety feature. + + C++ and/or Fortran + thread-safe is enforced as a non-supported + configuration. This matches the autotools. (DER - 2014/04/11) + + - CMake: Configuration of static HDF5 C library with the thread-safety + feature. + + Static + thread-safe + Win32 threads is not a supported configuration + due to the inability to automatically clean up thread-local storage. + This is expected to be fixed in a future release. In the meantime, a + work-around that uses internal functionality may allow the combination + to be used without resource leaks. Contact the help desk for more + information. (DER - 2014/04/11) + + - Autotools: Several changes were done to configure and installcheck. + + An export of LD_LIBRARY_PATH=<szip library location> was + removed from configure; make installcheck was revised to run + scripts installed in share/hdf5_examples to use the installed h5cc, etc. + to compile and run example source files also installed there. + + Make installcheck will now fail when a shared szip or other external lib + file cannot be found in the same manner that executables compiled and + linked with h5cc will fail to run when those lib files cannot be found + after install. Make installcheck should pass after setting + LD_LIBRARY_PATH to the szip location. (LRK - 2014/04/16) + + Library + ------- + - A Gnu Make directive (.NOTPARALLEL) is added to fortran/test/Makefile. + + AIX native make does not support this directive and would fail if + parallel make (e.g. make -j4) is used to build the library. AIX users + either do not use parallel make or install Gnu Make to build the library. + (AKC 2014/04/08 HDFFV-8738) + + - H5R.c: H5Rget_name gave an assertion failure if the "name" parameter + was NULL. + + Fixed H5Rget_name to return the size of the buffer needed to read a + name of the referenced object in this case. The size doesn't include + the NULL terminator. H5Rget_name returns negative on failure. + (MSB - 2014/01/22 HDFFV-8620) + + - H5Z.c: H5Zfilter_avail didn't check if a filter was available as a + dynamically loaded filter. The error manifested itself in the h5repack + tool when removing user-defined dynamically loaded filter. + + Added a code to find the filter among the dynamically loaded filters + after the function fails to find it among the registered filters. + (ADB - 2014/03/03 HDFFV-8629) + + - Memory leak: a memory leak was observed in conjunction to the + H5TS_errstk_key_g thread-local variable allocated in the H5E_get_stack + function in H5E.c. + + The shared HDF5 thread-safe library now no longer leaks thread-local + storage resources on Windows with Win32 threads. Currently, there is + no solution for this problem when HDF5 is statically built. We + disabled the build of the static HDF5 thread-safe library with + Win32 threads. (DER - 2014/04/11 HDFFV-8518) + + - H5Dio.c: Improved handling of NULL pointers to H5Dread/H5Dwrite + calls. Credit to Jason Newton (nevion@gmail.com) for the original patch. + + H5Dwrite/read failed when a NULL pointer was passed for a data buffer + and 0 elements were selected. Fixed. (QAK - 2014/04/16 HDFFV-8705) + + - Deprecated API (1_6 API): Improved handling of closing the library and + re-accessing it with a deprecated routine. + + When a program used a deprecated API (for example, H5Gcreate1), + closed the library, and reopened it again to access a group, dataset, + datatype, dataspace, attribute, or property list, HDF5 failed to + provide an identifier for the object. Fixed. + (NAF, QAK - 2014/04/16 HDFFV-8232) + + Parallel Library + ---------------- + - Fixed a missing H5F_Provisional module in HDF5mpio.f90 + (MSB - 2014/2/7 HDFFV-8651) + + Performance + ------------- + - None + + Tools + ----- + - The h5diff tool would report that a datafile compared with an exact + copy of the same datafile had differences. This was due to the issue + below of reading un-written chunks. This problem is also fixed. + (AKC - 2014/05/01 HDFFV-8637) + + - The h5dump and h5diff utilities occasionally produced different output + between Linux and Windows systems. This has been fixed. + + This happened to datasets that used chunked storage, with default fill + values, and some of the chunks had not been written. + When the dataset was read, the library failed to write the default fill + values to parts of the use buffer that were associated with the unwritten + chunks. (JP - 2014/05/01 HDFFV-8247) + + - The compress option is retired from bin/release. + (AKC - 2014/04/25 HDFFV-8755) + + - bin/release has a new option "zip" that produces a release zip file for + the Windows platform. (AKC - 2014/04/24 HDFFV-8433) + + - h5diff: Several failures relating to handling of strings attributes + are fixed. + + The tool crashed or gave an error message when one of the strings had + fixed size type and another variable-length size type. h5diff now flags such + strings as "not comparable". We plan to enhance the tool to handle + strings of the different types in the future releases. + (AKC - 2014/04/18 HDFFV-8625, 8639, 8745) + + - h5repack: h5repack would not remove user-defined filters. + Fixed by modifying h5repack to check if the filter is registered or + can be dynamically loaded. (ADB - 2014/03/03 HDFFV-8629) + + F90 API + ------- + - H5D_CHUNK_CACHE_NSLOTS_DFLT_F and H5D_CHUNK_CACHE_NBYTES_DFLT_F were + changed from the default KIND for INTEGER to INTEGER of KIND size_t. + (MSB - 2014/3/31 HDFFV-8689) + + C++ API + ------ + - Added throw() to all exception destructors. Credit to Jason Newton + (nevion@gmail.com) for the patch. (BMR - 2014/4/15 HDFFV-8623) + - Changed the default value for H5Location::getComment from 256 to 0 + to conform to C function and because it makes more sense. + (BMR - 2014/4/15) + + High-Level APIs: + ------ + - None + + Fortran High-Level APIs: + ------ + - None + + Testing + ------- + - testhdf5 now exits with EXIT_SUCCESS(0) if no errors, else + EXIT_FAILURE(1). (AKC - 2014/01/27 HDFFV-8572) + + - The big test now pays attention to the HDF5_DRIVER environment variable. + Previously, it would run all tests with the family, stdio, and sec2 + virtual file drivers (VFDs) for each VFD in the check-vfd make target, + regardless of the variable setting. It now checks the variable and + either runs the appropriate VFD-specific tests or skips as needed. + This saves much testing time. Fixes HDFFV-8554. (DER - 2014/04/11) + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + gmake v3.82 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 13.7-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 14.0.2 (Build 20140120) + + Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.11.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + IBM XL C/C++ V11.1 + IBM XL Fortran V13.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 w/ Intel Fortran 14 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 14 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.28(0.271/5/3) gcc(4.8.2) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 14 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 14 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake) + + Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (duck) Intel icc/icpc/ifort version 13.0.3 + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.0 from Xcode 5.0.2 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 14.0.2 + + Mac OS X Mavericks 10.9.2 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (wren/quail) Intel icc/icpc/ifort version 14.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y y +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.1 64-bit n y/y n y y y +AIX 5.3 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y +OpenVMS IA64 V8.4 n y/n n y y n + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +Mac OS X Mavericks 10.9.1 64-bit y n y y +AIX 5.3 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n +Linux 2.6.32-431.11.2.el6.ppc64 y y y n +OpenVMS IA64 V8.4 n n n n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1 compiled with + #1 SMP i686 i686 i386 gcc 4.8.2 and gfortran 4.8.2 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.8.2 and gfortran 4.8.2 + (platypus) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 + (loyalty) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 + (freedom) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.11.10-301.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7) + GNU Fortran (GCC) 4.8.2 20130603 (Red Hat 4.8.2-7) + (cmake and autotools) + + SUSE 13.1 3.11.6-4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 13.10 3.11.0-13-generic #20-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 + GNU Fortran (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 + (cmake and autotools) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== +* When reading or writing a dataset (H5Dread/H5Dwrite) with a large selection + size (e.g., 2GB ~= 500 million of 4 bytes integers or floating point + numbers), some I/O systems may not be able to process it correctly. + We advise users to find out system limits before using large selections. If + I/O size limits exist, application should use HDF5 partial I/O capabilities + (e.g., H5Sselect_hyperslab(...)) to divide large requests into smaller sizes. + In this case we also advise users not to use chunk storage sizes larger that + 2GB since the HDF5 library performs I/O on the entire chunk. We will work + on the HDF5 library to divide large data requests to smaller I/O requests. + (AKC 2014/05/02 HDFFV-8479) + +* Due to an Intel compiler bug introduced in version 14.0.1, the HDF5 FORTRAN + wrappers do not work with configure option --enable-fortran2003. + However, the option --enable-fortran works with Intel 14.0.1. The compiler + bug was fixed in Intel version 14.0.2 and resolved the issue. + (MSB - 2014/4/15) + +* Due to a PGI compiler bug introduced in versions before 13.3 and versions + after 14.2, the FORTRAN test 'Testing get file image' will fail. + (MSB - 2014/4/15) + +* On CYGWIN, when building the library dynamically, testing will fail on + dynamically loaded filters. The test process will build dynamic filter + libraries with the *.dll.a extension, and the HDF5 Library will be looking + for *.so libraries. Entered as issue HDFFV-8736. (ADB - 2014/04/14) + +* A Gnu Make directive (.NOTPARALLEL) is added to fortran/test/Makefile. + AIX native make does not support this directive and would fail if + parallel make (e.g. make -j4) is used to build the library. AIX users + either do not use parallel make or install Gnu Make to build the library. + (AKC 2014/04/08 HDFFV-8738) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro + DETECT_I in H5detect.c. Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior should not to be + used for H5detect.c. In the future, we can separate flags for H5detect.c + from the rest of the library. (SLU - 2013/10/16 HDFFV-8147) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i) + have bugs. They convert data between floating-point numbers and integers. + But the library's default is hard conversion. The user should avoid + explicitly enabling soft conversion between floating-point numbers and + integers. (Issue VMS-8; SLU - 2013/09/19) + +* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works + fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5; + SLU 2013/09/19) + +* When building using the Cray compilers on Cray machines, HDF5 + configure mistakenly thinks the compiler is an intel compiler and + sets the -std=c99 flag which breaks configure on Cray. To build HDF5 + properly on a Cray machine, please consult with the instructions in + INSTALL_parallel for building on Hopper. + (MSC - 2013/04/26 - HDFFV-8429) + +* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It + complains with this message: + "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. + + The reason is that __func__ is a predefined identifier in C99 standard. The + HDF5 C library uses it in H5private.h. The test ttypes.cpp includes + H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 + C++ compiler doesn't support __func__, thus fails to compile the C++ test. + But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler + knows this identifier, try to compile the following simple C++ program: + #include<stdio.h> + + int main(void) + { + printf("%s\n", __func__); + return 0; + } + (SLU - 2012/11/5) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set + to aprun -np X, because the H5lib_settings.c file was not generated + properly. Not setting those environment variables works, because + configure was able to automatically detect that it's a Cray system + and used the proper launch commands when necessary. + (MSC - 2012/04/18) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) doesn't have the problem. Users should lower the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + This will overwrite the library's default optimization level. + (SLU - 2012/02/07 - HDFFV-7829) + This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with + gcc 4.7.2. + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.12%%%% + + +HDF5 version 1.8.12 released on 2013-11-04 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.11 and +HDF5-1.8.12, and contains information on the platforms tested and +known problems in HDF5-1.8.12. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.12 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.12 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.12 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.12 (current +release) versus Release 1.8.11": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.11 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Added a configuration option to change the default plugin path. + The configure option is --with-default-plugindir=location. + The cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location. + HDFFV-8513. (ADB 2013/09/04) + - Renamed FFLAGS to FCFLAGS in configure. (ADB 2013/08/13) + - CMake can now package a compressed examples file, the default for + Windows binaries from HDF Group. (ADB - 2013/07/22) + + Library + ------- + - None + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5repack: Added the ability to use plugin filters to read and write + files. The option uses the filter number. HDFFV-8345 + (ADB - 2013/09/04). + - h5dump: Added the option -N --any_path, which searches the file for + paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). + - h5dump: Added the optional arg 0 to -A, which excludes attributes + from display. HDFFV-8134 (ADB - 2013/08/01). + + High-Level APIs + --------------- + - None + + Fortran API + ----------- + - None + + C++ API + ------- + - Added tutorial examples to C++/examples. They can be installed by + "make install-examples" and, in the installed directory, they can be + executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28) + - A new class, H5::H5Location, is added to represent the location concept + in the C library. It is a base class to H5::H5File and H5::H5Ojbect, + whose member functions are moved into H5::H5Location. H5::H5File can + now inherent those functions. As a result, an H5::H5File object can have + an attribute. (BMR - 2013/09/27) + - Added wrappers for H5Rget_obj_type2 to retrieve the type of the object + that an object reference points to. (BMR - 2013/09/27) + H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type) + - Added wrappers for H5Aexist to check whether an attribute exists given + a name. (BMR - 2013/09/27) + bool H5::H5Location::attrExists(const char* name) + bool H5::H5Location::attrExists(const H5std_string& name) + - Added a number of overloaded functions for convenience. (BMR - 2013/09/27) + + +Support for New Platforms, Languages, and Compilers +=================================================== + - None + +Bug Fixes since HDF5-1.8.11 +=========================== + + Configuration + ------------- + - Modified H5detect.c to scan floating point types for padding bits before + analyzing the type further. This should fix problems with gcc 4.8. + (NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500) + - HDF5 rpaths are no longer encoded in the library files when configured + with --disable-sharedlib-rpath. (LRK-2013-09-23 - HDFFV-8276) + + Library + ------- + - Added const qualifier to source buffer parameters in H5Dgather and + H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/09) + + - CMake now creates *.so.{lt_version} files with the same version as + configure. (ADB - 2013/06/05 HDFFV-8437) + + Parallel Library + ---------------- + - None + + Performance + ------------- + - None + + Tools + ----- + - h5dump: Added the option -N --any_path, which searches the file for + paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). + - h5dump: Added the optional arg 0 to -A, which excludes attributes + from display. HDFFV-8134 (ADB - 2013/08/01). + - h5dump correctly exports subsetted data to a file, using the --output + option. (ADB - 2013/06/07 HDFFV-8447) + - h5cc and other compile scripts now default to linking shared libraries + when HDF5 is configured with the --disable-static option. + (LRK - 2013-09-23 - HDFFV-8141) + + F90 API + ------- + - None + + C++ API + ------ + - None + + High-Level APIs: + ------ + - None + + Fortran High-Level APIs: + ------ + - None + + Testing + ------- + - test/big sometimes failed with the message of "file selection+offset not + within extent". This has been fixed. (AKC - 2013/09/28 HDFFV-8271). + - tools/h5diff/testh5diff.sh is run in every "make check", even after it + has passed in the previous run. It should not run again if there are no + code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392) + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.1 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 13.7-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 13.1.3 (Build 20130607) + + Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.1 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 13.1.3 (Build 20130607) + + Linux 2.6.32-358.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.1 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 13.1.3 (Build 20130607) + + Linux 2.6.32-358.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + IBM XL C/C++ V11.1 + IBM XL Fortran V13.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Visual Studio 2012 w/ Intel Fortran 13 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Visual Studio 2012 w/ Intel Fortran 13 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 13 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 13 (cmake) + + Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (fred) Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1 Build 20120928 + + Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (duck) Intel icc/icpc/ifort version 13.0.3 + + Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (wren) Intel icc/icpc/ifort version 13.0.3 + + OpenVMS IA64 V8.4 HP C V7.3-018 + HP Fortran V8.2-104939-50H96 + HP C++ V7.4-004 + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y +AIX 5.3 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y +OpenVMS IA64 V8.4 n y/n n y y n + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Snow Leopard 10.6.8 64-bit y n y n +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +AIX 5.3 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-358.2.1.el6.ppc64 y y y n +OpenVMS IA64 V8.4 n n n n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with + #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2 + (koala) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 + (loyalty) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 + (freedom) gcc 4.6.1 20110527 + g++ 4.6.1 20110527 + gfortran 4.6.1 20110527 + + Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.46-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora19 3.11.1-200.fc19.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1) + GNU Fortran (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1) + (cmake and autotools) + + SUSE 12.3 3.7.10-1.16-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.7.2 + GNU Fortran (SUSE Linux) 4.7.2 + (cmake and autotools) + + Ubuntu 13.04 3.8.0-30-generic #44-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 + GNU Fortran (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 + (cmake and autotools) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== +* Several HDF5 command-line tools and tests leave behind generated files + that are not cleaned up with "make clean" or "make distclean" when software + is built in place. The issue will be addressed in the 1.8.13 release. We + recommend to use build directory to compile and test HDF5 as described + in the INSTALL file, section 4.2. + +* Source directory names with spaces in them will cause failures in configure + or make on Mac (HDFFV-8152), Linux, and probably all other platforms. If a + configure command with a space is run from a build directory, it will exit + with an error message: "checking whether build environment is sane... + configure: error: unsafe srcdir value: '/scr/lrknox/hdf5 v1.8.12'". If + configure is run inside or below the directory with the space in the name, + libtool will get the directory path from the system, put the part of the + path before the space in the libdir variable in .../src/libhdf5.la, and + then fail to find the nonexistent directory. This is a known libtool issue + and the suggested workaround is to rename the directory without spaces. + (LRK - 2013/10/22) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro + DETECT_I in H5detect.c (HDFFV-8147). This issue will be addressed in the + next release. (SLU - 2013/10/16) + +* Running make check for the tools can fail in the tools tests if make was not + run prior. The tests for the tools use other tools in the tests, therefore + all the tools should be built before testing the tools. (ADB - 2013/10/09) + +* Make provided by Solaris fails in "make check". Solaris users should use + gmake to build and install HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) + +* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i) + have bugs. They convert data between floating-point numbers and integers. + But the library's default is hard conversion. The user should avoid + explicitly enabling soft conversion between floating-point numbers and + integers. (Issue VMS-8; SLU - 2013/09/19) + +* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works + fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5; + SLU 2013/09/19) + +* When building using the Cray compilers on Cray machines, HDF5 + configure mistakenly thinks the compiler is an intel compiler and + sets the -std=c99 flag which breaks configure on Cray. To build HDF5 + properly on a Cray machine, please consult with the instructions in + INSTALL_parallel for building on Hopper. + (MSC - 2013/04/26 - HDFFV-8429) + +* The h5dump and h5diff utilities occasionally produce different output + between Linux and Windows systems. This is caused by lower-level library + routines that fail to write fill values to the user's buffer when reading + unallocated chunks from datasets that have a fill value set to + H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of + spurious data values has only been encountered on Windows 32-bit systems. + (Issue HDFFV-8247; JP - 2013/03/27) + +* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It + complains with this message: + "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. + + The reason is that __func__ is a predefined identifier in C99 standard. The + HDF5 C library uses it in H5private.h. The test ttypes.cpp includes + H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 + C++ compiler doesn't support __func__, thus fails to compile the C++ test. + But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler + knows this identifier, try to compile the following simple C++ program: + #include<stdio.h> + + int main(void) + { + printf("%s\n", __func__); + return 0; + } + (SLU - 2012/11/5) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set + to aprun -np X, because the H5lib_settings.c file was not generated + properly. Not setting those environment variables works, because + configure was able to automatically detect that it is a Cray system + and used the proper launch commands when necessary. + (MSC - 2012/04/18) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) do not have the problem. Users should lower the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + This will overwrite the library's default optimization level. + (SLU - 2012/02/07 - HDFFV-7829) + This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with + gcc 4.7.2. + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.11%%%% + + +HDF5 version 1.8.11 released on 2013-05-08 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.10 and +HDF5-1.8.11-*, and contains information on the platforms tested and +known problems in HDF5-1.8.11-*. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.11 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.11 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.11 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.11 (current +release) versus Release 1.8.10": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.10 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Libtool version number is changed to 8.0.0 because there are API + changes. See below for details. (AKC - 2013/05/07 HDFFV-8435) + - Mac OS X 10.7 (Lion) and 10.8 (Mountain Lion) uses clang/clang++ as the + default C and C++ compilers. (AKC - 2013/04/19 HDFFV-8245) + - CMake minimum is now 2.8.10. (ADB 2013/1/14) + - A new tool, cmakehdf5, which is a build command script similar to + buildhdf5 is added and is available in the bin directory. + (AKC - 2013/01/16 HDFFV-8336) + + Library + ------- + - The library can load filter libraries dynamically during runtime. Users + can set the search path through environment variable HDF5_PLUGIN_PATH + and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) + - Added new API functions H5Dscatter and H5Dgather to scatter data to and + and gather data from a selection within a memory buffer. + (NAF - 2013/02/05) + - The library now supports the data conversion from enumeration to numeric + (integer and floating-point number) datatypes. See Issue HDFFV-8221. + (SLU - 2012/10/23) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5dump: added new option -O or -ddl to output the ddl text to a file. This + is a complement to the -o or --output option, which redirects the data to + a file. HDFFV-8229 (ADB - 2013/2/25) + + High-Level APIs + --------------- + - A new API function, H5DOwrite_chunk. This function writes a data chunk + directly into a file, bypassing hyperslab selection, data conversion, + and the filter pipeline. The user must be careful with the function and + clearly understand the I/O process of the library. (SLU - 2013/2/11) + + Fortran API + ----------- + - New API functions added (MSB - 2013/3/23): + + h5odecr_refcount_f, h5oexists_by_name_f, h5oget_comment_f, + h5oget_comment_by_name_f, h5oincr_refcount_f, h5oopen_by_idx_f, + h5oset_comment_f, h5oset_comment_by_name_f, h5oset_comment_by_name_f + + F2003: h5oget_info_f, h5oget_info_by_idx_f, h5ovisit_by_name_f + + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and + Sun Fortran 95 8.6 compiler. + - Visual Studio 2012 w/ Intel Fortran 13 on Windows 7 + - g95 released new version recently and is tested in this release. + +Bug Fixes since HDF5-1.8.10 +========================== + + Configuration + ------------- + - Fixed Thread-safe configure failure for the AIX platform. + (AKC - 2013/04/19 HDFFV-8390) + - Configure will check the result of header searches before searching for + the library. + Fixes HDFFV-8257 (ADB 2013/03/04) + - HDF does not support building SHARED Fortran libraries on OSX. Added + CMake code to check for this condition. + Fixes HDFFV-8227 (ADB 2013/03/04) + - CMake builds on Windows will no longer use legacy naming for libraries. + The "dll" tag will no longer be added to the name of *.lib and *.dll. + The option HDF_LEGACY_NAMING is now OFF by default. + Fixes HDFFV-8292 (ADB 2013/01/30) + + Library + ------- + - The library now behaves correctly when performing large I/O operations + on Mac OS-X. Previously, single I/O operations > 2 GB would fail + since the Darwin read/write calls cannot handle the number of bytes + that their parameter types imply. + Fixes HDFFV-7975 and HDFFV-8240 (DER 2013/01/07) + - Fixed a bug in the core VFD that causes failures when opening files + > 2 GB. + Fixes HDFFV-8124 and HDFFV-8158 (DER 2013/01/07) + - Fixed a bug where uninitialized memory was read during variable-length + type conversion. This caused segfaults in netCDF. Fixes HDFFV-8159. + (DER 2013/03/30) + - Removed the H5Pset/get_dxpl_multi functions from the library. The + intended functionality for them was never fully implemented, and they + have always been fundamentally broken. NOTE: This does not affect + setting the multi VFD or any expected VFD functionality. Multi VFD + usage remains unchanged. + Fixes HDFFV-8296. (DER 2013/03/30) + + Parallel Library + ---------------- + - None + + Performance + ------------- + - None + + Tools + ----- + - h5redeploy is changed to do this by default: + Installation directories: + prefix architecture-independent files. + exec_prefix architecture-dependent files, default is <prefix>. + libdir libraries, default is <exec_prefix>/lib. + includedir header files, default is <prefix/include>. + This allows users to just change the first line of prefix=<...> and the + effect will change libdir and includedir too. (AKC 2013/04/05 HDFFV-8358) + - h5repack: Fixed failure to convert the layout of a small chunked + dataset (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/26) + - h5dump: Fixed displaying compression ratio for unknown or user-defined + filters. HDFFV-8344 (XCAO 2013/03/19) + - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined + filter. HDFFV-8346 (XCAO 2013/03/19) + - h5diff: Fixed to return the correct exit code 1 when the program + detects a unique extra attribute. Prior to this fix, h5diff returned + exit code 0 indicating the two files are identical. + HDFFV-7643 (JKM 2013/02/15) + - h5dump: Fixed writing nulls to a binary file when exporting a dataset + with compound string datatype. HDFFV-8169 (ADB 2013/1/31) + - The following h5stat test case failed in BG/P machines (and potentially + other machines that display extra output if an MPI task returns with a + non-zero code.) + Testing h5stat notexist.h5 + The test script was fixed to ignore the extra output. HDFFV-8233 + (AKC - 2012/11/30) + - h5diff: Improved speed when comparing HDF5 files with lots of + attributes. Much slower performance was identified with release versions + from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19) + + F90 API + ------- + - The integer type of the 'offset' argument in h5pset_external_f and + h5pget_external_f was changed to INTEGER(KIND=OFF_T) to support 8-byte + integers, matching the C type definition of off_t. (MSB - 2013/3/23) + - h5fc updated to recognize .f95, .f03 and .f08 file extensions. + + C++ API + ------ + - The C++ wrappers DSetMemXferPropList::setMulti/getMulti were removed + because the C functions H5Pset/get_dxpl_multi functions are removed + from the library. Fixes HDFFV-8296 by DER. (BMR 2013/03/30) + - An exception thrown by an internal function was not propagating to the + test program during stack unwinding, so it couldn't be caught by the + test, and the program terminated "without an active exception." It + seemed that the problem happened when c_str() was used to generate + an equivalent const char* from a std::string and the resulting string + was passed to the internal function. As a work-around, we added a + try/catch around the the call to the internal function and when the + exception is caught there, it is re-thrown. Fixes HDFFV-8067. + (BMR 2013/03/30) + + High-Level APIs: + ------ + - Fixed a problem with H5DSget_scale_name including the NULL terminator + in the size calculation returned by the function. The API was changed + to NOT include the NULL terminator in the size of name returned + (MSB- 2013/2/10) + + Fortran High-Level APIs: + ------ + - None + + Testing + ------- + - In some Mac systems, testlibinfo.sh failed with this error: + Check file ../src/.libs/libhdf5.7.dylib + strings: object: ../src/.libs/libhdf5.7.dylib malformed object \ + (unknown load command 15) + The strings command of Mac systems inspects library files, and older + versions of strings may not know newer library formats, resulting + in errors. Fixed by sending the library file as stdin to the strings + command to avoid this problem. (AKC - 2013/03/08 HDFFV-8305) + - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation + faulted when used before. (AKC - 2013/02/12 HDFFV-8267) + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.6.3 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 11.9-0 + Version 12.5-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 12.1 (Build 20110811) + Version 12.1 (Build 20120212) + + Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.6.3 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 11.9-0 + Version 12.5-0 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 12.1 (Build 20110811) + Version 12.1 (Build 20120212) + + Linux 2.6.32-358.2.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 12.1 20120212 + + Linux 2.6.32-358.2.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + IBM XL C/C++ V11.1 + IBM XL Fortran V13.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Visual Studio 2012 w/ Intel Fortran 13 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Visual Studio 2012 w/ Intel Fortran 13 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (fred) Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1 Build 20120928 + + Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (duck) Intel icc/icpc/ifort version 13.0 + + Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (wren) Intel icc/icpc/ifort version 13.0.1.119 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y +AIX 5.3 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/n n y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Mac OS X Snow Leopard 10.6.8 64-bit y n y n +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +AIX 5.3 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-358.2.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with + #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2 + (koala) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Debian6.0.7 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + (cmake and autotools) + + Fedora18 3.7.9-205.fc18.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.7.2 20121109 (Red Hat 4.7.2-8) + GNU Fortran (GCC) 4.7.2 20120507 (Red Hat 4.7.2-8) + (cmake and autotools) + + SUSE 12.3 3.7.10-1.1-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.7.2 + GNU Fortran (SUSE Linux) 4.7.2 + (cmake and autotools) + + Ubuntu 12.10 3.5.0-25-generic #39-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 + GNU Fortran (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 + (cmake and autotools) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== + +* When building using the Cray compilers on Cray machines, HDF5 + configure mistakenly thinks the compiler is an intel compiler and + sets the -std=c99 flag which breaks configure on Cray. To build HDF5 + properly on a Cray machine, please consult with the instructions in + INSTALL_parallel for building on Hopper. + (MSC - 2013/04/26 - HDFFV-8429) + +* The h5dump and h5diff utilities occasionally produce different output + between Linux and Windows systems. This is caused by lower-level library + routines that fail to write fill values to the user's buffer when reading + unallocated chunks from datasets that have a fill value set to + H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of + spurious data values has only been encountered on Windows 32-bit systems. + (Issue HDFFV-8247; JP - 2013/03/27) + +* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It + complains with this message: + "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. + + The reason is that __func__ is a predefined identifier in C99 standard. The + HDF5 C library uses it in H5private.h. The test ttypes.cpp includes + H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 + C++ compiler doesn't support __func__, thus fails to compile the C++ test. + But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler + knows this identifier, try to compile the following simple C++ program: + #include<stdio.h> + + int main(void) + { + printf("%s\n", __func__); + return 0; + } + (SLU - 2012/11/5) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set + to aprun -np X, because the H5lib_settings.c file was not generated + properly. Not setting those environment variables works, because + configure was able to automatically detect that it's a Cray system + and used the proper launch commands when necessary. + (MSC - 2012/04/18) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) doesn't have the problem. Users should lower the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + This will overwrite the library's default optimization level. + (SLU - 2012/02/07 - HDFFV-7829) + This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with + gcc 4.7.2. + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. + (SLU - 2010/05/05 - HDFFV-1264) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.10-patch1%%%% + + +HDF5 version 1.8.10-patch1 released on 2013-01-22 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.9 and +HDF5 1.8.10, and contains information on the platforms tested and +known problems in HDF5-1.8.10. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.10 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.10 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.10 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.10 (current +release) versus Release 1.8.9": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.10 +- Bug Fixes since HDF5-1.8.9 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - A new tool, cmakehdf5, which is a build command script similar to + buildhdf5 is added and is available in the bin directory. + (AKC - 2013/01/21) + + Library + ------- + - Updated to latest autotools and changed all hard *.sh scripts to + configure managed *.sh.in files. Removed overloading of autotools + TESTS variable by examples and tests. Renamed configure.in to + configure.ac. (ADB - 2012/08/23 - HDFFV-8129) + - The data sieve buffer size was set for all the datasets in the file. It + could waste memory if any dataset size is smaller than the sieve buffer + size. Now the library picks the smaller one between the dataset size + and the sieve buffer size from the file access property. See Issue 7934. + (SLU - 2012/4/11) + + Parallel Library + ---------------- + - Added the H5Pget_mpio_no_collective_cause() function that retrieves + reasons why the collective I/O was broken during read/write IO access. + (JKM - 2012/08/30 HDFFV-8143) + + - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) + + Tools + ----- + - h5import: Changed to allow the use of h5dump output as input files to + h5import. h5dump must include the "-p" option to print the properties; + configuration file is captured output of h5dump. The restrictions are + that only one dataset with a simple datatype (integer, floating-point, + or string) can be processed. Integers and floating-point imports from + h5dump must use the "binary" option for the data file. The string version + uses the h5dump "-y --width=1" options to disable the indexing printouts, + print single columns, and obviously NOT use the "binary" option. + (ADB - 2012/07/19 HDFFV-721) + + High-Level APIs + --------------- + - None + + Fortran API + ----------- + - Fixed a typo in return value of the nh5dread_f_c function (was 1 + instead of 0 on success); fixed the return value to make it consistent + with other Fortran functions; cleaned debug statements from the code. + (EIP - 2012/06/23) + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - None + +Bug Fixes since HDF5-1.8.10 +=========================== + Library + ------- + - The library now behaves correctly when performing large I/O operations on + Mac OS-X. Previously, single I/O operations > 2 GB would fail since the + Darwin read/write calls cannot handle the number of bytes that their + parameter types imply. + Fixes HDFFV-7975 and HDFFV-8240 (DER - 07 JAN 2013) + - Fixed a bug in the core VFD that cause failures when opening files > 2 GB. + Fixes HDFFV-8124 and HDFFV-8158 (DER - 07 JAN 2013) + + Tools + ----- + - The following h5stat test case failed in BG/P machines (and potentially + other machines that display extra output if an MPI task returns with a + non-zero code.) + Testing h5stat notexist.h5 + The test script was fixed to ignore the extra output. + HDFFV-8233 (AKC - 2012/12/17) + - h5diff: Fixed slowness when comparing HDF5 files with many attributes. + Much slower performance was identified with later release version + (from 1.8.7 to 1.8.10) compared to 1.8.6. The issue was introduced + from fixing an attribute related bug for 1.8.7 release in the past. + HDFFV-8145 (JKM 2012/12/13) + + Testing + ------- + - None + +Bug Fixes since HDF5-1.8.9 +========================== + + Configuration + ------------- + - Fixed configure --enable-production to not use -O optimization for Lion + and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2 + (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of + the hard conversion code in test/dt_arith.c to fail. HDFFV-8017. + (AKC - 2012/10/10) + - Fixed AIX Fortran compiler flags to use appropriate settings for + debugging, profiling, and optimization situations. HDFFV-8069. + (AKC 2012/09/27) + + Library + ------- + - Fixed a memory leak exposed when inserting/removing a property + from a property list several times. HDFFV-8022. (MSC 2012/05/18) + - The file_image test will fail in the "initial file image and callbacks in + the core VFD" sub-test if the source directory is read-only as the test + fails to create its test files in the build directory. This has been + fixed. HDFFV-8009 (AKC - 2012/07/06) + + + Parallel Library + ---------------- + - The MPI-POSIX VFD was updated to include the POSIX and Windows + correctness features added that had already been added to the other VFDs. + HDFFV-8058/7845. (DER 2012/09/17) + + Performance + ------------- + - Removed program perform/benchpar from the enable-build-all list. The + program will be retired or moved to another location. HDFFV-8156 + (AKC 2012/10/01) + - Retired program perform/mpi-perf. Its purpose has been incorporated + into h5perf. (AKC 2012/09/21) + + Tools + ----- + - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if + source file contains chunked dataset and a chunk dim is bigger than + the dataset dim. Another issue is that the command changed max dims + if chunk dim is smaller than the dataset dim. These issue occurred + when dataset size is smaller than 64k (compact size limit) Fixed both. + HDFFV-8012 (JKM 2012/09/24) + - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no + longer add together the differences between datasets and the differences + between attributes of those datasets. This change makes the output of + verbose mode consistent for datasets, groups, and committed datatypes. + HDFFV-5919 (JKM 2012/09/10) + - h5diff: Fixed the incorrect result when comparing attribute data + values and the data type has the same class but different sizes. + HDFFV-7942 (JKM 2012/08/15) + - h5dump: Replaced single element fwrite with block writes. + HDFFV-1208 (ADB 2012/08/13) + - h5diff: Fixed test failure for "make check" due to failure of + copying test files when performed in HDF5 source tree. Also applied + to other tools. HDFFV-8107 (JKM 2012/08/01) + - ph5diff: Fixed intermittent hang issue on a certain operation in + parallel mode. It was detected by daily test for comparing + non-comparable objects, but it could have occurred in other + operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01) + - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh + to better report when there is an error in the file copying. + HDFFV-8105 (AKC 2012/07/22) + - h5dump: Fixed the sort by name display to maintain correct parent/child + relationships between ascending/descending order. + HDFFV-8095 (ADB 2012/07/12) + - h5dump: Fixed the display by creation order when using option -n + (print contents). + HDFFV-5942 (ADB 2012/07/09) + - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output. + Used technique similar to what was done in h5ls (matches library + options). + HDFFV-7999 (ADB 2012/05/23) + - h5diff: Fixed the tool so that it will not check and display the status + of dangling links without setting the --follow-symlinks option. This + also improved performance when comparing lots of external links without + the --follow-symlinks option. + HDFFV-7998 (JKM 2012/04/26) + + F90 API + ------- + + - Fixed a typo in return value of the nh5dread_f_c function (was 1 + instead of 0 on success); fixed the return value to make it consistent + with other Fortran functions; cleaned debug statements from the code. + (EIP - 2012/06/23) + + - Fixed a problem writing/reading control characters to a dataset; writing + a string containing alerts, backspace, carriage_return, form_feed, + horizontal_tab, vertical_tab, or new_line is now tested and working. + (MSB - 2012/09/01) + + - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) + + - Corrected the number of continuation lines in the src files + to be less than 32 lines for F95 compliance. (MSB - 2012/10/01) + + C++ API + ------ + - None + + High-Level APIs: + ------ + + - Fixed problem with H5TBdelete_record destroying all data following the + deletion of a row. (MSB- 2012/7/26) + + - Fixed H5LTget_attribute_string not closing an object identifier when an + error occurs. (MSB- 2012/7/21) + + - Corrected the return type of H5TBAget_fill from herr_t to htri_t to + reflect that a return value of 1 indicates that a fill value is + present, 0 indicates a fill value is not present, and <0 indicates an + error. + + Fortran High-Level APIs: + ------ + - None + +Supported Platforms +=================== + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.6.3 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 11.9-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 12.1 + MPICH mpich2-1.4.1p1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.6.3 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 11.9-0 + Version 12.5-0 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 12.1 (Build 20110811) + Version 12.1 (Build 20120212) + MPICH mpich2-1.4.1p1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 + (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) + + Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers + ch5.x86_64 GNU/Linux Version 12.1.5.339 + (LLNL Aztec) + + IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 + (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 + XL Fortran for Blue Gene/P, bgxlf90 V11.1 + + SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 + (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 + Sun C++ 5.9 Sun OS_sparc Patch 124863-26 + Sun C 5.11 SunOS_sparc + Sun Fortran 95 8.5 SunOS_sparc + Sun C++ 5.11 SunOS_sparc + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + (fred) gfortran GNU Fortran (GCC) 4.6.2 + Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1.0.038 Build 20110811 + + Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 + (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1.0.038 Build 20110811 + + Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + (duck) gfortran GNU Fortran (GCC) 4.6.2 + + Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 + (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 + gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + gfortran GNU Fortran (GCC) 4.6.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.10 32-bit n y/y n y y y +Solaris2.10 64-bit n y/n n y y y +Windows 7 y y/n n y y y +Windows 7 x64 y y/n n y y y +Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n +Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y +Mac OS X Lion 10.7.3 32-bit n y/y n y y n +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n +AIX 5.3 32- and 64-bit y y/n y y y y +CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y +CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y +Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit n n n n +Windows 7 y y y y +Windows 7 x64 y y y y +Mac OS X Snow Leopard 10.6.8 32-bit y n y n +Mac OS X Snow Leopard 10.6.8 64-bit y n y n +Mac OS X Lion 10.7.3 32-bit y n y y +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +AIX 5.3 32- and 64-bit n n n y +CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n +CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n +Linux 2.6.32-220.7.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + (cmake and autotools) + + Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + (cmake and autotools) + + Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + (cmake and autotools) + + Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + (cmake and autotools) + + SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux + gcc (SUSE Linux) 4.7.1 + GNU Fortran (SUSE Linux) 4.7.1 + (cmake and autotools) + + SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.7.1 + GNU Fortran (SUSE Linux) 4.7.1 + (cmake and autotools) + + Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + (cmake and autotools) + + Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + (cmake and autotools) + (Use optimization level -O1) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set + to aprun -np X, because the H5lib_settings.c file was not generated + properly. Not setting those environment variables works, because + configure was able to automatically detect that it's a Cray system + and used the proper launch commands when necessary. + (MSC - 2012/04/18) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) doesn't have the problem. Users should lower the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + This will overwrite the library's default optimization level. + (SLU - 2012/02/07 - HDFFV-7829) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. + (SLU - 2010/05/05 - HDFFV-1264) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.10%%%% + + +HDF5 version 1.8.10 released on 2012-10-26 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.9 and +HDF5 1.8.10, and contains information on the platforms tested and +known problems in HDF5-1.8.10. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.10 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.10 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.10 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.10 (current +release) versus Release 1.8.9": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.9 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + ------------- + - None + + Library + ------- + - Updated to latest autotools and changed all hard *.sh scripts to + configure managed *.sh.in files. Removed overloading of autotools + TESTS variable by examples and tests. Renamed configure.in to + configure.ac. (ADB - 2012/08/23 - HDFFV-8129) + - The data sieve buffer size was set for all the datasets in the file. It + could waste memory if any dataset size is smaller than the sieve buffer + size. Now the library picks the smaller one between the dataset size + and the sieve buffer size from the file access property. See Issue 7934. + (SLU - 2012/4/11) + + Parallel Library + ---------------- + - Added the H5Pget_mpio_no_collective_cause() function that retrieves + reasons why the collective I/O was broken during read/write IO access. + (JKM - 2012/08/30 HDFFV-8143) + + - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) + + Tools + ----- + - h5import: Changed to allow the use of h5dump output as input files to + h5import. h5dump must include the "-p" option to print the properties; + configuration file is captured output of h5dump. The restrictions are + that only one dataset with a simple datatype (integer, floating-point, + or string) can be processed. Integers and floating-point imports from + h5dump must use the "binary" option for the data file. The string version + uses the h5dump "-y --width=1" options to disable the indexing printouts, + print single columns, and obviously NOT use the "binary" option. + (ADB - 2012/07/19 HDFFV-721) + + High-Level APIs + --------------- + - None + + Fortran API + ----------- + - Fixed a typo in return value of the nh5dread_f_c function (was 1 + instead of 0 on success); fixed the return value to make it consistent + with other Fortran functions; cleaned debug statements from the code. + (EIP - 2012/06/23) + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - None + +Bug Fixes since HDF5-1.8.9 +========================== + + Configuration + ------------- + - Fixed configure --enable-production to not use -O optimization for Lion + and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2 + (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of + the hard conversion code in test/dt_arith.c to fail. HDFFV-8017. + (AKC - 2012/10/10) + - Fixed AIX Fortran compiler flags to use appropriate settings for + debugging, profiling, and optimization situations. HDFFV-8069. + (AKC 2012/09/27) + + Library + ------- + - Fixed a memory leak exposed when inserting/removing a property + from a property list several times. HDFFV-8022. (MSC 2012/05/18) + - The file_image test will fail in the "initial file image and callbacks in + the core VFD" sub-test if the source directory is read-only as the test + fails to create its test files in the build directory. This has been + fixed. HDFFV-8009 (AKC - 2012/07/06) + + + Parallel Library + ---------------- + - The MPI-POSIX VFD was updated to include the POSIX and Windows + correctness features added that had already been added to the other VFDs. + HDFFV-8058/7845. (DER 2012/09/17) + + Performance + ------------- + - Removed program perform/benchpar from the enable-build-all list. The + program will be retired or moved to another location. HDFFV-8156 + (AKC 2012/10/01) + - Retired program perform/mpi-perf. Its purpose has been incorporated + into h5perf. (AKC 2012/09/21) + + Tools + ----- + - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if + source file contains chunked dataset and a chunk dim is bigger than + the dataset dim. Another issue is that the command changed max dims + if chunk dim is smaller than the dataset dim. These issue occurred + when dataset size is smaller than 64k (compact size limit) Fixed both. + HDFFV-8012 (JKM 2012/09/24) + - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no + longer add together the differences between datasets and the differences + between attributes of those datasets. This change makes the output of + verbose mode consistent for datasets, groups, and committed datatypes. + HDFFV-5919 (JKM 2012/09/10) + - h5diff: Fixed the incorrect result when comparing attribute data + values and the data type has the same class but different sizes. + HDFFV-7942 (JKM 2012/08/15) + - h5dump: Replaced single element fwrite with block writes. + HDFFV-1208 (ADB 2012/08/13) + - h5diff: Fixed test failure for "make check" due to failure of + copying test files when performed in HDF5 source tree. Also applied + to other tools. HDFFV-8107 (JKM 2012/08/01) + - ph5diff: Fixed intermittent hang issue on a certain operation in + parallel mode. It was detected by daily test for comparing + non-comparable objects, but it could have occurred in other + operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01) + - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh + to better report when there is an error in the file copying. + HDFFV-8105 (AKC 2012/07/22) + - h5dump: Fixed the sort by name display to maintain correct parent/child + relationships between ascending/descending order. + HDFFV-8095 (ADB 2012/07/12) + - h5dump: Fixed the display by creation order when using option -n + (print contents). + HDFFV-5942 (ADB 2012/07/09) + - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output. + Used technique similar to what was done in h5ls (matches library + options). + HDFFV-7999 (ADB 2012/05/23) + - h5diff: Fixed the tool so that it will not check and display the status + of dangling links without setting the --follow-symlinks option. This + also improved performance when comparing lots of external links without + the --follow-symlinks option. + HDFFV-7998 (JKM 2012/04/26) + + F90 API + ------- + + - Fixed a typo in return value of the nh5dread_f_c function (was 1 + instead of 0 on success); fixed the return value to make it consistent + with other Fortran functions; cleaned debug statements from the code. + (EIP - 2012/06/23) + + - Fixed a problem writing/reading control characters to a dataset; writing + a string containing alerts, backspace, carriage_return, form_feed, + horizontal_tab, vertical_tab, or new_line is now tested and working. + (MSB - 2012/09/01) + + - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) + + - Corrected the number of continuation lines in the src files + to be less than 32 lines for F95 compliance. (MSB - 2012/10/01) + + C++ API + ------ + - None + + High-Level APIs: + ------ + + - Fixed problem with H5TBdelete_record destroying all data following the + deletion of a row. (MSB- 2012/7/26) + + - Fixed H5LTget_attribute_string not closing an object identifier when an + error occurs. (MSB- 2012/7/21) + + - Corrected the return type of H5TBAget_fill from herr_t to htri_t to + reflect that a return value of 1 indicates that a fill value is + present, 0 indicates a fill value is not present, and <0 indicates an + error. + + Fortran High-Level APIs: + ------ + - None + +Supported Platforms +=================== + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.6.3 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 11.9-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 12.1 + MPICH mpich2-1.4.1p1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.6.3 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 11.9-0 + Version 12.5-0 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 12.1 (Build 20110811) + Version 12.1 (Build 20120212) + MPICH mpich2-1.4.1p1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 + (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) + + Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers + ch5.x86_64 GNU/Linux Version 12.1.5.339 + (LLNL Aztec) + + IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 + (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 + XL Fortran for Blue Gene/P, bgxlf90 V11.1 + + SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 + (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 + Sun C++ 5.9 Sun OS_sparc Patch 124863-26 + Sun C 5.11 SunOS_sparc + Sun Fortran 95 8.5 SunOS_sparc + Sun C++ 5.11 SunOS_sparc + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) + (cmake and autotools) + + Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + (fred) gfortran GNU Fortran (GCC) 4.6.2 + Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1.0.038 Build 20110811 + + Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 + Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 + (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1.0.038 Build 20110811 + + Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + (duck) gfortran GNU Fortran (GCC) 4.6.2 + + Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 + (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 + gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + gfortran GNU Fortran (GCC) 4.6.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.10 32-bit n y/y n y y y +Solaris2.10 64-bit n y/n n y y y +Windows 7 y y/n n y y y +Windows 7 x64 y y/n n y y y +Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n +Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y +Mac OS X Lion 10.7.3 32-bit n y/y n y y n +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n +AIX 5.3 32- and 64-bit y y/n y y y y +CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y +CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y +Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit n n n n +Windows 7 y y y y +Windows 7 x64 y y y y +Mac OS X Snow Leopard 10.6.8 32-bit y n y n +Mac OS X Snow Leopard 10.6.8 64-bit y n y n +Mac OS X Lion 10.7.3 32-bit y n y y +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +AIX 5.3 32- and 64-bit n n n y +CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n +CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n +Linux 2.6.32-220.7.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + (cmake and autotools) + + Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + (cmake and autotools) + + Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + (cmake and autotools) + + Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) + (cmake and autotools) + + SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux + gcc (SUSE Linux) 4.7.1 + GNU Fortran (SUSE Linux) 4.7.1 + (cmake and autotools) + + SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.7.1 + GNU Fortran (SUSE Linux) 4.7.1 + (cmake and autotools) + + Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + (cmake and autotools) + + Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 + (cmake and autotools) + (Use optimization level -O1) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== +* The following h5stat test case fails in BG/P machines (and potentially other + machines that display extra output if an MPI task returns with a non-zero + code.) + Testing h5stat notexist.h5 + + The test actually runs and passes as expected. It is the extra output from + the MPI process that causes the test script to fail. This will be fixed + in the next release. (AKC - 2012/10/25 - HDFFV-8233) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set + to aprun -np X, because the H5lib_settings.c file was not generated + properly. Not setting those environment variables works, because + configure was able to automatically detect that it's a Cray system + and used the proper launch commands when necessary. + (MSC - 2012/04/18) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) doesn't have the problem. Users should lower the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + This will overwrite the library's default optimization level. + (SLU - 2012/02/07 - HDFFV-7829) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14 - HDFFV-8235) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. + (SLU - 2010/05/05 - HDFFV-1264) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + + +%%%%1.8.9%%%% + + +HDF5 version 1.8.9 released on 2012-05-09 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.8 and +HDF5 1.8.9. It also contains information on the platforms tested and +known problems in HDF5-1.8.9. + +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.9 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.9 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.9 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.9 (current +release) versus Release 1.8.8": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.8 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - None + + Library + ------- + - Added new feature to merge committed datatypes when copying objects, + using new H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG, modified by new API + routines: H5Padd_merge_committed_dtype_path(), + H5Pfree_merge_committed_dtype_paths(), H5Pset_mcdt_search_cb() and + H5Pget_mcdt_search_cb(). (QAK - 2012/03/30) + - Added new feature which allows working with files in memory in the + same ways files are worked with on disk. New API routines include + H5Pset_file_image, H5Pget_file_image, H5Pset_file_image_callbacks, + H5Pget_file_image_callbacks, H5Fget_file_image, and + H5LTopen_file_image. (QAK - 2012/04/17) + + Parallel Library + ---------------- + - Corrected memory allocation error in MPI datatype construction code. + (QAK - 2012/04/23) + - Add two new routines to set/get the atomicity parameter in the + MPI library to perform atomic operations. Some file systems (for + example PVFS2) do not support atomic updates, so those routines + would not be supported. (MSC - 2012/03/27 - HDFFV-7961) + + Tools + ----- + - h5repack: Added ability to set the metadata block size of the output + file, with the '-M'/'--metadata_block_size' command line parameter. + (QAK - 2012/03/30) + - h5stat: Added ability to display a summary of the file space usage for a + file, with the '-S'/'--summary' command line parameter. (QAK - 2012/03/28) + - h5dump: Added capability for "-a" option to show attributes containing "/" + by using an escape character. For example, for a dataset "/dset" + containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" + to show the content of the attribute. (PC - 2012/03/12 - HDFFV-7523) + - h5dump: Added ability to apply command options across multiple files using a + wildcard in the filename. Unix example; "h5dump -H -d Dataset1 tarr*.h5". + Cross platform example; "h5dump -H -d Dataset1 tarray1.h5 tarray2.h5 tarray3.h5". + (ADB - 2012/03/12 - HDFFV-7876). + - h5dump: Added new option --no-compact-subset. This option will not + interpret the '[' character as starting the compact form of + subsetting. This is useful when the "h5dump error: unable to + open dataset "datset_name"" message is output because a dataset + name contains a '[' character. (ADB - 2012/03/05 - HDFFV-7689). + - h5repack: Improved performance for big chunked datasets (size > 128MB) + when used with the layout (-l) or compression (-f) options. + Before this change, repacking datasets with chunks with a large first + dimension would take extremely long. For example, repacking a dataset + with chunk dimensions of 1024x5x1 might take many hours to process + while changing a dataset with chunk dimensions set to 1x5x1024 + might take under an hour. After this change, processing the dataset + with chunk dimensions of 1024x5x1 takes about 15 minutes, and processing + a dataset with chunk dimensions of 1x5x1024 takes about 14 minutes. + (JKM - 2012/03/01 - HDFFV-7862) + + High-Level APIs + --------------- + - New API: H5LTpath_valid (Fortran: h5ltpath_valid_f) checks + if a path is correct, determines if a link resolves to a valid + object, and checks that the link does not dangle. (MSB - 2012/03/15) + + Fortran API + ----------- + + - Added for the C API the Fortran wrapper: + h5ocopy_f (MSB - 2012/03/22) + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - None + +Bug Fixes since HDF5-1.8.8 +========================== + + Configuration + ------------- + - Fixed Makefile issue in which "-Wl," was not properly specified + prior to -rpath when building parallel Fortran libraries with + an Intel compiler. (MAM - 2012/03/26) + - Makefiles generated by other packages using h5cc as the compiler + no longer error when 'make' is invoked more than once in order + to 'rebuild' after changes to source. (MAM - 2012/03/26) + - Added code to display the version information of XL Fortran and C++ + in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793) + - Updated all CMakeLists.txt files to indicate the minimum CMake version is + the current standard of 2.8.6 (ADB - 2011/12/05 - HDFFV-7854) + + Library + ------- + - Windows and STDIO correctness changes have been propagated from the SEC2 + and old Windows drivers to the STDIO VFD. (DER - 2012/03/30 - HDFFV-7917) + - Fixed an error that would occur when copying an object with attribute + creation order tracked and indexed. (NAF - 2012/03/28 - HDFFV-7762) + - Fixed a bug in H5Ocopy(): When copying an opened object, call the + object's flush class action to ensure that cached data is flushed so + that H5Ocopy will get the correct data. (VC - 2012/03/27 - HDFFV-7853) + - The istore test will now skip the sparse 50x50x50 test when the VFD does + not support sparse files on that platform. The most important platforms + on which this will be skipped are Windows (NTFS sparse files are not + supported) and Mac OS-X (HFS sparse files are not supported). This + fixes CTest timeout issues on Windows. (DER - 2012/03/27 - HDFFV-7769) + - Windows and POSIX correctness changes have been propagated from the SEC2 + VFD to the Core VFD. This mainly affects file operations on the + driver's backing store and fixes a problem on Windows where large files + could not be read. (DER - 2012/03/27 - HDFFV-7916 - HDFFV-7603) + - When an application tries to write or read many small data chunks and + runs out of memory, the library had a segmentation fault. The fix is to + return the error stack with proper information. + (SLU - 2012/03/23 - HDFFV-7785) + - H5Pset_data_transform had a segmentation fault in some cases like x*-100. + It works correctly now and handles other cases like 100-x or 2/x. + (SLU - 2012/03/15 - HDFFV-7922) + - Fixed rare corruption bugs that could occur when using the new object + header format. (NAF - 2012/03/15 - HDFFV-7879) + - Fixed an error that occurred when creating a contiguous dataset with a + zero-sized dataspace and space allocation time set to 'early'. + (QAK - 2012/03/12) + - Changed Windows thread creation to use _beginthread() instead of + CreateThread(). Threads created by the latter can be killed in + low-memory situations. (DER - 2012/02/10 - HDFFV-7780) + - Creating a dataset in a read-only file caused a segmentation fault when + the file is closed. It's fixed. The attempt to create a dataset will + fail with an error indicating the file is read-only. + (SLU - 2012/01/25 - HDFFV-7756) + - Fixed a segmentation fault that could occur when shrinking a dataset + with chunks larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833) + - Fixed a bug that could cause H5Oget_info to return the wrong address + after copying a committed (named) datatype. (NAF - 2011/11/14) + - The library allowed the conversion of strings between ASCII and UTF8 + We have corrected it to report an error under this situation. + (SLU - 2011/11/8 - HDFFV-7582) + - Fixed a segmentation fault when the library tried to shrink the size + of a compound datatype through H5Tset_size immediately after the + datatype was created. (SLU - 2011/11/4 - HDFFV-7618) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5unjam: Fixed a segmentation fault that occurred when h5unjam was used + with the -V (show version) option. (JKM - 2012/04/19 - HDFFV-8001) + - h5repack: Fixed a failure that occurred when repacking the chunk size + of a specified chunked dataset with unlimited max dims. + (JKM - 2012/04/11 - HDFFV-7993) + - h5diff: Fixed a failure when comparing groups. Before the fix, if an + object in a group was compared with an object in another group where + both had the same name but the object type was different, then h5diff + would fail. After the fix, h5diff detects such cases as non-comparable + and displays appropriate error messages. + (JKM - 2012/03/28 - HDFFV-7644) + - h5diff: If unique objects exist only in one file and if h5diff is set to + exclude the unique objects with the --exclude-path option, then h5diff + might miss excluding some objects. This was fixed to correctly exclude + objects. (JKM - 2012/03/20 - HDFFV-7837) + - h5diff: When two symbolic dangling links are compared with the + --follow-symlinks option, the result should be the same. This worked when + comparing two files, but didn't work when comparing two objects. + h5diff now works when comparing two objects. + (JKM - 2012/03/09 - HDFFV-7835) + - h5dump: Added the tools library error stack to properly catch error + information generated within the library. (ADB - 2012/03/12 - HDFFV-7958) + - h5dump: Changed the process where an open link used to fail. Now dangling + links no longer throw error messages. (ADB - 2012/03/12 - HDFFV-7839) + - h5dump: Refactored code to remove duplicated functions. Split XML + functions from DDL functions. Corrected indentation and formatting + errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified + all tools call tools_init() in main. The USER_BLOCK data now correctly + displays within the SUPER_BLOCK info. NOTE: WHITESPACE IN THE OUTPUT + HAS CHANGED. (ADB - 2012/02/17 - HDFFV-7560) + - h5diff: Fixed to prevent from displaying error stack message when + comparing two dangling symbolic links with the follow-symlinks option. + (JKM - 2012/01/13 - HDFFV-7836) + - h5repack: Fixed a memory leak that occurred with the handling of + variable length strings in attributes. + (JKM - 2012/01/10 - HDFFV-7840) + - h5ls: Fixed a segmentation fault that occurred when accessing region + reference data in an attribute. (JKM - 2012/01/06 - HDFFV-7838) + + F90 API + ------- + - None + + C++ API + ------ + - None + + High-Level APIs: + ------ + - None + + Fortran High-Level APIs: + ------ + - h5ltget_attribute_string_f: The h5ltget_attribute_string_f used to return + the C NULL character in the returned character buffer. The returned + character buffer now does not return the C NULL character; the buffer + is blank-padded if needed. (MSB - 2012/03/23) + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) g++ 4.2.1 [FreeBSD] 20070719 + gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) g++ 4.2.1 [FreeBSD] 20070719 + gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Linux 2.6.18-194.3.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.5.2 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 11.8-0 + Version 11.9-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 12.0 + Version 12.1 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.18-308.1.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) + Version 4.5.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 11.9-0 (64-bit) + Version 11.8-0 (32-bit) + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 12.0 + Version 12.1 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 + (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) + + Linux 2.6.18-108chaos Intel C, C++, Fortran Compilers Version 11.1 + #1 SMP x86_64 GNU/Linux + (LLNL Aztec) + + IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 + (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 + XL Fortran for Blue Gene/P, bgxlf0 V11.1 + + SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 + (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 + Sun C++ 5.9 Sun OS_sparc Patch 124863-26 + Sun C 5.11 SunOS_sparc + Sun Fortran 95 8.5 SunOS_sparc + Sun C++ 5.11 SunOS_sparc + + SGI Altix UV Intel(R) C, Fortran Compilers + SGI ProPack 7 Linux Version 11.1 20100806 + 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02 + default #1 SMP + (NCSA ember) + + Dell NVIDIA Cluster Intel(R) C, Fortran Compilers + Red Hat Enterprise Linux 6 Version 12.0.4 20110427 + 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4 + (NCSA forge) + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 w/ Intel Fortran 12 (cmake) + Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) + + Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc) + Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++) + Intel 64-bit (Apple Inc. build 5666) (dot 3) + (fred) GNU Fortran (GCC) 4.6.1 (gfortran) + Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1.0.038 Build 20110811 + + Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc) + Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++) + Intel 32-bit (Apple Inc. build 5666) (dot 3) + (tejeda) GNU Fortran (GCC) 4.6.1 (gfortran) + Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1.0.038 Build 20110811 + + Mac OS X Lion 10.7.3 GCC 4.2.1 gcc + 32- and 64-bit GNU Fortran (GCC) 4.6.1 gfortran + (duck) GCC 4.2.1. g++ + + Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + + Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + + Fedora16 3.2.9-2.fc16.i6866 #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) + GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) + + Fedora16 3.2.9-2.fc16.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) + GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) + + SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux + gcc (SUSE Linux) 4.6.2 + GNU Fortran (SUSE Linux) 4.6.2 + + SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.6.2 + GNU Fortran (SUSE Linux) 4.6.2 + + Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 + GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1 + + Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 + GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 + + Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74 + hopper.nersc.gov pgcc 11.9-0 64-bit target on x86-64 Linux -tp k8e + pgf90 11.9-0 64-bit target on x86-64 Linux -tp k8e + pgCC 11.9-0 64-bit target on x86-64 Linux -tp k8e + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +Windows XP n y(4) n y y y +Windows XP x64 n y(4) n y y y +Windows Vista n y(4) n y y y +Windows Vista x64 n y(4) n y y y +Mac OS X Snow Leopard 10.6.8 32-bit n y n y y n +Mac OS X Snow Leopard 10.6.8 64-bit n y n y y y +Mac OS X Lion 10.7.3 32-bit n y n y y n +Mac OS X Lion 10.7.3 64-bit n y n y y y +AIX 5.3 32- and 64-bit y y y y y y +FreeBSD 8.2-STABLE 32&64 bit n x n x y y +CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y +CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y y +CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y y +CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y(3) y y y y +CentOS 5.5 Linux 2.6.18 x86_64 Intel W n y n y y y +CentOS 5.5 Linux 2.6.18 x86_64 PGI W n y n y y y +Linux 2.6.32-220.7.1.el6.ppc64 n y n y y y +SGI ProPack 7 Linux 2.6.32.24 y y y y y y +Red Hat Enterprise Linux 6 y y y y y y +CLE hopper.nersc.gov y y(3) y y y n + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit n n n n +Windows XP y y(4) y n +Windows XP x64 y y(4) y n +Windows Vista y y(4) y y +Windows Vista x64 y y(4) y y +Mac OS X Snow Leopard 10.6.8 32-bit y n y n +Mac OS X Snow Leopard 10.6.8 64-bit y n y n +Mac OS X Lion 10.7.3 32-bit y n y y +Mac OS X Lion 10.7.3 64-bit y n y y +AIX 5.3 32- and 64-bit n n n y +FreeBSD 8.2-STABLE 32&64 bit y x x y +CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y +CentOS 5.5 Linux 2.6.18-194 i686 Intel W y y y n +CentOS 5.5 Linux 2.6.18-194 i686 PGI W y y y n +CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y y y +CentOS 5.5 Linux 2.6.18 x86_64 Intel W y y y n +CentOS 5.5 Linux 2.6.18 x86_64 PGI W y y y n +Linux 2.6.32-220.7.1.el6.ppc64 y y y n +SGI ProPack 7 Linux 2.6.32.24 y y y n +Red Hat Enterprise Linux 6 y y y n +CLE hopper.nersc.gov n n n n + + (1) Fortran compiled with gfortran. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) + (5) C and C++ shared libraries will not be built when Fortran is enabled. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* The h5repacktst test fails on AIX 32-bit because the test uses more + memory than the default amount. The failure message typically looks like: + + "time: 0551-010 The process was stopped abnormally. Try again." + + This is an issue with the test only and does not represent a problem with + the library. To allow the test to pass, request more memory when testing + via appropriate command such as: + + $ env LDR_CNRTL=MAXDATA=0x20000000@DSA make check + + (AKC - 2012/05/09 - HDFFV-8016) + +* The file_image test will fail in the "initial file image and callbacks in + the core VFD" sub-test if the source directory is read-only as the test + fails to create its test files in the build directory. This will be + resolved in a future release. + (AKC - 2012/05/05 - HDFFV-8009) + +* The dt_arith test reports several errors involving "long double" on + Mac OS X 10.7 Lion when any level of optimization is enabled. The test does + not fail in debug mode. This will be addressed in a future release. + (SLU - 2012/05/08) + +* The following h5dump test case fails in BG/P machines (and potentially other + machines that use a command script to launch executables): + + h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" + tno-subset.h5 + + This is due to the embedded spaces in the dataset name being interpreted + by the command script launcher as meta-characters, thus passing three + arguments to h5dump's -d flag. The command passes if run by hand, just + not via the test script. + (AKC - 2012/05/03) + +* The ph5diff (parallel h5diff) tool can intermittently hang in parallel mode + when comparing two HDF5 files that contain objects with the same names but + with different object types. + (JKM - 2012/04/27) + +* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set + to aprun -np X, because the H5lib_settings.c file was not generated + properly. Not setting those environment variables works, because + configure was able to automatically detect that it's a Cray system + and used the proper launch commands when necessary. + (MSC - 2012/04/18) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) doesn't have the problem. Users should lower the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + This will overwrite the library's default optimization level. + (SLU - 2012/02/07 - HDFFV-7829) + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release. + (DER - 2011/10/14) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in a future release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. + (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. + (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. + (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. + (SLU - 2010/05/05 - HDFFV-1264) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* MinGW has a missing libstdc++.dll.a library file and will not successfully link + C++ applications/tests. Do not use the enable-cxx configure option. Read all of + the INSTALL_MINGW.txt file for all restrictions. + (ADB - 2009/11/11) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not + exist. This is due to the MPI_File_open() call failing if the mode has + the MPI_MODE_EXCL bit set. + (AKC - 2009/08/11 - HDFFV-988) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. + (CMC - 2009/04/28) + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + (AKC - 2008/11/10) + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect to see this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + (AKC - 2008/05/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + (AKC - 2004/12/08) + + +%%%%1.8.8%%%% + + +HDF5 version 1.8.8 released on 2011-11-15 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.7 and +HDF5 1.8.8, and contains information on the platforms tested and +known problems in HDF5-1.8.8. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.8 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.8 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.8 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.8 (current +release) versus Release 1.8.7": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.7 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Added the --enable-fortran2003 flag to enable Fortran2003 support + in the HDF5 Fortran library. The flag should be used along with the + --enable-fortran flag and takes affect only when the Fortran compiler + is Fortran2003 compliant. (EIP - 2011/11/14) + - Added checks for clock_gettime and mach/mach_time.h to both configure and + CMake. This will support the move from gettimeofday to clock_gettime's + monotonic timer in the profiling code in a future release. + (DER - 2011/10/12) + + Library + ------- + - The Windows VFD code has been removed with the exception of the functions + which set it (H5Pset_fapl_windows, for example). Setting the Windows + VFD now really sets the SEC2 VFD. The WINDOWS_MAX_BUF and + WINDOWS_USE_STDIO configuration options and #defines have also been + removed. NOTE: Since the Windows VFD was a clone of the SEC2 VFD, this + change should be transparent to users. + (DER - 2011/10/12 - HDFFV-7740, HDFFV-7744) + - H5Tcreate now supports the string type (fixed-length and variable- + length). (SLU - 2011/05/20) + + Parallel Library + ---------------- + - Added new H5Pget_mpio_actual_chunk_opt_mode and + H5Pget_mpio_actual_io_mode API routines for querying whether/how + a collective I/O operation completed. (QAK - 2011/10/12) + + Tools + ----- + - None + + High-Level APIs + --------------- + - Added the following Fortran wrappers for the Dimension Scale APIs: + h5dsset_scale_f + h5dsattach_scale_f + h5dsdetach_scale_f + h5dsis_attached_f + h5dsis_scale_f + h5dsset_label_f + h5dsget_label_f + h5dsget_scale_name_f + h5dsget_num_scales_f + (EIP for SB - 2011/10/13 - HDFFV-3797) + + Fortran API + ----------- + - The HDF5 Fortran library was enhanced to support the Fortran 2003 standard. + The following features are available when the HDF5 library is configured + using the --enable-fortran and --enable-fortran2003 configure flags AND + if the Fortran compiler is Fortran 2003 compliant: + + - Subroutines overloaded with the C_PTR derived type: + h5pget_f + h5pget_fill_value_f + h5pinsert_f + h5pregister_f + h5pset_f + h5pset_fill_value_f + h5rcreate_f + h5rderefrence_f + h5rget_name_f + h5rget_obj_type_f + - Subroutines overloaded with the C_PTR derived type + and simplified signatures: + h5aread_f + h5awrite_f + h5dread_f + h5dwrite_f + - New subroutines + h5dvlen_reclaim_f + h5literate_by_name_f + h5literate_f + h5ovisit_f + h5tconvert_f + h5pset_nbit_f + h5pset_scaleoffset_f + - Subroutines with additional optional parameters: + h5pcreate_class_f + (EIP - 2011/10/14) + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - None + +Bug Fixes since HDF5-1.8.7 +========================== + + Configuration + ------------- + - Changed the size of H5_SIZEOF_OFF_T to 4 bytes (was 8) in the VMS + h5pubconf.h based on the output of a test program. (DER - 2011/10/12) + - The Windows and VMS versions of H5pubconf.h were brought into sync with + the linux/posix version. (DER - 2011/10/12) + - Fixed a bug in the bin/trace Perl script where API functions + that take a variable number of arguments were not processed for + trace statement fixup. (DER - 2011/08/25) + - The --enable-h5dump-packed-bits configure option has been removed. + The h5dump code that this option conditionally enabled is now always + compiled into h5dump. Please refer to the h5dump reference manual for + usage of the packed bits feature. (MAM - 2011/06/23 - HDFFV-7592) + - Configure now uses the same flags and symbols in its tests that are + used to build the library. (DER - 2011/05/24) + + Library + ------- + - Corrected the error when copying attributes between files which are using + different versions of the file format. (QAK - 2011/10/20 - HDFFV-7718) + - Corrected the error when loading local heaps from the file, which could + cause the size of the local heap's data block to increase dramatically. + (QAK - 2011/10/14 - HDFFV-7767) + - An application does not need to do H5O_move_msgs_forward() when writing + attributes. Tests were checked into the performance suite. + (VC - 2011/10/13 - HDFFV-7640) + - Fixed a bug that occurred when using H5Ocopy on a committed datatype + containing an attribute using that committed datatype. + (NAF - 2011/10/13 - HDFFV-5854) + - Added generic VFD I/O types to the SEC2 and log VFDs to ensure correct + I/O sizes (and remove compiler warnings) between Windows and true POSIX + systems. (DER - 2011/10/12) + - Corrected some Windows behavior in the SEC2 and log VFDs. This mainly + involved datatype correctness fixes, Windows API call error checks, + and adding the volume serial number to the VFD cmp functions. + (DER - 2011/10/12) + - Converted post-checks for the appropriate POSIX I/O sizes to pre-checks + in order to avoid platform-specific or undefined behavior. + (DER - 2011/10/12) + - #ifdef _WIN32 instances have been changed to #ifdef H5_HAVE_WIN32_API. + H5_HAVE_VISUAL_STUDIO checks have been added where necessary. This is in + CMake only as configure never sets _WIN32. (ADB - 2011/09/12) + - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + discovered 3 problems in tests and tools' library: + 1. In dsets.c, left shifting an unsigned int for 32 bits or more + caused undefined behavior. + 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow + when the value is a negative minimal and is being subtracted from one. + 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits + or more caused undefined behavior. + All the problems have been corrected. (SLU - 2011/09/02 - HDFFV-7674) + - H5Epush2() now has the correct trace functionality (this is related to the + bin/trace Perl script bug noted in the configure section). + (DER - 2011/08/25) + - Corrected mismatched function name typo of h5pget_dxpl_mpio_c and + h5pfill_value_defined_c. (AKC - 2011/08/22 - HDFFV-7641) + - Corrected an internal error in the library where objects that use committed + (named) datatypes and were accessed from two different file IDs could confuse + the two and cause erroneous failures. (QAK - 2011/07/18 - HDFFV-7638) + - In v1.6 of the library, there was an EOA for the whole MULTI file saved in the + super block. We took it out in v1.8 of the library because it's meaningless + for the MULTI file. v1.8 of the library saves the EOA for the metadata file + instead, but this caused a backward compatibility problem. + A v1.8 library couldn't open the file created with the v1.6 library. We + fixed the problem by checking the EOA value to detect the file + created with v1.6 library. (SLU - 2011/06/22) + - When a dataset had filters and reading data failed, the error message + didn't say which filter wasn't registered. It's fixed now. (SLU - 2011/06/03) + + Parallel Library + ---------------- + - The Special Collective IO (IO when some processes do not contribute to the + IO) and the Complex Derived Datatype MPI functionalities are no longer + conditionally enabled in the library by configure. They are always + enabled in order to take advantage of performance boosts from these + behaviors. Older MPI implementations that do not allow for these + functionalities can no longer by used by HDF5. + (MAM - 2011/07/08 - HDFFV-7639). + + Tools + ----- + - h5diff: fixed segfault over non-comparable attribute with different + dimension or rank, along with '-c' option to display details. + (JKM - 2011/10/24 - HDFFV-7770) + - Fixed h5diff to display all the comparable objects and attributes + regardless of detecting non-comparables. (JKM - 2011/09/16 - HDFFV-7693) + - Fixed h5repack to update the values of references(object and region) of + attributes in h5repack for 1) references, 2) arrays of references, + 3) variable-length references, and 4) compound references. + (PC - 2011/09/14 - HDFFV-5932) + - h5diff: fixed a segfault over a dataset with container types + array and variable-length (vlen) along with multiple nested compound types. + Example: compound->array->compound, compound->vlen->compound. + (JKM - 2011/09/01 - HDFFV-7712) + - h5repack: added macro to handle a failure in H5Dread/write when memory + allocation failed inside the library. (PC - 2011/08/19) + - Fixed h5jam to not to allow the specifying of an HDF5 formatted file as + an input file for the -u (user block file) option. The original HDF5 file + would not be accessible if this behavior was allowed. + (JKM - 2011/08/19 - HDFFV-5941) + - Revised the command help pages of h5jam and h5unjam. The descriptions + were not up to date and some were missing. + (JKM - 2011/08/15 - HDFFV-7515) + - Fixed h5dump to correct the schema location: + <hdf5:HDF5-File + xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File + http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> + (ADB - 2011/08/10) + - h5repack: h5repack failed to copy a dataset if the layout is changed + from chunked with unlimited dimensions to contiguous. + (PC - 2011/07/15 - HDFFV-7649) + - Fixed h5diff: the "--delta" option considers two NaN of the same type + are different. This is wrong based on the h5diff description in the + Reference Manual. (PC - 2011/07/15 - HDFFV-7656) + - Fixed h5diff to display an instructive error message and exit with + an instructive error message when mutually exclusive options + (-d, -p and --use-system-epsilon) are used together. + (JKM - 2011/07/07 - HDFFV-7600) + - Fixed h5dump so that it displays the first line of each element in correct + position for multiple dimension array types. Before this fix, + the first line of each element in an array was + displayed after the last line of previous element without + moving to the next line (+indentation). + (JKM - 2011/06/15 - HDFFV-5878) + - Fixed h5dump so that it will display the correct value for + H5T_STD_I8LE datasets on the Blue-gene system (ppc64, linux, Big-Endian, + clustering). (AKC & JKM - 2011/05/12 - HDFFV-7594) + - Fixed h5diff to compare a file to itself correctly. Previously h5diff + reported either the files were different or not compatible in certain + cases even when comparing a file to itself. This fix also improves + performance when comparing the same target objects through verifying + the object and file addresses before comparing the details + in the objects. Examples of details are datasets and attributes. + (XCAO & JKM - 2011/05/06 - HDFFV-5928) + + F90 API + ------- + - Modified the h5open_f and h5close_f subroutines to not to call H5open + and H5close correspondingly. While the H5open call just adds overhead, + the H5close call called by a Fortran application shuts down the HDF5 + library. This makes the library inaccessible to the application. + (EIP & SB - 2011/10/13 - HDFFV-915) + - Fixed h5tget_tag_f where the length of the C string was used to + repack the C string into the Fortran string. This lead to memory + corruption in the calling program. (SB - 2011/07/26) + - Added defined constants: + H5T_ORDER_MIXED_F (HDFFV-2767) + H5Z_SO_FLOAT_DSCALE_F + H5Z_SO_FLOAT_ESCALE_F + H5Z_SO_INT_F + H5Z_SO_INT_MINBITS_DEFAULT_F + H5O_TYPE_UNKNOWN_F + H5O_TYPE_GROUP_F + H5O_TYPE_DATASET_F + H5O_TYPE_NAMED_DATATYPE_F + H5O_TYPE_NTYPES_F + + C++ API + ------ + - None + + High-Level APIs: + ------ + - Fixed the H5LTdtype_to_text function. It had some memory problems when + dealing with some complicated data types. (SLU - 2011/10/19 - HDFFV-7701) + - Fixed H5DSset_label seg faulting when retrieving the length of a + dimension label that was not set. (SB - 2011/08/07 - HDFFV-7673) + - Fixed a dimension scale bug where if you create a dimscale, attach two + datasets to it, and then unattach them, you get an error if they are + unattached in order, but no error if you unattach them in reverse order. + (SB - 2011/06/07 - HDFFV-7605) + + Fortran High-Level APIs: + ------ + - None + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 5.3 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) g++ 4.2.1 [FreeBSD] 20070719 + gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) g++ 4.2.1 [FreeBSD] 20070719 + gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + IBM Blue Gene/P bgxlc 9.0.0.9 + (LLNL uDawn) bgxlf90 11.1.0.7 + bgxlC 9.0.0.9 + + Linux 2.6.16.60-0.54.5-smp Intel(R) C, C++, Fortran Compilers + x86_64 Version 11.1 20090630 + (INL Icestorm) + + Linux 2.6.18-194.el5 x86_64 Intel(R) C, C++, Fortran Compilers + (INL Fission) Version 12.0.2 20110112 + + Linux 2.6.18-108chaos x86_64 Intel(R) C, C++, Fortran Compilers + (LLNL Aztec) Version 11.1 20090630 + + Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 + #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 + (jam) (Red Hat 4.1.2-48) and 4.4.2 + PGI C, Fortran, C++ 10.4-0 32-bit + PGI C, Fortran, C++ 10.6-0 32-bit + Intel(R) C Compiler for 32-bit + applications, Version 11.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 11.1 + Intel(R) Fortran Compiler for 32-bit + applications, Version 11.1 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.18-238.12.1.el5 gcc 4.1.2 and 4.4.2 + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 + (koala) (Red Hat 4.1.2-46) and 4.4.2 + tested for both 32- and 64-bit binaries + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64, + Version 11.1. + PGI C, Fortran, C++ Version 9.0-4 + for 64-bit target on x86-64 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + SGI Altix UV Intel(R) C, Fortran Compilers + SGI ProPack 7 Linux Version 11.1 20100806 + 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02 + default #1 SMP + (NCSA ember) + + Dell NVIDIA Cluster Intel(R) C, Fortran Compilers + Red Hat Enterprise Linux 6 Version 12.0.4 20110427 + 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4 + (NCSA forge) + + SunOS 5.10 32- and 64-bit Sun C 5.11 SunOS_sparc 2010/08/13 + Sun Fortran 95 8.5 SunOS_sparc 2010/08/13 + Sun C++ 5.11 SunOS_sparc 2010/08/13 + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 (cmake) + Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 (cmake) + Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) + + Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Mac OS X 10.8.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) + Darwin Kernel Version 10.8.0 GNU Fortran (GCC) 4.6.1 + Intel C, C++ and Fortran compilers 12.1.0 + + Mac OS X 10.8.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) + Darwin Kernel Version 10.8.0 GNU Fortran (GCC) version 4.6.1 + Intel C, C++ and Fortran compilers 12.1.0 + + Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux + gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) + GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) + + Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + + Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + + Fedora15 2.6.40.6-0.fc15.i686.PAE #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) + GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) + + Fedora15 2.6.40.6-0.fc15.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) + GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) + + SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux + gcc (SUSE Linux) 4.5.1 20101208 + GNU Fortran (SUSE Linux) 4.5.1 20101208 + + SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.5.1 20101208 + GNU Fortran (SUSE Linux) 4.5.1 20101208 + + Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 + GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1 + + Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 + GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 + + OpenVMS Alpha 8.3 HP C V7.3-009 + HP Fortran V8.2-104679-48H9K + HP C++ V7.3-009 + + Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74 + hopper.nersc.gov pgcc 11.7-0 64-bit target on x86-64 Linux -tp k8e + franklin.nersc.gov pgf90 11.7-0 64-bit target on x86-64 Linux -tp k8e + pgCC 11.7-0 64-bit target on x86-64 Linux -tp k8e + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +Windows XP n y(4) n y y y +Windows XP x64 n y(4) n y y y +Windows Vista n y(4) n y y y +Windows Vista x64 n y(4) n y y y +OpenVMS Alpha n y n y y n +Mac OS X 10.8 Intel 32-bit n y n y y y +Mac OS X 10.8 Intel 64-bit n y n y y y +AIX 5.3 32- and 64-bit n y n y y y +FreeBSD 8.2-STABLE 32&64 bit n x n x y y +CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y +CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n +CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n +CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y +CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n +CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y +Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y +SGI ProPack 7 Linux 2.6.32.24 y y y y y y +Red Hat Enterprise Linux 6 y y y y y y +CLE hopper.nersc.gov y y(3) y y y n +CLE franklin.nersc.gov y y(3) y y y n + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +Windows XP y y(4) y n +Windows XP x64 y y(4) y n +Windows Vista y y(4) y y +Windows Vista x64 y y(4) y y +OpenVMS Alpha n n n n +Mac OS X 10.8 Intel 32-bit y(5) n y n +Mac OS X 10.8 Intel 64-bit y(5) n y n +AIX 5.3 32- and 64-bit n n n y +FreeBSD 8.2-STABLE 32&64 bit y x x y +CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y +CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n +CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n +CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y +CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n +CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n +Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y +SGI ProPack 7 Linux 2.6.32.24 y y y n +Red Hat Enterprise Linux 6 y y y n +CLE hopper.nersc.gov n n n n +CLE franklin.nersc.gov n n n n + + (1) Fortran compiled with gfortran. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) + (5) C and C++ shared libraries will not be built when Fortran is enabled. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== + +* The STDIO VFD does not work on some architectures, possibly due to 32/64 + bit or large file issues. The basic STDIO VFD test is known to fail on + 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin + 10.7.0. The STDIO VFD test has been disabled while we investigate and + a fix should appear in a future release, possibly 1.8.9. + (DER - 2011/10/14) + +* h5diff can report inconsistent results when comparing datasets of enum type + that contain invalid values. This is due to how enum types are handled in + the library and will be addressed in the next release. + (DER - 2011/10/14 - HDFFV-7527) + +* The links test can fail under the stdio VFD due to some issues with external + links. This will be investigated and fixed in a future release. + (DER - 2011/10/14 - HDFFV-7768) + +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 - HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + (NAF - 2011/01/19) + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. + (SLU - 2010/05/05 - HDFFV-1264) + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + (SLU - 2010/02/02) + +* MinGW has a missing libstdc++.dll.a library file and will not successfully link + C++ applications/tests. Do not use the enable-cxx configure option. Read all of + the INSTALL_MINGW.txt file for all restrictions. (ADB - 2009/11/11) + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + (MAM - 2009/11/04) + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not + exist. This is due to the MPI_File_open() call failing if the mode has + the MPI_MODE_EXCL bit set. (AKC - 2009/08/11 - HDFFV-988) + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. (CMC - 2009/04/28) + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + (AKC - 2008/11/10) + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect to see this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + (AKC - 2008/05/28) + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + (SLU - 2005/06/30) + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + (AKC - 2004/12/08) + + +%%%%1.8.7%%%% + + +HDF5 version 1.8.7 released on Tue May 10 09:24:44 CDT 2011 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.6 and +HDF5 1.8.7, and contains information on the platforms tested and +known problems in HDF5-1.8.7. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.7 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.7 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.7 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.7 (current +release) versus Release 1.8.6": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.6 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Configure now generates Makefiles that build in "silent make mode" + by default in which compile and link lines are significantly + simplified for clarity. To override this and view actual compile and + link lines during building, the --disable-silent-rules flag can be used + at configure time, or the 'make' command can be followed by V=1, to + indicate a "verbose" make. (MAM - 2011/4/14). + - Added mpicc and mpif90 as the default C and Fortran compilers for Linux + systems when --enable-parallel is specified but no $CC or $FC is defined. + (AKC - 2011/2/7) + - Added a new configure option, "--enable-unsupported", which can + be used to stop configure from preventing the use of unsupported + configure option combinations, such as c++ in parallel or Fortran + with threadsafe. Use at your own risk, as it may result in a + library that won't compile or run as expected! + (MAM - 2010/11/17 - Bug 2061) + + Library + ------- + - The library allows the dimension size of a dataspace to be zero. In + the past, the library would allow this only if the maximal dimension + size was unlimited. Now there is no such restriction, but no data + can be written to this kind of dataset. (SLU - 2011/4/20) + - We added two new macros, H5_VERSION_GE and H5_VERSION_LE, to let users + compare certain version numbers with the library being used. (SLU - + 2011/4/20) + - Added ability to cache files opened through external links. Added new + public functions H5Pset_elink_file_cache_size(), + H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache(). + (NAF - 2011/02/17) + - Finished implementing all options for 'log' VFD. (QAK - 2011/1/25) + - Removed all old code for Metrowerks compilers, bracketed by + __MWERKS__). Metrowerks compiler is long gone. (AKC - 2010/11/17) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5diff: Added new "verbose with levels" option, '-vN, --verbose=N'. + The old '-v, --verbose' option is deprecated but remains available; + it is exactly equivalent to '-v0, --verbose=0'. + The new levels 1 ('-v1' or '--verbose=1') and 2 ('-v2' or + '--verbose=2') can be specified to view more information regarding + attributes differences. Bug #2121 (JKM 2011/3/23) + - h5dump: Added new option --enable-error-stack. This option will + display error stack information in the output stream. This is + useful when the "h5dump: Unable to print data" message is output. + (ADB - 2011/03/03) + + High-Level APIs + --------------- + - Fortran LT make datasets routines (H5LTmake_dataset_f, + h5ltmake_dataset_int_f, h5ltmake_dataset_float_f, h5ltmake_dataset_double_f) + and LT read datasets routines (h5ltread_dataset_f,h5ltread_dataset_int_f, + h5ltread_dataset_float_f, 5ltread_dataset_double_f) can now handle + 4-dimensional to 7-dimensional rank datasets. HDFFV-1217 (MSB-2011/4/24/2011) + + F90 API + ------- + - None + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) + + + +Bug Fixes since HDF5-1.8.6 +========================== + + Configuration + ------------- + - Shared C++ and HL libraries on AIX should now be working correctly. + Note that Fortran shared libraries are still not working on AIX. + (See the Known Problems section, below). (MAM - 2011/4/20) + - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file, + ibm-aix. (AKC - 2011/4/14) + - Shared C libraries are no longer disabled on Mac when Fortran + is enabled. Shared Fortran libraries are still not supported on Mac, + so configure will disable them by default, but this is overridable + with the new --enable-unsupported configure option. The configure + summary has been updated to reflect the fact that the shared-ness of + the C++/Fortran wrapper libraries may not align with the C library. + (MAM - 2011/04/11 - HDFFV-4353). + + Library + ------- + - Changed assertion failure when decoding a compound datatype with no + fields into a normal error failure. Also prohibit using this sort + of datatype for creating an attribute (as is already the case for + datasets and committed (named) datatypes). (QAK - 2011/04/15, Jira + issue #HDFFV-2766) + - Tell the VFL flush call that the file will be closing, allowing + the VFDs to avoid sync'ing the file (particularly valuable in parallel). + (QAK - 2011/03/09) + - The datatype handler created with H5Tencode/decode used to have the + reference count 0 (zero); it now has the reference count 1 (one). + (SLU - 2011/2/18) + - Fixed the definition of H5_HAVE_GETTIMEOFDAY on Windows so that + HDgettimeofday() is defined and works properly. Bug HDFFV-5931 + (DER - 2011/04/14) + - Added basic VFD tests for the Windows, STDIO and log VFD tests. + (DER - 2011/04/11) + + Parallel Library + ---------------- + - None + + Tools + ----- + - Updated h5dump test case script to prevent entire test failure when + source directory is read-only. Bug #HDFFV-4342 (JKM 2011/4/12) + - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in + attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type, + so h5dump is supposed to display -2 instead of 254. It worked correctly + on Little-Endian system , but not on Big-Endian system. Bug #HDFFV-4358 + (JKM 04/08/2011) + - Updated some HDF5 tools to standardize the option name as + '--enable-error-stack' for printing HDF5 error stack messages. h5ls and + h5dump have been updated. For h5ls, this replaces "-e/--errors" option, + which is deprecated. For h5dump, this is a new option. Bug #2182 + (JKM 2011/3/30) + - Fixed the h5diff --use-system-epsilon option. The formula used in the + calculation was changed from ( |a - b| / b ) to ( |a - b| ). + This was done to improve performance. Bug #2184 (JKM 2011/3/24) + - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document + the output of a H5T_REFERENCE should be followed by the type; + <reference> ::= H5T_REFERENCE { <ref_type> } + <ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG + Previously this was only displayed if the -R option was used. + Bug #1725 (ADB 2011/3/28) + - Fixed two h5diff issues. 1) h5diff compared attributes correctly only + when two objects had the same number of attributes and the attribute + names were identical. 2) h5diff did not display useful information about + attribute differences. Bug #2121 (JKM 2011/3/17) + - Fixed a memory leak in h5diff that occurred when accessing symbolic links + with the --follow-symlink option. Bug #2214 (JKM 2011/3/18) + - Fixed a memory leak in h5diff that occurred when accessing variable length + string data. Bug #2216 (JKM 2011/3/18) + - Fixed and improved the help page for h5ls -a, --address option. + Bug #1904 (JKM 2011/3/11) + - Fixed h5copy to enable copying an object into the same HDF5 file. + Previously h5copy displayed an error message when the target file + was the same as the source file. (XCAO 2011/3/8) + - Fixed an h5dump problem that caused the tool to skip some data elements + in large datasets with a large array datatype on Windows. This issue + arose only on Windows due to the different return behavior of the + _vsnprintf() function. Bug #2161 (JKM 2011/3/3) + - Fixed h5dump which was skipping some array indices in large datasets + with a relatively large array datatype. The interval of skipped indices + varied according to the size of the array. Bug #2092 (JKM 2011/2/15) + - Fixed h5diff which was segfaulting when comparing compound datasets + with a combination of fixed-length string datatypes and variable-length + string datatypes in certain orders. Bug #2089 (JKM 2010/12/28) + - Improved h5diff performance. 1) Now use HDmemcmp() before comparing two + elements. 2) Replace expensive H5Tequals() calls. 3) Retrieve datatype + information at dataset level, not at each element level for compound + datasets. HDFFV-7516 (JKM 2011/4/18) + - Fixed h5ls to display nested compound types with curly brackets + when -S (--simple) option is used with -l (--label), so it shows + which members (in curly brackets) belong to which nested compound type, + making the output clearer. Bug #1979 (JKM 2010/11/09) + - Fixed h5diff to handle variable-length strings in a compound dataset + and variable-length string arrays in a compound dataset correctly. + Garbage values were previously displayed when h5diff compared multiple + variable-length strings in a compound type dataset. + Bug #1989 (JKM 2010/10/28) + - Fixed h5copy to fail gracefully when copying an object to a non- + existing group without the -p option. Bug #2040 (JKM 2010/10/18) + + F90 API + ------ + - None + + C++ API + ------ + - None + + High-Level APIs: + ------ + - None + + Fortran High-Level APIs: + ------ + - h5tbmake_table_f: Fixed error in passing an array of characters with different + length field names. + - h5tget_field_info_f: Fixed error with packing the C strings into a Fortran + array of strings. Added optional argument called 'maxlen_out' which returns + the maximum string character length in a field name element. + Bug HDFFV-1255 (MSB- 4/17/2011) + + + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 6.1 xlc 11.1.0.3 + (NCSA BP) xlC 11.1.0.3 + xlf90 13.1.0.3 + mpcc_r 11.1.0.3 + mpxlf90_r 13.1.0.3 + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) g++ 4.2.1 [FreeBSD] 20070719 + gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) g++ 4.2.1 [FreeBSD] 20070719 + gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 + #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) + (jam) GNU Fortran (GCC) 4.1.2 20080704 + (Red Hat 4.1.2-48) and 4.4.2 + PGI C, Fortran, C++ 10.4-0 32-bit + PGI C, Fortran, C++ 10.6-0 32-bit + Intel(R) C Compiler for 32-bit + applications, Version 11.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 11.1 + Intel(R) Fortran Compiler for 32-bit + applications, Version 11.1 + Absoft 32-bit Fortran 95 10.0.7 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2 + #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) + (amani) tested for both 32- and 64-bit binaries + GNU Fortran (GCC) 4.1.2 20080704 + (Red Hat 4.1.2-46) and 4.4.2 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64, + Version 11.1. + PGI C, Fortran, C++ Version 9.0-4 + for 64-bit target on x86-64 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806 + 2.6.32.24-0.2.1.2230.2.PTF- Intel(R) Fortran Version 11.1 20100806 + default #1 SMP SGI MPT 2.01 + SGI Altix UV + (NCSA ember) + + SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 + (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 + Sun C++ 5.9 Sun OS_sparc Patch 124863-26 + Sun C 5.10 SunOS_sparc Patch 141861-07 + Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06 + Sun C++ 5.10 SunOS_sparc 128228-11 + + Intel Xeon Linux 2.6.18- gcc 4.2.4 + 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017 + perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017 + (NCSA abe) Open MPI 1.3.2 + MVAPICH2-1.5.1_pgi-10.8 + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 (cmake) + Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 (cmake) + Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) + + Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Mac OS X 10.7.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 + Darwin Kernel Version 10.7.0 GNU Fortran (GCC) 4.6.0 20101106 (experimental) + Intel C, C++ and Fortran compilers 12.0.1.122 20101110 + + Mac OS X 10.7.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) + Darwin Kernel Version 10.7.0 GNU Fortran (GCC) version 4.4.0 20090123 (experimental) + [trunk revision 143587] + + Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux + gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) + GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) + + Debian6.01 2.6.32-5-686 #1 SMP i686 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + + Debian6.01 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.4.5-8) 4.4.5 + GNU Fortran (Debian 4.4.5-8) 4.4.5 + + Fedora14 2.6.35.12-88.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + + Fedora14 2.6.35.12-88.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + + SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux + gcc (SUSE Linux) 4.5.1 20101208 + GNU Fortran (SUSE Linux) 4.5.1 20101208 + + SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.5.1 20101208 + GNU Fortran (SUSE Linux) 4.5.1 20101208 + + Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + + Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + + OpenVMS Alpha 8.3 HP C V7.3-009 + HP Fortran V8.2-104679-48H9K + HP C++ V7.3-009 + +Tested Configuration Features Summary +======================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +Windows XP n y(4) n y y y +Windows XP x64 n y(4) n y y y +Windows Vista n y(4) n y y y +Windows Vista x64 n y(4) n y y y +OpenVMS Alpha n y n y y n +Mac OS X 10.7 Intel 32-bit n y n y y y +Mac OS X 10.7 Intel 64-bit n y n y y y +AIX 6.1 32- and 64-bit y y y y y y +FreeBSD 8.2-STABLE 32&64 bit n x n x y y +CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y +CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n +CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n +CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y +CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n +CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y +RedHat EL4 2.6.18 Xeon Lustre C y y y y y n +Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y +SGI Linux 2.6.32.19 y y y y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +Windows XP y y(4) y n +Windows XP x64 y y(4) y n +Windows Vista y y(4) y y +Windows Vista x64 y y(4) y y +OpenVMS Alpha n n n n +Mac OS X 10.7 Intel 32-bit y(5) n y n +Mac OS X 10.7 Intel 64-bit y(5) n y n +AIX 6.1 32- and 64-bit n n n y +FreeBSD 8.2-STABLE 32&64 bit y x x y +CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y +CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n +CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n +CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y +CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n +CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n +RedHat EL4 2.6.18 Xeon Lustre C y y y n +Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y +SGI Linux 2.6.32.19 y y y y + + (1) Fortran compiled with gfortran. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) + (5) C and C++ shared libraries will not be built when Fortran is enabled. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* After the shared library support was fixed for some bugs, it was discovered + that "make prefix=XXX install" no longer works for shared libraries. It + still works correctly for static libraries. Therefore, if you want to + install the HDF5 shared libraries in a location such as /usr/local/hdf5, + you need to specify the location via the --prefix option during configure + time. E.g, ./configure --prefix=/usr/local/hdf5 ... + (AKC - 2011/05/07 HDFFV-7583) + +* The parallel test, t_shapesame, in testpar/, may run for a long time and may + be terminated by the alarm signal. If that happens, one can increase the + alarm seconds (default is 1200 seconds = 20 minutes) by setting the + environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 + (60 minutes). Note that the t_shapesame test may fail in some systems + (see the "While working on the 1.8.6 release..." problem below). If + it does, it will waste more time if $HDF5_ALARM_SECONDS is set + to a larger value. (AKC - 2011/05/07) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD. + (QAK - 2011/04/26) + +* Shared Fortran libraries are not quite working on AIX. While they are + generated when --enable-shared is specified, the fortran and hl/fortran + tests fail. We are looking into the issue. HL and C++ shared libraries + should now be working as intended, however. (MAM - 2011/04/20) + +* The --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10 + +* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command + sometimes fails in the perform directory due to the attempt to remove the + executable of h5perf or h5perf_serial by two "parallel" commands. This error + has no consequence on the functionality of the HDF5 library or install. It + is fixed in the next release. AKC - 2011/01/25 + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or file systems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. Please see bug #1813. + SLU - 2010/5/5 + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added in. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug in 1.8 library. Because there's only one user + complaining about it, we (Elena, Quincey, and I) decided to leave it as + it is (see bug report #1279). Quincey will make a plan for 1.10. + SLU - 2010/2/2 + +* MinGW has a missing libstdc++.dll.a library file and will not successfully link + C++ applications/tests. Do not use the enable-cxx configure option. Read all of + the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not + exist. This is due to the MPI_File_open() call failing if the mode has + the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. CMC - 2009/04/28 + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + AKC - 2008/11/10 + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect to see this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + +* There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which + is the default on that system) does not work properly and results in + failures during make check (in a static build) and make installcheck (during + a shared build). This appears to be a compiler optimization problem. + Reducing optimization by setting CFLAGS to -O1 or below resolves the issue. + Alternatively, using a newer version of the compiler (11.0) also works as + intended. MAM - 2010/06/01 + +* h5diff will not report enum value differences when one or both of the values + is not a valid enumeration value. The source of this bug has been identified + and it will be fixed in 1.8.8. DER - 2011/04/27 + + +%%%%1.8.6%%%% + + +HDF5 version 1.8.6 released on Mon Feb 14 10:26:30 CST 2011 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.5 and +HDF5 1.8.6, and contains information on the platforms tested and +known problems in HDF5-1.8.6. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.6 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.6 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.6 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.6 (current +release) versus Release 1.8.5": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.5 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - CMake: Improved CPack packaging, added parallel commands, improved + configuration options (better similarity to configure), added more + tests, better support for use in external cmake projects. + (ADB - 2010/10/07) + - The default configuration setting for official releases is + --enable-production. For unofficial releases, the default configuration + setting has been --disable-production. (AKC - 2010/05/28) + Library + ------- + - Added support for thread safety on Windows using the Windows threads + library. Use the HDF5_ENABLE_THREADSAFE option in CMake on a Windows + platform to enable this functionality. This is supported on Windows + Vista and newer Windows operating systems. (MAM - 2010/09/10) + - H5Tset_order and H5Tget_order now support all datatypes. A new byte + order, H5T_ORDER_MIXED, has been added specifically for a compound + datatype and its derived type. (SLU - 2010/8/23) + - Improved performance of metadata I/O by changing the default algorithm + to perform I/O from all processes (instead of just process 0) when using + parallel I/O drivers. (QAK - 2010/07/19) + - Improved performance of I/O on datasets with the same shape, but + different rank. (QAK - 2010/07/19) + - Improved performance of the chunk cache by avoiding unnecessary b-tree + lookups of chunks already in cache. (NAF - 2010/06/15) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5diff: Added a new flag: --exclude-path. The specified path to an + object will be excluded when comparing two files or two groups. If a + group is specified to be excluded, all member objects of that group + will be excluded. (JKM - 2010/09/16). + - h5ls: Added a new flag: --no-dangling-links. See --help output for + details. (JKM - 2010/06/15) + - h5ls: Added a new flag --follow-symlinks. See --help output for + details. (JKM - 2010/05/25) + + High-Level APIs + --------------- + - None + + F90 API + ------- + - None + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Sun C and C++ 5.10 and Sun Fortran 95 8.4. + - Mac OS X 10.6.4 with gcc 4.2.1 and gfortran 4.6 + + +Bug Fixes since HDF5-1.8.5 +========================== + + Configuration + ------------- + - The default number of MPI processes for testing purposes has been + changed from 3 to 6. (AKC - 2010/11/11) + - Some tests in tools/h5repack may fail in AIX systems when -q32 mode is + used. The error is caused by not requesting enough memory in default. + Added "env LDR_CNTRL=MAXDATA=0x20000000@DSA" into the $RUNSERIAL and + $RUNPARALLE in the AIX config file so that executables are tested with + more memory. (AKC - 2010/11/11) + - Removed recognition of the parallel compilers of LAM(hcc) and + ChMPIon(cmpicc) since we have no access to these two MPI implementations + and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921) + - PHDF5 was changed to use "mpiexec" instead of mpirun as the default + MPI applications startup command as defined in the MPI-2 definition, + section 4.1. (AKC - 2010/06/11 - Bug 1921) + + Library + ------- + - Fixed a bug that caused big endian machines to generate corrupt files + when using the scale-offset filter with floating point data or fill + values. Note that such datasets will no longer be readable by any + by any machine after this patch. (NAF - 2010/02/02 - Bug 2131) + - Retrieving a link's name by index in the case where the link is external + and the file that the link refers to doesn't exist will now fail + gracefully rather than cause a segmentation fault. (MAM - 2010/11/17) + - Modified metadata accumulator to better track accumulated dirty metadata + in an effort to reduce unnecessary I/O in certain situations and to + fix some other corner cases which were prone to error. (MAM - 2010/10/15) + - Added a new set of unit tests that are run during 'make check' to verify + the behavior of the metadata accumulator. (MAM - 2010/10/15) + - Modified library to always cache symbol table information. Libraries + from version 1.6.3 and earlier have a bug which causes them to require + this information for some operations. (NAF - 2010/09/21 - Bug 1864) + - Fixed a bug where the library could generate an assertion/core dump when + a file that had been created with H5Pset_libver_bounds(fapl, + H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) but didn't have a superblock + extension was later reopened. (QAK - 2010/09/16 - Bug 1968) + - Fixed a bug that could occur when getting information for a new-style + group that was previously opened through a file handle that was later + closed. (NAF - 2010/09/15) + - Added define check in H5public.h if stdint.h is supported by the C++ + compiler. This define is only available on Windows with VS2010 and using + CMake to build the library. (ADB - 2010/09/13 - Bug 1938) + - When a mandatory filter failed to write data chunks, the dataset + couldn't close (bug 1260). The fix releases all resources and closes + the dataset but returns a failure. (SLU - 2010/09/08) + - H5Eset_current_stack now also closes the error stack set as the + default. This is to avoid a potential problem. + (SLU - 2010/09/07 - Bug 1799) + - Corrected situation where 1-D chunked dataset could get created by an + application without calling H5Pset_chunk(). H5Pset_chunk is now + required for creating all chunked datasets. (QAK - 2010/09/02) + - Fixed many memory issues that valgrind exposed. (QAK - 2010/08/24) + - Fixed the bug in the filter's public CAN_APPLY function. The return + value should be htri_t not herr_t. (SLU - 2010/08/05 - Bug 1239) + - Fixed the STDIO VFD to use fseeko64 instead of fseek64 for 64-bit I/O + support. (AKC - 2010/7/30) + - Fixed a bug in the direct I/O driver that could render files with certain + kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28) + - valgrind reported an error of copying data to itself when a new attribute + is written. Fixed by taking out the memcpy step in the attribute code. + (SLU - 2010/07/28 - Bug 1956) + - Corrected various issues in the MPI datatype creation code which could + cause resource leaks or incorrect behavior (and may improve the + performance as well). (QAK - 2010/07/19) + - Fixed a bug that could cause file corruption when using non-default sizes + of addresses and/or lengths. This bug could also cause uncorrupted files + with this property to be unreadable. This bug was introduced in 1.8.5. + (NAF - 2010/07/16 - Bug 1951) + + Parallel Library + ---------------- + - None + + Tools + ----- + - Fixed h5diff to compare member objects and groups recursively when + two files or groups are compared. (JKM - 2010/9/16 - Bug 1975) + - Fixed h5repack to be able to convert a dataset to COMPACT layout. + (JKM - 2010/09/15 - Bug 1896) + - Changed h5ls to not interpret special characters in object or attribute + names for output. (JKM - 2010/06/28 - Bug 1784) + - Revised the order of arguments for h5cc, h5fc, h5c++, h5pcc and h5pfc. + CPPFLAGS, CFLAGS, LDFLAGS, and LIBS have been duplicated with an H5BLD_ + prefix to put the flags and paths from the hdf5 build in the correct + places and allow the script user to add entries in CPPFLAGS, CFLAGS, + LDFLAGS, and LIBS that will take precedence over those from the hdf5 + build. The user can make these entries persistent by editing + CFLAGSBASE, CPPFLAGSBASE, LDFLAGSBASE, and LIBSBASE near the top of + the script or temporary by setting HDF5_CFLAGS, HDF5_CPPFLAGS, + HDF5_LDFLAGS, or HDF5_LIBS in the environment. The new order of + arguments in these scripts is $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS + $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args + $shared_link. (LRK - 2010/10/25 - Bug 1973) + + F90 API + ------ + - None + + C++ API + ------ + - None + + High-Level APIs: + ------ + - None + + Fortran High-Level APIs: + ------ + - None + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 6.1 xlc 11.1.0.3 + (NCSA BP) xlC 11.1.0.3 + xlf 13.1.0.3 + mpcc_r 11.1.0.3 + mpxlf_r 13.1.0.3 + + FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.4.5 20100803 + g++ 4.4.5 20100803 + gfortran 4.4.5 20100803 + + FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.4.5 20100803 + g++ 4.4.5 20100803 + gfortran 4.4.5 20100803 + + Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 + #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) + (jam) GNU Fortran (GCC) 4.1.2 20080704 + (Red Hat 4.1.2-48) and 4.4.2 + PGI C, Fortran, C++ 10.4-0 32-bit + PGI C, Fortran, C++ 10.6-0 32-bit + Intel(R) C Compiler for 32-bit + applications, Version 11.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 11.1 + Intel(R) Fortran Compiler for 32-bit + applications, Version 11.1 + Absoft 32-bit Fortran 95 10.0.7 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2 + #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) + (amani) tested for both 32- and 64-bit binaries + GNU Fortran (GCC) 4.1.2 20080704 + (Red Hat 4.1.2-46) and 4.4.2 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64, + Version 11.1. + PGI C, Fortran, C++ Version 9.0-4 + for 64-bit target on x86-64 + MPICH mpich2-1.3.1 compiled with + gcc 4.1.2 and gfortran 4.1.2 + + SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806 + 2.6.32.19-0.3.1.1982.0.PTF- Intel(R) Fortran Version 11.1 20100806 + default #1 SMP SGI MPT 2.01 + SGI Altix UV + (NCSA ember) + + SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 + (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 + Sun C++ 5.9 Sun OS_sparc Patch 124863-62 + Sun C 5.10 SunOS_sparc Patch 141861-07 + Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06 + Sun C++ 5.10 SunOS_sparc 128228-11 + + Intel Xeon Linux 2.6.18- gcc 4.2.4 + 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017 + perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017 + (NCSA abe) Open MPI 1.3.2 + MVAPICH2-1.5.1_pgi-10.8 + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 (cmake) + Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + Visual Studio 2010 (cmake) + Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) + + Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) + Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) + + Mac OS X 10.6.3 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 + Darwin Kernel Version 10.3.1 GNU Fortran (GCC) 4.5.0 20090910 + Intel C, C++ and Fortran compilers 11.1 20100806 + + Mac OS X 10.6.4 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 + Darwin Kernel Version 10.4.0 GNU Fortran (GCC) 4.6.0 20101106 + Intel C, C++ and Fortran compilers 12.0.0 20101110 + + Mac OS X 10.6.4 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659) + Darwin Kernel Version 10.6.0 GNU Fortran (GCC) 4.5.0 20090910 + Intel C, C++ and Fortran compilers 11.1 20100806 + + Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux + gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) + GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) + + Debian5.06 2.6.26-2-686 #1 SMP i686 GNU/Linux + gcc (Debian 4.3.2-1.1) 4.3.2 + GNU Fortran (Debian 4.3.2-1.1) 4.3.2 + + Debian5.06 2.6.26-2-amd64 #1 SMP x86_64 GNU/Linux + gcc (Debian 4.3.2-1.1) 4.3.2 + GNU Fortran (Debian 4.3.2-1.1) 4.3.2 + + Fedora14 2.6.35.6-48.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + + Fedora14 2.6.35.6-48.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) + + SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux + gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] + GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] + + SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] + GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] + + Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + + Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 + + OpenVMS Alpha 8.3 HP C V7.3-009 + HP Fortran V8.2-104679-48H9K + HP C++ V7.3-009 + +Tested Configuration Features Summary +======================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +Windows XP n y(4) n y y y +Windows XP x64 n y(4) n y y y +Windows Vista n y(4) n y y y +Windows Vista x64 n y(4) n y y y +OpenVMS Alpha n y n y y n +Mac OS X 10.6 Intel n y n y y y +AIX 6.1 32- and 64-bit y y y y y y +FreeBSD 6.3-STABLE 32&64 bit n y n y y y +CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y +CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n +CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n +CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y +CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n +CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y +RedHat EL4 2.6.18 Xeon Lustre C y y y y y n +Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y +SGI Linux 2.6.32.19 y y y y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +Windows XP y y(4) y n +Windows XP x64 y y(4) y n +Windows Vista y y(4) y y +Windows Vista x64 y y(4) y y +OpenVMS Alpha n n n n +Mac OS X 10.6 y(5) n y n +AIX 6.1 32- and 64-bit n n n y +FreeBSD 6.3-STABLE 32&64 bit y n y y +CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y +CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n +CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n +CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y +CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n +CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n +RedHat EL4 2.6.18 Xeon Lustre C y y y n +Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y +SGI Linux 2.6.32.19 y y y y + + (1) Fortran compiled with gfortran. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) + (5) C and C++ shared libraries will not be built when Fortran is enabled. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* examples/run-all-ex.sh does not work on Cygwin. (NAF - 2011/02/11) + +* Parallel test, t_shapesame in testpar, is rather unstable as it continues to + have occasional errors in AIX and quite often in NCSA Abe. It is being built + but it is not run automatically in the "make check" command. One would have to + run it by hand to see if it works in a particular machine. AKC - 2011/01/28 + +* Although OpenVMS Alpha is supported, there are several problems with the C + test suite - getname.c, lheap.c, lheap.c, mtime.c, and stab.c. The test + suite for h5diff also fails. These failures are from the tests, not the + library. We have fixed these failures. But it's too late to put the fixes + into this release. If you install the 1.8.6 library, it should still work + despite of these test failures. If you want the working copy without any + test failure, you can request it from us. SLU - 2011/01/26 + +* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command + sometimes fails in the perform directory due to the attempt to remove the + executable of h5perf or h5perf_serial by two "parallel" commands. This error + has no consequence on the functionality of the HDF5 library or install. It + is fixed in the next release. AKC - 2011/01/25 + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or filesystems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + +* The h5diff tool can display garbage values when variable-length strings in + a compound type dataset are compared. This also occurs with variable-length + string arrays in a compound type dataset. See bug #1989. This will be fixed + in the next release. JKM - 2010/11/05 + +* The AIX --enable-shared setting does not quite work. It can produce a shared + library, but there cannot be more than one shared library that is + interlinked. This means that the high level APIs will not work which is not + very useful. We hope to have a solution in the next release. + (AKC - 2010/10/15) + +* H5Eset_auto can cause a seg fault for a library API call if the application + compiles with -DH5_USE_16_API (see bug 1707). It will be fixed in the + next release. SLU - 2010/10/5 + +* The library's test dt_arith.c showed a compiler's rounding problem on + Cygwin when converting an unsigned long long to a long double. The + library's own conversion works fine. We defined a macro for Cygwin to + skip this test until we can solve the problem. Please see bug #1813. + SLU - 2010/5/5 + +* All the VFL drivers aren't backwardly compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. A new parameter was added to the + get_eoa and set_eoa callback functions, and a new callback function + get_type_map was added. The public function H5FDrealloc was taken out in + 1.8. The problem only happens when users define their own driver for 1.6 + and try to plug in a 1.8 library. This will be fixed in 1.10. SLU - 2010/2/2 + +* MinGW has a missing libstdc++.dll.a library file and will not successfully link + C++ applications/tests. Do not use the enable-cxx configure option. Read all of + the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not + exist. This is due to the MPI_File_open() call failing if the amode has + the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. CMC - 2009/04/28 + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of their sub-tests. These + sub-tests are expected to fail and should exit with a non-zero code but + the yod command does not propagate the exit code of the executables. Yod + always returns 0 if it can launch the executable. The test suite shell + expects a non-zero for this particular test. Therefore, it concludes the + test has failed when it receives 0 from yod. To skip all the "failing" + tests for now, change them as shown below. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + AKC - 2008/11/10 + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message "yod allocation delayed for node recovery." This interferes + with test suites that do not expect to see this message. See the "Red Storm" + section in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use the -mp -O1 compilation flags to build the libraries. A higher level + of optimization causes failures in several HDF5 library tests. + +* On mpich 1.2.5 and 1.2.6 on a system using four processors, if more than + two processes contribute no I/O and the application asks to do collective + I/O, we have found that a simple collective write will sometimes hang. This + can be verified with the t_mpi test under testpar. + +* A dataset created or rewritten with a v1.6.3 or later library cannot be + read with the v1.6.2 or earlier library when the Fletcher32 EDC filter + is enabled. There was a bug in the calculation of the Fletcher32 checksum + in the library before v1.6.3; the checksum value was not consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value was no + longer the same as before on little-endian system. Library releases after + 1.6.4 can still read datasets created or rewritten with an HDF5 library of + v1.6.2 or earlier. SLU - 2005/6/30 + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. To + work around this, set the environment variable MP_INFOLEVEL to 0 to + minimize the messages and run the tests again. The tests may fail with + messages like "The socket name is already in use", but HDF5 does not use + sockets. This failure is due to problems with the poe command trying to + set up the debug socket. To resolve this problem, check to see whether + there are any old /tmp/s.pedb.* files around. These are sockets used by + the poe command and left behind if the command failed at some point. To + resolve this, ask your system administrator to remove the + old/tmp/s.pedb.* files, and then ask IBM to provide a means to run poe + without the debug socket. + +* The --enable-static-exec configure flag will only statically link + libraries if the static version of that library is present. If only the + shared version of a library exists (i.e., most system libraries on + Solaris, AIX, and Mac, for example, only have shared versions), the flag + should still result in a successful compilation, but note that the + installed executables will not be fully static. Thus, the only guarantee + on these systems is that the executable is statically linked with just + the HDF5 library. + +* On an SGI Altix SMP ia64 system, the Intel compiler version 10.1 (which + is the default on that system) does not work properly and results in + failures during the make check (in a static build) and the make + installcheck (in a shared build). This appears to be a compiler + optimization problem. Reducing the optimization by setting CFLAGS to + -O1 or below resolves the issue. Using a newer version of the compiler + (11.0) avoids the issue. MAM - 2010/06/01 + +* On solaris systems, when running the examples with the scripts installed in + .../share/hdf5_examples, two of the c tests, h5_extlink and h5_elink_unix2win + may fail or generate HDF5 errors because the script commands in c/run-c-ex.sh + fail to create test directories red, blue, and u2w. Moving the '!' in lines + 67, 70, 73 of run-c-ex.sh will fix the problem. For example the script command + "if ! test -d red; then" will work on solaris if changed to + "if test ! -d red; then". + + +%%%%1.8.5%%%% + + +HDF5 version 1.8.5 released on Fri Jun 4 13:27:31 CDT 2010 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.4 and HDF5 1.8.5, and +contains information on the platforms tested and known problems in HDF5-1.8.5. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt +in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.5 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.5 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.5 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.5 (current +release) versus Release 1.8.4": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.4 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - CMake Early Access: This release adds support for building HDF5 using + the CMake system. Initial work has targeted Windows, but other platforms + can be used. See the CMake.TXT file for more information. Version + 2.8.1 of CMake is required. + - Configure now adds appropriate defines for supporting large (64-bit) + files on all systems, where supported, by default, instead of only Linux. + This large file support is controllable with the --enable-largefile + configure option. The Linux-specific --enable-linux-lfs option has been + deprecated in favor of this new option. Please note that specifying + --disable-large does NOT attempt to "turn off" largefile support if it + is natively supported by the compiler, but rather just disables + configure from actively trying to add any additional compiler flags. + (MAM - 2010/05/05 - Bug # 1772/1434) + - Fixed an signal handling mask error in H5detect that might result in + SIGBUS or SIGSEGV failures in some platforms such as Linux on Sparc. + (AKC - 2010/4/28 - Bug # 1764) + - Fixed various "strict aliasing" problems, allowing higher levels + of compiler optimization (in particular, allowing '-O3' to work + with recent versions of GCC). (QAK - 2010/04/26) + - Upgraded versions of autotools used to generate configuration suite. + We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b. + (MAM - 2010/04/15) + - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM + compilers so that the IBM compiler options can be added properly. This + allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be + recognized. (AKC - 2009/11/26) + + Library + ------- + - Performance is substantially improved when extending a dataset with early + allocation. (NAF - 2010/03/24 - Bug # 1637) + - Added support for filtering densely stored groups. Many of the API + functions related to filters have been extended to support dense groups + as well as datasets. Pipeline messages can now be stored in a group's + object header. (NAF/QAK - 2009/11/3) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5dump: Added the new packed bits feature which prints packed bits stored + in an integer dataset. (AKC/ADB - 2010/5/7) + - h5diff: Fixed incorrect behavior (hang) in parallel mode when specifying + invalid options (ex: -v and -q). (JKM - 2010/02/17) + - h5diff: Added new flag --no-dangling-links (see --help for details). + (JKM - 2010/02/10) + - h5diff: Added new flag --follow-symlinks (see --help for details). + (JKM - 2010/01/25) + - h5diff: Added a fix to correct the display of garbage values when + displaying big-endian data on a little-endian machine. (JKM - 2009/11/20) + + High-Level APIs + --------------- + - None + + F90 API + ------- + - None + + C++ API + ------- + - New member functions + + Overloaded CommonFG::getObjnameByIdx to take char* for name. + + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*. + (BMR - 2010/05/10) + + Added DataSet::getInMemDataSize() to simplify getting the dataset's + data size in memory. (BMR - 2009/07/26) + + +Support for New Platforms, Languages, and Compilers +=================================================== + - AIX 6.1 has been added. (AKC - 2010/1/4) + + +Bug Fixes since HDF5-1.8.4 +========================== + + Configuration + ------------- + - Fixed various "strict aliasing" problems, allowing higher levels + of compiler optimization (in particular, allowing '-O3' to work + with recent versions of GCC). (QAK - 2010/04/26) + + Library + ------- + - Fixed a file corruption bug that could happen when shrinking a compressed + dataset. (NAF - 2010/05/20) + - Fixed some memory leaks in VL datatype conversion when strings are + used as fill values. (MAM - 2010/05/12 - Bug # 1826) + - Fixed an H5Rcreate failure when passing in a -1 for the dataspace + identifier. (ADB - 2010/4/28) + - Fixed a bug when copying objects with NULL references with the + H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - Bug # 1815) + - Added a mechanism to the H5I interface to save returned object identifier + structures for immediate re-use if needed. This addresses a potential + performance issue by delaying the case when the next identifier to be + registered has grown so large that it wraps around and needs to be + checked to see whether it is available for distribution. + (MAM - 2010/03/15 - Bug # 1730) + - Files can now be concurrently opened more than once using the core file + driver, as long as the backing store is used. (NAF - 2010/03/09) + - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External + links will now be expanded if this flag is set. + (NAF - 2010/03/05 - Bug # 1733) + - Fixed a bug where the library, when traversing an external link, would + reopen the source file if nothing else worked. (NAF - 2010/03/05) + - Fixed a bug where fractal heap identifiers for attributes and shared + object header messages could be incorrectly encoded in the file for + files created on big-endian platforms. + Please see http://www.hdfgroup.org/HDF5/release/known_problems if you + suspect you have a file with this problem. + (QAK - 2010/02/23 - Bug # 1755) + - Fixed an intermittent bug in the b-tree code which could be triggered + by expanding and shrinking chunked datasets in certain ways. + (NAF - 2010/02/16) + - H5Tdetect_class said a VL string is a string type. But when it's in + a compound type, it said it's a VL type. THis has been fixed to be + consistent; it now always returns a string type. + (SLU - 2009/12/10 - Bug # 1584) + - Allow "child" files from external links to be correctly located when + relative to a "parent" file that is opened through a symbolic link. + (QAK - 2009/12/01) + + Parallel Library + ---------------- + - Parallel mode in AIX will fail some of the testcheck_version.sh tests + where it treats "exit(134) the same as if process 0 had received an abort + signal. Fixed. (AKC - 2009/11/3) + + Tools + ----- + - Fixed h5ls to return exit code 1 (error) when a non-existent file is + specified. (JKM - 2010/04/27 - Bug # 1793) + - Fixed h5copy failure when copying a dangling link that is specified + directly. (JKM - 2010/04/22 - Bug # 1817) + - Fixed an h5repack failure that lost attributes from a dataset of + reference type. (JKM - 2010/3/25 - Bug # 1726) + - Fixed h5repack error that set NULL for object reference values for + datasets, groups, or named datatypes. (JKM - 2010/03/19 - Bug # 1814) + + F90 API + ------ + - None + + C++ API + ------ + - The constructor PropList::PropList(id) was fixed to act properly + according to the nature of 'id'. When 'id' is a property class + identifier, a new property list will be created. When 'id' is a + property list identifier, a copy of the property list will be made. + (BMR - 2010/5/9) + - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and + CommonFG::getComment, respectively, now have default values for the + user's convenience. (BMR - 2009/10/23) + - NULL pointer accessing was fixed. (BMR - 2009/10/05 - Bug # 1061) + - Read/write methods of DataSet and Attribute classes were fixed + to handle string correctly. (BMR - 2009/07/26) + + High-Level APIs: + ------ + - Fixed a bug in H5DSattach_scale, H5DSis_attached, and H5DSdetach_scale + caused by using the H5Tget_native_type function to determine the native + type for reading the REFERENCE_LIST attribute. This bug was exposed + on Mac PPC. (EIP - 2010/05/22 - Bug # 1851) + - Fixed a bug in the H5DSdetach_scale function when 0 bytes were + allocated after the last reference to a dimension scale was removed + from the list of references in a VL element of the DIMENSION_LIST + attribute. Modified the function to comply with the specification: + the DIMENSION_LIST attribute is now deleted when no dimension scales + are left attached. (EIP - 2010/05/14 - Bug # 1822) + + Fortran High-Level APIs: + ------ + - None + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 5.3 xlc 7.0.0.9, 8.0.0.20, 9.0.0.4 + (LLNL Up) xlC 7.0.0.9, 8.0.0.20, 9.0.0.4 + xlf 9.1.0.9, 10.1.0.9, 11.1.0.7 + mpcc_r 7.0.0.9 + mpxlf_r 09.01.0000.0008 + + AIX 6.1 xlc 10.1.0.6 + (NCSA BP) xlC 10.1.0.6 + xlf 12.1.0.7 + + Cray XT3 (2.1.56) cc (pgcc) 10.0-0 + (SNL red storm) ftn (pgf90) 10.0-0 + CC (pgCC) 10.0-0 + + FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.3.4 20090419 + g++ 4.3.4 20090419 + gfortran 4.3.4 20090419 + + FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.4.1 20090421 + g++ 4.4.1 20090421 + gfortran 4.4.1 20090421 + + Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 20080704 and 4.4.2 + #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2 + (jam) g++ (GCC) 4.1.2 20080704 and 4.4.2 + G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) + Absoft 32-bit Fortran 95 10.0.7 + PGI C, Fortran, C++ 10.4-0 32-bit + Intel(R) C, C++, Fortran Compilers for 32-bit + applications, Version 11.1 Build 20090827 + MPICH mpich2-1.0.8 compiled with + gcc 4.1.2 and GNU Fortran (GCC) 4.1.2 + + Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 and gcc 4.4.2 + x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2 + (amani) g++ (GCC) 4.1.2 20080704 and 4.4.2 + G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64, + Version 11.1 Build 20090827. + PGI C, Fortran, C++ Version 10.4-0 + for 32 & 64-bit target on x86-64 + MPICH mpich2-1.0.8 compiled with + gcc 4.1.2 and GNU Fortran (GCC) 4.1.2 + + Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 11.0.074 + SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 11.0.074 + (cobalt) SGI MPI 1.38 + + SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-14 + (linew) Sun Fortran 95 8.3 SunOS_sparc + Patch 127000-13 + Sun C++ 5.9 SunOS_sparc Patch 124863-23 + + Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 + 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 + perfctr #7 SMP Open MPI 1.2.2 + (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 + compiled with icc v10.0.026 and ifort 10.0.026 + + Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for + SMP x86_64 GNU/Linux applications running on Intel(R) 64, + (SNL Glory) Versions 11.1. + + Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 + Cygwin(1.7.5 native gcc(4.3.4) compiler and + gfortran) + + Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 + + Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 + + Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 + + MAC OS 10.6.3 (Intel) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 + (pahra) GNU Fortran (GCC) 4.5.0 20090910 + i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 + Intel C, C++ and Fortran compilers 11.1 + + MAC OS 10.5.8 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 + (tejeda) + + MAC OS 10.5 (PPC) powerpc-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 + (juniper-w) + + OpenVMS Alpha V8.3 HP C V7.3-009 + HP C++ V7.3-009 + HP Fortran V8.0-1-104669-48GBT + +Supported Configuration Features Summary +======================================== + + In the tables below + y = tested and supported + n = not supported or not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +Windows XP n y(4) n(4) y y y +Windows XP x64 n y(4) n(4) y y y +Windows Vista n y(4) n(4) y y y +Windows Vista x64 n y(4) n(4) y y y +Mac OS X 10.5 PPC n n n n y n +Mac OS X 10.5 Intel n y n y y y +Mac OS X 10.6 Intel n y n y y y +AIX 5.3 32- and 64-bit n y n y y n +AIX 6.1 32- and 64-bit n y n y y n +FreeBSD 6.3-STABLE 32&64 bit n y n y y y +RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y +RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y +RedHat EL5 2.6.18-128 i686 Intel W n y n y y n +RedHat EL5 2.6.18-128 i686 PGI W n y n y y n +SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y +SuSe Linux 2.6.16 x86_64 Intel W n y n y y n +SuSe Linux 2.6.16 x86_64 PGI W n y n y y y +SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y +RedHat EL4 2.6.18 Xeon Lustre C y y y y y n +Cray XT3 2.1.56 y y y y y n +OpenVMS Alpha V8.3 n y n y y n + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +Windows XP y y(4) y n +Windows XP x64 y y(4) y n +Windows Vista y y(4) y n +Windows Vista x64 y y(4) y n +Mac OS X 10.5 PPC y n n n +Mac OS X 10.5 (Intel) y(5) n y n +Mac OS X 10.6 (Intel) y(5) n y n +AIX 5.3 32- and 64-bit n n n n +AIX 6.1 32- and 64-bit n n n n +FreeBSD 6.3-STABLE 32&64 bit y n y y +RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y +RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y +RedHat EL5 2.6.18-128 i686 Intel W y y y n +RedHat EL5 2.6.18-128 i686 PGI W y y y n +SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y +SuSe Linux 2.6.16 x86_64 Intel W y y y n +SuSe Linux 2.6.16 x86_64 PGI W y y y n +SuSe Linux 2.6.16 SGI Altix ia64 C y n +RedHat EL4 2.6.18 Xeon Lustre C y y y n +Cray XT3 2.1.56 n n n n +OpenVMS Alpha V8.3 n n n n + + (1) Fortran compiled with g95. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2008. (Cygwin shared libraries are not + supported.) + (5) Shared C and C++ are disabled when Fortran is configured in. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* The library's test dt_arith.c exposed a compiler's rounding problem on + Cygwin when converting from unsigned long long to long double. The + library's own conversion works correctly. A macro is defined for Cygwin + to skip this test until we can solve the problem. (Please see bug #1813.) + SLU - 2010/5/5 + +* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the + structure H5FD_class_t changed in 1.8. There is a new parameter added to + get_eoa and set_eoa callback functions. A new callback function + get_type_map was added. The public function H5FDrealloc was taken + out in 1.8. The problem only happens when users define their own driver + for 1.6 and try to plug it into a 1.8 library. This affects a very small + number of users. (See bug report #1279.) SLU - 2010/2/2 + +* MinGW has a missing libstdc++.dll.a library file and will not successfully + link C++ applications/tests. Do not use the enable-cxx configure option. + Read all of the INSTALL_MINGW.txt file for all restrictions. + ADB - 2009/11/11 + +* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. + The error is due to insufficient memory requested. Request a large amount + of runtime memory by setting the following environment variable for more + memory. + LDR_CNTRL=MAXDATA=0x20000000@DSA + AKC - 2009/10/31 + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not + existing. This is due to the MPI_File_open() call failing if the amode has + the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. CMC - 2009/04/28 + +* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c + would fail to compile. Actually bad H5Tinit.c is produced. If -O (same + as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. + When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all + tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. + AKC - 2009/04/20 + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + AKC - 2008/11/10 + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect seeing this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use," + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + +* There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +* On FREE-BSD systems when shared libraries are disabled, make install fails + in install-examples with the error '"Makefile", line 635: Need an operator'. + When this error occurs removing or commenting out the line "export + LD_LIBRARY_PATH=$(LL_PATH)" (line 635 in examples/Makefile) will allow make + install to finish installing examples. The problem will be fixed in the + next release. LRK - 2010/05/26 + +* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which + is the default on that system) does not work properly and results in + failures during make check (in a static build) and make installcheck (during + a shared build). This appears to be a compiler optimization problem. + Reducing optimization by setting CFLAGS to -O1 or below resolves the issue. + Alternatively, using a newer version of the compiler (11.0) also works as + intended. MAM - 2010/06/01 + + +%%%%1.8.4%%%% + + +HDF5 version 1.8.4 released on Tue Nov 10 15:33:14 CST 2009 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.3 and +HDF5 1.8.4, and contains information on the platforms tested and +known problems in HDF5-1.8.4 +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.4 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.4 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.4 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.4 (current +release) versus Release 1.8.3": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.3 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Configuration suite now uses Automake 1.11 and Autoconf 2.64. + MAM 2009/08/31. + - Changed default Gnu fortran compiler from g95 to gfortran since + gfortran is more likely installed with gcc now. -AKC 2009/07/19- + + Library + ------- + - The embedded library information is displayed by H5check_version() if a + version mismatch is detected. Also changed H5check_version() to + suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 + or higher. (Old behavior treated 3 or higher the same as 1, that is + print a warning and allows the program to continue. (AKC - 2009/9/28) + - If a user does not care for the extra library information insert + in the executables, he may turn it off by --disable-embedded-libinfo + during configure. (AKC - 2009/9/15) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5diff: h5diff treats two INFINITY values different. Fixed by checking + (value==expect) before call ABS(...) at h5diff_array.c. This will make + that (INF==INF) is true (INF is treated as an number instead of NaN) + (PC -- 2009/07/28) + - h5diff: add option "--use-system-epsilon" to print difference if + (|a-b| > EPSILON). + Change default to use strict equality (PC -- 2009/09/12) + + High-Level APIs + --------------- + - None + + F90 API + ------- + - Added H5Oopen_by_addr_f MSB - 9/14/09 + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - PathScale compilers are recognized and can build the HDF5 library + properly. AKC - 2009/7/28 - + + +Bug Fixes since HDF5-1.8.3 +========================== + + Configuration + ------------- + - Removed the following config files, as we no longer support them: + config/dec-osf*, config/hpux11.00, config/irix5.x, + config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* + MAM - 2009/10/08 + - Modified configure and make process to properly preserve user's CFLAGS + (and company) environment variables. Build will now properly use + automake's AM_CFLAGS for any compiler flags set by the configure + process. Configure will no longer modify CFLAGS directly, nor will + setting CFLAGS during make completely replace what configure has set up. + MAM - 2009/10/08 + - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS + machine has long retired. AKC - 2009/10/06. + - Added $(EXEEXT) extension to H5detect when it's executed in the + src/Makefile to generate H5Tinit.c so it works correctly on platforms + that require the full extension when running executables. + MAM - 2009/10/01 - BZ #1613 + - Configure will now set FC and CXX to "no" when fortran and c++ + are not being compiled, respectively, so configure will not run + some of the compiler tests for these languages when they are not + being used. MAM - 2009/10/01 + - The --enable-static-exec flag will now properly place the -static flag + on the link line of all installed executables. This will force the + executable to link with static libraries over shared libraries, provided + the static libraries are available. MAM - 2009/08/31 - BZ #1583 + - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to + recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - + + Library + ------- + - Fixed a bug where writing and deleting many global heap objects (i.e. + variable length data) would render the file unreadable. Previously + created files exhibiting this problem should now be readable. + NAF - 2009/10/27 - 1483 + - Fixed error in library's internal caching mechanisms which could cause + an assertion failure (and attendant core dump) when encountering an + unusually formatted file. (QAK - 2009/10/13) + - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628 + - Fixed an assertion failure that occurred when H5Ocopy was called on a + dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597 + - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. + NAF - 2009/09/25 - 1620 + - Fixed a bug where properties weren't being compared with the registered + compare callback. NAF - 2009/09/25 - 1555 + - Corrected problem where library would re-write the superblock in a file + opened for R/W access, even when no changes were made to the file. + (QAK - 2009/08/20, Bz#1473) + - Fixed a bug where H5Pget_filter_by_id would succeed when called for a + filter that wasn't present. NAF - 2009/06/25 - 1250 + - Fixed an issue with committed compound datatypes containing a vlen. Also + fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593 + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5dump/h5ls display buffer resize fixed in tools library. + ADB - 2009/7/21 - 1520 + - perf_serial test added to Windows projects and check batch file. + ADB - 2009/06/11 -1504 + + + F90 API + ------ + - Fixed bug in h5lget_info_by_idx_f by adding missing arguments, + consequently changing the API. New API is: + + SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, & + link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id) + + MSB - 2009/9/17 - 1652 + + - Corrected the values for the H5L_flags FORTRAN constants: + H5L_LINK_ERROR_F, H5L_LINK_HARD_F, H5L_LINK_SOFT_F, H5L_LINK_EXTERNAL_F + MSB - 2009-09-17 - 1653 + + - Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F + MSB - 2009-9-24 - 1471 + + C++ API + ------ + - None + + High-Level APIs: + ------ + - Fixed a bug where the H5TB API would forget the order of fields when added + out of offset order. NAF - 2009/10/27 - 1582 + - H5DSis_attached failed to account for different platform types. Added a + get native type call. ADB - 2009/9/29 - 1562 + + Fortran High-Level APIs: + ------ + - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions + had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 + + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 5.3 xlc 7.0.0.8 + (LLNL Up) xlf 09.01.0000.0008 + xlC 7.0.0.8 + mpcc_r 7.0.0.8 + mpxlf_r 09.01.0000.0008 + + Cray XT3 (2.0.41) cc (pgcc) 7.1-4 + (SNL red storm) ftn (pgf90) 7.1-4 + CC (pgCC) 7.1-4 + + FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.3.5 20091004 + g++ 4.3.5 20091004 + gfortran 4.3.5 20091004 + + FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.4.2 20091006 + g++ 4.4.2 20091006 + gfortran 4.4.2 20091006 + + Linux 2.6.18-164.el5 gcc (GCC) 4.1.2 20080704 + #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) + (jam) GNU Fortran (GCC) 4.1.2 20080704 + (Red Hat 4.1.2-46) + PGI C, Fortran, C++ 8.0-5 32-bit + PGI C, Fortran, C++ 8.0-1 32-bit + Intel(R) C Compiler for 32-bit + applications, Versions 11.0, 11.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 11.0, 11.1 + Intel(R) Fortran Compiler for 32-bit + applications, Version 11.0, 11.1 + Absoft 32-bit Fortran 95 10.0.7 + MPICH mpich2-1.0.8 compiled with + gcc (GCC) 4.1.2 and G95 + (GCC 4.0.3 (g95 0.92!) + + Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 + x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) + (amani) tested for both 32- and 64-bit binaries + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64, + Versions 11.1. + PGI C, Fortran, C++ Version 9.0-4 + for 64-bit target on x86-64 + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + MPICH mpich2-1.0.8 compiled with + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + GNU Fortran (GCC) 4.1.2 20080704 + (Red Hat 4.1.2-46) + + + Linux 2.6.16.60-0.42.5 #1 Intel(R) C++ Version 10.1.017 + SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 + (cobalt) SGI MPI 1.38 + + SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-11 2009/04/30 + (linew) Sun Fortran 95 8.3 SunOS_sparc + Patch 127000-11 2009/10/06 + Sun C++ 5.9 SunOS_sparc + Patch 124863-16 2009/09/15 + + Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 + 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 + perfctr #6 SMP Open MPI 1.2.2 + (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 + compiled with icc v10.0.026 and ifort 10.0.026 + + IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 + #1 SMP ia64 Intel(R) C++ Version 8.1.037 + (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 + mpich-gm-1.2.7p1..16-intel-8.1.037-r1 + + Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for + .1.4.11.1smp #1 SMP applications running on Intel(R) 64, + SMP x86_64 GNU/Linux Versions 10.1. + (SNL Thunderbird) + + Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for + SMP x86_64 GNU/Linux applications running on Intel(R) 64, + (SNL Glory) Versions 10.1. + + Windows XP Visual Studio 2005 w/ Intel Fortran 9.1 + Cygwin(native gcc compiler and g95) + + Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 + + Windows Vista Visual Studio 2005 w/ Intel Fortran 9.1 + + Windows Vista x64 Visual Studio 2005 w/ Intel Fortran 9.1 + + MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 + GNU Fortran (GCC) 4.3.0 20070810 + G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) + Intel C, C++ and Fortran compilers 10.1 + + +Supported Configuration Features Summary +======================================== + + In the tables below + y = tested and supported + n = not supported or not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +Windows XP n y(4) n(4) y y y +Windows XP x64 n y(4) n(4) y y y +Windows Vista n n n y y y +Mac OS X 10.5 Intel n y n y y y +AIX 5.3 32- and 64-bit n y n y y n +FreeBSD 6.3-STABLE 32&64 bit n y n y y y +RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y y y +RedHat EL5 2.6.18-164 i686 Intel W n y n y y n +RedHat EL5 2.6.18-164 i686 PGI W n y n y y n +RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y(3) y y y y +RedHat EL5 2.6.18-164 x86_64 IntelW n y n y y n +RedHat EL5 2.6.18-164 x86_64 PGI W n y n y y y +SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y +RedHat EL4 2.6.18 Xeon Lustre C y y y y y n +SuSe Linux 2.4.21 ia64 Intel C y y y y y n +Cray XT3 2.0.62 y y y y y n + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +Windows XP y y(4) y y +Windows XP x64 y y(4) y y +Windows Vista y n n y +Mac OS X 10.5 y n y n +AIX 5.3 32- and 64-bit n n n n +FreeBSD 6.3-STABLE 32&64 bit y y y y +RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y +RedHat EL5 2.6.18-164 i686 Intel W y y y n +RedHat EL5 2.6.18-164 i686 PGI W y y y n +RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y y y +RedHat EL5 2.6.18-164 x86_64 IntelW y y y n +RedHat EL5 2.6.18-164 x86_64 PGI W y y y n +SuSe Linux 2.6.16 SGI Altix ia64 C y n +RedHat EL4 2.6.18 Xeon Lustre C y y y n +SuSe Linux 2.4.21 ia64 Intel C y y y n +Cray XT3 2.0.62 n n n n + + (1) Fortran compiled with g95. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2005 or Cygwin + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* Parallel mode in AIX will fail some of the testcheck_version.sh tests where + it treats "exit(134) the same as if process 0 had received an abort signal. + This is fixed and will be available in the next release. AKC - 2009/11/3 + +* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. + The error is due to insufficient memory requested. Request a large amount + of runtime memory by setting the following environment variable for more + memory. + LDR_CNTRL=MAXDATA=0x20000000@DSA + AKC - 2009/10/31 + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not + existing. This is due to the MPI_File_open() call failing if the amode has + the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. CMC - 2009/04/28 + +* There is a known issue in which HDF5 will change the timestamp on a file + simply by opening it with read/write permissions, even if the file is not + modified in any way. This is due to the way in which HDF5 manages the file + superblock. A fix is currently underway and should be included in the 1.8.4 + release of HDF5. MAM - 2009/04/28 + +* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c + would fail to compile. Actually bad H5Tinit.c is produced. If -O (same + as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. + When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all + tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. + AKC - 2009/04/20 + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + AKC - 2008/11/10 + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect seeing this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + +* There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +%%%%1.8.3%%%% + + +HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.2 and +HDF5 1.8.3, and contains information on the platforms tested and +known problems in HDF5-1.8.3. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.3 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.3 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.3 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.3 (current +release) versus Release 1.8.2": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.2 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Added libtool version numbers to generated c++, fortran, and + hl libraries. MAM 2009/04/19. + - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. + - Added a Make target of check-all-install to test the correctness of + installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 + + Library + ------- + - Embed the content of libhdf5.settings into the hdf5 executables + so that an "orphaned" executables can display (via the Unix + strings command, for example) the library settings used to build + the executables. This is a prototype implementation. Improvement will + be added in next release. AKC - 2009/04/20 + - Separated "factory" free list class from block free lists. These free + lists are dynamically created and manage blocks of a fixed size. + H5set_free_list_limits() will use the same settings specified for block + free lists for factory free lists. NAF - 2009/04/08 + - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29 + - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a + user-defined callback function for external link traversal. + NAF - 2009/01/08 + - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to + allow the user to specify the file access flags used to open the target + file of an external link. NAF - 2009/01/08 + - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow + individual rdcc configuration for each dataset. Added + H5Dget_access_plist() function to retrieve a dataset access property + list from a dataset. NAF - 2008/11/12 + - Added H5Iis_valid() function to check if an id is valid without + producing an error message. NAF - 2008/11/5 + - Added code to maintain a min_clean_fraction in the metadata cache when + in serial mode. MAM - 2009/01/9 + + Parallel Library + ---------------- + - Modified parallel tests to run with arbitrary number of processes. The + modified tests are testphdf5 (parallel dataset access), t_chunk_alloc + (chunk allocation), and t_posix_compliant (posix compliance). The rest of + the parallel tests already use in the code the number of processes + available in the communicator. (CMC - 2009/04/28) + + Tools + ----- + - h5diff new flag, -c, --compare, list objects that are not comparable. + PVN - 2009/4/2 - 1368 + - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2 + - h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519 + - h5repack now handles group creation order. PVN - 2009/4/2 - 1402 + - h5repack: When user doesn't specify a chunk size, h5repack now + defines a default chunk size as the same size of the size of the + hyperslab used to read the chunks. The size of the hyperslabs are + defined as the size of each dimension or a predefined constant, + whatever is smaller. This assures that the chunk read fits in the + chunk cache. PVN - 2008/11/21 + + High-Level APIs + --------------- + - Table: In version 3.0 of Table, the writing of the "NROWS" attribute + (used to store number of records) was deprecated. PVN - 2008/11/24 + + F90 API + ------- + - Added for the C APIs the Fortran wrappers: + h5dget_access_plist_f + h5iis_valid_f + h5pset_chunk_cache_f + h5pget_chunk_cache_f + MSB - 2009/04/17 + + C++ API + ------- + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + + +Bug Fixes since HDF5-1.8.2 +========================== + + Configuration + ------------- + - The --includedir=DIR configuration option now works as intended, and + can be used to specify the location to install C header files. The + default location remains unchanged, residing at ${prefix}/include. + MAM - 2009/03/10 - BZ #1381 + - Configure no longer removes the '-g' flag from CFLAGS when in production + mode if it has been explicitly set in the CFLAGS environment variable + prior to configuration. MAM - 2009/03/09 - BZ #1401 + + Library + ------- + - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 + API. NAF - 2009/04/20 - 1533 + - Fixed a problem with using data transforms with non-native types in the + file. NAF - 2009/04/20 - 1548 + - Added direct.h include file to windows section of H5private.h + to fix _getcwd() warning. ADB - 2009/04/14 - 1536 + - Fixed a bug that prevented external links from working after calling + H5close(). NAF - 2009/04/10 - 1539 + - Modified library to write cached symbol table information to the + superblock, to allow library versions 1.3.0 to 1.6.3 to read files created + by this version. NAF - 2009/04/08 - 1423 + - Changed skip lists to use a deterministic algorithm. The library should + now never call rand() or srand(). NAF - 2009/04/08 - 503 + - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups + when that property was set. NAF - 2009/04/07 - 1526 + - Fixed a bug that caused files with a user block to grow by the size of the + user block every time they were opened. NAF - 2009/03/26 - 1499 + - Fixed a rare problem that could occur with files using the old (pre 1.4) + array datatype. NAF - 2009/03/23 + - Modified library to be able to open files with corrupt root group symbol + table messages, and correct these errors if they are found. Such files + can only be successfully opened with write access. NAF - 2009/03/23 - 1189 + - Removed the long_long #define and replaced all instances with + "long long". This caused problems with third party products. All + currently supported compilers support the type. ADB - 2009/03/05 + - Fixed various bugs that could prevent the fill value from being written + in certain rare cases. NAF - 2009/02/26 - 1469 + - Fixed a bug that prevented more than one dataset chunk from being cached + at a time. NAF - 2009/02/12 - 1015 + - Fixed an assertion failure caused by opening an attribute multiple times + through multiple file handles. NAF - 2009/02/12 - 1420 + - Fixed a problem that could prevent the user from adding attributes (or any + object header message) in some circumstances. NAF - 2009/02/12 - 1427 + - Fixed a bug that could cause problems when an attribute was added to a + committed datatype using the committed datatype's datatype. + NAF - 2009/02/12 + - Fixed a bug that could cause problems when copying an object with a shared + message in its own object header. NAF - 2009/01/29 + - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes. + NAF - 2009/01/27 - 1443 + - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise + packed compound type. NAF - 2009/01/14 + - Fixed up some old v2 btree assertions that get run in debug mode that + were previously failing on compilation, and removed some of the + more heavily outdated and non-rewritable ones. MAM - 2008/12/15 + - Fixed a bug that could cause problems when "automatically" unmounting + multiple files. NAF - 2008/11/17 + - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. + PVN - 2009/01/8 + + Parallel Library + ---------------- + - None + + Tools + ----- + - Fixed many problems that could occur when using h5repack with named + datatypes. NAF - 2009/4/20 - 1516/1466 + - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets + that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant + defined as 1024Kb, such as array types with large dimensions. + PVN - 2009/4/1 - 1501 + - h5import: By selecting a compression type, a big endian byte order + was being selected. PVN - 2009/3/11 - 1462 + - zip_perf.c had missing argument on one of the open() calls. Fixed. + AKC - 2008/12/9 + + F90 API + ------ + - None + + C++ API + ------ + - None + + High-Level APIs: + ------ + - Dimension scales: The scale index return value in H5DSiterate_scales + was not always incremented. PVN - 2009/4/8 - 1538 + + Fortran High-Level APIs: + ------ + - Lite: The h5ltget_dataset_info_f function (gets information about + a dataset) was not correctly returning the dimension array + PVN - 2009/3/23 + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 5.3 xlc 7.0.0.8 + (LLNL Up) xlf 09.01.0000.0008 + xlC 7.0.0.8 + mpcc_r 7.0.0.8 + mpxlf_r 09.01.0000.0008 + + Cray XT3 (2.0.41) cc (pgcc) 7.1-4 + (SNL red storm) ftn (pgf90) 7.1-4 + CC (pgCC) 7.1-4 + + FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.3.4 20090419 + g++ 4.3.4 20090419 + gfortran 4.3.4 20090419 + + FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.4.1 20090421 + g++ 4.4.1 20090421 + gfortran 4.4.1 20090421 + + IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m + F90 MIPSpro 7.4.4m + C++ MIPSpro cc 7.4.4m + + Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 + #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) + (jam) PGI C, Fortran, C++ 7.2-1 32-bit + PGI C, Fortran, C++ 8.0-1 32-bit + Intel(R) C Compiler for 32-bit + applications, Versions 10.1, 11.0 + Intel(R) C++ Compiler for 32-bit + applications, Version 10.1, 11.0 + Intel(R) Fortran Compiler for 32-bit + applications, Version 10.1, 11.0 + Absoft 32-bit Fortran 95 10.0.7 + MPICH mpich2-1.0.8 compiled with + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + + Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 + SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) + (kagiso) MPICH mpich2-1.0.8 compiled with + gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) + + Linux 2.6.16.60-0.37-smp #1 gcc 4.1.2 + SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) + (smirom) Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64, + Versions 10.1, 11.0. + PGI C, Fortran, C++ Version 7.2-1, 8.0-1 + for 64-bit target on x86-64 + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + MPICH mpich2-1.0.8 compiled with + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + tested for both 32- and 64-bit binaries + + Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 + SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 + (cobalt) SGI MPI 1.38 + + SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09 + (linew) Sun WorkShop 6 update 2 Fortran 95 8.3 + Patch 127000-07 + Sun WorkShop 6 update 2 C++ 5.8 + Patch 124863-11 + + Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404 + 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026 + perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026 + (abe) Open MPI 1.2.2 + MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 + compiled with icc v10.0.026 and ifort 10.0.026 + + IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 + #1 SMP ia64 Intel(R) C++ Version 8.1.037 + (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 + mpich-gm-1.2.7p1..16-intel-8.1.037-r1 + + Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for + .1.4.11.1smp #1 SMP applications running on Intel(R) 64, + SMP x86_64 GNU/Linux Versions 9.1. + (SNL Spirit) + + Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for + .1.4.11.1smp #1 SMP applications running on Intel(R) 64, + SMP x86_64 GNU/Linux Versions 10.1. + (SNL Thunderbird) + + Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for + SMP x86_64 GNU/Linux applications running on Intel(R) 64, + (SNL Glory) Versions 10.1. + + Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for + SMP x86_64 GNU/Linux applications running on Intel(R) 64, + (LLNL Zeus) Versions 9.1. + gcc/gfortran/g++ (GCC) 4.1.2. + + Windows XP Visual Studio .NET + Visual Studio 2005 w/ Intel Fortran 9.1 + Cygwin(native gcc compiler and g95) + + Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 + + Windows Vista Visual Studio 2005 + + MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 + GNU Fortran (GCC) 4.3.0 20070810 + G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) + Intel C, C++ and Fortran compilers 10.1 + + +Supported Configuration Features Summary +======================================== + + In the tables below + y = tested and supported + n = not supported or not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +IRIX64_6.5 32-bit n n n n y y +IRIX64_6.5 64-bit n y y y y y +Windows XP n y(4) n(4) y y y +Windows XP x64 n y(4) n(4) y y y +Windows Vista n n n y y y +Mac OS X 10.5 Intel n y n y y y +AIX 5.3 32- and 64-bit n y n y y n +FreeBSD 6.3-STABLE 32&64 bit n y n y y y +RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y +RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y +RedHat EL5 2.6.18-128 i686 Intel W n y n y y n +RedHat EL5 2.6.18-128 i686 PGI W n y n y y n +SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y +SuSe Linux 2.6.16 x86_64 Intel W n y n y y n +SuSe Linux 2.6.16 x86_64 PGI W n y n y y y +SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y +RedHat EL4 2.6.18 Xeon Lustre C y y y y y n +SuSe Linux 2.4.21 ia64 Intel C y y y y y n +Cray XT3 2.0.41 y y y y y n + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +IRIX64_6.5 32-bit y dna y y +IRIX64_6.5 64-bit y y n y +Windows XP y y(4) y y +Windows XP x64 y y(4) y y +Windows Vista y n n y +Mac OS X 10.5 y n y n +AIX 5.3 32- and 64-bit n n n n +FreeBSD 6.3-STABLE 32&64 bit y n y y +RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y +RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y +RedHat EL5 2.6.18-128 i686 Intel W y y y n +RedHat EL5 2.6.18-128 i686 PGI W y y y n +SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y +SuSe Linux 2.6.16 x86_64 Intel W y y y n +SuSe Linux 2.6.16 x86_64 PGI W y y y n +SuSe Linux 2.6.16 SGI Altix ia64 C y n +RedHat EL4 2.6.18 Xeon Lustre C y y y n +SuSe Linux 2.4.21 ia64 Intel C y y y n +Cray XT3 2.0.41 n n n n + + (1) Fortran compiled with g95. + (2) With PGI and Absoft compilers. + (3) With PGI compiler for Fortran. + (4) Using Visual Studio 2005 or Cygwin + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. CMC - 2009/04/28 + +* There is a known issue in which HDF5 will change the timestamp on a file + simply by opening it with read/write permissions, even if the file is not + modified in any way. This is due to the way in which HDF5 manages the file + superblock. A fix is currently underway and should be included in the 1.8.4 + release of HDF5. MAM - 2009/04/28 + +* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c + would fail to compile. Actually bad H5Tinit.c is produced. If -O (same + as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. + When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all + tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. + AKC - 2009/04/20 + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + AKC - 2008/11/10 + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect seeing this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* We have discovered two problems when running collective IO parallel HDF5 + tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a + Linux cluster at NCSA. + + Under some complex selection cases: + 1) MPI_Get_element returns the wrong value. + 2) MPI_Type_struct also generates the wrong derived datatype and corrupt + data may be generated. + These issues arise only when turning on collective IO with chunking storage + with some complex selections. We have not found these problems on other + MPI-IO compilers. If you encounter these problems, you may use independent + IO instead. + + To avoid this behavior, change the following line in your code + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + to + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); + KY - 2007/08/24 + +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* For LLNL, uP: both serial and parallel tests pass. + Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. + ubgl: Serial tests pass but parallel tests fail. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* On IRIX6.5, when the C compiler version is greater than 7.4, complicated + MPI derived datatype code will work. However, the user should increase + the value of the MPI_TYPE_MAX environment variable to some appropriate value + to use collective irregular selection code. For example, the current + parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag fails to compile for Solaris + platforms. This is due to the fact that not all of the system libraries on + Solaris are available in a static format. + + The --enable-static-exec configure flag also fails to correctly compile + on IBM SP2 platforms for serial mode. The parallel mode works fine with + this option. + + It is suggested that you do not use this option on these platforms + during configuration. + +* There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +* Information about building with PGI and Intel compilers is available in + the INSTALL file sections 4.7 and 4.8. + + +%%%%1.8.2%%%% + + +HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2, +and contains information on the platforms tested and known problems in +HDF5-1.8.2. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.2 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.2 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.2 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.2 (current +release) versus Release 1.8.1": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.8.1 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15). + + Library + ------- + - Added two new public routines: H5Pget_elink_fapl() and + H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) + - Improved free space tracking in file to be faster. (QAK - 2008/10/06) + - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5repack: added new options -u and -b to add a userblock to an HDF5 + file during the repack. (PVN - 2008/08/26) + - h5repack: added options -t and -a to call H5Pset_alignment while + creating a repacked file. (PVN - 2008/08/29) + - h5ls: added capability to traverse through external links when the -r + (recursive) flag is given. (NAF - 2008/09/16) + - h5ls: added -E option to enable traversal of external links. + h5ls will not traverse external links without this flag being set. + (NAF - 2008/10/06) + - h5dump: when -b flag is used without a keyword after it, binary + output defaults to NATIVE. MEMORY keyword was deprecated + and replaced by NATIVE keyword. (PVN - 2008/10/30) + - h5diff: returns 1 when file graphs differ by any object. + Error return code was changed to 2 from -1. (PVN - 2008/10/30) + - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP + instead (PVN - 2008/10/30) + + + + F90 API + ------ + - Added optional parameter 'mounted' to H5Gget_info_f, + H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24) + - Added H5Tget_native_type_f (MSB - 2008/09/30) + + + C++ API + ------ + - These member functions were added as wrapper for H5Rdereference to + replace the incorrect IdComponent::dereference(). + void H5Object::dereference(H5Object& obj, void* ref, + H5R_type_t ref_type=H5R_OBJECT) + void H5Object::dereference(H5File& h5file, void* ref, + H5R_type_t ref_type=H5R_OBJECT) + void H5Object::dereference(Attribute& obj, void* ref, + H5R_type_t ref_type=H5R_OBJECT) + + In addition, these constructors were added to create the associated + objects by way of dereference: + DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) + DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) + DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) + Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) + Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) + Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) + DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) + DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) + DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) + (BMR - 2008/10/29) + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Intel 10.1 is supported on Mac OS X 10.5.4. + Note: + When Fortran is enabled, configure automatically + disables the build of shared libraries (i.e., only + static C and C++ HDF5 libraries will be built + along with the static HDF5 Fortran library). + Intel 10.1 C and C++ compilers require + "-no-multibyte-chars" compilation flag due to the known + bug in the compilers. + (EIP - 2008/10/30) + + +Bug Fixes since HDF5-1.8.1 +========================== + + Configuration + ------------- + - Fixed error with 'make check install' failing due to h5dump + needing other tools built first. (MAM - 2008/10/15). + - When using shared szip, it is no longer necessary to specify + the path to the shared szip libraries in LD_LIBRARY_PATH. + (MAM - 2008/10/15). + - The file libhdf5_fortran.settings is not installed since its content + is included in libhdf5.settings now. (AKC - 2008/10/21) + - "make DESTDIR=xxx install" failed to install some tools and files + (e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8). + + Library + ------- + - H5Ovisit and H5Ovisit_by_name will now properly terminate when the + callback function returns a positive value on the starting object. + (NAF - 2008/11/03) + - Fixed an error where a null message could be created that was larger + than could be written to the file. (NAF - 2008/10/23) + - Corrected error with family/split/multi VFD not updating driver info + when "latest" version of the file format used. (QAK - 2008/10/14) + - Corrected alignment+threshold errors to work correctly when metadata + aggregation is enabled. (QAK - 2008/10/06) + - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects + registered by the library for internal library use. + (NAF - 2008/10/06) + - Fixed potential memory leak during compound conversion. + (NAF - 2008/10/06) + - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. + Also changed the return value of H5Fget_obj_ids from HERR_T to + SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T. + (SLU - 2008/09/26) + - Fixed an issue that could cause data to be improperly overwritten + during compound type conversion. (NAF - 2008/09/19) + - Fixed pointer alignment violations that could occur during vlen + conversion. (NAF - 2008/09/16) + - Fixed problem where library could cause a segmentation fault when + an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) + - Fixed improper shutdown when objects have reference count > 1. The + library now tracks reference count due to the application separately + from that due to internal library routines. (NAF - 2008/08/19) + - Fixed assertion failure caused by incorrect array datatype version. + (NAF - 2008/08/08) + - Fixed an issue where mount point traversal would fail when using + multiple handles for the child. (NAF - 2008/08/07) + - Fixed an issue where mount points were inaccessible when using + multiple file handles for the parent. The mount table is now in + the shared file structure (the parent pointer is still in the + top structure). (NAF - 2008/08/07) + - Fixed assertion failure caused by incorrect array datatype version. + (NAF - 2008/08/04) + - Fixed issue where a group could have a file mounted on it twice. + (QAK - 2008/07/15) + - When an attribute was opened twice and data was written with + one of the handles, the file didn't have the data. It happened + because each handle had its own object structure, and the empty + one overwrote the data with fill value. This is fixed by making + some attribute information like the data be shared in the + attribute structure. (SLU - 2008/07/07) + - Fixed a Windows-specific issue in the ohdr test which was causing + users in some timezones to get false errors. This a deficiency in + the Windows mktime() function, and has been handled properly. + (SJW - 2008/06/19) + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5dump now checks for uniqueness of committed datatypes. + (NAF - 2008/10/15) + - Fixed unnecessary indentation of committed datatypes in h5dump. + (NAF - 2008/10/15) + - Fixed bugs in h5stat: segmemtation fault when printing groups and + print warning message when traversal of objects is unsuccessful. + (see bug #1253) (VC- 2008/10/13) + - Fixed bug in h5ls that prevented relative group listings (like + "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) + - h5dump: when doing binary output (-b), the stdout printing of + attributes was done incorrectly. Removed printing of attributes + when doing binary output. (PVN - 2008/06/05) + + + F90 API + ------ + - h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND + and H5S_SELECT_PREPEND (MSB - 2008/09/30) + - h5sget_select_elem_pointlist: Fixed list of returned points by + rearranging the point list correctly by accounting for C + conventions. (MSB - 2008/09/30) + - h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension + of arrays.(MSB - 2008/9/30) + - h5sget_select_bounds_f: Swapped array bounds to account for C and + Fortran reversed array notation (MSB - 2008/9/30) + - Changed to initializing string to a blank character instead of a + null type in tH5P.f90 to fix compiling error using AIX 5.3.0 + (MSB - 2008/7/29) + - Fixed missing commas in H5test_kind.f90 detected by NAG compiler + (MSB - 2008/7/29) + - Fixed passing and array to a scalar in tH5A_1_8.f90 detected by + NAG compiler (MSB - 2008/7/29) + - Added the ability of the test programs to use the status of + HDF5_NOCLEANUP to determine if the *.h5 files should be removed + or not after the tests are completed (MSB - 2008/10/1) + - In nh5tget_offset_c: (MSB 9/12/2008) + If offset was equal to 0 it returned the error code of -1, + this was changed to return an error code of -1 when the offset + value is < 0. + - Uses intrinsic Fortran function SIZEOF if available when detecting + type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3) + - Put the DOUBLE PRECISION interfaces in a separate module and + added a USE statement for the module. The interfaces are + included/excluded depending on the state of FORTRAN_DEFAULT_REAL + is DBLE_F which detects if the default REAL is DOUBLE PRECISION. + This allows the library to be compiled with -r8 Fortran flag + without the user needing to edit the source code. + (MSB - 200/8/27) + - Enable building shared library for fortran by adding the flag -fPIC + to the compile flags for versions of Intel Fortran compiler >=9 + (MSB - 2008/8/26) + + C++ API + ------ + - Fixed a design bug which allowed an Attribute object to create/modify + attributes (bugzilla #1068). The API class hierarchy was revised + to address the problem. Classes AbstractDS and Attribute are moved + out of H5Object. Class Attribute now multiply inherits from + IdComponent and AbstractDs and class DataSet from H5Object and + AbstractDs. In addition, the data member IdComponent::id was + moved into subclasses: Attribute, DataSet, DataSpace, DataType, + H5File, Group, and PropList. (BMR - 2008/05/20) + - IdComponent::dereference was incorrect and replaced as described + in "New Features" section. + (BMR - 2008/10/29) + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + AIX 5.3 xlc 7.0.0.8 + xlf 09.01.0000.0008 + xlC 7.0.0.8 + mpcc_r 7.0.0.8 + mpxlf_r 09.01.0000.0008 + + Cray XT3 (2.0.41) cc (pgcc) 7.1-4 + (red storm) ftn (pgf90) 7.1-4 + CC (pgCC) 7.1-4 + + FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.2.5 20080702 + g++ 4.2.5 20080702 + gfortran 4.2.5 20080702 + + FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.2.5 20080702 + g++ 4.2.5 20080702 + gfortran 4.2.5 20080702 + + IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m + F90 MIPSpro 7.4.4m + C++ MIPSpro cc 7.4.4m + + Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 + SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007) + (kagiso) PGI C, Fortran, C++ 7.2-1 32-bit + Intel(R) C Compiler for 32-bit + applications, Version 10.1 + Intel(R) C++ Compiler for 32-bit + applications, Version 10.1 + Intel(R) Fortran Compiler for 32-bit + applications, Version 10.1 + Absoft 32-bit Fortran 95 10.0.4 + MPICH mpich-1.2.7 compiled with + gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) + MPICH mpich2-1.0.6p1 compiled with + gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) + + Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T + SMP x86_64 GNU/Linux Ver. 10.1.013 + (smirom) Intel(R) Fortran Intel(R) EM64T + Ver. 10.1.013 + PGI C, Fortran, C++ Version 7.2-1 + for 64-bit target on x86-64 + MPICH mpich-1.2.7 compiled with + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + MPICH mpich2-1.0.7 compiled with + gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) + tested for both 32- and 64-bit binaries + + Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 + Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 + (cobalt) SGI MPI 1.16 + + SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 + (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 + Sun WorkShop 6 update 2 C++ 5.8 + Patch 121019-06 + + Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp + (abe) Intel(R) C++ Version 10.0.026 + Intel(R) Fortran Compiler Version 10.0.026 + Open MPI 1.2.2 + MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 + compiled with icc v10.0.026 and + ifort 10.0.026 + + IA-64 Linux 2.4.21-309.tg1 #1 SMP + ia64 gcc (GCC) 3.2.2 + (NCSA tg-login) Intel(R) C++ Version 8.1.037 + Intel(R) Fortran Compiler Version 8.1.033 + mpich-gm-1.2.7p1..16-intel-8.1.037-r1 + + Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp + (abe) gcc 3.4.6 20060404 + Intel(R) C++ Version 10.0 + Intel (R) Fortran Compiler Version 10.0 + mvapich2-0.9.8p2patched-intel-ofed-1.2 + + Windows XP Visual Studio .NET + Visual Studio 2005 w/ Intel Fortran 9.1 + Cygwin(native gcc compiler and g95) + + Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 + + Windows Vista Visual Studio 2005 + + MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 + GNU Fortran (GCC) 4.3.0 20070810 + G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) + Intel C, C++ and Fortran compilers 10.1 + + +Supported Configuration Features Summary +======================================== + + In the tables below + y = tested and supported + n = not supported or not tested in this release + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +Solaris2.10 32-bit n y n y y y +Solaris2.10 64-bit n y n y y y +IRIX64_6.5 32-bit n n n n y y +IRIX64_6.5 64-bit n y y y y y +Windows XP n y(15) n(15) y y y +Windows XP x64 n y(15) n(15) y y y +Windows Vista n n n y y y +Mac OS X 10.5 Intel n y n y y y +AIX 5.3 32- and 64-bit n y n y y n +FreeBSD 6.3-STABLE +32&64 bit n y n y y y +RedHat EL4 (3) W y(1) y(10) y(1) y y y +RedHat EL4 Intel (3) W n y n y y n +RedHat EL4 PGI (3) W n y n y y n +SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y +SuSe x86_64 Int(3,12) W n y(13) n y y n +SuSe x86_64 PGI(3,12) W n y(8) n y y y +Linux 2.6 SuSE ia64 C + Intel (3,7) y y y y y n +Linux 2.6 SGI Altix + ia64 Intel (3) y y y y y y +Linux 2.6 RHEL C + Lustre Intel (5) y(4) y y(4) y y n +Cray XT3 2.0.41 y y y y y n + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 32-bit y y y y +Solaris2.10 64-bit y y y y +IRIX64_6.5 32-bit y dna y y +IRIX64_6.5 64-bit y y n y +Windows XP y y(15) y y +Windows XP x64 y y(15) y y +Windows Vista y n n y +Mac OS X 10.5 y n y n +AIX 5.3 32- and 64-bit n n n n +FreeBSD 6.2 32&64 bit y n y y +RedHat EL4 (3) W y y(10) y y +RedHat EL4 Intel (3) W y y y n +RedHat EL4 PGI (3) W y y y n +SuSe x86_64 GNU(3,12) W y y y y +SuSe x86_64 Int(3,12) W y y y n +SuSe x86_64 PGI(3,12) W y y y n +Linux 2.4 SuSE C + ia64 C Intel (7) y y y n +Linux 2.4 SGI Altix C + ia64 Intel y n +Linux 2.6 RHEL C + Lustre Intel (5) y y y n +Cray XT3 2.0.41 n n n n + + Notes: (1) Using mpich2 1.0.6. + (2) Using mpich2 1.0.7. + (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. + W or C indicates workstation or cluster, respectively. + (4) Using mvapich2 0.9.8. + (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre + and Intel compilers + (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre + and Intel compilers + (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers + (8) pgf90 + (9) With Compaq Visual Fortran 6.6c compiler. + (10) With PGI and Absoft compilers. + (11) PGI and Intel compilers for both C and Fortran + (12) AMD Opteron x86_64 + (13) ifort + (14) Yes with C and Fortran, but not with C++ + (15) Using Visual Studio 2005 or Cygwin + (16) Not tested for this release. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and + tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests + are expected to fail and should exit with a non-zero code but the yod + command does not propagate the exit code of the executables. Yod always + returns 0 if it can launch the executable. The test suite shell expects + a non-zero for this particular test, therefore it concludes the test has + failed when it receives 0 from yod. Skip all the "failing" test for now + by changing them as following. + + ======== Original tools/h5ls/testh5ls.sh ========= + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Change to =============================== + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ================================================== + + ======== Original tools/h5copy/testh5copy.sh ========= + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + H5LSTEST $FILEOUT + ======== Change to =============================== + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets + echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested + echo SKIP H5LSTEST $FILEOUT + ================================================== + AKC - 2008/11/10 + +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect seeing this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* We have discovered two problems when running collective IO parallel HDF5 + tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a + Linux cluster at NCSA. + + Under some complex selection cases: + 1) MPI_Get_element returns the wrong value. + 2) MPI_Type_struct also generates the wrong derived datatype and corrupt + data may be generated. + These issues arise only when turning on collective IO with chunking storage + with some complex selections. We have not found these problems on other + MPI-IO compilers. If you encounter these problems, you may use independent + IO instead. + + To avoid this behavior, change the following line in your code + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + to + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); + + KY - 2007/08/24 + +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* For LLNL, uP: both serial and parallel tests pass. + Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. + ubgl: Serial tests pass but parallel tests fail. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* On IRIX6.5, when the C compiler version is greater than 7.4, complicated + MPI derived datatype code will work. However, the user should increase + the value of the MPI_TYPE_MAX environment variable to some appropriate value + to use collective irregular selection code. For example, the current + parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag fails to compile for Solaris + platforms. This is due to the fact that not all of the system libraries on + Solaris are available in a static format. + + The --enable-static-exec configure flag also fails to correctly compile + on IBM SP2 platforms for serial mode. The parallel mode works fine with + this option. + + It is suggested that you do not use this option on these platforms + during configuration. + +* There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +* Information about building with PGI and Intel compilers is available in + the INSTALL file sections 4.7 and 4.8. + + + + +%%%%1.8.1%%%% + + +HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between the HDF5-1.8.1 release +and HDF5 1.8.0, and contains information on the platforms tested and known +problems in HDF5-1.8.1. For more details, see the files +HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory +of the HDF5 source. + +Links to the HDF5 1.8.1 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.1 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.1 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.1 (current +release) versus Release 1.8.0": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.8.0 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + Configuration + ------------- + - The lib/libhdf5.settings file contains much more configure + information. (AKC - 2008/05/18) + + - The new configure option "--disable-sharedlib-rpath" disables + embedding the '-Wl,-rpath' information into executables when + shared libraries are produced, and instead solely relies on the + information in LD_LIBRARY_PATH. (MAM - 2008/05/15) + + - Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and + Libtool 2.2.2 (MAM - 2008/05/01) + + Source code distribution + ======================== + + Library + ------- + - None + + Parallel Library + ---------------- + - None + + Tools + ----- + - h5repack: Reinstated the -i and -o command line flags to specify + input and output files. h5repack now understands both the old + syntax (with -i and -o) and the new syntax introduced in Release + 1.8.0. (PVN - 2008/05/23) + - h5dump: Added support for external links, displaying the object that + an external link points to. (PVN - 2008/05/12) + - h5dump: Added an option, -m, to allow user-defined formatting in the + output of floating point numbers. (PVN - 2008/05/06) + - h5dump, in output of the -p option: Added effective data compression + ratio to the dataset storage layout output when a compression filter + has been applied to a dataset. (PVN - 2008/05/01) + + F90 API + ------ + - New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were + added. See "Release 1.8.1 (current release) versus Release 1.8.0" in + the document "HDF5 Software Changes from Release to Release" + (http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the + complete list of the new APIs. + + C++ API + ------ + - None + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Both serial and parallel HDF5 are supported for the Red Storm machine + which is a Cray XT3 system. + + - The Fortran library will work correctly if compiled with the -i8 + flag. This has been tested with the g95, PGI and Intel Fortran + compilers. + + +Bug Fixes since HDF5-1.8.0 +========================== + + Configuration + ------------- + - None + + Source code distribution + ======================== + + Library + ------- + - Chunking: Chunks greater than 4GB are disallowed. + (QAK - 2008/05/16) + - Fixed the problem with searching for a target file when following + an external link. The search pattern will depend on whether the + target file's pathname is an absolute or a relative path. + Please see the H5Lcreate_external description in the "HDF5 + Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html). + (VC - 2008/04/08) + - Fixed possible file corruption bug when encoding datatype + descriptions for compound datatypes whose size was between + 256 and 511 bytes and the file was opened with the "use the + latest format" property enabled (with H5Pset_libver_bounds). + (QAK - 2008/03/13) + - Fixed bug in H5Aget_num_attrs() routine to correctly handle an + invalid location identifier. (QAK - 2008/03/11) + + Parallel Library + ---------------- + - None + + Tools + ----- + - Fixed bug in h5diff that prevented datasets and attributes with + variable-length string elements from comparing correctly. + (QAK - 2008/02/28) + - Fixed bug in h5dump that caused binary output to be made only for + the first dataset, when several datasets were requested. + (PVN - 2008/04/07) + + F90 API + ------ + - The h5tset(get)_fields subroutines were missing the parameter to + specify a sign position; fixed. (EIP - 2008/05/23) + - Many APIs were fixed to work with the 8-byte integers in Fortran vs. + 4-byte integers in C. This change is transparent to user applications. + + C++ API + ------ + - The class hierarchy was revised to address the problem reported + in bugzilla #1068, Attribute should not be derived from base + class H5Object. Classes AbstractDS was moved out of H5Object. + Class Attribute now multiply inherits from IdComponent and + AbstractDs and class DataSet from H5Object and AbstractDs. + In addition, data member IdComponent::id was moved into subclasses: + Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList. + (BMR - 2008/05/20) + - IdComponent::dereference was incorrect; it was changed from: + void IdComponent::dereference(IdComponent& obj, void* ref) + to: + void H5Object::dereference(H5File& h5file, void* ref) + void H5Object::dereference(H5Object& obj, void* ref) + (BMR - 2008/05/20) + - Revised Attribute::write and Attribute::read wrappers to handle + memory allocation/deallocation properly. (bugzilla 1045) + (BMR - 2008/05/20) + + +Platforms Tested +================ +The following platforms and compilers have been tested for this release. + + Cray XT3 (2.0.41) cc (pgcc) 7.1-4 + (red storm) ftn (pgf90) 7.1-4 + CC (pgCC) 7.1-4 + mpicc 1.0.2 + mpif90 1.0.2 + + FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.2.1 20080123 + g++ 4.2.1 20080123 + gfortran 4.2.1 20070620 + + FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.2.1 20080123 + g++ 4.2.1 20080123 + gfortran 4.2.1 20080123 + + IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m + F90 MIPSpro 7.4.4m + C++ MIPSpro cc 7.4.4m + + Linux 2.6.9 (RHEL4) Intel 10.0 compilers + (abe.ncsa.uiuc.edu) + + Linux 2.4.21-47 gcc 3.2.3 20030502 + (osage) + + Linux 2.6.9-42.0.10 gcc,g++ 3.4.6 20060404, G95 (GCC 4.0.3) + (kagiso) PGI 7.1-6 (pgcc, pgf90, pgCC) + Intel 9.1 (icc, ifort, icpc) + + Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, + (smirom) g95 (GCC 4.0.3) + PGI 7.1-6 (pgcc, pgf90, pgCC) + Intel 9.1 (icc, ifort, icpc) + + Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 + SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 + (cobalt) SGI MPI + + SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 + (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 + Sun WorkShop 6 update 2 C++ 5.3 + + SunOS 5.10 cc: Sun C 5.8 + (linew) f90: Sun Fortran 95 8.2 + CC: Sun C++ 5.8 + + Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre + (tungsten) gcc 3.2.2 20030222 + Intel(R) C++ Version 9.0 + Intel(R) Fortran Compiler Version 9.0 + + IA-64 Linux 2.4.21.SuSE_309.tg1 ia64 + (NCSA tg-login) gcc 3.2.2 + Intel(R) C++ Version 8.1 + Intel(R) Fortran Compiler Version 8.1 + mpich-gm-1.2.6..14b-intel-r2 + + Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp + (abe) gcc 3.4.6 20060404 + Intel(R) C++ Version 10.0 + Intel (R) Fortran Compiler Version 10.0 + mvapich2-0.9.8p2patched-intel-ofed-1.2 + + Windows XP Visual Studio .NET + Visual Studio 2005 w/ Intel Fortran 9.1 + Cygwin(native gcc compiler and g95) + MinGW(native gcc compiler and g95) + + Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 + + Windows Vista Visual Studio 2005 + + MAC OS 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 + GNU Fortran (GCC) 4.3.0 20070810 + G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) + + +Supported Configuration Features Summary +======================================== + + In the tables below + y = tested and supported + n = not supported or not tested in this release + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +SunOS5.10 64-bit n y n y y y +SunOS5.10 32-bit n y n y y y +IRIX64_6.5 64-bit n y y y y y +IRIX64_6.5 32-bit n n n n y y +Windows XP n y(15) n(15) y y y +Windows XP x64 n y(15) n(15) y y y +Windows Vista n n n y y y +Mac OS X 10.5 Intel n y n y y y +FreeBSD 4.11 n n n y y y +RedHat EL3 W (3) y(1) y(10) y(1) y y y +RedHat EL3 W Intel (3) n y n y y n +RedHat EL3 W PGI (3) n y n y y n +SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y +SuSe x86_64 Int (3,12) n y(13) n y y n +SuSe x86_64 PGI (3,12) n y(8) n y y y +Linux 2.4 Xeon C + Lustre Intel (3,6) n y n y y n +Linux 2.6 SuSE ia64 C + Intel (3,7) y y y y y n +Linux 2.6 SGI Altix + ia64 Intel (3) y y y y y y +Linux 2.6 RHEL C + Lustre Intel (5) y(4) y y(4) y y n +Cray XT3 2.0.41 y y y y y n + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.10 64-bit y y y y +Solaris2.10 32-bit y y y y +IRIX64_6.5 64-bit y y n y +IRIX64_6.5 32-bit y dna y y +Windows XP y y(15) y y +Windows XP x64 y y(15) y y +Windows Vista y n n y +Mac OS X 10.3 y n +FreeBSD 4.11 y n y y +RedHat EL3 W (3) y y(10) y y +RedHat EL3 W Intel (3) y y y n +RedHat EL3 W PGI (3) y y y n +SuSe x86_64 W GNU (3,12) y y y y +SuSe x86_64 W Int (3,12) y y y n +SuSe x86_64 W PGI (3,12) y y y n +Linux 2.4 Xeon C + Lustre Intel (6) y y y n +Linux 2.4 SuSE + ia64 C Intel (7) y y y n +Linux 2.4 SGI Altix + ia64 Intel y n +Linux 2.6 RHEL C + Lustre Intel (5) y y y n +Cray XT3 2.0.41 n n n n n + + Notes: (1) Using mpich2 1.0.6. + (2) Using mpich2 1.0.7. + (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. + W or C indicates workstation or cluster, respectively. + (4) Using mvapich2 0.9.8. + (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre + and Intel compilers + (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre + and Intel compilers + (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers + (8) pgf90 + (9) With Compaq Visual Fortran 6.6c compiler. + (10) With PGI and Absoft compilers. + (11) PGI and Intel compilers for both C and Fortran + (12) AMD Opteron x86_64 + (13) ifort + (14) Yes with C and Fortran, but not with C++ + (15) Using Visual Studio 2005 or Cygwin + (16) Not tested for this release. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* For Red Storm, a Cray XT3 system, the yod command sometimes gives the + message, "yod allocation delayed for node recovery". This interferes with + test suites that do not expect seeing this message. See the section of "Red + Storm" in file INSTALL_parallel for a way to deal with this problem. + AKC - 2008/05/28 + +* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on + the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is + expected to fail and exit with a non-zero code but the yod command does + not propagate the exit code of the executables. Yod always returns 0 if it + can launch the executable. The test suite shell expects a non-zero for + this particular test, therefore it concludes the test has failed when it + receives 0 from yod. To bypass this problem for now, change the following + lines in the tools/h5ls/testh5ls.sh. + ======== Original ========= + # The following combination of arguments is expected to return an error message + # and return value 1 + TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== Skip the test ========= + echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 + ======== end of bypass ======== + AKC - 2008/05/28 + +* We have discovered two problems when running collective IO parallel HDF5 + tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a + Linux cluster at NCSA. + + Under some complex selection cases: + 1) MPI_Get_element returns the wrong value. + 2) MPI_Type_struct also generates the wrong derived datatype and corrupt + data may be generated. + These issues arise only when turning on collective IO with chunking storage + with some complex selections. We have not found these problems on other + MPI-IO compilers. If you encounter these problems, you may use independent + IO instead. + + To avoid this behavior, change the following line in your code + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + to + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); + + KY - 2007/08/24 + +* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel + tests failed with MPI-IO file locking message. AKC - 2007/6/25 + +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* For LLNL, uP: both serial and parallel tests pass. + Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. + ubgl: Serial tests pass but parallel tests fail. + +* Configuring with --enable-debug=all produces compiler errors on most + platforms: Users who want to run HDF5 in debug mode should use + --enable-debug rather than --enable-debug=all to enable debugging + information on most modules. + +* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long + double to (unsigned) long long and from (unsigned) long long to long double. + +* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 + optimization flag. + +* On VAX, the Scaleoffset filter is not supported. The Scaleoffset filter + supports only the IEEE standard for floating-point data; it cannot be applied + to HDF5 data generated on VAX. + +* On Cray X1, a lone colon on the command line of h5dump --xml (as in + the testh5dumpxml.sh script) is misinterpereted by the operating system + and causes an error. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* On IRIX6.5, when the C compiler version is greater than 7.4, complicated + MPI derived datatype code will work. However, the user should increase + the value of the MPI_TYPE_MAX environment variable to some appropriate value + to use collective irregular selection code. For example, the current + parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculation of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD + Opteron processor, there is a bug in the compiler for optimization(-O2). + The library failed in several tests, all related to the MULTI driver. + The problem has been reported to the vendor. + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag fails to compile for Solaris + platforms. This is due to the fact that not all of the system libraries on + Solaris are available in a static format. + + The --enable-static-exec configure flag also fails to correctly compile + on IBM SP2 platforms for serial mode. The parallel mode works fine with + this option. + + It is suggested that you do not use this option on these platforms + during configuration. + +* With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during + compilation. The ANSI version of the compiler complains about not being + able to handle the `long long' datatype with the warning: + + warning: ANSI C does not support `long long' + + This warning is innocuous and can be safely ignored. + +* The ./dsets tests fail on the TFLOPS machine if the test program, + dsets.c, is compiled with the -O option. The HDF5 library still works + correctly with the -O option. The test program works fine if it is + compiled with -O1 or -O0. Only -O (same as -O2) causes the test + program to fail. + +* Not all platforms behave correctly with Szip's shared libraries. Szip is + disabled in these cases, and a message is relayed at configure time. Static + libraries should be working on all systems that support Szip and should be + used when shared libraries are unavailable. + + There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +* On some platforms that use Intel and Absoft compilers to build the HDF5 + Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 + and fflush2.f90 complaining about the exit subroutine. Comment out the line + IF (total_error .ne. 0) CALL exit (total_error). + +* Information about building with PGI and Intel compilers is available in + the INSTALL file sections 4.7 and 4.8. + +* On at least one system, SDSC DataStar, the scheduler (in this case + LoadLeveler) sends job status updates to standard error when you run + any executable that was compiled with the parallel compilers. + + This causes problems when running "make check" on parallel builds, as + many of the tool tests function by saving the output from test runs, + and comparing it to an exemplar. + + The best solution is to reconfigure the target system so it no longer + inserts the extra text. However, this may not be practical. + + In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to + the configure and build. This will cause "make check" to continue after + detecting errors in the tool tests. However, in the case of SDSC DataStar, + it also leaves you with some 150 "failed" tests to examine by hand. + + A second solution is to write a script to run serial tests and filter + out the text added by the scheduler. A sample script used on SDSC + DataStar is given below, but you will probably have to customize it + for your installation. + + Observe that the basic idea is to insert the script as the first item + on the command line which executes the the test. The script then + executes the test and filters out the offending text before passing + it on. + + #!/bin/csh + + set STDOUT_FILE=~/bin/serial_filter.stdout + set STDERR_FILE=~/bin/serial_filter.stderr + + rm -f $STDOUT_FILE $STDERR_FILE + + ($* > $STDOUT_FILE) >& $STDERR_FILE + + set RETURN_VALUE=$status + + cat $STDOUT_FILE + + tail +3 $STDERR_FILE + + exit $RETURN_VALUE + + You get the HDF5 make files and test scripts to execute your filter script + by setting the environment variable "RUNSERIAL" to the full path of the + script prior to running configure for parallel builds. Remember to + "unsetenv RUNSERIAL" before running configure for a serial build. + + Note that the RUNSERIAL environment variable exists so that we can + prefix serial runs as necessary on the target system. On DataStar, + no prefix is necessary. However on an MPICH system, the prefix might + have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to + get the serial tests to run at all. + + In such cases, you will have to include the regular prefix in your + filter script. + +* H5Ocopy() does not copy reg_ref attributes correctly when shared-message + is turn on. The value of the reference in the destination attriubte is + wrong. This H5Ocopy problem will affect the h5copy tool. + +* In the C++ API, it appears that there are bugs in Attribute::write/read + and DataSet::write/read for fixed- and variable-len strings. The problems + are being worked on and a patch will be provided when the fixes are + available. + + +%%%%1.8.0%%%% + + +HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between the HDF5-1.6.x release series +and HDF5 1.8.0, and contains information on the platforms tested and known +problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt +file in the +release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.0 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + http://www.hdfgroup.org/products/hdf5/ + +The HDF5 1.8.0 release can be obtained from: + + http://www.hdfgroup.org/HDF5/release/obtain5.html + +User documentation for 1.8.0 can be accessed directly at this location: + + http://www.hdfgroup.org/HDF5/doc/ + +New features in 1.8.0, including brief general descriptions of some new +and modified APIs, are described in the "What's New in 1.8.0?" document: + + http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.0 (current +release) versus Release 1.6.x": + + http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Removed Feature +- Support for new platforms and languages +- Bug Fixes since HDF5-1.6.0 +- Platforms Tested +- Supported Configuration Features Summary +- Known Problems + + +New Features +============ + + HDF5 Release 1.8.0 is a major release with many changes and new features. + + New format and interface features discussed in the "What's New in + HDF5 1.8.0" document include the following: + + Enhanced group object management + Enhanced attribute management and more efficient meta data handling + Expanded datatype features + Creation order tracking and indexing + Improved meta data caching and cache control + UTF-8 encoding + New I/O filters: n-bit and scale+offset compression + New link (H5L) and object (H5O) interfaces and features + External and user-defined links + New high-level APIs: + HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS) + C++ and Fortran interfaces for older high-level APIs: + H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB) + New and improved tools + And more... + + http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + + + New APIs associated with these features, other interface changes + (e.g., ENUM and struct definitions), and new library configuration flags + are listed in the "Release 1.8.0 (current release) versus Release 1.6.x" + section of "HDF5 Software Changes from Release to Release." + + http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html + +Compatibility +------------- + Many HDF5 users and user communities have existing applications that + they may wish to port to Release 1.8.0. Alternatively, some users may + wish to take advantage of Release 1.8.0's improved performance without + having to port such applications. To facilitate managing application + compatibility and porting applications from release to release, the HDF + Team has implemented the following features: + Individually-configurable macros that selectively map common + interface names to the old and new interfaces + Library configuration options to configure the macro mappings + + Two related documents accompany this release: + "API Compatibility Macros in HDF5" discusses the specifics of the + new individually-configurable macros and library configuration + options. + http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html + + "New Features in HDF5 Release 1.8.0 and Backward/Forward Format + Compatibility Issues" discusses each new feature with regard to + its impact on format compatibility. + http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html + +Referenced documents +-------------------- + http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + "What's New in HDF5 1.8.0" + + http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html + The "Release 1.8.0 (current release) versus Release 1.6.x " + section in "HDF5 Software Changes from Release to Release" + + http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html + "API Compatibility Macros in HDF5" + + http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html + "New Features in HDF5 Release 1.8.0 and Backward/Forward Format + Compatibility Issues" + + +Removed Feature +=============== +The stream virtual file driver (H5FD_STREAM) have been removed in this +release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream +and the constant H5FD_STREAM. + +This virtual file driver will be available at +http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release, +the transition is still in progress; the necessary integration tools may +not be available when HDF5 Release 1.8.0 first comes out. + + +Support for New Platforms, Languages, and Compilers +=================================================== + - Support for Open VMS 7.3 was added. + + +Bug Fixes since HDF5-1.6.0 +========================== + This release contains numerous bug fixes. For details, see the + "Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for + this release. + + +Platforms Tested +================ +The following platforms and compilers have been tested for for this release. + + AIX 5.2 (32/64 bit) xlc 8.0.0.11 + xlC 8.0 + xlf 10.01.0000.0 + mpcc_r 6.0.0.8 + mpxlf_r 8.1.1.7 + + FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 + (duty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.2.1 20080123 + g++ 4.2.1 20080123 + gfortran 4.2.1 20070620 + + FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 + (liberty) g++ 3.4.6 [FreeBSD] 20060305 + gcc 4.2.1 20080123 + g++ 4.2.1 20080123 + gfortran 4.2.1 20080123 + + IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m + F90 MIPSpro 7.4.4m + C++ MIPSpro cc 7.4.4m + + Linux 2.6.9 (RHEL4) Intel 10.0 compilers + (abe.ncsa.uiuc.edu) + + Linux 2.4.21-47 gcc 3.2.3 20030502 + (osage) + + Linux 2.6.9-42.0.10 gcc 3.4.6 20060404 + (kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC) + Intel 9.1 (icc, ifort, icpc) + + Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, + (smirom) g95 (GCC 4.0.3) + PGI 6.2-5 (pgcc, pgf90, pgCC) + Intel 9.1 (icc, iort, icpc) + + Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 + SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 + (cobalt) SGI MPI + + SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 + (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 + Sun WorkShop 6 update 2 C++ 5.3 + + SunOS 5.10 cc: Sun C 5.8 + (linew) f90: Sun Fortran 95 8.2 + CC: Sun C++ 5.8 + + Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre + (tungsten) gcc 3.2.2 20030222 + Intel(R) C++ Version 9.0 + Intel(R) Fortran Compiler Version 9.0 + + IA-64 Linux 2.4.21.SuSE_292.til1 ia64 + (NCSA tg-login) gcc 3.2.2 + Intel(R) C++ Version 8.1 + Intel(R) Fortran Compiler Version 8.1 + mpich-gm-1.2.5..10-intel-r2 + + Windows XP Visual Studio .NET + Visual Studio 2005 w/ Intel Fortran 9.1 + Cygwin(native gcc compiler and g95) + MinGW(native gcc compiler and g95) + + Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 + + Windows Vista Visual Studio 2005 + + MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 + G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) + + Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD + HP Fortran V7.6-3276 + Compaq C++ V6.5-004 + + +Supported Configuration Features Summary +======================================== + + In the tables below + y = tested and supported + n = not supported or not tested in this release + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90 F90 C++ zlib SZIP + parallel parallel +SunOS5.8 64-bit n y n y y y +SunOS5.8 32-bit n y n y y y +SunOS5.10 64-bit y(1) y n y y y +SunOS5.10 32-bit y(1) y n y y y +IRIX64_6.5 64-bit n y y y y y +IRIX64_6.5 32-bit n n n n y y +AIX-5.2 32-bit y y y y y y +AIX-5.2 64-bit y y y y y y +Windows XP n y(15) n(15) y y y +Windows XP x64 n y(15) n(15) y y y +Windows Vista n n n y y y +Mac OS X 10.4 PowerPC n n +Mac OS X 10.4 Intel n y n y y y +FreeBSD 4.11 n n n y y y +RedHat EL3 W (3) y(1a) y(10) y(1a) y y y +RedHat EL3 W Intel (3) n y n y y n +RedHat EL3 W PGI (3) n y n y y n +SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y +SuSe x86_64 Int (3,12) n y(13) n y y n +SuSe x86_64 PGI (3,12) n y(8) n y y y +Linux 2.4 Xeon C + Lustre Intel (3,6) n y n y y n +Linux 2.6 SuSE ia64 C + Intel (3,7) y y y y y n +Linux 2.6 SGI Altix + ia64 Intel (3) y y y y y y +Alpha OpenVMS 7.3.2 n y n y n n + + + +Platform Shared Shared Shared static- Thread- + C libs F90 libs C++ libs exec safe +Solaris2.8 64-bit y y y x y +Solaris2.8 32-bit y y y x y +Solaris2.10 64-bit y x y +Solaris2.10 32-bit y x y +IRIX64_6.5 64-bit y y n y y +IRIX64_6.5 32-bit y dna y y y +AIX-5.2 & 5.3 32-bit n n n y n +AIX-5.2 & 5.3 64-bit n n n y n +Windows XP y y(15) y y y +Windows XP x64 y y(15) y y y +Windows Vista y n n y y +Mac OS X 10.3 y y n +FreeBSD 4.11 y n y y y +RedHat EL3 W (3) y y(10) y y y +RedHat EL3 W Intel (3) y y y y n +RedHat EL3 W PGI (3) y y y y n +SuSe x86_64 W GNU (3,12) y y y y y +SuSe x86_64 W Int (3,12) y y y y(14) n +SuSe x86_64 W PGI (3,12) y y y y(14) n +Linux 2.4 Xeon C + Lustre Intel (6) y y y y n +Linux 2.4 SuSE + ia64 C Intel (7) y y y y n +Linux 2.4 SGI Altix + ia64 Intel y y n +Alpha OpenVMS 7.3.2 n n n y n + + Notes: (1) Using mpich 1.2.6. + (1a) Using mpich2 1.0.6. + (2) Using mpt and mpich 1.2.6. + (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. + W or C indicates workstation or cluster, respectively. + + (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre + and Intel compilers + (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel +compilers + (8) pgf90 + (9) With Compaq Visual Fortran 6.6c compiler. + (10) With PGI and Absoft compilers. + (11) PGI and Intel compilers for both C and Fortran + (12) AMD Opteron x86_64 + (13) ifort + (14) Yes with C and Fortran, but not with C++ + (15) Using Visual Studio 2005 or Cygwin + (16) Not tested for this release. + Compiler versions for each platform are listed in the preceding + "Platforms Tested" table. + + +Known Problems +============== +* We have discovered two problems when running collective IO parallel HDF5 + tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a + Linux cluster at NCSA. + + Under some complex selection cases: + 1) MPI_Get_element returns the wrong value. + 2) MPI_Type_struct also generates the wrong derived datatype and corrupt + data may be generated. + These issues arise only when turning on collective IO with chunking storage + with some complex selections. We have not found these problems on other + MPI-IO compilers. If you encounter these problems, you may use independent + IO instead. + + To avoid this behavior, change the following line in your code + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + + to + H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); + + KY - 2007/08/24 + +* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel + tests failed with MPI-IO file locking message. AKC - 2007/6/25 + +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, + use -mp -O1 compilation flags to build the libraries. A higher level of + optimization causes failures in several HDF5 library tests. + +* For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass + when run against the parallel library; the parallel tests also pass, but + with lots of non-fatal error messages. + +* For LLNL, uP: both serial and parallel tests pass. + Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. + ubgl: Serial tests pass but parallel tests fail. + +* On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with + Attributes" test. + +* Configuring with --enable-debug=all produces compiler errors on most + platforms: Users who want to run HDF5 in debug mode should use + --enable-debug rather than --enable-debug=all to enable debugging + information on most modules. + +* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long + double to (unsigned) long long and from (unsigned) long long to long double. + +* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 + optimization flag. + +* On VAX, the Scaleoffset filter is not supported. The filter cannot be + applied to HDF5 data generated on VAX. The Scaleoffset filter only supports + the IEEE standard for floating-point data. + +* On Cray X1, a lone colon on the command line of h5dump --xml (as in + the testh5dumpxml.sh script) is misinterpereted by the operating system + and causes an error. + +* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and + the application asks to do collective IO, we have found that when using 4 + processors, a simple collective write will sometimes be hung. This can be + verified with t_mpi test under testpar. + +* On IRIX6.5, when the C compiler version is greater than 7.4, complicated + MPI derived datatype code will work. However, the user should increase + the value of the MPI_TYPE_MAX environment variable to some appropriate value + to use collective irregular selection code. For example, the current + parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. + +* A dataset created or rewritten with a v1.6.3 library or after cannot be read + with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. + There was a bug in the calculating code of the Fletcher32 checksum in the + library before v1.6.3; the checksum value was not consistent between big- + endian and little-endian systems. This bug was fixed in Release 1.6.3. + However, after fixing the bug, the checksum value was no longer the same as + before on little-endian system. Library releases after 1.6.4 can still read + datasets created or rewritten with an HDF5 library of v1.6.2 or before. + SLU - 2005/6/30 + +* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD + Opteron processor, there is a bug in the compiler for optimization(-O2). + The library failed in several tests, all related to the MULTI driver. + The problem has been reported to the vendor. + +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command `poe'. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + + The tests may fail with messages like "The socket name is already in use", + but HDF5 does not use sockets. This failure is due to problems with the + poe command trying to set up the debug socket. To resolve this problem, + check to see whether there are many old /tmp/s.pedb.* files staying around. + These are sockets used by the poe command and left behind due to failed + commands. First, ask your system administrator to clean them out. + Lastly, request IBM to provide a means to run poe without the debug socket. + +* The --enable-static-exec configure flag fails to compile for Solaris + platforms. This is due to the fact that not all of the system libraries on + Solaris are available in a static format. + + The --enable-static-exec configure flag also fails to correctly compile + on IBM SP2 platform for the serial mode. The parallel mode works fine with + this option. + + It is suggested that you do not use this option on these platforms + during configuration. + +* With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during + compilation. The ANSI version of the compiler complains about not being + able to handle the `long long' datatype with the warning: + + warning: ANSI C does not support `long long' + + This warning is innocuous and can be safely ignored. + +* The ./dsets tests fail on the TFLOPS machine if the test program, + dsets.c, is compiled with the -O option. The HDF5 library still works + correctly with the -O option. The test program works fine if it is + compiled with -O1 or -O0. Only -O (same as -O2) causes the test + program to fail. + +* Not all platforms behave correctly with Szip's shared libraries. Szip is + disabled in these cases, and a message is relayed at configure time. Static + libraries should be working on all systems that support Szip and should be + used when shared libraries are unavailable. + + There is also a configure error on Altix machines that incorrectly reports + when a version of Szip without an encoder is being used. + +* On some platforms that use Intel and Absoft compilers to build the HDF5 + Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 + and fflush2.f90 complaining about the exit subroutine. Comment out the line + IF (total_error .ne. 0) CALL exit (total_error). + +* Information about building with PGI and Intel compilers is available in + the INSTALL file sections 4.7 and 4.8. + +* On at least one system, SDSC DataStar, the scheduler (in this case + LoadLeveler) sends job status updates to standard error when you run + any executable that was compiled with the parallel compilers. + + This causes problems when running "make check" on parallel builds, as + many of the tool tests function by saving the output from test runs, + and comparing it to an exemplar. + + The best solution is to reconfigure the target system so it no longer + inserts the extra text. However, this may not be practical. + + In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to + the configure and build. This will cause "make check" to continue after + detecting errors in the tool tests. However, in the case of SDSC DataStar, + it also leaves you with some 150 "failed" tests to examine by hand. + + A second solution is to write a script to run serial tests and filter + out the text added by the scheduler. A sample script used on SDSC + DataStar is given below, but you will probably have to customize it + for your installation. + + Observe that the basic idea is to insert the script as the first item + on the command line which executes the the test. The script then + executes the test and filters out the offending text before passing + it on. + + #!/bin/csh + + set STDOUT_FILE=~/bin/serial_filter.stdout + set STDERR_FILE=~/bin/serial_filter.stderr + + rm -f $STDOUT_FILE $STDERR_FILE + + ($* > $STDOUT_FILE) >& $STDERR_FILE + + set RETURN_VALUE=$status + + cat $STDOUT_FILE + + tail +3 $STDERR_FILE + + exit $RETURN_VALUE + + You get the HDF5 make files and test scripts to execute your filter script + by setting the environment variable "RUNSERIAL" to the full path of the + script prior to running configure for parallel builds. Remember to + "unsetenv RUNSERIAL" before running configure for a serial build. + + Note that the RUNSERIAL environment variable exists so that we can + can prefix serial runs as necessary on the target system. On DataStar, + no prefix is necessary. However on an MPICH system, the prefix might + have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to + get the serial tests to run at all. + + In such cases, you will have to include the regular prefix in your + filter script. + +* H5Ocopy() does not copy reg_ref attributes correctly when shared-message + is turn on. The value of the reference in the destination attriubte is + wrong. This H5Ocopy problem will affect the h5copy tool. + diff --git a/release_docs/HISTORY-1_8_0-1_10_0.txt b/release_docs/HISTORY-1_8_0-1_10_0.txt new file mode 100644 index 0000000..7b84fbc --- /dev/null +++ b/release_docs/HISTORY-1_8_0-1_10_0.txt @@ -0,0 +1,1739 @@ +HDF5 HISTORY +============= + + +INTRODUCTION + +This document describes the development history between the HDF5-1.8.0 and +HDF5 1.10.0 releases. For more information see the SVN log. + +Information about supported and tested platforms is provided for historical +reasons only and may not be accurate. + + +For more information, see the HDF5 home page: + + http://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.8.0 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration: + ------------- + - Java JNI library API wrappers and supporting files added as HDF_JAVA language + option. Both configure and CMake disable this option by default. + HDFFV-9552 (ADB 2016/02.28) + - CMake minimum is now 3.1.0. (ADB 2015/11/14) + - cmakehdf5: configure options added to enable or disable the building of + different API's and testings. See "cmakehdf5 --help" for details. + (AKC - 2014/12/09 HDFFV-8932) + - Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08) + - CMake: Moved minimum CMake version to 2.8.11 which enables better library + include processing. (ADB - 2014/03/26) + - New configuration option added to change the default plugin path. + configure option is --with-default-plugin=location + cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location + HDFFV-8513. (ADB 2013/09/04) + - Rename FFLAGS to FCFLAGS in configure (ADB 2013/08/13) + - CMake minimum is now 2.8.10. (ADB 2013/01/14) + - A new tool, cmakehdf5, which is a build command script similar to + buildhdf5 is added and is available in the bin directory. + (AKC - 2012/12/12) + - Fixed AIX Fortran compiler flags to use appropriate settings for + debugging, profiling, optimization situations. HDFFV-8069. (AKC + 2012/09/27) + - Updated to latest autotools and changed all hard *.sh scripts to + configure managed *.sh.in files. Removed overloading of autotools + TESTS variable by examples and tests. Renamed configure.in to + configure.ac. (ADB - 2012/08/23 - HDFFV-8129) + - Added code to display the version information of XL fortran and C++ + in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793) + - Configure now generates Makefiles that build in "silent make mode" + by default in which compile and link lines are significantly + simplified for clarity. To override this and view actual compile and + link lines during building, the --disable-silent-rules flag can be used + at configure time, or the 'make' command can be followed by V=1, to + indicate a "verbose" make. (MAM - 2011/4/14). + - Added mpicc and mpif90 as the default C and Fortran compilers for Linux + systems when --enable-parallel is specified but no $CC or $FC is defined. + (AKC - 2011/2/7) + - Added a new configure option, "--enable-unsupported", which can + be used to stop configure from preventing the use of unsupported + configure option combinations, such as c++ in parallel or parallel + HDF5 with threadsafe. Use at your own risk, as it may result in a + library that won't compile or run as expected! + (MAM - 2010/11/17 - Bug 2061) + - PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI + applications startup command as defined in the MPI-2 definition, section + 4.1. (AKC - 2010/6/11 - Bug 1921) + - Configure now adds appropriate defines for supporting large (64-bit) + files on all systems, where supported, by default, instead of only linux. + This largefile support is controllable with the --enable-largefile + configure option. This is replacing the linux-specific --enable-linux-lfs + option, which has been removed from configure. + (MAM - 2010/05/05 - 1772/1434) + - Upgraded versions of autotools used to generate configuration suite. + We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b. + MAM 2010/04/15. + - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM + compilers so that the ibm compiler options can be added properly. This + allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be + recognized. AKC 2009/11/26. + - Configuration suite now uses Automake 1.11 and Autoconf 2.64. + MAM 2009/08/11. + - Changed default Gnu fortran compiler from g95 to gfortran since + gfortran is more likely installed with gcc now. -AKC 2009/07/19- + - Added libtool version numbers to generated c++, fortran, and + hl libraries. MAM 2009/04/19. + - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. + - Added a Make target of check-all-install to test the correctness of + installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 + - Configuration suite now uses Libtool 2.2.6a. MAM 2008/10/24 + + - Configuration suite now uses Autoconf 2.61, Automake 1.10.1. + MAM 2008/05/05. + + - The new configure option "--disable-sharedlib-rpath" disables + embedding the '-Wl,-rpath' information into executables when + shared libraries are produced, and instead solely relies on the + information in LD_LIBRARY_PATH. (MAM - 2008/05/15) + + Library: + -------- + + - Virtual Dataset feature was added + (NAF - 2015-10-05, VDS-193) + + - H5F_ACC_DEBUG labeled "deprecated" + + The symbol was originally used to emit some extra debugging + informationi in the multi VFD. The underlying functionality + was removed due to disuse in HDF5 1.8.16 though the symbol + remained defined since it was visible in H5Fpublic.h. + + In this release, the symbol has been labeled deprecated and will + not be defined when H5_NO_DEPRECATED_SYMBOLS is defined. + + (DER - 2015-04-30, HDFFV-1074) + + - The library can load filter libraries dynamically during runtime. Users + can set the search path through environment variable HDF5_PLUGIN_PATH + and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) + - Added new API functions H5Dscatter and H5Dgather to scatter data to and + and gather data from a selection within a memory buffer. + (NAF - 2013/02/05) + - The library now supports the data conversion from enumeration to numeric + (integer and floating-point number) datatypes. See Issue 8221. + (SLU - 2012/10/23) + - The data sieve buffer size was for all the datasets in the file. It + could waste memory if any dataset size is smaller than the sieve buffer + size. Now the library picks the smaller one between the dataset size + and the sieve buffer size from the file access property. See Issue 7934. + (SLU - 2012/4/2) + - I added a new parameter of object access property list to the function + H5Rdereference (Issue 2763). It's called H5Rdereference2 now. The former + H5Rdereference function has been deprecated to H5Rdereference1. (SLU - + 2011/7/18) + - H5Tcreate now supports string type (fixed-length and variable-length). + (SLU - 2011/05/20) + - Added ability to cache files opened through external links. Added new + public functions H5Pset_elink_file_cache_size(), + H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache(). + (NAF - 2011/02/17) + - Removed all old code for Metraowerks compilers, bracketed by + __MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17) + - Added support for threadsafety on windows using the windows threads + library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a + windows platform to enable this functionality. This is supported on + Windows Vista and newer Windows operating systems. (MAM - 2010/09/10) + - When a mandatory filter failed to write data chunks, the dataset + couldn't close (bug 1260). The fix releases all resources and closes + the dataset but returns a failure. (SLU - 2010/9/8) + - H5Tset_order and H5Tget_order now support all data types. A new byte + order H5T_ORDER_MIXED has been added specifically for compound datatype + and its derived type. Please see bug #1934. (SLU - 2010/8/23) + - Improved performance of the chunk cache by avoiding unnecessary b-tree + lookups of chunks already in cache. (NAF - 2010/06/15) + - Greatly improved performance of extending a dataset with early + allocation. (NAF - 2010/03/24 - 1637) + - Added support for filtering densely stored groups. Many of the API + functions related to filters have been extended to support dense groups + as well as datasets. Pipeline messages can now be stored in a group's + object header. (NAF/QAK - 2009/10/8) + - The embedded library information is displayed by H5check_version() if a + version mismatch is detected. Also changed H5check_version() to + suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 + or higher. (Old behavior treated 3 or higher the same as 1, that is + print a warning and allows the program to continue. (AKC - 2009/9/28) + - If a user does not care for the extra library information insert + in the executables, he may turn it off by --disable-embedded-libinfo + during configure. (AKC - 2009/9/15) + - Corrected problem where library would re-write the superblock in a file + opened for R/W access, even when no changes were made to the file. + (QAK - 2009/08/20, Bz#1473) + - Separated "factory" free list class from block free lists. These free + lists are dynamically created and manage blocks of a fixed size. + H5set_free_list_limits() will use the same settings specified for block + free lists for factory free lists. (NAF - 2009/04/08) + - Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29) + - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a + user-defined callback function for external link traversal. + (NAF - 2009/01/08) + - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to + allow the user to specify the file access flags used to open the target + file of an external link. (NAF - 2009/01/08) + - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow + individual rdcc configuration for each dataset. Added + H5Dget_access_plist() function to retrieve a dataset access property + list from a dataset. (NAF - 2008/11/12) + - Added H5Iis_valid() function to check if an id is valid without producing + an error message. (NAF - 2008/11/5) + - Added two new public routines: H5Pget_elink_fapl() and + H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) + - Improved free space tracking in file to be faster. (QAK - 2008/10/06) + - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) + + Parallel Library: + ----------------- + - Add H5Pget_mpio_no_collective_cause() function that retrieve reasons + why the collective I/O was broken during read/write IO access. + (JKM - 2012/08/30 HDFFV-8143) + - Special Collective IO (IO when some processes do not contribute to the + IO) and Complex Derived Datatype MPI functionalities are no longer + conditionally enabled in the library by configure. They are always + enabled in order to take advantage of performance boosts from these + behaviors. Older MPI implementations that do not allow for these + functionalities can no longer by used by HDF5. (MAM - 2011/07/08). + - Modified parallel tests to run with arbitrary number of processes. The + modified tests are testphdf5 (parallel dataset access), t_chunk_alloc + (chunk allocation), and t_posix_compliant (posix compliance). The rest of + the parallel tests already use in the code the number of processes + available in the communicator. (CMC - 2009/04/28) + + Fortran Library: + ---------------- + + - Added parallel routine H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) + + - Added for the C API the Fortran wrapper: + h5ocopy_f (MSB - 2012/03/22) + + + HDF5 Fortran library was enhanced to support Fortran 2003 standard. + The following features are available when the HDF5 library is configured + using --enable-fortran --enable-fortran2003 configure flags AND + if fortran compiler is Fortran2003 compliant: + + - Subroutines overloaded with the C_PTR derived type: + h5pget_f + h5pget_fill_value_f + h5pinsert_f + h5pregister_f + h5pset_f + h5pset_fill_value_f + h5rcreate_f + h5rderefrence_f + h5rget_name_f + h5rget_obj_type_f + - Subroutines overloaded with the C_PTR derived type and simplified signatures: + h5aread_f + h5awrite_f + h5dread_f + h5dwrite_f + - New subroutines + h5dvlen_reclaim_f + h5literate_by_name_f + h5literate_f + h5ovisit_f + h5tconvert_f + + - Subroutines with additional optional parameters: + h5pcreate_class_f + (EIP - 2011/10/14) + + - Added for the C APIs the Fortran wrappers: + h5dget_access_plist_f + h5iis_valid_f + h5pset_chunk_cache_f + h5pget_chunk_cache_f + (MSB - 2009/04/17) + + + + C++ Library: + ------------ + - New member function added + + The assignment operator ArrayType::operator= is added because ArrayType + has pointer data members. + + (BMR, 2016/03/07, HDFFV-9562) + + - New member functions + + Overloaded CommonFG::getObjnameByIdx to take char* for name + + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*. + (BMR - 2010/05/02) + + DataSet::getInMemDataSize() to simplify getting the dataset's + data size in memory. (BMR - 2009/07/26) + - These member functions were added as wrapper for H5Rdereference to + replace the incorrect IdComponent::dereference(). + void H5Object::dereference(H5File& h5file, void* ref) + void H5Object::dereference(H5Object& obj, void* ref) + In addition, these constructors were added to create the associated + objects by way of dereference: + Attribute(H5Object& obj, void* ref); + Attribute(H5File& file, void* ref); + DataSet(H5Object& obj, void* ref); + DataSet(H5File& file, void* ref); + DataType(H5Object& obj, void* ref); + DataType(H5File& file, void* ref); + Group(H5Object& obj, void* ref); + Group(H5File& obj, void* ref); + (BMR - 2008/08/10) + + + + Tools: + ------ + - h5repack: Added ability to use plugin filters. HDFFV-8345 (ADB - 2013/09/04). + - h5dump: Added option -N --any_path, which searches the file for paths that + match the search path. HDFFV-7989 (ADB - 2013/08/12). + - h5dump: Added optional arg 0 to -A, which excludes attributes from display. + HDFFV-8134 (ADB - 2013/08/01). + - h5dump: Fixed displaying compression ratio for unknown or user-defined + filters. HDFFV-8344 (XCAO 2013/03/19) + - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter. + HDFFV-8346 (XCAO 2013/03/19) + - h5dump: Added capability for "-a" option to show attributes containing "/" + by using an escape character. For example, for a dataset "/dset" + containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" + to show the content of the attribute. See details at HDFFV-7523 + (PC -- 2012/03/12) + - h5dump: Added ability to apply command options across multiple files using a + wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5". + HDFFV-7876 (ADB - 2012/03/12). + - h5repack: Improved performance for big chunked datasets (size > 128MB) + when used with layout (-l) or compression (-f) option. + It would perform much better prior to the improvement, + especially for cases that chunk dimensions looks like + "1024x5x1" (compare to "1x5x1024"). When bigger numbers + are toward front and smaller number is toward back in chunk + dimensions. HDFFV-7862 (JKM - 2012/03/01) + - h5dump: Added new option --no-compact-subset. This option will not + interpret the '[' character as starting the compact form of + subsetting. This is useful when the "h5dump error: unable to + open dataset "datset_name"" message is output because a dataset + name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31) + - h5dump: Corrected schema location: + <hdf5:HDF5-File + xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File + http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> + (ADB - 2011/08/10) + - h5diff: Added new level for -v (verbose) option. The new levels are + 1 and 2. So -v1 and -v2 can be specified to view more + information about attributes differences. + Bug#2121 (JKM 2011/3/23) + - h5dump: Added new option --enable-error-stack. This option will display + error stack information in the output stream. This is useful + when the "h5dump: Unable to print data" message is output. + (ADB - 2011/02/24) + - h5diff: Add a new flag --exclude-path. Specified path to an object will + be excluded from comparing the two files or two groups. If group + is specified all the member objects will be excluded. + (JKM - 2010/09/16). + - h5ls: Add new flag --no-dangling-links. (refer to --help for details) + (JKM - 2010/06/15) + - h5ls: Add new flag --follow-symlinks. (refer to --help for details) + (JKM - 2010/05/25) + - h5diff: Add new flag --no-dangling-links. (refer to --help for details) + (JKM - 2010/02/10) + - h5diff: Add new flag --follow-symlinks. (refer to --help for details) + (JKM - 2010/01/25) + - h5diff: fix for displaying garbage value on LE machine for BE data. + (JKM - 2009/11/20) + - h5dump: subsetting now allows default for count. Also trailing ; in short form + can be omitted after last specified value. + (ADB - 2009/09/04) + - h5dump/h5ls: now can display data in region references + using new -R, --region flag. + (ADB - 2009/09/04) + - h5diff: new flag, -c, --compare, list objects that are not comparable. + (PVN - 2009/4/10 - 1368) + - h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10) + - h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519) + - h5repack now handles group creation order. (PVN - 2009/4/2 - 1402) + - h5dump: added a printing of the compression ratio of uncompressed and compressed + sizes for cases where compression filters are present. (PVN - 2008/05/01) + - h5dump: added an option to allow a user defined formatting string for printf + regarding floating point numbers. (PVN - 2008/05/06) + - h5dump: support for external links, display the object that the external link + points to. (PVN - 2008/05/12) + - h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26) + - h5repack: add 2 options that call H5Pset_alignment in the repacked file. (PVN - 2008/08/29) + - h5ls: added capability to traverse through external links when the -r + (recursive) flag is given. (NAF - 2008/09/16) + - h5ls: added -E option to enable traversal of external links. h5ls will + not traverse external links without this flag being set. + (NAF - 2008/10/06) + - h5diff: added support for long double (PVN - 2008/10/28) + - h5dump: binary output defaults to NATIVE with -b optionally accepting + the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/10/30) + - h5diff: return 1 for file differences when both file graphs differ by any object. + Error return code was changed to 2 from -1. (PVN - 2008/10/30) + - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP + instead (PVN - 2008/10/30) + - h5repack: When user doesn't specify a chunk size, h5repack now defines a default + chunk size as the same size of the size of the hyperslab used to read the chunks. + The size of the hyperslabs are defined as the size of each dimension or a + predefined constant, whatever is smaller. This assures that the chunk + read fits in the chunk cache. (PVN - 2008/11/21) + - h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect) + before call ABS(...) at h5diff_array.c This will make that (INF==INF) is true + (INF is treated as an number instead of NaN) (PC -- 2009/07/28) + - h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON) + Change default to use strict equality (PC -- 2009/09/12) + + + High-Level APIs: + --------------- + + C Packet Table API + ------------------ + - Replacement of a public function + + The existing function H5PTcreate_fl limits applications to deflate + compression only. The public function H5PTcreate is added to replace + H5PTcreate_fl. H5PTcreate takes a property list ID to provide + flexibility on creation properties. + + hid_t H5PTcreate(hid_t loc_id, const char *dset_name, + hid_t dtype_id, hsize_t chunk_size, hid_t plist_id); + (BMR, 2016/03/04, HDFFV-8623) + + - New public functions + + Two accessor functions were added per HDFFV-8623/patch 003. + /* Returns the ID of the dataset associated with the packet table */ + hid_t H5PTget_dataset(hid_t table_id); + + /* Returns the ID of the datatype the packet table uses */ + hid_t H5PTget_type(hid_t table_id); + (BMR, 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks are removed from the PT library source + except the following cases: + + H5PTis_varlen() is made available again. + + H5PTfree_vlen_readbuff() now became H5PTfree_vlen_buff() + (BMR, 2016/03/04, HDFFV-442) + + C++ Packet Table API + -------------------- + - New constructor + + An overloaded constructor is added to FL_PacketTable and takes a property + list ID to provide flexibility on creation properties. + + FL_PacketTable(hid_t fileID, hid_t plist_id, const char* name, hid_t dtypeID, hsize_t chunkSize); + (BMR, 2016/03/08, HDFFV-8623) + + - New public functions + + Two accessor wrappers to class PacketTable, per HDFFV-8623/patch 004. + /* Returns the ID of the dataset associated with the packet table */ + hid_t PacketTable::GetDataset() + + /* Returns the ID of the datatype the packet table uses */ + hid_t PacketTable::GetDataset() + (BMR, 2016/03/04, HDFFV-8623) + + - Member functions having "char*" as an argument + + Overloaded functions were added to provide "const char*" argument, the + existing version will be deprecated. + (BMR, 2016/03/04) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks are removed from the PT library source + except the following cases: + + VL_PacketTable::IsVariableLength() is moved to PacketTable + + VL_PacketTable::FreeReadBuff() now became PacketTable::FreeBuff() + + (BMR, 2016/03/04, HDFFV-442) + + + Internal header file + -------------------- + - A new API function H5DOwrite_chunk. It writes a data chunk directly + into a file bypassing hyperslab selection, data conversion, and + filter pipeline. The user must be careful with the function and + clearly understand the I/O process of the library. + (SLU - 2013/2/11) + - New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks + if a path is correct and determines if a link resolves to a valid + object and checks that the link does not dangle. (MSB- 2012/3/15) + + - Added Fortran wrappers for Dimension Scale APIs. HDFFV-3797 + h5dsset_scale_f + h5dsattach_scale_f + h5dsdetach_scale_f + h5dsis_attached_f + h5dsis_scale_f + h5dsset_label_f + h5dsget_label_f + h5dsget_scale_name_f + h5dsget_num_scales_f + (EIP for SB - 2011/10/13) + + - Table: In version 3.0 of Table, "NROWS" (used to store number of records) was + deprecated (PVN - 2008/11/24) + + Documentation + ------------- + +Support for new platforms, languages and compilers. +======================================= + - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) + - PathScale compilers are recognized and can build the HDF5 library + properly. AKC - 2009/7/28 - + - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and + Sun Fortran 95 8.6 compiler. (SLU - 2013/04/15) + +Bug Fixes since HDF5-1.8.0 release +================================== + + Library + ------- + - Incorrect usage of list in CMake COMPILE_DEFINITIONS set_property + + The CMake command, set_property with COMPILE_DEFINITIONS property + needs a quoted semi-colon separated list of values. CMake will + transform the list to a series of -D{value} for the compile. + + (ADB - 2014/12/09, HDFV-9041) + + - H5Z.c: H5Zfilter_avail(H5Z_filter_t id) + Added else block if the call to the internal H5Z_filter_avail(id) does not + fail and returns FALSE. This block calls the H5PL_load(H5PL_TYPE_FILTER, (int)id) + function to attempt to dynamically load the filter plugin. + (ADB - 2014/03/03 HDFFV-8629) + - Added const qualifier to source buffer parameters in H5Dgather and + H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/02) + - Fixed an error involving failure to write fill values to the user's + buffer when reading unallocated chunks from datasets that have a + fill value set to H5D_FILL_VALUE_DEFAULT. A consequence of this + was the reporting of spurious data values in h5dump and h5diff + output. + (HDFFV-8247; JP - 2013/05/03) + - Fixed an error that could occur when calling H5Ocopy within an + H5Literate callback (and possibly other situations). + (NAF - 2012/7/25 - HDFFV-5853) + - Fixed an error that would occur when copying an object with attribute + creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762) + - Fixed a bug in H5Ocopy(): When copying an opened object, call the + object's flush class action to ensure that cached data is flushed + so that H5Ocopy will get the correct data. + (VC - 2012/3/27 - HDFFV-7853) + - When an application tries to write or read many small data chunks and + runs out of memory, the library had a seg fault. The fix is to + return the error stack with proper information. (SLU - 2012/3/23. + Issue 7785) + - H5Pset_data_transform had seg fault in some cases like x*-100. It + works correctly now and handles other cases like 100-x or 2/x. + (SLU - 2012/3/15. Issue 7922) + - Fixed rare corruption bugs that could occur when using the new object + header format. (NAF - 2012/3/15 - HDFFV-7879) + - Creating a dataset in a read-only file caused seg fault when the file + is closed. It's fixed. The attempt to create a dataset will fail + with the error stack indicating the file is read-only. (SLU - + 2012/1/25. Issue 7756) + - Fixed a seg fault that could occur when shrinking a dataset with chunks + larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833) + - Fixed a bug that could cause file corruption when copying named + datatypes to a file using shared messages. (NAF - 2011/11/14) + - Fixed a bug that could cause H5Oget_info to return the wrong address + after copying a named datatype. (NAF - 2011/11/14) + - The library allowed the conversion of strings between ASCII and UTF8 + (Issue 7582). We have corrected it to report an error under this + situation. (SLU - 2011/11/8) + - The library had seg fault when it tried to shrink the size of compound type + through H5Tset_size immediately after the type was created (Issue + 7618). It's fixed now. (SLU - 2011/10/26) + - Fixed a bug that occurred when using H5Ocopy on a committed datatype + containing an attribute using that committed datatype. + (NAF - 2011/10/13 - Issue 5854) + - #ifdef _WIN32 instances changed to #ifdef H5_HAVE_WIN32_API and added + H5_HAVE_VISUAL_STUDIO checks where necessary. CMake only as configure + never set _WIN32. + - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + discovered 3 problems in tests and tools' library (Issue 7674): + 1. In dsets.c, left shifting an unsigned int for 32 bits or more + caused undefined behavior. + 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow + when the value is negative minimal and is being subtracted one. + 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits + or more caused undefined behavior. + All the problems have been corrected. (SLU - 2011/9/2) + - In v1.6 library, there was EOA for the whole MULTI file saved in the + super block. We took it out in v1.8 library because it's meaningless + for the MULTI file. v1.8 library saves the EOA for the metadata file, + instead. But this caused some backward compatibility problem. + v1.8 library couldn't open the file created with v1.6 library. We + fixed the problem by checking the EOA value to detect the file + created with v1.6 library. (SLU - 2011/6/22) + - When a dataset had filters and reading data failed, the error message + didn't say which filter isn't registered. It's fixed now. + (SLU - 2011/6/3) + - The datatype handler created with H5Tencode/decode used to have the + reference count 0 (zero). I have fixed it. It is 1 (one) now. + (SLU - 2011/2/18) + - Fixed a bug that caused big endian machines to generate corrupt files + when using the scale-offset filter with floating point data or + fill values. Note that such datasets will no longer be readable + by any machine after this patch. (NAF - 2010/02/02 - Bug 2131) + - Retrieving a link's name by index in the case where the link is + external and the file that the link refers to doesn't exist will + now fail gracefully rather than cause a segmentation fault. + (MAM - 2010/11/17) + - Modified library to always cache symbol table information. Libraries + version 1.6.3 have a bug which causes them to require this + information for some operations. (NAF - 2010/09/21 - 1864) + - Fixed a bug that could occur when getting information for a new-style + group that was previously opened through a file handle that was + later closed. (NAF - 2010/09/15) + - Added define check in H5public.h if stdint.h is supported by the C++ + compiler. This define is only available on Windows with VS2010 and + using CMake to build the library. (ADB - 2010/09/13 - Bug 1938) + - H5Eset_current_stack now also closes the error stack to be set as the + default. This is to avoid a potential problem (Bug 1799). + (SLU - 2010/9/7) + - Fixed the bug in the filter's public CAN_APPLY function. The return + value should be htri_t not herr_t (Bug #1239). (SLU - 2010/8/5) + - Fixed a bug in the direct I/O driver that could render files with + certain kinds of unaligned data unreadable or corrupt them. + (NAF - 2010/07/28) + - valgrind reported an error of copying data to itself when a new attribute + is written (Bug #1956). I fixed it by taking out the memcpy step in + the attribute code. (SLU - 2010/07/28) + - Fixed a bug that could cause file corruption when using non-default + sizes of addresses and/or lengths. This bug could also cause + uncorrupted files with this property to be unreadable. This bug + was introduced in 1.8.5. (NAF - 2010/07/16 - 1951) + - Fixed a file corruption bug that could happen when shrinking a + compressed dataset. (NAF - 2010/05/20) + - Fixed some memory leaks in VL datatype conversion when strings are + used as fill values. (MAM - 2010/05/12 - BZ# 1826) + - Fixed a bug when copying objects with NULL references with the + H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815) + - Files can now be concurrently opened more than once using the core file + driver, as long as the backing store is used. (NAF - 2010/03/09) + - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External + links will now be expanded if this flag is set. + (NAF - 2010/03/05 - 1733) + - Fixed a bug where the library, when traversing an external link, would + reopen the source file if nothing else worked. (NAF - 2010/03/05) + - Fixed an intermittent bug in the b-tree code which could be triggered + by expanding and shrinking chunked datasets in certain ways. + (NAF - 2010/02/16) + - H5Tdetect_class said a VL string is a string type. But when it's + in a compound type, it said it's a VL type (Bug #1584). I fixed it + to be consistent. It always return string type. (SLU - 2009/12/10) + - Fixed a bug where writing and deleting many global heap objects (i.e. + variable length data) would render the file unreadable. Previously + created files exhibiting this problem should now be readable. + (NAF - 2009/10/27 - 1483) + - Fixed incorrect return value for H5Pget_preserve. (AKC - 2009/10/08 - 1628) + - Fixed an assertion failure that occurred when H5Ocopy was called on a + dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597) + - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. + (NAF - 2009/09/25 - 1620) + - Fixed a bug where properties weren't being compared with the registered + compare callback. (NAF - 2009/09/25 - 1555) + - Fixed a bug where H5Pget_fitler_by_id would succeed when called for a + filter that wasn't present. (NAF - 2009/06/25 - 1250) + - Fixed an issue with committed compound datatypes containing a vlen. + Also fixed memory leaks involving committed datatypes. + (NAF - 2009/06/10 - 1593) + - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 + API. (NAF - 2009/04/20 - 1533) + - Fixed a problem with using data transforms with non-native types in the + file. (NAF - 2009/04/20 - 1548) + - Added direct.h include file to windows section of H5private.h + to fix _getcwd() warning. (ADB - 2009/04/14 - 1536) + - Fixed a bug that prevented external links from working after calling + H5close(). (NAF - 2009/04/10 - 1539) + - Modified library to write cached symbol table information to the + superblock, to allow library versions 1.3.0 to 1.6.3 to read files + created by this version. (NAF - 2009/04/08 - 1423) + - Changed skip lists to use a deterministic algorithm. The library should + now never call rand() or srand(). (NAF - 2009/04/08 - 503) + - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate + groups when that property was set. (NAF - 2009/04/07 - 1526) + - Fixed a bug that caused files with a user block to grow by the size of + the user block every time they were opened. + (NAF - 2009/03/26 - 1499) + - Fixed a rare problem that could occur with files using the old (pre 1.4) + array datatype. (NAF - 2009/03/23) + - Modified library to be able to open files with corrupt root group symbol + table messages, and correct these errors if they are found. Such + files can only be successfully opened with write access. + (NAF - 2009/03/23 - 1189) + - Removed the long_long #define and replaced all instances with + "long long". This caused problems with third party products. All + currently supported compilers support the type. (ADB - 2009/03/05) + - Fixed various bugs that could prevent the fill value from being written + in certain rare cases. (NAF - 2009/02/26 - 1469) + - Fixed a bug that prevented more than one dataset chunk from being cached + at a time. (NAF - 2009/02/12 - 1015) + - Fixed an assertion failure caused by opening an attribute multiple times + through multiple file handles. (NAF - 2009/02/12 - 1420) + - Fixed a problem that could prevent the user from adding attributes (or + any object header message) in some circumstances. + (NAF - 2009/02/12 - 1427) + - Fixed a bug that could cause problems when an attribute was added to a + committed datatype using the committed datatype's datatype. + (NAF - 2009/02/12) + - Fixed a bug that could cause problems when copying an object with a + shared message in its own object header. (NAF - 2009/01/29) + - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most + datatypes. (NAF - 2009/01/27 - 1443) + - Fixed a bug where H5Tpack wouldn't remove trailing space from an + otherwise packed compound type. (NAF - 2009/01/14) + - Fixed up some old v2 btree assertions that get run in debug mode that + were previously failing on compilation, and removed some of the + more heavily outdated and non-rewritable ones. (MAM - 2008/12/15) + - Fixed a bug that could cause problems when "automatically" unmounting + multiple files. (NAF - 2008/11/17) + - H5Ovisit and H5Ovisit_by_name will now properly terminate when the + callback function returns a positive value on the starting object. + (NAF - 2008/11/03) + - Fixed an error where a null message could be created that was larger + than could be written to the file. (NAF - 2008/10/23) + - Corrected error with family/split/multi VFD not updating driver info + when "latest" version of the file format used. (QAK - 2008/10/14) + - Corrected alignment+threshold errors to work correctly when metadata + aggregation is enabled. (QAK - 2008/10/06) + - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered + by the library for internal library use. (NAF - 2008/10/06) + - Fixed potential memory leak during compound conversion. + (NAF - 2008/10/06) + - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also + changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and + the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26) + - Fixed an issue that could cause data to be improperly overwritten + during compound type conversion. (NAF - 2008/09/19) + - Fixed pointer alignment violations that could occur during vlen + conversion. (NAF - 2008/09/16) + - Fixed problem where library could cause a segmentation fault when + an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) + - Fixed improper shutdown when objects have reference count > 1. The + library now tracks reference count due to the application separately + from that due to internal library routines. (NAF - 2008/08/19) + - Fixed assertion failure caused by incorrect array datatype version. + (NAF - 2008/08/08) + - Fixed an issue where mount point traversal would fail when using + multiple handles for the child. (NAF - 2008/08/07) + - Fixed an issue where mount points were inaccessible when using multiple + file handles for the parent. The mount table is now in the shared + file structure (the parent pointer is still in the top structure). + (NAF - 2008/08/07) + - when an attribute was opened twice and data was written with one of the handles, + the file didn't have the data. It happened because each handle had its own + object structure, and the empty one overwrote the data with fill value. This is + fixed by making some attribute information like the data be shared in the + attribute structure. SLU - 2008/07/22 + - Fixed issue where a group could have a file mounted on it twice. + (QAK - 2008/07/15) + - Fixed a Windows-specific issue in the ohdr test which was causing users + in some timezones to get false errors. This a deficiency in the Windows + mktime() function, and has been handled properly. SJW - 2008/06/19 + - Fixed the problem with the searching of target file for H5Lcreate_external(). + The searching pattern will depend on whether the target file's + pathname is an absolute or a relative path. Please see the description + in the RM for H5Lcreate_external(). (VC - 2008/04/08) + - Fixed possible file corruption bug when encoding datatype + descriptions for compound datatypes whose size was between + 256 & 511 bytes and the file was opened with the "use the + latest format" property enabled (with H5Pset_libver_bounds). + (QAK - 2008/03/13) + - Fixed bug in H5Aget_num_attrs() routine to handle invalid location + ID correctly. (QAK - 2008/03/11) + - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. + (PVN - 2009/01/8) + - Added code to maintain a min_clean_fraction in the metadata cache when + in serial mode. (MAM - 2009/01/9) + + + + Configuration + ------------- + - CMake: When CMake commands are executed individually on the command line + and the external filters are being built, the CMAKE_BUILD_TYPE define + must be set to the same value as the configuration + (-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed + by the the szip and zlib filter build commands. (ADB - HDFFV-8695) + - CMake: Remove use of XLATE_UTILITY program. (ADB - 2014/03/28 HDFFV-8640) + - CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the + MPI option. (ADB - 2014/02/27 HDFFV-8674) + - Modified H5detect.c to scan floating point types for padding bits before + analyzing the type further. This should fix problems with gcc 4.8 + (NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500) + - Fixed Makefile issue in which "-Wl," was not properly specified + prior to -rpath when building parallel fortran libraries with + an Intel compiler. (MAM - 2012/03/26) + - Makefiles generated by other packages using h5cc as the compiler + no longer error when 'make' is invoked more than once in order + to 'rebuild' after changes to source. (MAM - 2012/03/26) + - Added --enable-fortran2003 flag to enable Fortran2003 support + in the HDF5 Fortran library. The flag should be used along with the + --enable-fortran flag and takes affect only when Fortran compiler + is Fortran2003 compliant. (EIP - 2011/11/14) + + - In Windows platform, the default VFD, was Windows VFD, is restored back + to the SEC2, aka POSIX, VFD. The Windows VFD is deprecated. HDFFV-7740 + (AKC 2011/09/26) + - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file, + ibm-aix. (AKC - 2011/4/14) + - Shared C libraries are no longer disabled on Mac when Fortran + is enabled. Shared Fortran libraries are still not supported on Mac, + so configure will disable them by default, but this is overridable + with the new --enable-unsupported configure option. The configure + summary has been updated to reflect the fact that the shared-ness of + the C++/Fortran wrapper libraries may not align with the C library. + (MAM - 04/11/2011 - HDFFV-4353). + - Removed recognition of the parallel compilers of LAM(hcc) and + ChMPIon(cmpicc) since we have no access to these two MPI implementations + and cannot verify their correctness. (AKC - 2010/7/14 - Bug 1921) + - Removed the following config files, as we no longer support them: + config/dec-osf*, config/hpux11.00, config/irix5.x, + config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* + MAM - 2009/10/08 + - Modified configure and make process to properly preserve user's CFLAGS + (and company) environment variables. Build will now properly use + automake's AM_CFLAGS for any compiler flags set by the configure + process. Configure will no longer modify CFLAGS directly, nor will + setting CFLAGS during make completely replace what configure has set up. + MAM - 2009/10/08 + - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS + machine has long retired. AKC - 2009/10/06. + - Added $(EXEEXT) extension to H5detect when it's executed in the + src/Makfile to generate H5Tinit.c so it works correctly on platforms + that require the full extension when running executables. + MAM - 2009/10/01 - BZ #1613 + - Configure will now set FC and CXX to "no" when fortran and c++ + are not being compiled, respectively, so configure will not run + some of the compiler tests for these languages when they are not + being used. MAM - 2009/10/01 + - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to + recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - + - The --enable-static-exec flag will now properly place the -static flag + on the link line of all installed executables. This will force the + executable to link with static libraries over shared libraries, provided + the static libraries are available. MAM - 2009/08/31 - BZ #1583 + - The --includedir=DIR configuration option now works as intended, and can + be used to specify the location to install C header files. The default + location remains unchanged, residing at ${prefix}/include. + MAM - 2009/03/10 - BZ #1381 + - Configure no longer removes the '-g' flag from CFLAGS when in production + mode if it has been explicitly set in the CFLAGS environment variable + prior to configuration. MAM - 2009/03/09 - BZ #1401. + - Fixed error with 'make check install' failing due to h5dump + needing other tools built first. MAM - 2008/10/24. + - Wpen using shared szip, it is no longer necessary to specify + the path to the shared szip libraries in LD_LIBRARY_PATH. MAM - + 2008/10/24. + - The file libhdf5_fortran.settings is not installed since its content + is included in libhdf5.settings now. AKC - 2008/10/21 + - "make DESTDIR=xxx install" failed to install some tools and files + (e.g., h5cc and fortran modules). Fixed. AKC - 2008/10/8. + - Autotools: An export of LD_LIBRARY_PATH=<szip library location> was + removed from configure and make installcheck was revised to run + scripts installed in share/hdf5_examples to use the installed h5cc, etc. + to compile and run example source files also installed there. Make + installcheck will now fail when a shared szip or other external lib file + cannot be found in the same manner that executables compiled and linked + with h5cc will fail to run when those lib files cannot be found after + install. Make installcheck should pass after setting LD_LIBRARY_PATH to the + szip location. + (LRK - 2014/04/16) + + Performance + ------------- + - Removed program perform/benchpar from the enable-build-all list. The + program will be retired or moved to another location. HDFFV-8156 + (AKC 2012/10/01) + - Retired program perform/mpi-perf. Its purpose has been incorporated + into h5perf before. (AKC 2012/09/20) + - ifdefs added to tests around include unistd.h and function to simulate + getlogin() on Windows. + (ADB - 2011/08/15) + - perf_serial test added to Windows projects and check batch file. + (ADB - 2009/06/11) + + Fortran + -------- + - Fixed a typo in return value of the nh5dread_f_c function ( was 1 + instead of 0 on success); fixed the return value to make it consistent + with other Fortran functions; cleaned the code from debug statements. + (EIP - 2012/06/23) + + - Fixed problem writing/reading control characters to a dataset; writing + a string containing: alerts, backspace, carriage_return, form_feed, + horizontal_tab, vertical_tab, new_line is now tested and working. + (MSB - 2012/09/01) + + - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) + + - Corrected the number of continuation lines in the src files + to be less then 32 lines for F95 compliance. (MSB - 2012/10/01) + + Tools + ----- + - h5dump subsetting fixed for dims greater then two + When a dataset has more then two dimensions, subsetting would incorrectly + calculate the data that needed to be displayed. + Added in block and stride calculation that account for dimensions greater + then two. NOTE: lines that have line breaks inserted because of display + length calculations, may have index info that is incorrect until the next + dimension break. (ADB, 2016/03/04, HDFFV-9698) + - h5repack: h5repack would not attempt to remove UD filters. Added a + check to h5repack for UD filters that checks if the filter can + be dynamically loaded. This will require a change in the library to + add the H5PL_load() to the H5Zfilter_avail(). (ADB - 2014/03/03 HDFFV-8629) + - h5repack: Fixed failure for converting a layout of small chunked dataset + (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/18) + - h5diff: Fixed to return correct exit code 1 when detect unique extra + attribute. Prior to this fix, h5diff returned exit code 0 indicating + two files are identical. HDFFV-7643 (JKM 2013/02/15) + - h5diff: Improved speed when comparing HDF5 files with lots of + attributes. Much slower performance was identified with release + version from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19) + - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if + source file contains chunked dataset and a chunk dim is bigger than + the dataset dim. Another issue is that the command changed max dims + if chunk dim is smaller than the dataset dim. + These issue occurred when dataset size is smaller than 64k (compact + size limit) Fixed both. + HDFFV-8012 (JKM 2012/09/24) + - h5diff: Fixed not to accumulate attribute difference to dataset + difference in verbose mode (-v, -r), which caused incorrect + difference between dataset and group/datatype object if attribute + exist with any differences. This also lead to fix inconsistent + format indicating difference between dataset and group/datatype + object. HDFFV-5919 (JKM 2012/09/05) + - h5diff: Fixed the incorrect result when comparing attribute data + values and the data type has same class but different size. + HDFFV-7942 (JKM 2012/08/15) + - ph5diff: Fixed intermittent hang issue on a certain operation in + parallel mode. It was detected by daily test for comparing + non-comparable objects, but it could have occurred in other + operations depend on machine condition. HDFFV-8003 (JKM 2012/08/01) + - h5diff: Fixed test failure for "make check" due to failure of + copying test files when performed in HDF5 source tree. Also applied + to other tools. + HDFFV-8107 (JKM 2012/08/01) + - h5diff: Fixed the Function COPY_TESTFILES_TO_TESTDIR() of + testh5diff.sh to better report when there is an error in the file + copying. HDFFV-8105 (AKC -2012/07/22) + - h5diff: Fixed not to check and display dangling link status without + --follow-symlinks option. This also improved performance when + comparing lots of external links without the --follow-symlinks + option. HDFFV-7998 (JKM 2012/04/26) + - h5unjam: Fixed sefgault when used -V (show version) option. + HDFFV-8001 (JKM 2012/04/19) + - h5repack: Fixed a failure when change the chunk size of a specified + chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11) + - h5diff: Fixed failure for comparing same named object with different + object types in comparing groups. Prior to the fix, h5diff resulted + in error. After the fix, h5diff detects such case as non-comparable + and display messages accordingly. HDFFV-7664 (JKM 2012/03/28) + - h5diff: If unique objects exists only in one file and try to exclude + the unique objects with --exclude-path option, h5diff missed + excluding some objects. + Fixed to exclude objects correctly in such case. + HDFFV-7837 (JKM 2012/03/20) + - h5dump: Added tools library error stack to properly catch error + information generated within the library. + HDFFV-7958 (ADB 2012/03/12) + - h5dump: Dangling links no longer throw error message, change process + when open link fails. + HDFFV-7839 (ADB 2012/03/12) + - h5diff: When two symbolic dangling links are compared with + --follow-symlinks option, the result should be same. It worked for + comparing two files, but didn't work for comparing two objects. + HDFFV-7835 (JKM 2012/03/09) + - h5dump: Refactored code to remove duplicated functions. Split XML + functions from DDL functions. Corrected indentation and formatting + errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified + all tools call tools_init() in main. + HDFFV-7560 (ADB 2012/02/17) + - h5diff: fixed to prevent from displaying error stack message when + comparing the two dangling symlinks with follow-symlinks option. + HDFFV-7836 (JKM 2012/01/13) + - h5repack: fixed memory leak for handling variable length string in + attribute. HDFFV-7840 (JKM 2012/01/06) + - h5ls: fixed segfault when access region reference data in an + attribute. HDFFV-7838 (JKM 2011/12/29) + - h5diff: fixed segfault over non-comparable attribute with different + dimension or rank, along with '-c' option to display details. + HDFFV-7770 (JKM 2011/10/24) + - Fixed h5diff to display all the comparable object and attribute + regardless of non-comparables. HDFFV-7693 (JKM 2011/09/16) + - Fixed h5repack to update values of references(object and region) of + attributes in h5repack for 1) references, 2) ARRAY of references, + 3) VLEN of references, and 4) COMPOUND of references. + (JIRA HDF5 5932) PC -2011/09/14 + - h5diff: fixed segfault over dataset with container types + (array,lven) with multiple nested compound types. + (ex: compound->array->compound, compound->vlen->compound) + HDFFV-7712 JKM (2011/09/01) + - h5repack: added macro to handle failure in H5Dread/write when memory + allocation failed inside the library. (PC -- 2011/08/19) + - Fixed h5jam not to allow specifying an HDF5 formatted file as input + file for -u (user block file) option, because the original HDF5 file + will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15) + - Revised command help pages of h5jam and h5unjam. The descriptions + were not up to date and some were missing. + HDFFV-7515 (JKM 2011/08/15) + - h5repack: h5repack failed to copy dataset if the layout is changed + from chunked with unlimited dims to contiguous. HDFFV-7649 + (PC -- 2011/07/15) + - h5diff: "--delta" option considers two NaN of the same type are + different, which is wrong based on h5diff description in Reference + Manual. HDFFV-7656 (PC -- 2011/07/15) + - Fixed h5diff to display instructive error message and exit with 1 + when mutually exclusive options (-d, -p and --use-system-epsilon) + are used together. HDFFV-7600 (JKM 2011/07/07) + - Fixed h5dump to display the first line of each element into correct + position for multiple dimension array type. + Before this fix, the first line of each element in array were + displayed after the last line of previous element without + moving to the next line (+indentation). + Bug #HDFFV-5878 (JKM 2011/06/15) + - Fixed h5dump to display correct value for H5T_STD_I8LE dataset + on a system (ppc64, linux, Big-Endian, clustering). + Bug #HDFFV-7594 (ABERT & JKM 2011/05/12) + - Fixed h5diff to compare file itself correctly. Previously h5diff + reported either different or not compatible in certain cases even + comparing file itself. This fix also improve performance when + comparing same target objects through verifying the obj&file + addresses before comparing the details in the objects (ex: datasets + or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06) + - Updated h5dump test case script to prevent entire test failure upon + source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12) + - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in + attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type, + so h5dump is supposed to display -2 instead of 254. It worked + correctly on Little-Endian system , but not on Big-Endian system. + Bug #HDFFV-4358 (JKM 2011/04/08) + - Updated to unify option name to '--enable-error-stack' for printing + HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now. + For h5ls, this replaces "-e/--errors" option, which is deprecated. + Bug#2182 (JKM 2011/3/30) + - Fix h5diff for --use-system-epsilon option: the calculation changed + from ( |a - b| / b ) to ( |a - b| ). This was decided for better + performance. Bug#2184 (JKM 2011/3/24) + - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document + the output of a H5T_REFERENCE should be followed by the type; + <reference> ::= H5T_REFERENCE { <ref_type> } + <ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG + Previously this was only displayed if the -R option was used. + Bug#1725 (ADB 2011/3/28) + - Fix h5diff issues for #1: h5diff compared attributes correctly only + when two objects have the same number of attributes and attribute + names are identical, #2: didn't display useful information about + attribute difference. Bug#2121 (JKM 2011/3/17) + - Fixed memory leak for h5diff when accessing symbolic links with + --follow-symlink option. Bug#2214 (JKM 2011/3/18) + - Fixed memory leak for h5diff when access variable length string + data. Bug#2216 (JKM 2011/3/18) + - Fixed and improved help page for -a option of h5ls. + Bug#1904 (JKM 2011/3/11) + - Fixed h5dump not to include attribute values in the output file when + h5dump "-y -o output_file" options were used. The problem was introduced + in HDF5 1.8.6 by showing data pointed by region references. (XCAO 2011/3/9) + - Fixed h5copy to be able to copy any object into the same HDF5 file. + Previously h5copy displayed error message when target file is same + as source file. (XCAO 2011/3/8) + - Fixed h5dump for skipping some values for long array type dataset on + Windows. This issue only occurred on Windows due to the different + return behavior from _vsnprintf() function. Bug#2161 (JKM 2011/3/3) + - Fixed h5dump for skipping array indices every certain number + when the array type dataset is relatively big. The certain number + varies according to the size of array. Bug#2092 (JKM 2011/2/15). + - Fixed h5diff for the segfault when compares compound datasets + with combination of fixed length string types and vlen string types + in certain orders. bug#2089 (JKM 2010/12/28) + - Improve h5diff performance. 1) use HDmemcmp() before comparing each + elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype + information at dataset level not each element level for compound + datasets + - Fixed h5ls to display nested compound type with curly bracket + when -S (--simple) option is used with -l (--label), so it shows + which member (in curly bracket) belong to which nested compound type + and make the output make sense. bug#1979 (JKM 2010/11/09) + - Fixed h5diff to handle variable-length strings in a compound dataset + correctly. (also variable-length string array in a compound dataset) + Garbage values were displayed when h5diff compared multiple + variable-length strings in a compound type dataset. + Bug#1989 (JKM 2010/10/28) + - Fixed h5copy to fail gracefully when copying object to non-exist + group without -p option. Bug#2040 (JKM 2010/10/18) + - Fixed to compare member objects and groups recursively when two + files or groups are specified to be compared. Bug#1975 + (JKM 2010/9/16) + - Make h5repack be able to convert a layout to COMPACT for small size + dataset as default. bug#1896 (JKM 2010/09/15) + - Change h5ls not to manipulate special characters in object name or + attribute name for smart display. bug#1784 (JKM 2010/06/28) + - Fixed h5ls to return exit code 1 (error) when non-existent file is + specified. bug#1793. (JKM 2010/04/27) + - h5copy failed to copy dangling link when the link is specified + directly. bug#1817. (JKM 2010/04/22) + - h5repack lost attributes from a dataset of reference type. bug#1726. + (JKM 2010/3/25) + - h5repack sets NULL for object reference value for group or + named datatype. bug#1814. (JKM 2010/03/19) + - h5diff: fixed incorrect behavior (hang) in parallel mode when + specify invalid options (ex: -v and -q) (JKM 2010/02/17) + - h5dump/h5ls display buffer resize fixed in tools library. + (ADB - 2009/07/21 - 1520) + - Fixed many problems that could occur when using h5repack with named + datatypes. (NAF - 2009/4/20 - 1516/1466) + - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets + that have a datatype datum size greater than H5TOOLS_BUFSIZE, a + constant defined as 1024Kb, such as array types with large + dimensions (PVN - 2009/4/1 - 1501) + - h5import: By selecting a compression type, a big endian byte order was being + selected (PVN - 2009/3/11 - 1462) + - zip_perf.c had missing argument on one of the open() calls. Fixed. + (AKC - 2008/12/9) + - h5dump now checks for uniqueness of committed datatypes. + (NAF - 2008/10/15) + - Fixed unnecessary indentation of committed datatypes in h5dump. + (NAF - 2008/10/15) + - Fixed bugs in h5stat:segmemtation fault when printing groups and + print warning message when traversal of objects is unsuccessful. + (see bug #1253) (VC- 2008/10/13) + - Fixed bug in h5ls that prevented relative group listings (like + "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) + - Fixed bug in h5diff that prevented datasets & attributes with + variable-length string elements from comparing correctly. + (QAK - 2008/02/28) + - h5import bug on Windows w/binary datasets. fread in windows needs a + binary file to be open with 'rb' instead of 'r' otherwise it + terminates execution if an end of file character is found on the + input file. Besides that the binary file generated needs to be open + with 'wb' , otherwise an end of line character is read twice. + (PVN - 2008/02/19) + - Fixed bug in h5dump that caused binary output to be made only for the first + dataset, when several datasets were requested. (PVN - 2008/04/07) + - h5dump: when doing binary output (-b), the stdout printing of attributes + was done incorrectly. Removed printing of attributes when doing binary + output. PVN - 2008/06/05 + + + High-Level APIs: + ------ + - Packet Table is updated. + + In the Packet Table C API, there are changes with the following functions, + which had been ifdef'ed out with VLPT_REMOVED since 2006 + * H5PTcreate_vl, is removed from this release + * H5PTfree_vlen_readbuff, is renamed to H5PTfree_vlen_buff + * H5PTis_varlen, is made available again + + Various cleanup: replacing 0/-1 with SUCCEED/FAIL and H5I_BADID with + H5I_INVALID_HID. (BMR, 2016/03/04, HDFFV-442) + + - Fixed problem with H5DSget_scale_name including the NULL terminator in + the size calculation returned by the function. The API does not + include the NULL terminator in the size returned (MSB- 2013/2/10) + + - Fixed problem with H5TBdelete_record destroying all data following the deletion + of a row. (MSB- 2012/7/26) + + - Fixed H5LTget_attribute_string not closing an object identifier when an + error occurs. (MSB- 2012/7/21) + + - Fixed the H5LTdtype_to_text function. It had some memory problems when + dealing with some complicated data types. HDFFVI-7701 (SLU - 2011/10/19) + + - Fixed a bug in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale + caused by using H5Tget_native_type function to determine the native + type for reading REFERENCE_LIST attribute. The bug was exposed + on Mac PPC. + (EIP - 2010/05/22 -1851) + - Fixed a bug in the H5DSdetach_scale function when 0 bytes + were allocated after the last reference to a dim. scale + was removed from the list of references in a VL element of the + DIMENSION_LIST attribute; modified the function to comply + with the Spec: DIMENSION_LIST attribute is deleted now when no + dimension scales left attached. + (EIP - 2010/05/14 -1822) + - Fixed a bug where the H5TB API would forget the order of fields when + added out of offset order. (NAF - 2009/10/27 - 1582) + - H5DSis_attached failed to account for different platform types. Added a + get native type call. (ADB - 2009/9/29 - 1562) + - Dimension scales: The scale index return value in H5DSiterate_scales was not always + incremented. (PVN - 2009/4/8 - 1538) + + Fortran High-Level APIs: + ------ + + - Lite: The h5ltget_attribute_string_f used to return the C NULL character in the + returned character buffer. The returned Fortran character buffer now does + not return the C NULL character. (MSB - 2012/3/23) + - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) + was not correctly returning the dimension array. (PVN - 2009/3/23) + - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions + had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 + + + Documentation + ------------- + + + F90 APIs + -------- + - Modified the h5open_f and h5close_f subroutines to not to call H5open + and H5close correspodningly. While the H5open call just adds overhead, + the H5close call called by an Fortran application shuts down the HDF5 + library making it unaccessible to the application. + HDFFV-915 (EIP & SB - 2011/10/13) + + + C++ APIs + -------- + - The constructor PropList::PropList(id) was fixed to act properly + according to the nature of 'id'. When 'id' is a property class id, + a new property list will be created. When 'id' id a property list id, + a copy of the property list will be made. (BMR - 2010/5/9) + - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and + CommonFG::getComment, respectively, now have default values for + user's convenience. (BMR - 2009/10/23) + - NULL pointer accessing was fixed, bugzilla 1061. (BMR - 2009/10/05) + - read/write methods of DataSet and Attribute classes were fixed + to handle string correctly. (BMR - 2009/07/26) + - Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20) + - Fixed bug in PropList::getClassName to use portable HDfree instead + of free. (BMR - 2008/04/20) + - Fixed a design bug which allowed an Attribute object to create/modify + attributes (bugzilla #1068). The API class hierarchy was revised + to address the problem. Classes AbstractDS and Attribute are moved + out of H5Object. Class Attribute now multiply inherits from + IdComponent and AbstractDs and class DataSet from H5Object and + AbstractDs. In addition, the data member IdComponent::id was + moved into subclasses: Attribute, DataSet, DataSpace, DataType, + H5File, Group, and PropList. (BMR - 2008/08/10) + - IdComponent::dereference was incorrect and replaced as described + in "New Features" section. + (BMR - 2008/08/10) + + Testing + ------- + - tools/h5diff/testh5diff.sh is run in every "make check", even after it + has passed in the previous run. It should not run again if there is no + code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392) + - In some Mac system, testlibinfo.sh failed with this error: + Check file ../src/.libs/libhdf5.7.dylib + strings: object: ../src/.libs/libhdf5.7.dylib malformed object \ + (unknown load command 15) + The strings command of Mac inspects library files and older + versions of strings may not know newer library format, resulting + in errors. Fixed by sending the library file as stdin to the strings + command to avoid this problem. (AKC - 2013/03/08 HDFFV-8305) + + - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation + faulted when used before. (AKC - 2013/02/12 HDFFV-8267) + + +Supported Platforms +=================== + AIX 6.1 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 13.7-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 14.0.2 (Build 20140120) + + Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers + ch5.x86_64 GNU/Linux Version 12.1.5.339 + (LLNL Aztec) + + IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 + (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 + XL Fortran for Blue Gene/P, bgxlf90 V11.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + (duck) gfortran GNU Fortran (GCC) 4.6.2 + + Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 + (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 + gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + gfortran GNU Fortran (GCC) 4.6.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 8 y y/y n y y y +Windows 8 x64 y y/y n y y y +Mac OS X Lion 10.7.3 32-bit n y/y n y y n +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.1 64-bit n y/y n y y ? +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 8 y y y y +Windows 8 x64 y y y y +Mac OS X Lion 10.7.3 32-bit y n y y +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +Mac OS X Mavericks 10.9.1 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n +Linux 2.6.32-431.11.2.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with + #1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1 + (platypus) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Debian7.5.0 3.2.0-4-686 #1 SMP Debian 3.2.51-1 i686 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.i6866 #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT i686 athlon i386 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== +* "make check" fails on CYGWIN when building shared lib files is enabled. The + default on Cygwin has been changed to disable shared. It can be enabled with + the --enable-shared configure option but is likely to fail "make check" + with GCC compilers. (LK -2015/04/16) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It + complains with this message: + "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. + + The reason is that __func__ is a predefined identifier in C99 standard. The + HDF5 C library uses it in H5private.h. The test ttypes.cpp includes + H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 + C++ compiler doesn't support __func__, thus fails to compile the C++ test. + But 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this + identifier, try to compile the following simple C++ program: + #include<stdio.h> + + int main(void) + { + printf("%s\n", __func__); + return 0; + } + (SLU - 2012/11/5) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The data conversion test dt_arith.c has failures (segmentation fault) from + "long double" to other datatypes during hard conversion when the library + is built with the default GCC 4.2.1 on Mac Lion system. It only happens + with optimization (-O3, -O2, and -O1). Some newer versions of GCC do not + have this problem. Users should disable optimization or try newer version + of GCC. (Issue 8017. SLU - 2012/6/12) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel + (3.2.2 on Fedora) doesn't have the problem. Users should lower down the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + It will overwrite the library's default optimization level. (Issue 7829. + SLU - 2012/2/7) + +* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or filesystems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + +* Parallel mode in AIX will fail some of the testcheck_version.sh tests where + it treats "exit(134) the same as if process 0 had received an abort signal. + This is fixed and will be available in the next release. AKC - 2009/11/3 + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not + existing. This is due to the MPI_File_open() call failing if the amode has + the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. (CMC - 2009/04/28) + +* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel + tests failed with MPI-IO file locking message. AKC - 2007/6/25. +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use + -mp -O1 compilation flags to build the libraries. Higher level of optimization + causes failures in several HDF5 library tests. +* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the + shared libraries (tested for 1.8.0-beta2) +* For SNL, Red Storm: only parallel HDF5 is supported. The serial tests pass + and the parallel tests also pass with lots of non-fatal error messages. +* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test +* configuring with --enable-debug=all produces compiler errors on most + platforms. Users who want to run HDF5 in debug mode should use + --enable-debug rather than --enable-debug=all to enable debugging + information on most modules. +* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long + double to (unsigned) long long and from (unsigned)long long to long double. +* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3 + optimization flag. +* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to + HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard + for floating-point data. +* On Cray X1, a lone colon on the command line of h5dump --xml (as in + the testh5dumpxml.sh script) is misinterpereted by the operating system + and causes an error. +* On mpich 1.2.5 and 1.2.6, we found that if more than two processes + contribute no IO and the application asks to do IO with collective, we found + that when using 4 processors, a simple collective write will be hung + sometimes. This can be verified with t_mpi test under testpar. +* The dataset created or rewritten with the v1.6.3 library or after can't + be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is + enabled. There was a bug in the calculating code of the Fletcher32 + checksum in the library before v1.6.3. The checksum value wasn't consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value is no + longer the same as before on little-endian system. The library release + after 1.6.4 can still read the dataset created or rewritten with the library + of v1.6.2 or before. SLU - 2005/6/30 +* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron + processor, there's a bug in the compiler for optimization(-O2). The library + failed in several tests but all related to multi driver. The problem has + been reported to the vendor. +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command poe. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + The tests may fail with messages like "The socket name is already + in use". HDF5 does not use sockets (except for stream-VFD). This is + due to problems of the poe command trying to set up the debug socket. + Check if there are many old /tmp/s.pedb.* staying around. These are + sockets used by the poe command and left behind due to failed commands. + Ask your system administrator to clean them out. Lastly, request IBM + to provide a mean to run poe without the debug socket. + +* The C++ library's tests fails when compiling with PGI C++ compiler. The + workaround until the problem is correctly handled is to use the + flag "--instantiate=local" prior to the configure and build steps, as: + setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher + + +* The stream-vfd test uses ip port 10007 for testing. If another + application is already using that port address, the test will hang + indefinitely and has to be terminated by the kill command. To try the + test again, change the port address in test/stream_test.c to one not + being used in the host. + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + +* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during + compilation. The ANSI version of the compiler complains about not being + able to handle the `long long' datatype with the warning: + + warning: ANSI C does not support `long long' + + This warning is innocuous and can be safely ignored. + +* Certain platforms give false negatives when testing h5ls: + - Cray J90 and Cray T90IEEE give errors during testing when displaying + some floating-point values. These are benign differences due to + the different precision in the values displayed and h5ls appears to + be dumping floating-point numbers correctly. + +* Not all platforms behave correctly with szip's shared libraries. Szip is + disabled in these cases, and a message is relayed at configure time. Static + libraries should be working on all systems that support szip, and should be + used when shared libraries are unavailable. There is also a configure error + on Altix machines that incorrectly reports when a version of szip without + an encoder is being used. + +* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library, + compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 + complaining about exit subroutine. Comment out the line + IF (total_error .ne. 0) CALL exit (total_error) + +* Information about building with PGI and Intel compilers is available in + INSTALL file sections 5.7 and 5.8 + +* On at least one system, (SDSC DataStar), the scheduler (in this case + LoadLeveler) sends job status updates to standard error when you run + any executable that was compiled with the parallel compilers. + + This causes problems when running "make check" on parallel builds, as + many of the tool tests function by saving the output from test runs, + and comparing it to an exemplar. + + The best solution is to reconfigure the target system so it no longer + inserts the extra text. However, this may not be practical. + + In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to + the configure and build. This will cause "make check" to continue after + detecting errors in the tool tests. However, in the case of SDSC DataStar, + it also leaves you with some 150 "failed" tests to examine by hand. + + A second solution is to write a script to run serial tests and filter + out the text added by the scheduler. A sample script used on SDSC + DataStar is given below, but you will probably have to customize it + for your installation. + + Observe that the basic idea is to insert the script as the first item + on the command line which executes the the test. The script then + executes the test and filters out the offending text before passing + it on. + + #!/bin/csh + + set STDOUT_FILE=~/bin/serial_filter.stdout + set STDERR_FILE=~/bin/serial_filter.stderr + + rm -f $STDOUT_FILE $STDERR_FILE + + ($* > $STDOUT_FILE) >& $STDERR_FILE + + set RETURN_VALUE=$status + + cat $STDOUT_FILE + + tail +3 $STDERR_FILE + + exit $RETURN_VALUE + + You get the HDF make files and test scripts to execute your filter script + by setting the environment variable "RUNSERIAL" to the full path of the + script prior to running configure for parallel builds. Remember to + "unsetenv RUNSERIAL" before running configure for a serial build. + + Note that the RUNSERIAL environment variable exists so that we can + can prefix serial runs as necessary on the target system. On DataStar, + no prefix is necessary. However on an MPICH system, the prefix might + have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to + get the serial tests to run at all. + + In such cases, you will have to include the regular prefix in your + filter script. + +* H5Ocopy() does not copy reg_ref attributes correctly when shared-message + is turn on. The value of the reference in the destination attriubte is + wrong. This H5Ocopy problem will affect h5copy tool + diff --git a/release_docs/HISTORY-1_9.txt b/release_docs/HISTORY-1_9.txt deleted file mode 100644 index 8e7648a..0000000 --- a/release_docs/HISTORY-1_9.txt +++ /dev/null @@ -1,6 +0,0 @@ - HDF5 HISTORY - ============ - This file contains history of the HDF5 1.9 branch - - CONTENTS - diff --git a/release_docs/INSTALL b/release_docs/INSTALL index 2dcb9be..177f3b6 100644 --- a/release_docs/INSTALL +++ b/release_docs/INSTALL @@ -2,11 +2,12 @@ Instructions for the Installation of HDF5 Software ================================================== -This file provides instructions for installing the HDF5 software. -If you have any problems with the installation, please see The HDF Group's -support page at the following location: +This file provides instructions for installing the HDF5 software. - http://www.hdfgroup.org/services/support.html +For help with installing, questions can be posted to the HDF Forum or sent to the HDF Helpdesk: + + HDF Forum: https://forum.hdfgroup.org/ + HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk CONTENTS -------- @@ -31,59 +32,34 @@ CONTENTS 4.3. Configuring 4.3.1. Specifying the installation directories 4.3.2. Using an alternate C compiler - 4.3.3. Configuring for 64-bit support - 4.3.4. Additional compilation flags - 4.3.5. Compiling HDF5 wrapper libraries - 4.3.6. Specifying other programs - 4.3.7. Specifying other libraries and headers - 4.3.8. Static versus shared linking - 4.3.9. Optimization versus symbolic debugging - 4.3.10. Parallel versus serial library - 4.3.11. Threadsafe capability - 4.3.12. Backward compatibility + 4.3.3. Additional compilation flags + 4.3.4. Compiling HDF5 wrapper libraries + 4.3.5. Specifying other programs + 4.3.6. Specifying other libraries and headers + 4.3.7. Static versus shared linking + 4.3.8. Optimization versus symbolic debugging + 4.3.9. Parallel versus serial library + 4.3.10. Threadsafe capability + 4.3.11. Backward compatibility 4.4. Building 4.5. Testing 4.6. Installing HDF5 5. Using the Library - 6. Support - - A. Warnings about compilers - A.1. GNU (Intel platforms) - A.2. DEC - A.3. SGI (Irix64 6.2) - A.4. Windows/NT - - B. Large (>2GB) versus small (<2GB) file capability - - C. Building and testing with other compilers - C.1. Building and testing with Intel compilers - C.2. Building and testing with PGI compilers ***************************************************************************** 1. Obtaining HDF5 The latest supported public release of HDF5 is available from - ftp://ftp.hdfgroup.org/HDF5/current/src. For Unix and UNIX-like - platforms, it is available in tar format compressed with gzip. + https://www.hdfgroup.org/downloads/hdf5/. For Unix and UNIX-like + platforms, it is available in tar format compressed with gzip. For Microsoft Windows, it is in ZIP format. - The HDF team also makes snapshots of the source code available on - a regular basis. These snapshots are unsupported (that is, the - HDF team will not release a bug-fix on a particular snapshot; - rather any bug fixes will be rolled into the next snapshot). - Furthermore, the snapshots have only been tested on a few - machines and may not test correctly for parallel applications. - Snapshots, in a limited number of formats, can be found on THG's - development FTP server: - - ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots - 2. Quick installation For those who don't like to read ;-) the following steps can be used - to configure, build, test, and install the HDF5 Library, header files, + to configure, build, test, and install the HDF5 library, header files, and support programs. For example, to install HDF5 version X.Y.Z at location /usr/local/hdf5, use the following steps. @@ -101,14 +77,14 @@ CONTENTS $ tar zxf hdf5-X.Y.Z.tar.gz <configure_flags> above refers to the configure flags appropriate - to your installation. For example, to install HDF5 with the - Fortran and C++ interfaces and with SZIP compression, the + to your installation. For example, to install HDF5 with the + Fortran and C++ interfaces and with SZIP compression, the configure line might read as follows: - + $ ./configure --prefix=/usr/local/hdf5 --enable-fortran \ --enable-cxx --with-szlib=PATH_TO_SZIP - In this case, PATH_TO_SZIP would be replaced with the path to the + In this case, PATH_TO_SZIP would be replaced with the path to the installed location of the SZIP library. 2.1. Windows @@ -125,36 +101,38 @@ CONTENTS 3. HDF5 dependencies 3.1. Zlib - The HDF5 Library includes a predefined compression filter that + The HDF5 library includes a predefined compression filter that uses the "deflate" method for chunked datasets. If zlib-1.1.2 or later is found, HDF5 will use it. Otherwise, HDF5's predefined compression method will degenerate to a no-op; the compression filter will succeed but the data will not be compressed. 3.2. Szip (optional) - The HDF5 Library includes a predefined compression filter that + The HDF5 library includes a predefined compression filter that uses the extended-Rice lossless compression algorithm for chunked - datasets. For more information about Szip compression and license - terms, see http://hdfgroup.org/doc_resource/SZIP/. + datasets. For information on Szip compression, license terms, + and obtaining the Szip source code, see: + + https://portal.hdfgroup.org/display/HDF5/Szip+Compression+in+HDF+Products - The Szip source code can be obtained from the HDF5 Download page - http://www.hdfgroup.org/HDF5/release/obtain5.html#extlibs. Building - instructions are available with the Szip source code. + Building instructions are available with the Szip source code. The HDF Group does not distribute separate Szip precompiled libraries, - but the HDF5 binaries available from - http://www.hdfgroup.org/HDF5/release/obtain5.html include - the Szip encoder enabled binary for the corresponding platform. + but the HDF5 pre-built binaries provided on The HDF Group download page + include the Szip library with the encoder enabled. These can be found + here: - To configure the HDF5 Library with the Szip compression filter, use + https://www.hdfgroup.org/downloads/hdf5/ + + To configure the HDF5 library with the Szip compression filter, use the '--with-szlib=/PATH_TO_SZIP' flag. For more information, see section 4.3.7, "Specifying other libraries and headers." Please notice that if HDF5 configure cannot find a valid Szip library, - configure will not fail; in this case, the compression filter will + configure will not fail; in this case, the compression filter will not be available to the applications. - To check if Szip compression was successfully configured in, + To check if Szip compression was successfully configured in, check the "I/O filters (external):" line in the configure output, summary section, printed to the standard output. @@ -204,27 +182,13 @@ CONTENTS $ cd build-fortran $ ../hdf5-X.Y.Z/configure --enable-fortran ... - Unfortunately, this does not work on recent Irix platforms (6.5? - and later) because that `make' does not understand the VPATH variable. - However, HDF5 also supports Irix `pmake' which has a .PATH target - which serves a similar purpose. Here's what the Irix man pages say - about VPATH, the facility used by HDF5 makefiles for this feature: - - The VPATH facility is a derivation of the undocumented - VPATH feature in the System V Release 3 version of make. - System V Release 4 has a new VPATH implementation, much - like the pmake(1) .PATH feature. This new feature is also - undocumented in the standard System V Release 4 manual - pages. For this reason it is not available in the IRIX - version of make. The VPATH facility should not be used - with the new parallel make option. 4.3. Configuring HDF5 uses the GNU autoconf system for configuration, which detects various features of the host system and creates the Makefiles. On most systems it should be sufficient to say: - $ ./configure + $ ./configure Or $ sh configure @@ -243,7 +207,7 @@ CONTENTS 4.3.1. Specifying the installation directories The default installation location is the HDF5 directory created in the build directory. Typing `make install' will install the HDF5 - Library, header files, examples, and support programs in hdf5/lib, + library, header files, examples, and support programs in hdf5/lib, hdf5/include, hdf5/doc/hdf5/examples, and hdf5/bin. To use a path other than hdf5, specify the path with the `--prefix=PATH' switch: @@ -254,15 +218,15 @@ CONTENTS before the library and executables are built. HDF5 can be installed into a different location than the prefix - specified at configure time; see section 4.6, "Installing HDF5," + specified at configure time; see section 4.6, "Installing HDF5," for more details. 4.3.2. Using an alternate C compiler By default, configure will look for the C compiler by trying `gcc' and `cc'. However, if the environment variable "CC" is set - then its value is used as the C compiler. For instance, one would - use the following line to specify the native C compiler on a system - that also has the GNU gcc compiler (users of csh and derivatives + then its value is used as the C compiler. For instance, one would + use the following line to specify the native C compiler on a system + that also has the GNU gcc compiler (users of csh and derivatives will need to prefix the commands below with `env'): $ CC=cc ./configure @@ -275,46 +239,25 @@ CONTENTS $ CC=/usr/local/mpi/bin/mpicc ./configure -4.3.3. Configuring for 64-bit support - Several machine architectures support 32-bit or 64-bit binaries. - The options below describe how to enable support for different options. - - On Irix64, the default compiler is `cc'. To use an alternate compiler, - specify it with the CC variable: - - $ CC='cc -n32' ./configure - - Similarly, users compiling on a Solaris machine and desiring to - build the distribution with 64-bit support should specify the - correct flags with the CC variable: - $ CC='cc -m64' ./configure - - To configure AIX 64-bit support including the Fortran and C++ APIs, - (Note: need to set $AR to 'ar -X 64'.) - Serial: - $ CFLAGS=-q64 FCFLAGS=-q64 CXXFLAGS=-q64 AR='ar -X 64'\ - ./configure --enable-fortran - Parallel: (C++ not supported with parallel) - $ CFLAGS=-q64 FCFLAGS=-q64 AR='ar -X 64'\ - ./configure --enable-fortran - -4.3.4. Additional compilation flags - If addtional flags must be passed to the compilation commands, +4.3.3. Additional compilation flags + If additional flags must be passed to the compilation commands, specify those flags with the CFLAGS variable. For instance, to enable symbolic debugging of a production version of HDF5, one might say: - $ CFLAGS=-g ./configure --enable-production + $ CFLAGS=-g ./configure --enable-build-mode=production -4.3.5. Compiling HDF5 wrapper libraries - One can optionally build the Fortran and/or C++ interfaces to the - HDF5 C library. By default, both options are disabled. To build - them, specify `--enable-fortran' and `--enable-cxx', respectively. +4.3.4. Compiling HDF5 wrapper libraries + One can optionally build the Fortran, C++, and Java interfaces to + the HDF5 C library. By default, these options are disabled. To build + them, specify '--enable-fortran', '--enable-cxx', or '--enable-java', + respectively. $ ./configure --enable-fortran $ ./configure --enable-cxx - + $ ./configure --enable-java + Configuration will halt if a working Fortran 90 or 95 compiler or C++ compiler is not found. Currently, the Fortran configure tests for these compilers in order: f90, pgf90, f95. To use an @@ -322,16 +265,9 @@ CONTENTS $ FC=/usr/local/bin/g95 ./configure --enable-fortran - Note: The Fortran and C++ interfaces are not supported on all the - platforms the main HDF5 Library supports. Also, the Fortran - interface supports parallel HDF5 while the C++ interface does - not. - Note: See sections 4.7 and 4.8 for building the Fortran library with - Intel or PGI compilers. - -4.3.6. Specifying other programs - The build system has been tuned for use with GNU make but also +4.3.5. Specifying other programs + The build system has been tuned for use with GNU make but also works with other versions of make. If the `make' command runs a non-GNU version but a GNU version is available under a different name (perhaps `gmake'), then HDF5 can be configured to use it by @@ -346,12 +282,12 @@ CONTENTS the `ar' and `ranlib' (or `:') commands to override values detected by configure. - The HDF5 Library, include files, and utilities are installed + The HDF5 library, include files, and utilities are installed during `make install' (described below) with a BSD-compatible install program detected automatically by configure. If none is found, the shell script bin/install-sh is used. Configure does not - check that the install script actually works; if a bad install is - detected on your system (e.g., on the ASCI blue machine as of + check that the install script actually works; if a bad install is + detected on your system (e.g., on the ASCI blue machine as of March 2, 1999) you have two choices: 1. Copy the bin/install-sh program to your $HOME/bin @@ -364,7 +300,7 @@ CONTENTS because the HDF5 makefiles also use the install program to change file ownership and/or access permissions. -4.3.7. Specifying other libraries and headers +4.3.6. Specifying other libraries and headers Configure searches the standard places (those places known by the systems compiler) for include files and header files. However, additional directories can be specified by using the CPPFLAGS @@ -374,11 +310,11 @@ CONTENTS LDFLAGS=-L/home/robb/lib \ ./configure - HDF5 uses the zlib library to support the HDF5 deflate - data compression filter. Configure searches the standard places - (plus those specified above with the CPPFLAGS and LDFLAGS variables) - for the zlib headers and library. The search can be disabled by - specifying `--without-zlib' or alternate directories can be specified + HDF5 uses the zlib library to support the HDF5 deflate + data compression filter. Configure searches the standard places + (plus those specified above with the CPPFLAGS and LDFLAGS variables) + for the zlib headers and library. The search can be disabled by + specifying `--without-zlib' or alternate directories can be specified with `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and LDFLAGS variables: @@ -388,13 +324,13 @@ CONTENTS LDFLAGS=-L/usr/unsup/lib \ ./configure - HDF5 includes Szip as a predefined compression method (see 3.2). - To enable Szip compression, the HDF5 Library must be configured - and built using the Szip Library: + HDF5 includes Szip as a predefined compression method (see 3.2). + To enable Szip compression, the HDF5 library must be configured + and built using the Szip library: $ ./configure --with-szlib=/Szip_Install_Directory -4.3.8. Static versus shared linking +4.3.7. Static versus shared linking The build process will create static libraries on all systems and shared libraries on systems that support dynamic linking to a sufficient degree. Either form of the library may be suppressed by @@ -410,75 +346,96 @@ CONTENTS $ ./configure --enable-static-exec -4.3.9. Optimization versus symbolic debugging +4.3.8. Optimization versus symbolic debugging The library can be compiled to provide symbolic debugging support so it can be debugged with gdb, dbx, ddd, etc., or it can be compiled with various optimizations. To compile for symbolic - debugging (the default for snapshots), say `--disable-production'; - to compile with optimizations (the default for supported public - releases), say `--enable-production'. On some systems the library - can also be compiled for profiling with gprof by saying - `--enable-production=profile'. - - $ ./configure --disable-production #symbolic debugging - $ ./configure --enable-production #optimized code - $ ./configure --enable-production=profile #for use with gprof + debugging (the default for snapshots), say + `--enable-build-mode=debug'; to compile with optimizations + (the default for supported public releases), + say `--enable-build-mode=production'. For a 'clean slate' configuration + with optimization disabled and nothing turned on, + say `--enable-build-mode=clean'. On some systems the + library can also be compiled for profiling with gprof by saying + `--enable-profiling'. + + $ ./configure --enable-build-mode=debug #symbolic debugging + $ ./configure --enable-build-mode=production #optimized code + $ ./configure --enable-build-mode=clean #'clean slate' + $ ./configure --enable-profiling #for use with gprof Regardless of whether support for symbolic debugging is enabled, - the library can also perform runtime debugging of certain packages - (such as type conversion execution times and extensive invariant + the library can also perform runtime debugging of certain packages + (such as type conversion execution times and extensive invariant condition checking). To enable this debugging, supply a - comma-separated list of package names to to the `--enable-debug' - switch. See "Debugging HDF5 Applications" for a list of package - names: + comma-separated list of package names to the `--enable-internal-debug' + switch. - http://www.hdfgroup.org/HDF5/doc/H5.user/Debugging.html - - Debugging can be disabled by saying `--disable-debug'. + Debugging can be disabled by saying `--disable-internal-debug'. The default debugging level for snapshots is a subset of the available packages; the default for supported releases is no debugging (debugging can incur a significant runtime penalty). - $ ./configure --enable-debug=s,t #debug only H5S and H5T - $ ./configure --enable-debug #debug normal packages - $ ./configure --enable-debug=all #debug all packages - $ ./configure --disable-debug #no debugging + $ ./configure --enable-internal-debug=s,t #debug only H5S and H5T + $ ./configure --enable-internal-debug #debug normal packages + $ ./configure --enable-internal-debug=all #debug all packages + $ ./configure --disable-internal-debug #no debugging - HDF5 can also print a trace of all API function calls, their + HDF5 can also print a trace of all API function calls, their arguments, and the return values. To enable or disable the ability to trace the API say `--enable-trace' (the default for - snapthots) or `--disable-trace' (the default for public releases). - The tracing must also be enabled at runtime to see any output - (see "Debugging HDF5 Applications," reference above). + snapthots) or `--disable-trace' (the default for public releases). + The tracing must also be enabled at runtime to see any output. -4.3.10. Parallel versus serial library - The HDF5 Library can be configured to use MPI and MPI-IO for +4.3.9. Parallel versus serial library + The HDF5 library can be configured to use MPI and MPI-IO for parallelism on a distributed multi-processor system. Read the - file INSTALL_parallel for detailed explanations. + file INSTALL_parallel for detailed information. + + The threadsafe, C++ and Java interfaces are not compatible + with the parallel option. + Unless --enable-unsupported has been specified on the configure line, + the following options must be disabled: + --enable-threadsafe, --enable-cxx, --enable-java -4.3.11. Threadsafe capability - The HDF5 Library can be configured to be thread-safe (on a very + +4.3.10. Threadsafe capability + The HDF5 library can be configured to be thread-safe (on a very large scale) with the `--enable-threadsafe' flag to the configure script. Some platforms may also require the '-with-pthread=INC,LIB' (or '--with-pthread=DIR') flag to the configure script. - For further details, see "HDF5 Thread Safe Library": - - http://www.hdfgroup.org/HDF5/doc/TechNotes/ThreadSafeLibrary.html - -4.3.12. Backward compatibility - The 1.8 version of the HDF5 Library can be configured to operate - identically to the v1.6 library with the + For further information, see: + + https://portal.hdfgroup.org/display/knowledge/Questions+about+thread-safety+and+concurrent+access + + The high-level, C++, Fortran and Java interfaces are not compatible + with the thread-safety option because the lock is not hoisted + into the higher-level API calls. + Unless --enable-unsupported has been specified on the configure line, + the following options must be disabled: + --enable-hl, --enable-cxx, --enable-fortran, --enable-java + + +4.3.11. Backward compatibility + The 1.13 version of the HDF5 library can be configured to operate + identically to the v1.12 library with the + --with-default-api-version=v112 + configure flag, or identically to the v1.10 library with the + --with-default-api-version=v110 + configure flag, or identically to the v1.8 library with the + --with-default-api-version=v18 + configure flag, or identically to the v1.6 library with the --with-default-api-version=v16 configure flag. This allows existing code to be compiled with the - v1.8 library without requiring immediate changes to the application - source code. For addtional configuration options and other details, - see "API Compatibility Macros in HDF5": + v1.13 library without requiring immediate changes to the application + source code. For additional configuration options and other details, + see "API Compatibility Macros": - http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html + https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros 4.4. Building The library, confidence tests, and programs can be built by - saying just: + specifying: $ make @@ -493,9 +450,22 @@ CONTENTS $ make -j -l6 +4.4. Building doxygen + One can optionally build the doxygen files for the HDF5 C library. + By default, this option is disabled. To build the html files, specify + '--enable-doxygen'. + + $ ./configure --enable-doxygen + + Configuration will halt if the required applications are not available. + To build: + + $ make doxygen + + 4.5. Testing HDF5 comes with various test suites, all of which can be run by - saying + specifying: $ make check @@ -521,16 +491,16 @@ CONTENTS The HDF5 tests can take a long time to run on some systems. To perform a faster (but less thorough) test, set the HDF5TestExpress environment variable to 2 or 3 (with 3 being the shortest run). To perform a - longer test, set HDF5TestExpress to 0. 1 is the default. + longer test, set HDF5TestExpress to 0. 3 is the default. 4.6. Installing HDF5 - The HDF5 Library, include files, and support programs can be - installed in a (semi-)public place by saying `make install'. The - files are installed under the directory specified with - `--prefix=DIR' (default is 'hdf5') in directories named `lib', - `include', and `bin'. The directories, if not existing, will be - created automatically, provided the mkdir command supports the -p - option. + The HDF5 library, include files, and support programs can be + installed by specifying `make install'. The files are installed under the + directory specified with `--prefix=DIR' (or if not specified, in 'hdf5' + in the top directory of the HDF5 source code). They will be + placed in directories named `lib', `include', and `bin'. The directories, + if not existing, will be created automatically, provided the mkdir command + supports the -p option. If `make install' fails because the install command at your site somehow fails, you may use the install-sh that comes with the @@ -551,7 +521,7 @@ CONTENTS $ make install prefix=NEW_DIR - where NEW_DIR is the new directory where you wish to install HDF5. + where NEW_DIR is the new directory where you wish to install HDF5. If you do not use the deploy script, you should run h5redeploy in NEW_DIR/bin directory. This utility will fix the h5cc, h5fc and h5c++ scripts to reflect the new NEW_DIR location. @@ -574,7 +544,7 @@ CONTENTS The configuration information: ./src/H5pubconf.h - + The support programs that are useful are: ./tools/h5ls/h5ls (list file contents) ./tools/h5dump/h5dump (dump file contents) @@ -582,139 +552,20 @@ CONTENTS ./tools/misc/h5debug (low-level file debugging) ./tools/h5import/h5import (imports data to HDF5 file) ./tools/h5diff/h5diff (compares two HDF5 files) - ./tools/gifconv/h52gif (HDF5 to GIF converter) + ./tools/gifconv/h52gif (HDF5 to GIF converter) ./tools/gifconv/gif2h5 (GIF to HDF5 converter) 5. Using the Library - Please see the "HDF5 User's Guide" and the "HDF5 Reference Manual": - - http://www.hdfgroup.org/HDF5/doc/ - - Most programs will include <hdf5.h> and link with -lhdf5. - Additional libraries may also be necessary depending on whether - support for compression, etc., was compiled into the HDF5 Library. - - A summary of the HDF5 installation can be found in the - libhdf5.settings file in the same directory as the static and/or - shared HDF5 Libraries. - - -6. Support - Support is described in the README file. - - -***************************************************************************** - APPENDIX -***************************************************************************** - -A. Warnings about compilers - Output from the following compilers should be extremely suspected - when used to compile the HDF5 Library, especially if optimizations are - enabled. In all cases, HDF5 attempts to work around the compiler bugs. - -A.1. GNU (Intel platforms) - Versions before 2.8.1 have serious problems allocating registers - when functions contain operations on `long long' datatypes. - -A.2. COMPAQ/DEC - The V5.2-038 compiler (and possibly others) occasionally - generates incorrect code for memcpy() calls when optimizations - are enabled, resulting in unaligned access faults. HDF5 works - around the problem by casting the second argument to `char *'. - The Fortran module (5.4.1a) fails in compiling some Fortran - programs. Use 5.5.0 or higher. - -A.3. SGI (Irix64 6.2) - The Mongoose 7.00 compiler has serious optimization bugs and - should be upgraded to MIPSpro 7.2.1.2m. Patches are available - from SGI. - -A.4. Windows/NT - The Microsoft Win32 5.0 compiler is unable to cast unsigned long - long values to doubles. HDF5 works around this bug by first - casting to signed long long and then to double. - - A link warning: defaultlib "LIBC" conflicts with use of other libs - appears for debug version of VC++ 6.0. This warning will not affect - building and testing HDF5 Libraries. - - -B. Large (>2GB) versus small (<2GB) file capability - In order to read or write files that could potentially be larger - than 2GB, it is necessary to use the non-ANSI `long long' data - type on some platforms. However, some compilers (e.g., GNU gcc - versions before 2.8.1 on Intel platforms) are unable to produce - correct machine code for this datatype. - - -C. Building and testing with other compilers -C.1. Building and testing with Intel compilers - When Intel compilers are used (icc or ecc), you will need to modify - the generated "libtool" program after configuration is finished. - On or around line 104 of the libtool file, there are lines which - look like: - - # How to pass a linker flag through the compiler. - wl="" - - Change these lines to this: - - # How to pass a linker flag through the compiler. - wl="-Wl," - - UPDATE: This is now done automatically by the configure script. - However, if you still experience a problem, you may want to check this - line in the libtool file and make sure that it has the correct value. - - * To build the Fortran library using Intel compiler on Linux 2.4, - one has to perform the following steps: - x Use the -fpp -DDEC$=DEC_ -DMS$=MS_ compiler flags to disable - DEC and MS compiler directives in source files in the fortran/src, - fortran/test, and fortran/examples directories. - E.g., setenv F9X 'ifc -fpp -DDEC$=DEC_ -DMS$=MS_' - Do not use double quotes since $ is interpreted in them. - - x If Version 6.0 of Fortran compiler is used, the build fails in - the fortran/test directory and then in the fortran/examples - directory. To proceed, edit the work.pcl files in those - directories to contain two lines: - - work.pc - ../src/work.pc - - x Do the same in the fortran/examples directory. - - x A problem with work.pc files was resolved for the newest version - of the compiler (7.0). - - * To build the Fortran library on IA32, follow the steps described - above, except that the DEC and MS compiler directives should be - removed manually or use a patch from HDF FTP server: - - ftp://ftp.hdfgroup.org/HDF5/current/ - - -C.2. Building and testing with PGI compilers - When PGI C and C++ compilers are used (pgcc or pgCC), you will need to - modify the generated "libtool" program after configuration is finished. - On or around line 104 of the libtool file, there are lines which - look like this: - # How to pass a linker flag through the compiler. - wl="" + For information on using HDF5 see the documentation, tutorials and examples + found here: - Change these lines to this: + https://portal.hdfgroup.org/display/HDF5/HDF5 - # How to pass a linker flag through the compiler. - wl="-Wl," + A summary of the features included in the built HDF5 installation can be found + in the libhdf5.settings file in the same directory as the static and/or + shared HDF5 libraries. - UPDATE: This is now done automatically by the configure script. However, - if you still experience a problem, you may want to check this line in - the libtool file and make sure that it has the correct value. - To build the HDF5 C++ Library with pgCC (version 4.0 and later), set - the environment variable CXX to "pgCC -tlocal" - setenv CXX "pgCC -tlocal" - before running the configure script. diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt index c16b72d..b17a7e5 100644 --- a/release_docs/INSTALL_CMake.txt +++ b/release_docs/INSTALL_CMake.txt @@ -4,15 +4,15 @@ ************************************************************************ Table of Contents - + Section I: Preconditions -Section II: Quick Step Building HDF5 Libraries with CMake Script Mode +Section II: Quick Step Building HDF5 Libraries with CMake Script Mode Section III: Quick Step Building HDF5 Libraries with CMake Command Mode -Section IV: Further considerations +Section IV: Further considerations Section V: Options for building HDF5 Libraries with CMake command line Section VI: CMake option defaults for HDF5 Section VII: User Defined Options for HDF5 Libraries with CMake -Section VIII: Options for platform configuration files +Section VIII: User Defined Compile Flags for HDF5 Libraries with CMake ************************************************************************ @@ -20,202 +20,251 @@ Section VIII: Options for platform configuration files ======================================================================== I. Preconditions ======================================================================== -Obtaining HDF5 source code +Obtaining HDF5 source code 1. Create a directory for your development; for example, "myhdfstuff". 2. Obtain compressed (*.tar or *.zip) HDF5 source from - http://www.hdfgroup.org/ftp/HDF5/current/src/ + https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake and put it in "myhdfstuff". - Do not uncompress. + Uncompress the file. There should be a hdf5-1.13."X" folder. CMake version - 1. We suggest you obtain the latest CMake from the Kitware web site. - The HDF5 1.8."X" product requires a minimum CMake version 3.1.0, - where "X" is the current HDF5 release version. + 1. We suggest you obtain the latest CMake from the Kitware web site. + The HDF5 1.13."X" product requires a minimum CMake version 3.12, + where "X" is the current HDF5 release version. If you are using + VS2022, the minimum version is 3.21. + +Note: + To change the install prefix from the platform defaults initialize + the CMake variable, CMAKE_INSTALL_PREFIX. Users of build scripts + will use the INSTALLDIR option. ======================================================================== II. Quick Step Building HDF5 Libraries with CMake Script Mode ======================================================================== -This short set of instructions is written for users who want to quickly -build the HDF5 C, C++, Fortran, and High-level shared libraries and tools -from the HDF5 source code package using the CMake tools. This procedure -will use the default settings in the config/cmake/cacheinit.cmake file. +This short set of instructions is written for users who want to quickly +build the HDF5 C and C++ static libraries and tools with SZIP and ZLIB +compression included. This procedure will use the default settings in +the config/cmake/cacheinit.cmake file. HDF Group recommends using the ctest script mode to build HDF5. The following files referenced below are available at the HDF web site: - http://www.hdfgroup.org/HDF5/release/cmakebuild.html + https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake + +Single compressed file with all the files needed, including source: + CMake-hdf5-1.13.X.zip or CMake-hdf5-1.13.X.tar.gz +Individual files included in the above mentioned compressed files +----------------------------------------------- CMake build script: CTestScript.cmake External compression szip and zlib libraries: + LIBAEC.tar.gz SZip.tar.gz ZLib.tar.gz - -Platform configuration files: - HDF518Windows64CMake.cmake - HDF518Windows32CMake.cmake - HDF518LinuxCMake.cmake - HDF518MacCMake.cmake + +External compression plugin libraries: + hdf5_plugins.tar.gz + +Examples Source package: + HDF5Examples-2.0.x-Source.tar.gz + +Configuration files: + HDF5config.cmake + HDF5options.cmake + +Build scripts for windows or linux +----------------------------------------------- To build HDF5 with the SZIP and ZLIB external libraries you will need to: 1. Change to the development directory "myhdfstuff". - - 2. Download the SZip.tar.gz and ZLib.tar.gz to "myhdfstuff". - Do not uncompress the files. - - 3. Download the CTestScript.cmake file to "myhdfstuff". - CTestScript.cmake file should not be modified. - - 4. Download a platform configuration file to "myhdfstuff". - Do not modify the file unless you want to change default build - environment. - - 5. From the "myhdfstuff" directory execute the CTest Script with the - following options: - ctest -S <configuration file> -C Release -VV -O hdf5.log + 2. Download the CMake-hdf5-1.13.X.zip(.tar.gz) file to "myhdfstuff". + Uncompress the file. + + 3. Change to the source directory "hdf5-1.13.x". + CTestScript.cmake file should not be modified. - The command above will configure, build, test, and create an install - package in the myhdfstuff/hdf5-1.8/build folder. + 4. Edit the platform configuration file, HDF5options.cmake, if you want to change + the default build environment. + (See https://portal.hdfgroup.org/display/support/How+to+Change+HDF5+CMake+Build+Options) + + 5. From the "myhdfstuff" directory execute the CTest Script with the + following options: - The -S option uses the script version of ctest. - - The value for the -C option (as shown above, "-C Release") must - match the setting for CTEST_BUILD_CONFIGURATION in the platform - configuration file. - - The -VV option is for verbose; use -V for less verbose. - - The "-O hdf5.log" option saves the output to a log file hdf5.log. + On 32-bit Windows with Visual Studio 2019, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2019 -C Release -VV -O hdf5.log + On 64-bit Windows with Visual Studio 2019, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201964 -C Release -VV -O hdf5.log + On 32-bit Windows with Visual Studio 2017, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2017 -C Release -VV -O hdf5.log + On 64-bit Windows with Visual Studio 2017, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201764 -C Release -VV -O hdf5.log + On 32-bit Windows with Visual Studio 2015, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2015 -C Release -VV -O hdf5.log + On 64-bit Windows with Visual Studio 2015, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201564 -C Release -VV -O hdf5.log + On Linux and Mac, execute: + ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -VV -O hdf5.log + The supplied build scripts are versions of the above. + + The command above will configure, build, test, and create an install + package in the myhdfstuff folder. It will have the format: + HDF5-1.13.NN-<platform>.<zip or tar.gz> + + On Unix, <platform> will be "Linux". A similar .sh file will also be created. + On Windows, <platform> will be "win64" or "win32". If you have an + installer on your system, you will also see a similar file that ends + in either .exe (NSIS) or .msi (WiX). + + Notes on the command line options. + The -S option uses the script version of ctest. + + The value for the -C option (as shown above, "-C Release") must + match the setting for CTEST_CONFIGURATION_TYPE in the platform + configuration file. + + The -VV option is for most verbose; use -V for less verbose. + + The "-O hdf5.log" option saves the output to a log file hdf5.log. 6. To install, "X" is the current release version - - On Windows, execute: - HDF5-1.8."X"-win32.exe or HDF5-1.8."X"-win64.exe + + On Windows (with WiX installed), execute: + HDF5-1.13."X"-win32.msi or HDF5-1.13."X"-win64.msi By default this program will install the hdf5 library into the - "C:\Program Files" directory and will create the following + "C:\Program Files" directory and will create the following directory structure: HDF_Group --HDF5 - ----1.8."X" + ----1.13."X" ------bin ------include ------lib ------cmake - On Linux, change to the install destination directory + On Linux, change to the install destination directory (create it if doesn't exist) and execute: - <path-to>/myhdfstuff/hdf5-1.8/build/HDF5-1.8."X"-Linux.sh + <path-to>/myhdfstuff/HDF5-1.13."X"-Linux.sh After accepting the license, the script will prompt: By default the HDF5 will be installed in: - "<current directory>/HDF5-1.8."X"-Linux" - Do you want to include the subdirectory HDF5-1.8."X"-Linux? - Saying no will install in: "<current directory>" [Yn]: + "<current directory>/HDF5-1.13."X"-Linux" + Do you want to include the subdirectory HDF5-1.13."X"-Linux? + Saying no will install in: "<current directory>" [Yn]: Note that the script will create the following directory structure relative to the install point: HDF_Group --HDF5 - ----1.8."X" + ----1.13."X" ------bin ------include ------lib ------share - - On Mac you will find HDF5-1.8."X"-Darwin.dmg in the build folder. Click + + On Mac you will find HDF5-1.13."X"-Darwin.dmg in the myhdfstuff folder. Click on the dmg file to proceed with installation. After accepting the license, - there will be a folder with the following structure: + there will be a folder with the following structure: HDF_Group --HDF5 - ----1.8."X" + ----1.13."X" ------bin ------include ------lib ------share - + By default the installation will create the bin, include, lib and cmake - folders in the <install destination directory>/HDF_Group/HDF5/1.8. + folders in the <install destination directory>/HDF_Group/HDF5/1.13."X" + The <install destination directory> depends on the build platform; + Windows will set the default to: + C:/Program Files/HDF_Group/HDF5/1.13."X" + Linux will set the default to: + "myhdfstuff/HDF_Group/HDF5/1.13."X" + The default can be changed by adding ",INSTALLDIR=<my new dir>" to the + "ctest -S HDF5config.cmake..." command. For example on linux: + ctest -S HDF5config.cmake,INSTALLDIR=/usr/local/myhdf5,BUILD_GENERATOR=Unix -C Release -VV -O hdf5.log ======================================================================== III. Quick Step Building HDF5 C Static Libraries and Tools with CMake ======================================================================== -Notes: This short set of instructions is written for users who want to - quickly build the just the HDF5 C static library and tools from +Notes: This short set of instructions is written for users who want to + quickly build just the HDF5 C static library and tools from the HDF5 source code package using the CMake command line tools. - + Avoid the use of drive letters in paths on Windows. + Go through these steps: 1. Change to the development directory "myhdfstuff". 2. Uncompress the HDF5 source file - + 3. Create a folder "build" in the "myhdfstuff" directory. - - 4. Change into the "build" folder. - + + 4. Change into the "build" folder. + 5. Configure the C library, tools and tests with one of the following commands: On Windows 32 bit - cmake -G "Visual Studio 11" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-1.8."X" + cmake -G "Visual Studio 12 2013" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-1.13."X" On Windows 64 bit - cmake -G "Visual Studio 11 Win64" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-1.8."X" - + cmake -G "Visual Studio 12 2013 Win64" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-1.13."X" + On Linux and Mac - cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ../hdf5-1.8."X" + cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ../hdf5-1.13."X" where "X" is the current release version. - + 6. Build the C library, tools and tests with this command: cmake --build . --config Release - + 7. Test the C library and tools with this command: ctest . -C Release - + 8. Create an install image with this command: cpack -C Release CPackConfig.cmake - - 9. To install - On Windows, execute: - HDF5-1.8."X"-win32.exe or HDF5-1.8."X"-win64.exe + + 9. To install + On Windows (with WiX installed), execute: + HDF5-1.13."X"-win32.msi or HDF5-1.13."X"-win64.msi By default this program will install the hdf5 library into the - "C:\Program Files" directory and will create the following + "C:\Program Files" directory and will create the following directory structure: HDF_Group --HDF5 - ----1.8."X" + ----1.13."X" ------bin ------include ------lib ------cmake - On Linux, change to the install destination directory + On Linux, change to the install destination directory (create if doesn't exist) and execute: - <path-to>/myhdfstuff/build/HDF5-1.8."X"-Linux.sh + <path-to>/myhdfstuff/build/HDF5-1.13."X"-Linux.sh After accepting the license, the script will prompt: By default the HDF5 will be installed in: - "<current directory>/HDF5-1.8."X"-Linux" - Do you want to include the subdirectory HDF5-1.8."X"-Linux? - Saying no will install in: "<current directory>" [Yn]: + "<current directory>/HDF5-1.13."X"-Linux" + Do you want to include the subdirectory HDF5-1.13."X"-Linux? + Saying no will install in: "<current directory>" [Yn]: Note that the script will create the following directory structure relative to the install point: HDF_Group --HDF5 - ----1.8."X" + ----1.13."X" ------bin ------include ------lib ------share - - On Mac you will find HDF5-1.8."X"-Darwin.dmg in the build folder. Click + + On Mac you will find HDF5-1.13."X"-Darwin.dmg in the build folder. Click on the dmg file to proceed with installation. After accepting the license, - there will be a folder with the following structure: + there will be a folder with the following structure: HDF_Group --HDF5 - ----1.8."X" + ----1.13."X" ------bin ------include ------lib @@ -223,41 +272,65 @@ Notes: This short set of instructions is written for users who want to ======================================================================== -IV. Further considerations +IV. Further considerations ======================================================================== 1. We suggest you obtain the latest CMake for windows from the Kitware - web site. The HDF5 1.8."X" product requires a minimum CMake version 3.1.0. - + web site. The HDF5 1.13."X" product requires a minimum CMake version 3.18. + 2. If you plan to use Zlib or Szip: - A. Download the binary packages and install them in a central location. - For example on Windows, create a folder extlibs and install the + A. Download the binary packages and install them in a central location. + For example on Windows, create a folder extlibs and install the packages there. Add the following CMake options: -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include + -DZLIB_USE_EXTERNAL:BOOL=OFF -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include - where "some_location" is the full path to the extlibs folder. + -DSZIP_USE_EXTERNAL:BOOL=OFF + where "some_location" is the full path to the extlibs folder. + Also the appropriate environment variable must be set; + set(ENV{ZLIB_ROOT} "some_location") + set(ENV{SZIP_ROOT} "some_location") - B. Use source packages from an SVN server by adding the following CMake + B. Use source packages from an GIT server by adding the following CMake options: - HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="SVN" - ZLIB_SVN_URL:STRING="http://some_location/zlib/trunk" - SZIP_SVN_URL:STRING="http://some_location/szip/trunk" - where "some_location" is the URL to the SVN repository. Also set + HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT" + ZLIB_GIT_URL:STRING="http://some_location/zlib" + SZIP_GIT_URL:STRING="http://some_location/szip" + where "some_location" is the URL to the GIT repository. Also set CMAKE_BUILD_TYPE to the configuration type. - - C. Use source packages from a compressed file by adding the following + + C. Use source packages from a compressed file by adding the following CMake options: HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" ZLIB_TGZ_NAME:STRING="zlib_src.ext" SZIP_TGZ_NAME:STRING="szip_src.ext" TGZPATH:STRING="some_location" - where "some_location" is the URL or full path to the compressed + where "some_location" is the URL or full path to the compressed + file and ext is the type of compression file. Also set CMAKE_BUILD_TYPE + to the configuration type during configuration. See the settings in the + config/cmake/cacheinit.cmake file HDF uses for testing. + + 3. If you plan to use compression plugins: + A. Use source packages from an GIT server by adding the following CMake + options: + HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT" + PLUGIN_GIT_URL:STRING="http://some_location/plugins" + where "some_location" is the URL to the GIT repository. Also set + CMAKE_BUILD_TYPE to the configuration type. + + B. Use source packages from a compressed file by adding the following + CMake options: + HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" + PLUGIN_TGZ_NAME:STRING="plugin_src.ext" + TGZPATH:STRING="some_location" + where "some_location" is the URL or full path to the compressed file and ext is the type of compression file. Also set CMAKE_BUILD_TYPE - to the configuration type during configuration - - 3. If you are building on Apple Darwin platforms, you should add the + to the configuration type during configuration. See the settings in the + config/cmake/cacheinit.cmake file HDF uses for testing. + + 4. If you are building on Apple Darwin platforms, you should add the following options: Compiler choice - use xcode by setting the ENV variables of CC and CXX Shared fortran is not supported, build static: @@ -265,47 +338,87 @@ IV. Further considerations Additional options: CMAKE_ANSI_CFLAGS:STRING=-fPIC CTEST_USE_LAUNCHERS:BOOL=ON - CMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF - - 4. Windows developers should install NSIS to create an install image with CPack. + CMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF + + 5. Windows developers should install NSIS or WiX to create an install image with CPack. Visual Studio Express users will not be able to package HDF5 into an install image executable. - - 5. Developers can copy the config/cmake/cacheinit.cmake file and alter the + + 6. Developers can copy the config/cmake/cacheinit.cmake file and alter the the settings for the developers' environment. Then the only options needed on the command line are those options that are different. Example using HDF default cache file: - cmake -C ../config/cmake/cacheinit.cmake -G "Visual Studio 11" \ + cmake -C ../config/cmake/cacheinit.cmake -G "Visual Studio 12 2013" \ -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF \ -DCMAKE_BUILD_TYPE:STRING=Release .. + 7. CMake uses a toolchain of utilities to compile, link libraries and + create archives, and other tasks to drive the build. The toolchain + utilities available are determined by the languages enabled. In normal + builds, CMake automatically determines the toolchain for host builds + based on system introspection and defaults. In cross-compiling + scenarios, a toolchain file may be specified with information about + compiler and utility paths. + Variables and Properties + Several variables relate to the language components of a toolchain which + are enabled. CMAKE_<LANG>_COMPILER is the full path to the compiler used + for <LANG>. CMAKE_<LANG>_COMPILER_ID is the identifier used by CMake for + the compiler and CMAKE_<LANG>_COMPILER_VERSION is the version of the compiler. + + The CMAKE_<LANG>_FLAGS variables and the configuration-specific equivalents + contain flags that will be added to the compile command when compiling a + file of a particular language. + + As the linker is invoked by the compiler driver, CMake needs a way to + determine which compiler to use to invoke the linker. This is calculated + by the LANGUAGE of source files in the target, and in the case of static + libraries, the language of the dependent libraries. The choice CMake makes + may be overridden with the LINKER_LANGUAGE target property. + + See the CMake help for more information on using toolchain files. + + To use a toolchain file with the supplied cmake scripts, see the + HDF5options.cmake file under the toolchain section. + Notes: CMake and HDF5 - 1. Using CMake for building and using HDF5 is under active development. - While we have attempted to provide error-free files, please - understand that development with CMake has not been extensively + 1. Using CMake for building and using HDF5 is under active development. + While we have attempted to provide error-free files, please + understand that development with CMake has not been extensively tested outside of HDF. The CMake specific files may change before the next release. - - 2. CMake support for HDF5 development should be usable on any - system where CMake is supported. Please send us any comments on - how CMake support can be improved on any system. Visit the + + 2. CMake support for HDF5 development should be usable on any + system where CMake is supported. Please send us any comments on + how CMake support can be improved on any system. Visit the KitWare site for more information about CMake. - - 3. Build and test results can be submitted to our CDash server, - please read the HDF and CDash document at: - www.hdfgroup.org/CDash/HowToSubmit. - + + 3. Build and test results can be submitted to our CDash server: + The CDash server for community submissions of hdf5 is at + https://cdash.hdfgroup.org. + + Submitters are requested to register their name and contact info and + maintain their test sites. After your first submission, login and go + to your "My CDash" link and claim your site. + + We ask that all submissions include the configuration information and + contact information in the CTest Notes Files upload step. See the + current reports on CDash for examples. + + Please follow the convention that "NIGHTLY" submissions maintain the same + configuration every time. "EXPERIMENTAL" submissions can be expected to + be different for each submission. + 4. See the appendix at the bottom of this file for examples of using a ctest script for building and testing. Using a ctest script is preferred because of its flexibility. - + Notes: CMake in General - 1. More information about using CMake can be found at the KitWare site at + 1. More information about using CMake can be found at the KitWare site at www.cmake.org. - - 2. CMake uses the command line; however, the visual CMake tool is + + 2. CMake uses the command line; however, the visual CMake tool is available for the configuration step. The steps are similar for all the operating systems supported by CMake. @@ -330,36 +443,35 @@ These five steps are described in detail below. The visual CMake executable is named "cmake-gui.exe" on Windows and should be available in your Start menu. For Linux, UNIX, and Mac users the - executable is named "cmake-gui" and can be found where CMake was - installed. - - Specify the source and build directories. - + executable is named "cmake-gui" and can be found where CMake was + installed. + + Specify the source and build directories. + ***** Make the build and source directories different. ****** - - For example on Windows, if the source is at c:\MyHDFstuff\hdf5, - then use c:\MyHDFstuff\hdf5\build or c:\MyHDFstuff\build\hdf5 as the + + For example on Windows, if the source is at c:\MyHDFstuff\hdf5, + then use c:\MyHDFstuff\hdf5\build or c:\MyHDFstuff\build\hdf5 as the build directory. - + RECOMMENDED: - Users can perform the configuration step without using the visual - cmake-gui program. We use the file cacheinit.cmake in the - config/cmake source folder for our testing. This file enables all of the - basic options and we turn specific options on or off for testing + Users can perform the configuration step without using the visual + cmake-gui program. We use the file cacheinit.cmake in the + config/cmake source folder for our testing. This file enables all of the + basic options and we turn specific options on or off for testing using the following command line within the build directory: - + cmake -C <sourcepath>/config/cmake/cacheinit.cmake -G "<generator>" [-D<options>] <sourcepath> - - Where <generator> is + + Where <generator> is * MinGW Makefiles * NMake Makefiles * Unix Makefiles - * Visual Studio 12 - * Visual Studio 12 Win64 - * Visual Studio 11 - * Visual Studio 11 Win64 - * Visual Studio 10 - * Visual Studio 10 Win64 + * Visual Studio 14 2015 + * Visual Studio 14 2015 Win64 + * Visual Studio 15 2017 + * Visual Studio 15 2017 Win64 + * Visual Studio 16 2019 <options> is: * SZIP_INCLUDE_DIR:PATH=<path to szip includes directory> @@ -373,235 +485,382 @@ These five steps are described in detail below. ######################## # EXTERNAL cache entries ######################## - set (BUILD_SHARED_LIBS ON CACHE BOOL "Build Shared Libraries" FORCE) - set (BUILD_TESTING ON CACHE BOOL "Build HDF5 Unit Testing" FORCE) + set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Frameworks installation directory" FORCE) set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE) - set (HDF5_BUILD_CPP_LIB ON CACHE BOOL "Build HDF5 C++ Library" FORCE) - set (HDF5_BUILD_EXAMPLES ON CACHE BOOL "Build HDF5 Library Examples" FORCE) set (HDF5_BUILD_FORTRAN ON CACHE BOOL "Build FORTRAN support" FORCE) - set (HDF5_ENABLE_F2003 ON CACHE BOOL "Enable FORTRAN 2003 Standard" FORCE) - set (HDF5_BUILD_HL_LIB ON CACHE BOOL "Build HIGH Level HDF5 Library" FORCE) - set (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools" FORCE) - set (HDF5_BUILD_GENERATORS OFF CACHE BOOL "Build Test Generators" FORCE) set (HDF5_ENABLE_Z_LIB_SUPPORT ON CACHE BOOL "Enable Zlib Filters" FORCE) set (HDF5_ENABLE_SZIP_SUPPORT ON CACHE BOOL "Use SZip Filter" FORCE) set (HDF5_ENABLE_SZIP_ENCODING ON CACHE BOOL "Use SZip Encoding" FORCE) - set (HDF5_ENABLE_HSIZET ON CACHE BOOL "Enable datasets larger than memory" FORCE) - set (HDF5_ENABLE_UNSUPPORTED OFF CACHE BOOL "Enable unsupported combinations of configuration options" FORCE) - set (HDF5_ENABLE_DEPRECATED_SYMBOLS ON CACHE BOOL "Enable deprecated public API symbols" FORCE) - set (HDF5_ENABLE_DIRECT_VFD OFF CACHE BOOL "Build the Direct I/O Virtual File Driver" FORCE) - set (HDF5_ENABLE_PARALLEL OFF CACHE BOOL "Enable parallel build (requires MPI)" FORCE) set (MPIEXEC_MAX_NUMPROCS "3" CACHE STRING "Minimum number of processes for HDF parallel tests" FORCE) - set (HDF5_BUILD_PARALLEL_ALL OFF CACHE BOOL "Build Parallel Programs" FORCE) - set (HDF5_ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage for Libraries and Programs" FORCE) - set (HDF5_ENABLE_USING_MEMCHECKER OFF CACHE BOOL "Indicate that a memory checker is used" FORCE) - set (HDF5_DISABLE_COMPILER_WARNINGS OFF CACHE BOOL "Disable compiler warnings" FORCE) - set (HDF5_USE_FOLDERS ON CACHE BOOL "Enable folder grouping of projects in IDEs." FORCE) - set (HDF5_USE_16_API_DEFAULT OFF CACHE BOOL "Use the HDF5 1.6.x API by default" FORCE) - set (HDF5_ENABLE_THREADSAFE OFF CACHE BOOL "(WINDOWS)Enable Threadsafety" FORCE) - set (HDF5_PACKAGE_EXTLIBS OFF CACHE BOOL "(WINDOWS)CPACK - include external libraries" FORCE) - set (HDF5_NO_PACKAGES OFF CACHE BOOL "CPACK - Disable packaging" FORCE) - set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO SVN TGZ)" FORCE) - set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO SVN TGZ) + set (HDF5_ENABLE_ALL_WARNINGS ON CACHE BOOL "Enable all warnings" FORCE) + set (HDF_TEST_EXPRESS "2" CACHE STRING "Control testing framework (0-3)" FORCE) + set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE) + set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) set (SZIP_TGZ_NAME "SZip.tar.gz" CACHE STRING "Use SZip from compressed file" FORCE) + set (SZAEC_TGZ_NAME "LIBAEC.tar.gz" CACHE STRING "Use SZip AEC from compressed file" FORCE) + set (USE_LIBAEC ON CACHE BOOL "Use libaec szip replacement" FORCE) set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) + set (LIBAEC_PACKAGE_NAME "libaec" CACHE STRING "Name of AEC SZIP package" FORCE) set (SZIP_PACKAGE_NAME "szip" CACHE STRING "Name of SZIP package" FORCE) + ####################### + # filter plugin options + ####################### + set (PLUGIN_TGZ_NAME "hdf5_plugins.tar.gz" CACHE STRING "Use PLUGINS from compressed file" FORCE) + set (PLUGIN_PACKAGE_NAME "pl" CACHE STRING "Name of PLUGIN package" FORCE) + ############ + # bitshuffle + ########### + set (BSHUF_GIT_URL "https://someurl/bitshuffle.git" CACHE STRING "Use BSHUF from HDF repository" FORCE) + set (BSHUF_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (BSHUF_TGZ_NAME "bitshuffle.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE) + set (BSHUF_PACKAGE_NAME "bshuf" CACHE STRING "Name of BSHUF package" FORCE) + ####### + # blosc + ####### + set (BLOSC_GIT_URL "https://github.com/Blosc/c-blosc.git" CACHE STRING "Use BLOSC from Github" FORCE) + set (BLOSC_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (BLOSC_TGZ_NAME "c-blosc.tar.gz" CACHE STRING "Use BLOSC from compressed file" FORCE) + set (BLOSC_PACKAGE_NAME "blosc" CACHE STRING "Name of BLOSC package" FORCE) + set (ZLIB_GIT_URL "https://someurl/zlib.git" CACHE STRING "Use ZLIB from HDF repo" FORCE) + set (ZLIB_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) + set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) + ####### + # bzip2 + ###### + # + set (BZ2_GIT_URL "https://someurl/bzip2.git" CACHE STRING "Use BZ2 from HDF repository" FORCE) + set (BZ2_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (BZ2_TGZ_NAME "BZ2.tar.gz" CACHE STRING "Use BZ2 from compressed file" FORCE) + set (BZ2_PACKAGE_NAME "bz2" CACHE STRING "Name of BZ2 package" FORCE) + ####### + # fpzip + ####### + set (FPZIP_GIT_URL "https://https://github.com/LLNL/fpzip" CACHE STRING "Use FPZIP from github repository" FORCE) + set (FPZIP_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (FPZIP_TGZ_NAME "fpzip.tar.gz" CACHE STRING "Use FPZIP from compressed file" FORCE) + set (FPZIP_PACKAGE_NAME "fpzip" CACHE STRING "Name of FPZIP package" FORCE) + ###### + # jpeg + ###### + set (JPEG_GIT_URL "https://someurl/jpeg.git" CACHE STRING "Use JPEG from HDF repository" FORCE) + set (JPEG_GIT_BRANCH "jpeg9c" CACHE STRING "" FORCE) + #set (JPEG_TGZ_NAME "JPEG9c.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE) + set (JPEG_TGZ_NAME "JPEG.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE) + set (JPEG_PACKAGE_NAME "jpeg" CACHE STRING "Name of JPEG package" FORCE) + ###### + # lz4 + ###### + set (BUILD_LZ4_LIBRARY_SOURCE ON CACHE BOOL "build the lz4 library within the plugin" FORCE) + set (LZ4_GIT_URL "https://someurl/lz4.git" CACHE STRING "Use LZ4 from HDF repository" FORCE) + set (LZ4_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (LZ4_TGZ_NAME "lz4.tar.gz" CACHE STRING "Use LZ4 from compressed file" FORCE) + set (LZ4_PACKAGE_NAME "lz4" CACHE STRING "Name of LZ4 package" FORCE) + ###### + # lzf + ###### + set (LZF_GIT_URL "https://someurl/lzf.git" CACHE STRING "Use LZF from HDF repository" FORCE) + set (LZF_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (LZF_TGZ_NAME "lzf.tar.gz" CACHE STRING "Use LZF from compressed file" FORCE) + set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE) + ######## + # mafisc + ######## + #set (BUILD_MAFISC_LIBRARY_SOURCE OFF CACHE BOOL "build the mafisc library within the plugin" FORCE) + #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE) + ###### + # szf + ###### + set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE) + set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE) + set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE) + ###### + # zfp + ###### + set (ZFP_GIT_URL "https://github.com/LLNL/zfp.git" CACHE STRING "Use ZFP from Github" FORCE) + set (ZFP_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (ZFP_TGZ_NAME "zfp.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE) + set (ZFP_PACKAGE_NAME "zfp" CACHE STRING "Name of ZFP package" FORCE) + 2. Configure the cache settings - 2.1 Visual CMake users, click the Configure button. If this is the first time you are - running cmake-gui in this directory, you will be prompted for the - generator you wish to use (for example on Windows, Visual Studio 11). - CMake will read in the CMakeLists.txt files from the source directory and - display options for the HDF5 project. After the first configure you + 2.1 Visual CMake users, click the Configure button. If this is the first time you are + running cmake-gui in this directory, you will be prompted for the + generator you wish to use (for example on Windows, Visual Studio 12). + CMake will read in the CMakeLists.txt files from the source directory and + display options for the HDF5 project. After the first configure you can adjust the cache settings and/or specify the locations of other programs. - + Any conflicts or new values will be highlighted by the configure - process in red. Once you are happy with all the settings and there are no - more values in red, click the Generate button to produce the appropriate - build files. - - On Windows, if you are using a Visual Studio generator, the solution and + process in red. Once you are happy with all the settings and there are no + more values in red, click the Generate button to produce the appropriate + build files. + + On Windows, if you are using a Visual Studio generator, the solution and project files will be created in the build folder. - + On linux, if you are using the Unix Makefiles generator, the Makefiles will be created in the build folder. 2.2 Preferred command line example on Windows in c:\MyHDFstuff\hdf5\build directory: - - cmake -C ../config/cmake/cacheinit.cmake -G "Visual Studio 11" \ + + cmake -C ../config/cmake/cacheinit.cmake -G "Visual Studio 12 2013" \ -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF \ -DCMAKE_BUILD_TYPE:STRING=Release .. - 2.3 On Windows, if you are using a Visual Studio Express version you must + 2.3 On Windows, if you are using a Visual Studio Express version you must be sure that the following two options are correctly set/unset: - + HDF5_NO_PACKAGES:BOOL=ON HDF5_USE_FOLDERS:BOOL=OFF - + 3. Build HDF5 - - On Windows, you can build HDF5 using either the Visual Studio Environment + + On Windows, you can build HDF5 using either the Visual Studio Environment or the command line. The command line can be used on all platforms; Windows, linux, Unix, and Mac. To build from the command line, navigate to your build directory and execute the following: - - cmake --build . --config {Debug | Release} - + + cmake --build . --config {Debug | Release} + NOTE: "--config {Debug | Release}" may be optional on your platform. We - recommend choosing either Debug or Release on Windows. - - 3.1 If you wish to use the Visual Studio environment, open the solution - file in your build directory. Be sure to select either Debug or + recommend choosing either Debug or Release on Windows. + + 3.1 If you wish to use the Visual Studio environment, open the solution + file in your build directory. Be sure to select either Debug or Release and build the solution. - - 3.2.1 The external libraries (zlib and szip) can be configured - to allow building the libraries by downloading from an SVN repository. + + 3.2.1 The external libraries (zlib, szip and plugins) can be configured + to allow building the libraries by downloading from a GIT repository. The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT'; by adding the following configuration option: - -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="SVN" - - The options to control the SVN URL (config/cmake/cacheinit.cmake file) are: - ZLIB_SVN_URL:STRING="http://${svn_url}/zlib/trunk" - SZIP_SVN_URL:STRING="http://${svn_url}/szip/trunk" - ${svn_url} should be changed to your location. Also define CMAKE_BUILD_TYPE + -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT" + + The options to control the GIT URL (config/cmake/cacheinit.cmake file) are: + ZLIB_GIT_URL:STRING="http://${git_url}/zlib" + SZIP_GIT_URL:STRING="http://${git_url}/szip" + PLUGIN_GIT_URL:STRING="http://${git_url}/plugin" + ${git_url} should be changed to your location. Also define CMAKE_BUILD_TYPE to be the configuration type. - - 3.2.2 Or the external libraries (zlib and szip) can be configured + + 3.2.2 Or the external libraries (zlib, szip and plugins) can be configured to allow building the libraries by using a compressed file. - The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT' and is enabled by + The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT' and is enabled by adding the following configuration option: -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" - - The options to control the SVN URL (config/cmake/cacheinit.cmake + + The options to control the TGZ URL (config/cmake/cacheinit.cmake file) are: ZLIB_TGZ_NAME:STRING="zlib_src.ext" SZIP_TGZ_NAME:STRING="szip_src.ext" + LIBAEC_TGZ_NAME:STRING="libaec_src.ext" + PLUGIN_TGZ_NAME:STRING="plugin_src.ext" TGZPATH:STRING="some_location" - where "some_location/xxxx_src.ext" is the URL or full path to - the compressed file and where ext is the type of the compression + where "some_location/xxxx_src.ext" is the URL or full path to + the compressed file and where ext is the type of the compression file such as .bz2, .tar, .tar.gz, .tgz, or .zip. Also define CMAKE_BUILD_TYPE to be the configuration type. + NOTE: the USE_LIBAEC option will use the file named by LIBAEC_TGZ_NAME + to build SZIP instead of the file named by SZIP_TGZ_NAME. This option + is also used to account for the different headers and library names. + 4. Test HDF5 To test the build, navigate to your build directory and execute: - + ctest . -C {Debug | Release} - + NOTE: "-C {Debug | Release}" may be optional on your platform. We recommend choosing either Debug or Release to match the build - step on Windows. + step on Windows. 5. Packaging HDF5 (create an install image) - - To package the build into a simple installer using the NullSoft installer NSIS + + To package the build into a simple installer using WiX toolset or the NullSoft installer NSIS on Windows, or into compressed files (.tar.gz, .sh, .zip), use the CPack tool. To package the build, navigate to your build directory and execute; - + cpack -C {Debug | Release} CPackConfig.cmake - + NOTE: See note 8 of this document for NSIS information. - Also, if you are using a Visual Studio Express version or do not - want to enable the packaging components, set HDF5_NO_PACKAGES + See note 9 of this document for WiX information. + Also, if you are using a Visual Studio Express version or + want to disable the packaging components, set HDF5_NO_PACKAGES to ON (on the command line add -DHDF5_NO_PACKAGES:BOOL=ON) - - 6. The files that support building HDF5 with CMake are all the files in the - config/cmake folder, the CMakeLists.txt files in each source folder, and - CTestConfig.cmake. CTestConfig.cmake is specific to the internal testing - performed by The HDF Group. It should be altered for the user's + + 6. The files that support building HDF5 with CMake are all the files in the + config/cmake folder, the CMakeLists.txt files in each source folder, and + CTestConfig.cmake. CTestConfig.cmake is specific to the internal testing + performed by The HDF Group. It should be altered for the user's installation and needs. The cacheinit.cmake file settings are used by - The HDF Group for daily testing. It should be altered/ignored for the user's + The HDF Group for daily testing. It should be altered/ignored for the user's installation and needs. - 7. More information about using CMake can be found at the KitWare site, + 7. More information about using CMake can be found at the KitWare site, www.cmake.org. - + 8. Nullsoft Scriptable Install System - The Nullsoft Scriptable Install System (NSIS) is an open source installation - system. It was created by the WinAmp authors to distribute that application, - but it is now a general-purpose system which anyone might use. NSIS installers - recognize /S for silent installation and /D=dir to specify the - "output directory", which is where the program will be installed. These - options are case-sensitive, so be sure to type them in upper case. + The Nullsoft Scriptable Install System (NSIS) is an open source installation + system. It was created by the WinAmp authors to distribute that application, + but it is now a general-purpose system which anyone might use. NSIS installers + recognize /S for silent installation and /D=dir to specify the + "output directory", which is where the program will be installed. These + options are case-sensitive, so be sure to type them in upper case. + 9. WiX Toolset + WiX--the Windows Installer XML toolset--lets developers create installers for + Windows Installer, the Windows installation engine. See http://wixtoolset.org. ======================================================================== VI. CMake Option Defaults for HDF5 ======================================================================== -In the options listed below, there are three columns of information: -Option Name, Option Description, and Option Default. -The config/cmake/cacheinit.cmake file overrides the following values. +In the options listed below, there are three columns of information: +Option Name, Option Description, and Option Default. +The config/cmake/cacheinit.cmake file can override the following values. ---------------- General Build Options --------------------- -BUILD_SHARED_LIBS "Build Shared Libraries" OFF -BUILD_STATIC_EXECS "Build Static Executabless" OFF -BUILD_STATIC_PIC "Build Static PIC" OFF -BUILD_TESTING "Build HDF5 Unit Testing" OFF +BUILD_SHARED_LIBS "Build Shared Libraries" ON +BUILD_STATIC_LIBS "Build Static Libraries" ON +BUILD_STATIC_EXECS "Build Static Executables" OFF +BUILD_TESTING "Build HDF5 Unit Testing" ON ---------------- HDF5 Build Options --------------------- HDF5_BUILD_CPP_LIB "Build HDF5 C++ Library" OFF -HDF5_BUILD_EXAMPLES "Build HDF5 Library Examples" OFF +HDF5_BUILD_EXAMPLES "Build HDF5 Library Examples" ON HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF -HDF5_BUILD_HL_LIB "Build HIGH Level HDF5 Library" OFF -HDF5_BUILD_TOOLS "Build HDF5 Tools" OFF -if (HDF5_BUILD_FORTRAN) - HDF5_ENABLE_F2003 "Enable FORTRAN 2003 Standard" ON +HDF5_BUILD_JAVA "Build JAVA support" OFF +HDF5_BUILD_HL_LIB "Build HIGH Level HDF5 Library" ON +HDF5_BUILD_TOOLS "Build HDF5 Tools" ON +HDF5_BUILD_HL_TOOLS "Build HIGH Level HDF5 Tools" ON +HDF5_BUILD_HL_GIF_TOOLS "Build HIGH Level HDF5 GIF Tools" OFF + +---------------- HDF5 Folder Build Options --------------------- +Defaults relative to $<INSTALL_PREFIX> +HDF5_INSTALL_BIN_DIR "bin" +HDF5_INSTALL_LIB_DIR "lib" +HDF5_INSTALL_INCLUDE_DIR "include" +HDF5_INSTALL_MODULE_DIR "mod" +HDF5_INSTALL_CMAKE_DIR "cmake" +if (MSVC) + HDF5_INSTALL_DATA_DIR "." +else () + HDF5_INSTALL_DATA_DIR "share" +HDF5_INSTALL_DOC_DIR "HDF5_INSTALL_DATA_DIR" + +Defaults as defined by the `GNU Coding Standards` +HDF5_INSTALL_BIN_DIR "bin" +HDF5_INSTALL_LIB_DIR "lib" +HDF5_INSTALL_INCLUDE_DIR "include" +HDF5_INSTALL_MODULE_DIR "HDF5_INSTALL_INCLUDE_DIR/mod" +HDF5_INSTALL_CMAKE_DIR "HDF5_INSTALL_LIB_DIR/cmake" +HDF5_INSTALL_DATA_DIR "share" +HDF5_INSTALL_DOC_DIR "HDF5_INSTALL_DATA_DIR/doc/hdf5" ---------------- HDF5 Advanced Options --------------------- +HDF5_USE_GNU_DIRS "TRUE to use GNU Coding Standard install directory variables, + FALSE to use historical settings" FALSE +ONLY_SHARED_LIBS "Only Build Shared Libraries" OFF +ALLOW_UNSUPPORTED "Allow unsupported combinations of configure options" OFF +HDF5_EXTERNAL_LIB_PREFIX "Use prefix for custom library naming." "" HDF5_DISABLE_COMPILER_WARNINGS "Disable compiler warnings" OFF -HDF5_Enable_Clear_File_Buffers "Securely clear file buffers before writing to file" ON -HDF5_Enable_Instrument "Instrument The library" OFF +HDF5_ENABLE_ALL_WARNINGS "Enable all warnings" OFF HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." OFF HDF5_ENABLE_COVERAGE "Enable code coverage for Libraries and Programs" OFF +HDF5_ENABLE_DEBUG_APIS "Turn on extra debug output in all packages" OFF HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols" ON +HDF5_ENABLE_DIRECT_VFD "Build the Direct I/O Virtual File Driver" OFF HDF5_ENABLE_EMBEDDED_LIBINFO "embed library info into executables" ON -HDF5_ENABLE_HSIZET "Enable datasets larger than memory" ON -HDF5_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON HDF5_ENABLE_PARALLEL "Enable parallel build (requires MPI)" OFF +HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON HDF5_ENABLE_TRACE "Enable API tracing capability" OFF HDF5_ENABLE_USING_MEMCHECKER "Indicate that a memory checker is used" OFF -HDF5_METADATA_TRACE_FILE "Enable metadata trace file collection" OFF +HDF5_GENERATE_HEADERS "Rebuild Generated Files" ON +HDF5_BUILD_GENERATORS "Build Test Generators" OFF +HDF5_JAVA_PACK_JRE "Package a JRE installer directory" OFF HDF5_NO_PACKAGES "Do not include CPack Packaging" OFF +HDF5_PACK_EXAMPLES "Package the HDF5 Library Examples Compressed File" OFF +HDF5_PACK_MACOSX_FRAMEWORK "Package the HDF5 Library in a Frameworks" OFF +HDF5_BUILD_FRAMEWORKS "TRUE to build as frameworks libraries, + FALSE to build according to BUILD_SHARED_LIBS" FALSE HDF5_PACKAGE_EXTLIBS "CPACK - include external libraries" OFF HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks" OFF +HDF_TEST_EXPRESS "Control testing framework (0-3)" "3" HDF5_TEST_VFD "Execute tests with different VFDs" OFF -HDF5_USE_16_API_DEFAULT "Use the HDF5 1.6.x API by default" OFF -HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." OFF +HDF5_TEST_PASSTHROUGH_VOL "Execute tests with different passthrough VOL connectors" OFF +DEFAULT_API_VERSION "Enable default API (v16, v18, v110, v112, v114)" "v114" +HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." ON HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON HDF5_ENABLE_THREADSAFE "Enable Threadsafety" OFF -if (APPLE) +HDF5_MSVC_NAMING_CONVENTION "Use MSVC Naming conventions for Shared Libraries" OFF +HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF +if (APPLE) HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path" OFF -if (CMAKE_BUILD_TYPE MATCHES Debug) - HDF5_ENABLE_TRACE "Enable API tracing capability" ON -if (HDF5_TEST_VFD) +if (CMAKE_BUILD_TYPE MATCHES Debug) + HDF5_ENABLE_INSTRUMENT "Instrument The library" OFF +if (HDF5_TEST_VFD) HDF5_TEST_FHEAP_VFD "Execute fheap test with different VFDs" ON +if (HDF5_BUILD_FORTRAN) + HDF5_INSTALL_MOD_FORTRAN "Copy FORTRAN mod files to include directory (NO SHARED STATIC)" "XX" + if (BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED + if (BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED + if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is STATIC + if (NOT BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED +HDF5_BUILD_DOC "Build documentation" OFF +HDF5_ENABLE_ANALYZER_TOOLS "enable the use of Clang tools" OFF +HDF5_ENABLE_SANITIZERS "execute the Clang sanitizer" OFF +HDF5_ENABLE_FORMATTERS "format source files" OFF +TEST_SHELL_SCRIPTS "Enable shell script tests" ON ---------------- External Library Options --------------------- -HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building" "NO" -HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF -HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" OFF -ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 0 -SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 0 -HDF5_USE_FILTER_FLETCHER32 "Use the FLETCHER32 Filter" ON -HDF5_USE_FILTER_NBIT "Use the NBIT Filter" ON -HDF5_USE_FILTER_SCALEOFFSET "Use the SCALEOFFSET Filter" ON -HDF5_USE_FILTER_SHUFFLE "Use the SHUFFLE Filter" ON -if (HDF5_ENABLE_SZIP_SUPPORT) - HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" OFF +HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO" +HDF5_ENABLE_PLUGIN_SUPPORT "Enable PLUGIN Filters" OFF +HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF +HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" OFF +PLUGIN_USE_EXTERNAL "Use External Library Building for PLUGINS" 0 +ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 0 +SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 0 +if (HDF5_ENABLE_SZIP_SUPPORT) + HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" OFF + USE_LIBAEC "Use libaec szip replacement" OFF if (WINDOWS) H5_DEFAULT_PLUGINDIR "%ALLUSERSPROFILE%/hdf5/lib/plugin" -else (WINDOWS) +else () H5_DEFAULT_PLUGINDIR "/usr/local/hdf5/lib/plugin" -endif (WINDOWS) +endif () + +NOTE: + The BUILD_STATIC_EXECS ("Build Static Executables") option is only valid + on some unix operating systems. It adds the "-static" flag to cflags. This + flag is not available on windows and some modern linux systems will + ignore the flag. + +NOTE: + The HDF5_USE_GNU_DIRS option is usually recommended for linux platforms, but may + be useful on other platforms. See the CMake documentation for more details. + ---------------- Unsupported Library Options --------------------- + The threadsafe, C++ and Java interfaces are not compatible + with the HDF5_ENABLE_PARALLEL option. + Unless ALLOW_UNSUPPORTED has been specified, + the following options must be disabled: + HDF5_ENABLE_THREADSAFE, HDF5_BUILD_CPP_LIB, HDF5_BUILD_JAVA + + The high-level, C++, Fortran and Java interfaces are not compatible + with the HDF5_ENABLE_THREADSAFE option because the lock is not hoisted + into the higher-level API calls. + Unless ALLOW_UNSUPPORTED has been specified, + the following options must be disabled: + HDF5_BUILD_HL_LIB, HDF5_BUILD_CPP_LIB, HDF5_BUILD_FORTRAN, HDF5_BUILD_JAVA ======================================================================== @@ -611,134 +870,34 @@ VII. User Defined Options for HDF5 Libraries with CMake Support for User Defined macros and options has been added. The file UserMacros.cmake has an example of the technique. In the folder, config/cmake/UserMacros, is an implementation for Windows Visual Studio -users for linking libraries to the static CRT - Windows_MT.cmake. +users for linking libraries to the static CRT - Windows_MT.cmake. -Copy the contents of the file, both macro and option, into the +Copy the contents of the file, both macro and option, into the UserMacros.cmake file. Then enable the option to the CMake configuration, build and test process. + ======================================================================== -VIII. Options for Platform Configuration Files +VIII. User Defined Compile Flags for HDF5 Libraries with CMake ======================================================================== -Below is the HDF518LinuxCmake.cmake ctest script with extra comments. -The example is for a linux machine, but the same scripts can be used on -a Windows machine by adjusting the CTEST_CMAKE_GENERATOR option in the -platform configuration script. - - -############################################################################ -# Product specific script, HDF518LinuxCmake.cmake, that uses the -# CTestScript.cmake file. Usage: -# "ctest -S HDF518LinuxCmake.cmake -C Release -O hdf518shared.log" -############################################################################ -cmake_minimum_required(VERSION 3.1.0 FATAL_ERROR) - -# this is the location of the source hardcoded to hdf5-1.8.13 -set(CTEST_SOURCE_NAME hdf5-1.8.13) -# this is the location of the source with ctest parameter hdf5src -# "ctest -S HDF518LinuxCmake.cmake,hdf5src -C Release -O hdf518static.log" -#set(CTEST_SOURCE_NAME ${CTEST_SCRIPT_ARG}) - -# this is the location of the build directory -set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}/build) - -# this is the directory the script is executed from -set(CTEST_DASHBOARD_ROOT "${CTEST_SCRIPT_DIRECTORY}") - -# this is the full path of the source directory -set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_SOURCE_NAME}") - -# this is the full path of the build directory -set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_BINARY_NAME}") - - -################################################################### -### Following Line is one of [Release, RelWithDebInfo, Debug] ##### -set(CTEST_BUILD_CONFIGURATION "Release") -################################################################### - -################################################################### -######### Following describes compiler ############ -# this is for linux -set(CTEST_CMAKE_GENERATOR "Unix Makefiles") -# this is for windows 32 bit -#set(CTEST_CMAKE_GENERATOR "Visual Studio 11") -# this is for windows 64 bit -#set(CTEST_CMAKE_GENERATOR "Visual Studio 11 Win64") -# Visual Studio 2013 is 12, Visual Studio 2012 is 11, Visual Studio 2010 is 10 -################################################################### - -################################################################### -######### Following is for submission to CDash ############ -################################################################### -set(MODEL "Experimental") -######### Following describes computer ############ -## Set the following to unique id your computer ## -set(CTEST_SITE "LINUX.XXXX") -## following is optional to describe build ## -set(SITE_BUILDNAME_SUFFIX "SHARED") - -######### Following controls CDash submission ########## -#set(LOCAL_SUBMIT "TRUE") -######### Following controls test process ########## -#set(LOCAL_SKIP_TEST "TRUE") -#set(LOCAL_MEMCHECK_TEST "TRUE") -#set(LOCAL_COVERAGE_TEST "TRUE") -######### Following controls cpack command ########## -#set(LOCAL_NO_PACKAGE "TRUE") -######### Following controls source update ########## -#set(LOCAL_UPDATE "TRUE") -######### Following controls source repository ########## -#set(REPOSITORY_URL "http://svn.${hdfgroup_url}/hdf5/branches/hdf5_1_8") -#comment to use a uncompressed source folder -set(CTEST_USE_TAR_SOURCE "hdf5-1.8.13") -################################################################### - -################################################################### -#### Change default configuration of options in config/cmake/cacheinit.cmake file ### -#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") - -### uncomment/comment and change the following lines for configuration options - -### uncomment the following line to build static libraries -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF") - -#### ext libraries #### -### ext libs from tgz -set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}") -### ext libs from svn -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=SVN") -### ext libs on system -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include") -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include") - -#### fortran #### -### disable Fortran 2003 -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=OFF") -### disable Fortran -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") - -### Create install package with external libraries (szip, zlib) -set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON") - -### disable test program builds -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF") - -### disable packaging -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON") - -### disable building examples -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_EXAMPLES:BOOL=OFF") - -### disable building tests -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF") - -### change install prefix -#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=install") -################################################################### - -include(${CTEST_SCRIPT_DIRECTORY}/CTestScript.cmake) +Custom compiler flags can be added by defining the CMAKE_C_FLAGS and +CMAKE_CXX_FLAGS variables. +Using a cmake script: + set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O2") +Defined on the configure line: + cmake -G "Visual Studio 12 2013" -DCMAKE_C_FLAGS:STRING=-O2 .. + +Debug symbols are enabled with configuration selections Debug or RelWithDebInfo. +The difference between Debug and RelWithDebInfo configurations is that +RelWithDebInfo optimizes the code similar to Release. It produces fully optimized +code, but also creates the symbol table and the debug metadata to give the +debugger input to map the execution back to the original code. +RelwithDebInfo configuration should not affect the performance when the code +is run without a debugger attached. + +The HDF5_ENABLE_COVERAGE option will add "-g -O0 -fprofile-arcs -ftest-coverage" +to CMAKE_C_FLAGS. ======================================================================== diff --git a/release_docs/INSTALL_Cygwin.txt b/release_docs/INSTALL_Cygwin.txt index 2b72cac..34d3e5a 100644 --- a/release_docs/INSTALL_Cygwin.txt +++ b/release_docs/INSTALL_Cygwin.txt @@ -2,8 +2,8 @@ HDF5 Build and Install Instructions for Cygwin ************************************************************************ -This document is a instruction on how to build, test and install HDF5 libary on -Cygwin. See detailed information in hdf5/INSTALL. +This document is a instruction on how to build, test and install HDF5 library on +Cygwin. See detailed information in hdf5/INSTALL. NOTE: hdf5 can be built with CMake, see the INSTALL_CMake.txt file for more guidance. @@ -12,16 +12,16 @@ Preconditions: 1. Installed Cygwin 1.7.25 or higher - To install the Cygwin net release, go to http://www.cygwin.com and + To install the Cygwin net release, go to http://www.cygwin.com and click on "setup-x86.exe" (32-bit installation) under the heading - "Current Cygwin DLL version". This will download a GUI - installer called setup-x86.exe which can be run to download a complete - Cygwin installation via the internet. Then follow the instructions + "Current Cygwin DLL version". This will download a GUI + installer called setup-x86.exe which can be run to download a complete + Cygwin installation via the internet. Then follow the instructions on each screen to install Cygwin. - Cygwin uses packages to manage installing various software. Users can + Cygwin uses packages to manage installing various software. Users can choose to install or uninstall certain packages by running setup.exe. - http://www.cygwin.com/packages/ provides detailed information about + http://www.cygwin.com/packages/ provides detailed information about Cygwin packages. Most required dependencies can be satisfied by installing all packages in @@ -31,32 +31,32 @@ Preconditions: 2. Compilers, Libraries and Utilities Installed 2.1 Compilers Supported - + The following compilers are supported by HDF5 and included in the Cygwin package system: - gcc (4.7.3), which includes: + gcc (4.7.3 and 4.9.2), which includes: gcc4-core : C compiler gcc4-g++ : C++ compiler gcc4-fortran : fortran compiler - + 2.1.1 Using Compilers Not Supported - + By default the current configuration uses vendor compilers; to use another compiler run the following commands before running - configure: - + configure: + setenv CC "foo -flags" setenv FC "fffoo -flags" - For example, if users want to use pgf90 as fortran compiler, then + For example, if users want to use pgf90 as fortran compiler, then setenv FC pgf90 See the configure help page (configure --help) for a list of environment variables that have an affect on building the library. - + 2.2 HDF5 External Library Dependencies 2.2.1 Zlib @@ -66,164 +66,162 @@ Preconditions: 2.2.2 Szip The HDF5 library has a predefined compression filter that uses the extended-Rice lossless compression algorithm for chunked - datatsets. For more information about Szip compression and - license terms see - http://hdfgroup.org/HDF5/doc_resource/SZIP/index.html. - - The latest supported public release of SZIP is available from - ftp://ftp.hdfgroup.org/lib-external/szip/2.1. - - + datasets. For more information on Szip compression, license terms, + and obtaining the Szip source code, see: + + https://portal.hdfgroup.org/display/HDF5/Szip+Compression+in+HDF+Products + + 2.3 Additional Utilities - + The following standard utilities are also required to build and test HDF5: - + bison : yacc implementation flex : flex utility make : make utility - + 2.4 Alternate Build Process - - Download the CMake package and follow the notes in the "INSTALL_CMake.txt" + + Download the CMake package and follow the notes in the "INSTALL_CMake.txt" file to build HDF5 with the CMake utilities. - - - + + + Build, Test and Install HDF5 on Cygwin -------------------------------------- 1. Get HDF5 source code package Users can download HDF5 source code package from HDF website - (http://hdfgroup.org). - + (http://hdfgroup.org). + 2. Unpacking the distribution The HDF5 source code is distributed in a variety of formats which - can be unpacked with the following commands, each of which creates - an `hdf5-1.8.x' directory. + can be unpacked with the following commands, each of which creates + an `hdf5-1.13.x' directory. 2.1 Non-compressed tar archive (*.tar) - $ tar xf hdf5-1.8.x.tar + $ tar xf hdf5-1.13.x.tar 2.2 Gzip'd tar archive (*.tar.gz) - $ gunzip < hdf5-1.8.x.tar.gz | tar xf - + $ gunzip < hdf5-1.13.x.tar.gz | tar xf - 2.3 Bzip'd tar archive (*.tar.bz2) - $ bunzip2 < hdf5-1.8.x.tar.bz2 | tar xf - + $ bunzip2 < hdf5-1.13.x.tar.bz2 | tar xf - 2. Setup Environment In Cygwin, most compilers and setting are automatically detected during - the configure script. However, if you are building Fortran we recommend - that you explicitly set the "FC" variable in your environment to use the + the configure script. However, if you are building Fortran we recommend + that you explicitly set the "FC" variable in your environment to use the gfortran compiler. For example, issue the command: - + $ export FC=gfortran - -4. Configuring - - Notes: See detailed information in hdf5/release_docs/INSTALL, - part 5. Full installation instructions for source + +4. Configuring + + Notes: See detailed information in hdf5/release_docs/INSTALL, + part 5. Full installation instructions for source distributions - The host configuration file for cygwin i686-pc-cygwin is located - in the `config' directory and are based on architecture name, - vendor name, and operating system which are displayed near the + The host configuration file for cygwin i686-pc-cygwin is located + in the `config' directory and are based on architecture name, + vendor name, and operating system which are displayed near the beginning of the `configure' output. The host config file influences - the behavior of configure by setting or augmenting shell variables. - + the behavior of configure by setting or augmenting shell variables. + In short, - - To configure HDF5 C Library, using - + + To configure HDF5 C Library, using + $ ./configure - + To configure HDF5 C/C++ Library, using $ ./configure --enable-cxx - + To configure HDF5 C/Fortran Library, using $ ./configure --enable-fortran - + To configure HDF5 C with Szip library, using $ ./configure --with-szlib="path to szlib" - - For example, if szip library was installed in the directory + + For example, if szip library was installed in the directory /cygdrive/c/szip, which is parent directory of "include" and - "lib", then the following command will configure HDF5 C library + "lib", then the following command will configure HDF5 C library with szip enabled: - + $ ./configure --with-szlib=/cygdrive/c/szip - + To configure HDF5 C without Zlib, - + To disable zlib, using $ ./configure --without-zlib - + Two ways to configure HDF5 C with specified Zlib - + Using $ ./configure --with-zlib=INCDIR,LIBDIR For example, if the zlib library is installed in /cygdrive/c/usr, which is the parent directory of directories - "include" and "lib", + "include" and "lib", $ ./configure --with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib Through the CPPFLAGS and LDFLAGS Variables - - For example, if zlib was installed in the directory - /cygdrive/c/usr then using the following command to configure + + For example, if zlib was installed in the directory + /cygdrive/c/usr then using the following command to configure HDF5 with zib $ CPPFLAGS=-I/cygdrive/c/usr/include \ $ LDFLAGS=-L/cygdrive/c/usr/lib \ $ ./configure - To specify the installation directories, using + To specify the installation directories, using $ ./configure --prefix="path for installation" - - By default, HDF5 library, header files, examples, and + + By default, HDF5 library, header files, examples, and support programs will be installed in /usr/local/lib, /usr/local/include, /usr/local/doc/hdf5/examples, and - /usr/local/bin. To use a path other than /usr/local specify + /usr/local/bin. To use a path other than /usr/local specify the path with the `--prefix=PATH' switch as in the above command. - Combination of Switches + Combination of Switches - All of the above switches can be combined together. For - example, if users want to configure HDF5 C/C++/Fortran - library with szip library enabled, with zlib library at - /cygdrive/c/usr/, and install HDF5 into directory + All of the above switches can be combined together. For + example, if users want to configure HDF5 C/C++/Fortran + library with szip library enabled, with zlib library at + /cygdrive/c/usr/, and install HDF5 into directory /cygdrive/c/hdf5 using gcc/g++ as C/C++ compiler and gfortran as fortran compiler - + $ ./configure --with-szlib=/cygdrive/c/szip --with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib --prefix=/cygdrive/c/hdf5 --enable-cxx - --enable-fortran + --enable-fortran <"If no more switches, then hit Enter"> Notes: The command format above is for readilibity. In practice, please type in the command above with at least one - space between each line, No "Enter" until users finish - the switches and want to run the configure. + space between each line, No "Enter" until users finish + the switches and want to run the configure. + - or do it through CPPFLAGS and LDFLAGS variables: - + $ CPPFLAGS=-I/cygdrive/c/usr/include \ $ LDFLAGS=-L/cygdrive/c/usr/lib \ @@ -231,35 +229,41 @@ Build, Test and Install HDF5 on Cygwin --with-szlib=/cygdrive/c/szip --prefix=/cygdrive/c/hdf5 --enable-cxx - --enable-fortran + --enable-fortran <"If no more switches, then hit Enter"> - + 5. Make and Make Check After configuration is done successfully, run the following series of commands to build, test and install HDF5 - + $ make > "output file name" $ make check > "output file name" - + Before run "make install", check output file for "make check", there should be no failures at all. 6. Make Install $ make install > "output file name" - - + + 7. Check installed HDF5 library - After step 6, go to your installation directory, there should be + After step 6, go to your installation directory, there should be three subdirectories: "bin" "include" and "lib". -8. Known Problems - +8. Known Problems + dt_arith tests may fail due to the use of fork. This is a known issue with cygwin on Windows. + "make check" fails when building shared lib files is enabled. The default + on Cygwin has been changed to disable shared. It can be enabled with + the --enable-shared configure option but is likely to fail "make check" + with GCC compilers. + ----------------------------------------------------------------------- -Need Further assistance, email help@hdfgroup.org + HDF Forum: https://forum.hdfgroup.org/ + HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk diff --git a/release_docs/INSTALL_VMS.txt b/release_docs/INSTALL_VMS.txt deleted file mode 100644 index c2a1463..0000000 --- a/release_docs/INSTALL_VMS.txt +++ /dev/null @@ -1,77 +0,0 @@ - Building and installation instructions for Alpha Open VMS - HDF5 1.8.6 release - 18 February 2011 - - - - CONTENTS - -------- - - 1. Obtaining HDF5 - 2. Building and testing HDF5 C, Fortran and C++ libraries, - and utilities - 3. Installing HDF5 libraries - 4. Known problems - - - 1.Obtaining HDF5 - - Please see INSTALL file in this directory for downloading instructions. - - 2. Building and testing HDF5 C, Fortran and C++ libraries and utilities. - - IMPORTANT: This version REQUIRES GNU ZLIB library to be installed - on a system. You may download the source code from - http://www.zlib.net/ - - - Use tar command to untar HDF5 source ball - - tar -xvf <source>.tar - - - Change default directory to [.<source>.vms] - - Specify top HDF5 source directory in the build.com file - - Edit make.com: - specify path to ZLIB library - if necessary, modify compilation flags - Do NOT REMOVE /define=H5_VMS and /standard=strict_ansi qualifiers. - - Run build.com command file - @build - We recommend using batch queue to build and test this distribution. - The command file runs make.com and builds - C library, tests, and utilities - Fortran library and tests - C++ library and tests - It also runs test scripts to test C, Fortran and C++ libraries, and - h5dump, h5diff, h5ls, h5repack and h5import utilities. - - 3. Installing HDF5 libraries - - Modify install.com file to specify installation directory and run - @install - to install HDF5 C, Fortran, and C++ libraries, and utilities. - The script will create the directories shown below in the - installation directory: - - [.HDF5]... - [.HDF5.INCLUDE] - [.HDF5.LIB] - [.HDF5.BIN] - [.HDF5.EXAMPLES] - [.HDF5.EXAMPLES.C] - [.HDF5.EXAMPLES.F90] - [.HDF5.EXAMPLES.CXX] - - [.HDF5.EXAMPLES.*] directories contain make.com and check.com files - to build examples against the installed libraries and to verify - the installation. - - 3. Known problems - - - dsets test fails for test_scleoffset_double and - test_scleoffset_double_2 tests when G_FLOAT double is used - - There is no support for szip compression filter. - - Fortran multifile driver test fails; similar C test passes. - - - For help contact help@hdfgroup.org - diff --git a/release_docs/INSTALL_Warnings.txt b/release_docs/INSTALL_Warnings.txt new file mode 100644 index 0000000..97981be --- /dev/null +++ b/release_docs/INSTALL_Warnings.txt @@ -0,0 +1,469 @@ +*********************************************************************** +* COMPILER WARNINGS OPTIONS +*********************************************************************** + + Table of Contents + +Section I: Managing Warnings +Section II: Default Warnings +Section III: All Warnings +Section IV: Group 0 Warnings +Section V: Group 1 Warnings +Section VI: Group 2 Warnings +Section VII: Group 3 Warnings +Section VIII: Group 4 Warnings +Section IX: Disable Warnings + +************************************************************************ + + +======================================================================== +I. Managing Warnings +======================================================================== +Compiler warnings are managed by setting the compiler flags variables. + +Autotools uses the H5_CFLAGS and H5_CXXFLAGS, both variables set the flags nearly + identical, along with H5_FCFLAGS for Fortran. Autotools uses the type + and version of the compiler to determine which warning flags are used. + However, there is an option, enable-developer-warnings, to enable extra + flags for developers. + +CMake uses the CMAKE_C_FLAGS and CMAKE_CXX_FLAGS, both sets are nearly + identical, along with CMAKE_Fortran_FLAGS for Fortran. CMake has a + minimum set of flags for GNU type compilers and for MSVC compilers. In + addition, CMake breaks the list of flags into groups. The groups for + GNU are roughly associated with the version of the compiler, while + the MSVC groups are associated with the warning levels for the + Microsoft compilers. The CMake option for enabling extra developer + warnings is HDF5_ENABLE_DEV_WARNINGS. + +Custom settings can be used by setting; + Environment variables H5_CFLAGS and H5_CXXFLAGS for Autotools + CMake defines CMAKE_C_FLAGS and CMAKE_CXX_FLAGS for CMake + + +======================================================================== +II. Default Warnings +======================================================================== + +-------------------------------------------------- +Autotools UNIX warnings added to H5_CFLAGS +-------------------------------------------------- + -std=c99 + + the following warning switches should not raise warnings by the current code + -pedantic + -Wall + -Wextra + -Wbad-function-cast + -Wc++-compat + -Wcast-align + -Wcast-qual + -Wconversion + -Wdisabled-optimization + -Wfloat-equal + -Wformat=2 + -Winit-self + -Winvalid-pch + -Wmissing-declarations + -Wmissing-include-dirs + -Wmissing-prototypes + -Wnested-externs + -Wold-style-definition + -Wpacked + -Wpointer-arith + -Wredundant-decls + -Wshadow + -Wstrict-prototypes + -Wswitch-default + -Wswitch-enum + -Wundef + -Wunused-macros + -Wunsafe-loop-optimizations + -Wwrite-strings + + enable-developer-warnings=ON + -Winline + -Waggregate-return + -Wmissing-format-attribute + -Wmissing-noreturn + -Wunsuffixed-float-constants (gcc 4.5+) + enable-developer-warnings=OFF + -Wno-inline + -Wno-aggregate-return + -Wno-missing-format-attribute + -Wno-missing-noreturn + -Wno-unsuffixed-float-constants (gcc 4.5+) + +IF GCC <= 4.3 + -Wno-long-long + -Wvolatile-register-var + -Wstrict-overflow + +IF GCC <= 4.4 + -Wno-long-long + -Wvolatile-register-var + -Wstrict-overflow + -Wlogical-op + -Wvla + +IF GCC <= 4.5 + -Wno-long-long + -Wvolatile-register-var + -Wstrict-overflow + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + +IF GCC <= 4.6 + -Wno-long-long + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-aliasing + -Wstrict-overflow=5 + -Wjump-misses-init + +IF GCC <= 4.7 + -Wno-long-long + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-aliasing + -Wstrict-overflow=5 + -Wjump-misses-init + -Wdouble-promotion + -Wtrampolines + enable-developer-warnings=ON: + -Wsuggest-attribute=const + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + +IF GCC <= 4.8 + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-overflow=5 + -Wjump-misses-init + -Wdouble-promotion + -Wtrampolines + -Wstack-usage=8192 + -Wvector-operation-performance + enable-developer-warnings=ON: + -Wsuggest-attribute=const + -Wsuggest-attribute=pure + -Wsuggest-attribute=noreturn + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + -Wno-suggest-attribute=pure + -Wno-suggest-attribute=noreturn + +IF GCC <= 4.9 + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-overflow=5 + -Wjump-misses-init + -Wdouble-promotion + -Wtrampolines + -Wstack-usage=8192 + -Wvector-operation-performance + enable-developer-warnings=ON: + -Wsuggest-attribute=const + -Wsuggest-attribute=pure + -Wsuggest-attribute=noreturn + -Wsuggest-attribute=format + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + -Wno-suggest-attribute=pure + -Wno-suggest-attribute=noreturn + -Wno-suggest-attribute=format + +IF GCC < 5 + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-overflow=5 + -Wjump-misses-init + -Wdouble-promotion + -Wtrampolines + -Wstack-usage=8192 + -Wvector-operation-performance + -Wdate-time + enable-developer-warnings=ON: + -Wsuggest-attribute=const + -Wsuggest-attribute=pure + -Wsuggest-attribute=noreturn + -Wsuggest-attribute=format + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + -Wno-suggest-attribute=pure + -Wno-suggest-attribute=noreturn + -Wno-suggest-attribute=format + +IF GCC < 6 + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-overflow=5 + -Wjump-misses-init + -Wdouble-promotion + -Wtrampolines + -Wstack-usage=8192 + -Wvector-operation-performance + -Wdate-time + -Warray-bounds=2 + -Wc99-c11-compat + enable-developer-warnings=ON: + -Wsuggest-attribute=const + -Wsuggest-attribute=pure + -Wsuggest-attribute=noreturn + -Wsuggest-attribute=format + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + -Wno-suggest-attribute=pure + -Wno-suggest-attribute=noreturn + -Wno-suggest-attribute=format + +IF GCC < 7 + -Wlogical-op + -Wvla + -Wlarger-than=2048 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + -Wstrict-overflow=5 + -Wjump-misses-init + -Wdouble-promotion + -Wtrampolines + -Wstack-usage=8192 + -Wvector-operation-performance + -Wdate-time + -Warray-bounds=2 + -Wc99-c11-compat + -Wnull-dereference + -Wunused-const-variable + -Wduplicated-cond -Whsa + enable-developer-warnings=ON: + -Wsuggest-attribute=const + -Wsuggest-attribute=pure + -Wsuggest-attribute=noreturn + -Wsuggest-attribute=format + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + -Wno-suggest-attribute=pure + -Wno-suggest-attribute=noreturn + -Wno-suggest-attribute=format + + +-------------------------------------------- +CMake warnings added to CMAKE_C_FLAGS +-------------------------------------------- + +IF GNU GCC + -pedantic + -Wall + -Wextra + -Wbad-function-cast + -Wc++-compat + -Wcast-align + -Wcast-qual + -Wconversion + -Wdisabled-optimization + -Wfloat-equal + -Wformat=2 + -Winit-self + -Winvalid-pch + -Wmissing-declarations + -Wmissing-include-dirs + -Wmissing-prototypes + -Wnested-externs + -Wold-style-definition + -Wpacked + -Wpointer-arith + -Wredundant-decls + -Wshadow + -Wstrict-prototypes + -Wswitch-default + -Wswitch-enum + -Wundef + -Wunused-macros + -Wunsafe-loop-optimizations + -Wwrite-strings + + -fmessage-length=0 + HDF5_ENABLE_DEV_WARNINGS=ON + -Winline + -Waggregate-return + -Wunsuffixed-float-constants (gcc 4.5+) + HDF5_ENABLE_DEV_WARNINGS=OFF + -Wno-unused-parameter + -Wno-inline + -Wno-aggregate-return + -Wno-unsuffixed-float-constants (gcc 4.5+) + + +======================================================================== +III. All Warnings in CMake +======================================================================== + +Default: HDF5_ENABLE_DEV_WARNINGS:BOOL=OFF + For Visual Studio: + /W3 + +HDF5_ENABLE_ALL_WARNINGS:BOOL=ON + For Visual Studio: + /Wall + /wd4668 + + For GNU GCC + Group 0 flags + Group 1 flags + Group 2 flags + + +======================================================================== +IV. Group 0 Warnings in CMake +======================================================================== + +Default: HDF5_ENABLE_GROUPZERO_WARNINGS:BOOL=OFF + +HDF5_ENABLE_GROUPZERO_WARNINGS:BOOL=ON + For Visual Studio + /W1 + + For GNU GCC + Default Warnings + + +======================================================================== +V. Group 1 Warnings in CMake +======================================================================== + +Default: HDF5_ENABLE_GROUPONE_WARNINGS:BOOL=OFF + +HDF5_ENABLE_GROUPONE_WARNINGS:BOOL=ON + For Visual Studio + /W2 + + For GNU GCC + IF GCC >= 4.3 + -Wlogical-op + -Wvla + -Wlarger-than=2048 + IF GCC >= 4.4 + -Wsync-nand + -Wframe-larger-than=16384 + -Wpacked-bitfield-compat + IF GCC >= 4.5 + -Wstrict-overflow=5 + -Wjump-misses-init + + +======================================================================== +VI. Group 2 Warnings in CMake +======================================================================== + +Default: HDF5_ENABLE_GROUPTWO_WARNINGS:BOOL=OFF + +HDF5_ENABLE_GROUPTWO_WARNINGS:BOOL=ON + For Visual Studio + /W3 + + For GNU GCC + IF GCC >= 4.6 + -Wdouble-promotion + -Wtrampolines + enable-developer-warnings=ON: + -Wsuggest-attribute=const + enable-developer-warnings=OFF: + -Wno-suggest-attribute=const + IF GCC >= 4.7 + -Wstack-usage=8192 + -Wvector-operation-performance + enable-developer-warnings=ON: + -Wsuggest-attribute=pure + -Wsuggest-attribute=noreturn + enable-developer-warnings=OFF: + -Wno-suggest-attribute=pure + -Wno-suggest-attribute=noreturn + IF GCC >= 4.8 + enable-developer-warnings=ON: + -Wsuggest-attribute=format + enable-developer-warnings=OFF: + -Wno-suggest-attribute=format + IF GCC >= 4.8 + -Wdate-time + + +======================================================================== +VII. Group 3 Warnings in CMake +======================================================================== + +Default: HDF5_ENABLE_GROUPTHREE_WARNINGS:BOOL=OFF + +HDF5_ENABLE_GROUPTHREE_WARNINGS:BOOL=ON + For Visual Studio + /W4 + + For GNU GCC + IF GCC >= 5.1 + -Warray-bounds=2 + -Wc99-c11-compat + + +======================================================================== +VIII. Group 4 Warnings in CMake +======================================================================== + +Default: HDF5_ENABLE_GROUPFOUR_WARNINGS:BOOL=OFF + +HDF5_ENABLE_GROUPFOUR_WARNINGS:BOOL=ON + For GNU GCC + IF GCC >= 6.0 + -Wnull-dereference + -Wunused-const-variable + -Wduplicated-cond + -Whsa + + +======================================================================== +IX. Disable Warnings in CMake +======================================================================== + +Default: HDF5_DISABLE_COMPILER_WARNINGS:BOOL=OFF + +HDF5_DISABLE_COMPILER_WARNINGS:BOOL=ON + For Visual Studio + HDF5_WARNINGS_BLOCKED:BOOL=ON + /W0 + + For GNU GCC + -w + + +======================================================================== +For further assistance, send email to help@hdfgroup.org +======================================================================== + diff --git a/release_docs/INSTALL_Windows.txt b/release_docs/INSTALL_Windows.txt index 7873709..7af2571 100644 --- a/release_docs/INSTALL_Windows.txt +++ b/release_docs/INSTALL_Windows.txt @@ -9,8 +9,10 @@ We now recommend that users build, test and install HDF5 using CMake. Instructions for building and testing HDF5 using CMake can be found in the INSTALL_CMake.txt file found in this folder. -For instructions of building and testing an application with HDF5, see +For instructions of building and testing an application with HDF5, see USING_HDF5_CMake.txt file found in this folder. Users who want to build and run an application with HDF5 in Visual Studio -without using CMake should consult the USING_HDF5_VS.txt file. +without using CMake should consult the USING_HDF5_VS.txt file. Building +applications with the dynamic/shared hdf5 libraries requires that the +"H5_BUILT_AS_DYNAMIC_LIB" compile definition be used. diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index 2624b3b..d3d7830 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -1,6 +1,18 @@ Installation instructions for Parallel HDF5 ------------------------------------------- +0. Use Build Scripts +-------------------- +The HDF Group is accumulating build scripts to handle building parallel HDF5 +on various platforms (Cray, IBM, SGI, etc...). These scripts are being +maintained and updated continuously for current and future systems. The reader +is strongly encouraged to consult the repository at, + +https://github.com/HDFGroup/build_hdf5 + +for building parallel HDF5 on these system. All contributions, additions +and fixes to the repository are welcomed and encouraged. + 1. Overview ----------- @@ -28,9 +40,11 @@ and the parallel file system. 1.2. Further Help ----------------- -If you still have difficulties installing PHDF5 in your system, please send -mail to - help@hdfgroup.org + +For help with installing, questions can be posted to the HDF Forum or sent to the HDF Helpdesk: + + HDF Forum: https://forum.hdfgroup.org/ + HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk In your mail, please include the output of "uname -a". If you have run the "configure" command, attach the output of the command and the content of @@ -49,54 +63,15 @@ more detailed explanations. ---------------------------- HDF5 knows several parallel compilers: mpicc, hcc, mpcc, mpcc_r. To build parallel HDF5 with one of the above, just set CC as it and configure. -The "--enable-parallel" is optional in this case. - - $ CC=/usr/local/mpi/bin/mpicc ./configure --prefix=<install-directory> - $ make # build the library - $ make check # verify the correctness - # Read the Details section about parallel tests. - $ make install - -2.2. IBM SP ------------ -During the build stage, the H5detect is compiled and executed to generate -the source file H5Tinit.c which is compiled as part of the HDF5 library. In -parallel mode, make sure your environment variables are set correctly to -execute a single process mpi application. Otherwise, multiple processes -attempt to write to the same H5Tinit.c file, resulting in a scrambled -source file. Unfortunately, the setting varies from machine to machine. -E.g., the following works for the IBM SP machine at LLNL. - - setenv MP_PROCS 1 - setenv MP_NODES 1 - setenv MP_LABELIO no - setenv MP_RMPOOL 0 - setenv LLNL_COMPILE_SINGLE_THREADED TRUE # for LLNL site only - -The shared library configuration is problematic. So, only static library -is supported. - -Then do the following steps: - - $ ./configure --disable-shared --prefix=<install-directory> + $ CC=/usr/local/mpi/bin/mpicc ./configure --enable-parallel --prefix=<install-directory> $ make # build the library $ make check # verify the correctness # Read the Details section about parallel tests. $ make install -We also suggest that you add "-qxlf90=autodealloc" to FCFLAGS when building -parallel with fortran enabled. This can be done by invoking: - - setenv FCFLAGS -qxlf90=autodealloc # 32 bit build -or - setenv FCFLAGS "-q64 -qxlf90=autodealloc" # 64 bit build - -prior to running configure. Recall that the "-q64" is necessary for 64 -bit builds. - -2.3. Linux 2.4 and greater +2.2. Linux 2.4 and greater -------------------------- Be sure that your installation of MPICH was configured with the following configuration command-line option: @@ -107,99 +82,15 @@ This allows for >2GB sized files on Linux systems and is only available with Linux kernels 2.4 and greater. -2.4. Red Storm (Cray XT3) (for v1.8 and later) -------------------------- -Both serial and parallel HDF5 are supported in Red Storm. - -2.4.1 Building serial HDF5 for Red Storm ------------------------------------------- -The following steps are for building the serial HDF5 for the Red Storm -compute nodes. They would probably work for other Cray XT3 systems but have -not been verified. - -# Assume you already have a copy of HDF5 source code in directory `hdf5' and -# want to install the binary in directory `/project/hdf5/hdf5'. - -$ cd hdf5 -$ bin/yodconfigure configure -$ env RUNSERIAL="yod -sz 1" \ - CC=cc FC=ftn CXX=CC \ - ./configure --prefix=/project/hdf5/hdf5 -$ make -$ make check - -# if all is well, install the binary. -$ make install - -2.4.2 Building parallel HDF5 for Red Storm ------------------------------------------- -The following steps are for building the Parallel HDF5 for the Red Storm -compute nodes. They would probably work for other Cray XT3 systems but have -not been verified. - -# Assume you already have a copy of HDF5 source code in directory `hdf5' and -# want to install the binary in directory `/project/hdf5/phdf5'. You also -# have done the proper setup to have mpicc and mpif90 as the compiler commands. - -$ cd hdf5 -$ bin/yodconfigure configure -$ env RUNSERIAL="yod -sz 1" RUNPARALLEL="yod -sz 3" \ - CC=cc FC=ftn \ - ./configure --enable-parallel --prefix=/project/hdf5/phdf5 -$ make -$ make check - -# if all is well, install the binary. -$ make install - -2.4.3 Red Storm known problems ------------------------------- -For Red Storm, a Cray XT3 system, the yod command sometimes gives the -message, "yod allocation delayed for node recovery". This interferes with -test suites that do not expect seeing this message. To bypass this problem, -I launch the executables with a command shell script called "myyod" which -consists of the following lines. (You should set $RUNSERIAL and $RUNPARALLEL -to use myyod instead of yod.) -==== myyod ======= -#!/bin/sh -# sleep 2 seconds to allow time for the node recovery else it pops the -# message, -# yod allocation delayed for node recovery -sleep 2 -yod $* -==== end of myyod ======= - -For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on -the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is -expected to fail and exit with a non-zero code but the yod command does -not propagate the exit code of the executables. Yod always returns 0 if it -can launch the executable. The test suite shell expects a non-zero for -this particular test, therefore it concludes the test has failed when it -receives 0 from yod. To bypass this problem for now, change the following -lines in the tools/h5ls/testh5ls.sh. -======== Original ========= -# The following combination of arguments is expected to return an error message -# and return value 1 -TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 -======== Skip the test ========= -echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 -======== end of bypass ======== - -2.5. Hopper (Cray XE6) (for v1.8 and later) +2.3. Hopper (Cray XE6) (for v1.8 and later) ------------------------- -2.5.1 Building HDF5 for Hopper ------------------------------------------- The following steps are for building HDF5 for the Hopper compute nodes. They would probably work for other Cray systems but have not been verified. -Obtain a copy from the HDF ftp server: -http://www.hdfgroup.org/ftp/HDF5/current/src/ -(link might change, so always double check the HDF group website). - -$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-x.x.x.tar.gz -unpack the tarball +Obtain the HDF5 source code: + https://portal.hdfgroup.org/display/support/Downloads The entire build process should be done on a MOM node in an interactive allocation and on a file system accessible by all compute nodes. Request an interactive allocation with qsub: @@ -211,7 +102,7 @@ qsub -I -q debug -l mppwidth=8 - configure HDF5: RUNSERIAL="aprun -q -n 1" RUNPARALLEL="aprun -q -n 6" FC=ftn CC=cc /path/to/source/configure --enable-fortran --enable-parallel --disable-shared - RUNSERIAL and RUNPARALLEL tells the library how it should launch programs that are part of the build procedure. + RUNSERIAL and RUNPARALLEL tell the library how it should launch programs that are part of the build procedure. - Compile HDF5: gmake @@ -226,43 +117,6 @@ The build will be in build-hdf5/hdf5/ (or whatever you specify in --prefix). To compile other HDF5 applications use the wrappers created by the build (build-hdf5/hdf5/bin/h5pcc or h5fc) -2.5.2 Hopper known issues ------------------------------- -Issue 1: -Sometimes when building the library with make, you might get this problem: - -LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ -sed -e 's/-L/:/g' -e 's/ -//g'`" \ -./H5make_libsettings > H5lib_settings.c -|| \ -(test $HDF5_Make_Ignore && echo "*** Error ignored") -|| \ -(rm -f H5lib_settings.c ; exit 1) -/bin/sh: line 4: 9644 Segmentation fault -LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | sed -e 's/-L/:/g' -e 's/ -//g'`" ./H5make_libsettings > H5lib_settings.c - -If that happens, you are probable running with make -j <x>. In that -case, you need to cleanup everything and start again as detailed above -but use serial make (do not use -j <x>). - -Issue 2: -* When building using the Cray compilers on Cray machines, HDF5 - configure mistakenly thinks the compiler is an intel compiler and - sets the -std=c99 flag which breaks configure on Cray. To build HDF5 - properly on a Cray machine, please consult with the instructions in - INSTALL_parallel for building on Hopper. - (MSC - 2013/04/26 - HDFFV-8429) - -Issue 3: -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - 3. Detail explanation --------------------- @@ -293,28 +147,24 @@ a properly installed parallel compiler (e.g., MPICH's mpicc or IBM's mpcc_r) and supply the compiler name as the value of the CC environment variable. For examples, - $ CC=mpcc_r ./configure - $ CC=/usr/local/mpi/bin/mpicc ./configure - -If no such a compiler command is available then you must use your normal -C compiler along with the location(s) of MPI/MPI-IO files to be used. -For example, - - $ CPPFLAGS=-I/usr/local/mpi/include \ - LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ - ./configure --enable-parallel=mpich + $ CC=mpcc_r ./configure --enable-parallel + $ CC=/usr/local/mpi/bin/mpicc ./configure --enable-parallel If a parallel library is being built then configure attempts to determine how to run a parallel application on one processor and on many processors. If the compiler is `mpicc' and the user hasn't specified values for RUNSERIAL and RUNPARALLEL then configure chooses `mpiexec' from the same directory as `mpicc': - RUNSERIAL: /usr/local/mpi/bin/mpiexec -np 1 - RUNPARALLEL: /usr/local/mpi/bin/mpiexec -np $${NPROCS:=6} + RUNSERIAL: mpiexec -n 1 + RUNPARALLEL: mpiexec -n $${NPROCS:=6} The `$${NPROCS:=6}' will be substituted with the value of the NPROCS environment variable at the time `make check' is run (or the value 6). +Note that some MPI implementations (e.g. OpenMPI 4.0) disallow oversubscribing +nodes by default so you'll have to either set NPROCS equal to the number of +processors available (or fewer) or redefine RUNPARALLEL with appropriate +flag(s) (--oversubscribe in OpenMPI). 4. Parallel test suite ---------------------- diff --git a/release_docs/README_HDF5_CMake b/release_docs/README_HDF5_CMake new file mode 100644 index 0000000..8b30112 --- /dev/null +++ b/release_docs/README_HDF5_CMake @@ -0,0 +1,25 @@ +This tar file contains + + build-unix.sh script to build HDF5 with CMake on unix machines + build-unix-hpc.sh script to build HDF5 with CMake on unix machines and run + tests with batch scripts (sbatch). + CTestScript.cmake + HDF5config.cmake CMake scripts for building HDF5 + HDF5options.cmake + hdf5-1.13.2 HDF5 1.13.2 source + LIBAEC.tar.gz source for building SZIP replacement + ZLib.tar.gz source for building ZLIB + hdf5_plugins.tar.gz source for building compression plugins + HDF5Examples-2.0.1-Source.tar.gz source for building examples + +For more information about building HDF5 with CMake, see USING_HDF5_CMake.txt in +hdf5-1.13.2/release_docs, or +https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake. + +For more information about building HDF5 with CMake on HPC machines, including +cross compiling on Cray XC40, see README_HPC in hdf5-1.13.2/release_docs. + + + + + diff --git a/release_docs/README_HPC b/release_docs/README_HPC new file mode 100644 index 0000000..02034b4 --- /dev/null +++ b/release_docs/README_HPC @@ -0,0 +1,206 @@ +************************************************************************ +* Using CMake to build and test HDF5 source on HPC machines * +************************************************************************ + + Contents + +Section I: Prerequisites +Section II: Obtain HDF5 source +Section III: Using ctest command to build and test +Section IV: Cross compiling +Section V: Manual alternatives +Section VI: Other cross compiling options + +************************************************************************ + +======================================================================== +I. Prerequisites +======================================================================== + 1. Create a working directory that is accessible from the compute nodes for + running tests; the working directory should be in a scratch space or a + parallel file system space since testing will use this space. Building + from HDF5 source in a 'home' directory typically results in test + failures and should be avoided. + + 2. Load modules for desired compilers, module for cmake version 3.18 or greater, + and set any needed environment variables for compilers (i.e., CC, FC, CXX). + Unload any problematic modules (i.e., craype-hugepages2M). + +======================================================================== +II. Obtain HDF5 source +======================================================================== +Obtain HDF5 source code from the HDF5 repository using a git command or +from a release tar file in a working directory: + + git clone https://github.com/HDFGroup/hdf5.git + [-b branch] [source directory] + +If no branch is specified, then the 'develop' version will be checked out. +If no source directory is specified, then the source will be located in the +'hdf5' directory. The CMake scripts expect the source to be in a directory +named hdf5-<version string>, where 'version string' uses the format '1.xx.xx'. +For example, for the current 'develop' version, the "hdf5" directory should +be renamed "hdf5-1.13.0", or for the first hdf5_1_12_0 pre-release version, +it should be renamed "hdf5-1.12.0-5". + +If the version number is not known a priori, the version string +can be obtained by running bin/h5vers in the top level directory of the source clone, and +the source directory renamed 'hdf5-<version string>'. + +Release or snapshot tar files may also be extracted and used. + +======================================================================== +III. Using ctest command to build and test +======================================================================== + +The ctest command [1]: + + ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log + +will configure, build, test and package HDF5 from the downloaded source +after the setup steps outlined below are followed. + +CMake option variables are available to allow running test programs in batch +scripts on compute nodes and to cross-compile for compute node hardware using +a cross-compiling emulator. The setup steps will make default settings for +parallel or serial only builds available to the CMake command. + + 1. For the current 'develop' version the "hdf5" directory should be renamed + "hdf5-1.13.0". + + 2. Three cmake script files need to be copied to the working directory, or + have symbolic links to them, created in the working directory: + + hdf5-1.13.0/config/cmake/scripts/HDF5config.cmake + hdf5-1.13.0/config/cmake/scripts/CTestScript.cmake + hdf5-1.13.0/config/cmake/scripts/HDF5options.cmake + + should be copied to the working directory. + + 3. The resulting contents of the working directory are then: + + CTestScript.cmake + HDF5config.cmake + HDF5options.cmake + hdf5-1.13.0 + + Additionally, when the ctest command runs [1], it will add a build directory + in the working directory. + + 4. The following options (among others) can be added to the ctest + command [1], following '-S HDF5config.cmake,' and separated by ',': + + HPC=sbatch (or 'bsub' or 'raybsub') indicates which type of batch + files to use for running tests. If omitted, test + will run on the local machine or login node. + + KNL=true to cross-compile for KNL compute nodes on CrayXC40 + (see section IV) + + MPI=true enables parallel, disables c++, java, and threadsafe + + LOCAL_BATCH_SCRIPT_ARGS="--account=<account#>" to supply user account + information for batch jobs + + The HPC options will add BUILD_GENERATOR=Unix for the three HPC options. + An example ctest command for a parallel build on a system using sbatch is + + ctest -S HDF5config.cmake,HPC=sbatch,MPI=true -C Release -V -O hdf5.log + + Adding the option 'KNL=true' to the above list will compile for KNL nodes, + for example, on 'mutrino' and other CrayXC40 machines. + + Changing -V to -VV will produce more logging information in HDF5.log. + + More detailed CMake information can be found in the HDF5 source in + release_docs/INSTALL_CMake.txt. + +======================================================================== +IV. Cross-compiling +======================================================================== +For cross-compiling on Cray, set environment variables CC=cc, FC=ftn +and CXX=CC (for c++) after all compiler modules are loaded since switching +compiler modules may unset or reset these variables. + +CMake provides options for cross-compiling. To cross-compile for KNL hardware +on mutrino and other CrayXC40 machines, add HPC=sbatch,KNL=true to the +ctest command line. This will set the following options from the +config/cmake/scripts/HPC/sbatch-HDF5options.cmake file: + + set (COMPILENODE_HWCOMPILE_MODULE "craype-haswell") + set (COMPUTENODE_HWCOMPILE_MODULE "craype-mic-knl") + set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl") + set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl") + set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake") + +On the Cray XC40 the craype-haswell module is needed for configuring, and the +craype-mic-knl module is needed for building to run on the KNL nodes. CMake +with the above options will swap modules after configuring is complete, +but before compiling programs for KNL. + +The sbatch script arguments for running jobs on KNL nodes may differ on CrayXC40 +machines other than mutrino. The batch scripts knl_ctestS.sl and knl_ctestP.sl +have the correct arguments for mutrino: "#SBATCH -p knl -C quad,cache". For +cori, another CrayXC40, that line is replaced by "#SBATCH -C knl,quad,cache". +For cori (and other machines), the values in LOCAL_BATCH_SCRIPT_NAME and +LOCAL_BATCH_SCRIPT_PARALLEL_NAME in the config/cmake/scripts/HPC/sbatch-HDF5options.cmake +file can be replaced by cori_knl_ctestS.sl and cori_knl_ctestS.sl, or the lines +can be edited in the batch files in hdf5-1.13.0/bin/batch. + +======================================================================== +V. Manual alternatives +======================================================================== +If using ctest is undesirable, one can create a build directory and run the cmake +configure command, for example + +"/projects/Mutrino/hpcsoft/cle6.0/common/cmake/3.18/bin/cmake" +-C "<working directory>/hdf5-1.13.3/config/cmake/cacheinit.cmake" +-DCMAKE_BUILD_TYPE:STRING=Release -DHDF5_BUILD_FORTRAN:BOOL=ON +-DHDF5_BUILD_JAVA:BOOL=OFF +-DCMAKE_INSTALL_PREFIX:PATH=<working directory>/HDF_Group/HDF5/1.13.3 +-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF +-DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_BUILD_CPP_LIB:BOOL=OFF +-DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_ENABLE_THREADSAFE:BOOL=OFF +-DHDF5_PACKAGE_EXTLIBS:BOOL=ON -DLOCAL_BATCH_TEST:BOOL=ON +-DMPIEXEC_EXECUTABLE:STRING=srun -DMPIEXEC_NUMPROC_FLAG:STRING=-n +-DMPIEXEC_MAX_NUMPROCS:STRING=6 +-DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake +-DLOCAL_BATCH_SCRIPT_NAME:STRING=knl_ctestS.sl +-DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=knl_ctestP.sl -DSITE:STRING=mutrino +-DBUILDNAME:STRING=par-knl_GCC493-SHARED-Linux-4.4.156-94.61.1.16335.0.PTF.1107299-default-x86_64 +"-GUnix Makefiles" "" "<working directory>/hdf5-1.13.3" + +followed by make and batch jobs to run tests. + +To cross-compile on CrayXC40, run the configure command with the craype-haswell +module loaded, then switch to the craype-mic-knl module for the build process. + +Tests on machines using slurm can be run with + +"sbatch -p knl -C quad,cache ctestS.sl" + +or + +"sbatch -p knl -C quad,cache ctestP.sl" + +for parallel builds. + +Tests on machines using LSF will typically use "bsub ctestS.lsf", etc. + +======================================================================== +VI. Other cross compiling options +======================================================================== +Settings for two other cross-compiling options are also in the config/toolchain +files which do not seem to be necessary with the Cray PrgEnv-* modules + +1. HDF5_USE_PREGEN. This option, along with the HDF5_USE_PREGEN_DIR CMake + variable would allow the use of an appropriate H5Tinit.c file with type + information generated on a compute node to be used when cross compiling + for those compute nodes. The use of the variables in lines 110 and 111 + of HDF5options.cmake file seem to preclude needing this option with the + available Cray modules and CMake option. + +2. HDF5_BATCH_H5DETECT and associated CMake variables. This option when + properly configured will run H5detect in a batch job on a compute node + at the beginning of the CMake build process. It was also found to be + unnecessary with the available Cray modules and CMake options. diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 17f9ac1..baf85fb 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,39 +1,45 @@ -HDF5 version 1.9.216 currently under development +HDF5 version 1.15.0 currently under development ================================================================================ INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: -This document describes the differences between HDF5-1.9.0 and -HDF5 1.9.x snapshot, and contains information on the platforms -tested and known problems in HDF5-1.9.x. -For more details check the HISTORY*.txt files in the HDF5 source. + https://portal.hdfgroup.org/display/HDF5/HDF5 +The official HDF5 releases can be obtained from: -Links to HDF5 1.9.x source code can be found on The HDF Group's -development FTP server at the following location: - ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots -User documentation for the snapshot can be accessed directly at this location: - http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/ + https://www.hdfgroup.org/downloads/hdf5/ -For more information, see the HDF5 home page: - - http://www.hdfgroup.org/HDF5/ +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information If you have any questions or comments, please send them to the HDF Help Desk: - help@hdfgroup.org + help@hdfgroup.org CONTENTS +======== - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.8.0 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms +- Bug Fixes since HDF5-1.13.3 +- Platforms Tested - Known Problems +- CMake vs. Autotools installations New Features @@ -41,1586 +47,597 @@ New Features Configuration: ------------- - - cmakehdf5: configure options added to enable or disable the building of - different API's and testings. See "cmakehdf5 --help" for details. - (AKC - 2014/12/09 HDFFV-8932) - - Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08) - - CMake: Moved minimum CMake version to 2.8.11 which enables better library - include processing. (ADB - 2014/03/26) - - New configuration option added to change the default plugin path. - configure option is --with-default-plugin=location - cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location - HDFFV-8513. (ADB 2013/09/04) - - Rename FFLAGS to FCFLAGS in configure (ADB 2013/08/13) - - CMake minimum is now 2.8.10. (ADB 2013/01/14) - - A new tool, cmakehdf5, which is a build command script similar to - buildhdf5 is added and is available in the bin directory. - (AKC - 2012/12/12) - - Fixed AIX Fortran compiler flags to use appropriate settings for - debugging, profiling, optimization situations. HDFFV-8069. (AKC - 2012/09/27) - - Updated to latest autotools and changed all hard *.sh scripts to - configure managed *.sh.in files. Removed overloading of autotools - TESTS variable by examples and tests. Renamed configure.in to - configure.ac. (ADB - 2012/08/23 - HDFFV-8129) - - Added code to display the version information of XL fortran and C++ - in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793) - - Configure now generates Makefiles that build in "silent make mode" - by default in which compile and link lines are significantly - simplified for clarity. To override this and view actual compile and - link lines during building, the --disable-silent-rules flag can be used - at configure time, or the 'make' command can be followed by V=1, to - indicate a "verbose" make. (MAM - 2011/4/14). - - Added mpicc and mpif90 as the default C and Fortran compilers for Linux - systems when --enable-parallel is specified but no $CC or $FC is defined. - (AKC - 2011/2/7) - - Added a new configure option, "--enable-unsupported", which can - be used to stop configure from preventing the use of unsupported - configure option combinations, such as c++ in parallel or parallel - HDF5 with threadsafe. Use at your own risk, as it may result in a - library that won't compile or run as expected! - (MAM - 2010/11/17 - Bug 2061) - - PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI - applications startup command as defined in the MPI-2 definition, section - 4.1. (AKC - 2010/6/11 - Bug 1921) - - Configure now adds appropriate defines for supporting large (64-bit) - files on all systems, where supported, by default, instead of only linux. - This largefile support is controllable with the --enable-largefile - configure option. This is replacing the linux-specific --enable-linux-lfs - option, which has been removed from configure. - (MAM - 2010/05/05 - 1772/1434) - - Upgraded versions of autotools used to generate configuration suite. - We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b. - MAM 2010/04/15. - - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM - compilers so that the ibm compiler options can be added properly. This - allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be - recognized. AKC 2009/11/26. - - Configuration suite now uses Automake 1.11 and Autoconf 2.64. - MAM 2009/08/11. - - Changed default Gnu fortran compiler from g95 to gfortran since - gfortran is more likely installed with gcc now. -AKC 2009/07/19- - - Added libtool version numbers to generated c++, fortran, and - hl libraries. MAM 2009/04/19. - - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. - - Added a Make target of check-all-install to test the correctness of - installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 - - Configuration suite now uses Libtool 2.2.6a. MAM 2008/10/24 - - - Configuration suite now uses Autoconf 2.61, Automake 1.10.1. - MAM 2008/05/05. - - - The new configure option "--disable-sharedlib-rpath" disables - embedding the '-Wl,-rpath' information into executables when - shared libraries are produced, and instead solely relies on the - information in LD_LIBRARY_PATH. (MAM - 2008/05/15) + - Removal of MPE support + + The ability to build with MPE instrumentation has been removed along with + the following configure options: + + Autotools: + --with-mpe= + + CMake has never supported building with MPE support. + + (DER - 2022/11/08) + + - Removal of dmalloc support + + The ability to build with dmalloc support has been removed along with + the following configure options: + + Autotools: + --with-dmalloc= + + CMake: + HDF5_ENABLE_USING_DMALLOC + + (DER - 2022/11/08) + + - Removal of memory allocation sanity checks configure options + + With the removal of the memory allocation sanity checks feature, the + following configure options are no longer necessary and have been + removed: + + Autotools: + --enable-memory-alloc-sanity-check + + CMake: + HDF5_MEMORY_ALLOC_SANITY_CHECK + HDF5_ENABLE_MEMORY_STATS + + (DER - 2022/11/03) Library: -------- - - The library can load filter libraries dynamically during runtime. Users - can set the search path through environment variable HDF5_PLUGIN_PATH - and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) - - Added new API functions H5Dscatter and H5Dgather to scatter data to and - and gather data from a selection within a memory buffer. - (NAF - 2013/02/05) - - The library now supports the data conversion from enumeration to numeric - (integer and floating-point number) datatypes. See Issue 8221. - (SLU - 2012/10/23) - - The data sieve buffer size was for all the datasets in the file. It - could waste memory if any dataset size is smaller than the sieve buffer - size. Now the library picks the smaller one between the dataset size - and the sieve buffer size from the file access property. See Issue 7934. - (SLU - 2012/4/2) - - I added a new parameter of object access property list to the function - H5Rdereference (Issue 2763). It's called H5Rdereference2 now. The former - H5Rdereference function has been deprecated to H5Rdereference1. (SLU - - 2011/7/18) - - H5Tcreate now supports string type (fixed-length and variable-length). - (SLU - 2011/05/20) - - Added ability to cache files opened through external links. Added new - public functions H5Pset_elink_file_cache_size(), - H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache(). - (NAF - 2011/02/17) - - Removed all old code for Metraowerks compilers, bracketed by - __MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17) - - Added support for threadsafety on windows using the windows threads - library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a - windows platform to enable this functionality. This is supported on - Windows Vista and newer Windows operating systems. (MAM - 2010/09/10) - - When a mandatory filter failed to write data chunks, the dataset - couldn't close (bug 1260). The fix releases all resources and closes - the dataset but returns a failure. (SLU - 2010/9/8) - - H5Tset_order and H5Tget_order now support all data types. A new byte - order H5T_ORDER_MIXED has been added specifically for compound datatype - and its derived type. Please see bug #1934. (SLU - 2010/8/23) - - Improved performance of the chunk cache by avoiding unnecessary b-tree - lookups of chunks already in cache. (NAF - 2010/06/15) - - Greatly improved performance of extending a dataset with early - allocation. (NAF - 2010/03/24 - 1637) - - Added support for filtering densely stored groups. Many of the API - functions related to filters have been extended to support dense groups - as well as datasets. Pipeline messages can now be stored in a group's - object header. (NAF/QAK - 2009/10/8) - - The embedded library information is displayed by H5check_version() if a - version mismatch is detected. Also changed H5check_version() to - suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 - or higher. (Old behavior treated 3 or higher the same as 1, that is - print a warning and allows the program to continue. (AKC - 2009/9/28) - - If a user does not care for the extra library information insert - in the executables, he may turn it off by --disable-embedded-libinfo - during configure. (AKC - 2009/9/15) - - Corrected problem where library would re-write the superblock in a file - opened for R/W access, even when no changes were made to the file. - (QAK - 2009/08/20, Bz#1473) - - Separated "factory" free list class from block free lists. These free - lists are dynamically created and manage blocks of a fixed size. - H5set_free_list_limits() will use the same settings specified for block - free lists for factory free lists. (NAF - 2009/04/08) - - Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29) - - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a - user-defined callback function for external link traversal. - (NAF - 2009/01/08) - - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to - allow the user to specify the file access flags used to open the target - file of an external link. (NAF - 2009/01/08) - - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow - individual rdcc configuration for each dataset. Added - H5Dget_access_plist() function to retrieve a dataset access property - list from a dataset. (NAF - 2008/11/12) - - Added H5Iis_valid() function to check if an id is valid without producing - an error message. (NAF - 2008/11/5) - - Added two new public routines: H5Pget_elink_fapl() and - H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) - - Improved free space tracking in file to be faster. (QAK - 2008/10/06) - - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) + - Overhauled the Virtual Object Layer (VOL) + + The virtual object layer (VOL) was added in HDF5 1.12.0 but the initial + implementation required API-breaking changes to better support optional + operations and pass-through VOL connectors. The original VOL API is + now considered deprecated and VOL users and connector authors should + target the 1.14 VOL API. + + The specific changes are too extensive to document in a release note, so + VOL users and connector authors should consult the updated VOL connector + author's guide and the 1.12-1.14 VOL migration guide. + + (DER - 2022/12/28) + + - H5VLquery_optional() signature change + + The last parameter of this API call has changed from a pointer to hbool_t + to a pointer to uint64_t. Due to the changes in how optional operations + are handled in the 1.14 VOL API, we cannot make the old API call work + with the new scheme, so there is no API compatibility macro for it. + + (DER - 2022/12/28) + + - H5I_free_t callback signature change + + In order to support asynchronous operations and future IDs, the signature + of the H5I_free_t callback has been modified to take a second 'request' + parameter. Due to the nature of the internal library changes, no API + compatibility macro is available for this change. + + (DER - 2022/12/28) + + - Fix for CVE-2019-8396 + + Malformed HDF5 files may have truncated content which does not match + the expected size. When H5O__pline_decode() attempts to decode these it + may read past the end of the allocated space leading to heap overflows + as bounds checking is incomplete. + + The fix ensures each element is within bounds before reading. + + (2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209) + + - Removal of memory allocation sanity checks feature + + This feature added heap canaries and statistics tracking for internal + library memory operations. Unfortunately, the heap canaries caused + problems when library memory operations were mixed with standard C + library memory operations (such as in the filter pipeline, where + buffers may have to be reallocated). Since any platform with a C + compiler also usually has much more sophisticated memory sanity + checking tools than the HDF5 library provided (e.g., valgrind), we + have decided to to remove the feature entirely. + + In addition to the configure changes described above, this also removes + the following from the public API: + H5get_alloc_stats() + H5_alloc_stats_t + + (DER - 2022/11/03) Parallel Library: ----------------- - - Add H5Pget_mpio_no_collective_cause() function that retrive reasons - why the collective I/O was broken during read/write IO access. - (JKM - 2012/08/30 HDFFV-8143) - - Special Collective IO (IO when some processes do not contribute to the - IO) and Complex Derived Datatype MPI functionalities are no longer - conditionally enabled in the library by configure. They are always - enabled in order to take advantage of performance boosts from these - behaviors. Older MPI implementations that do not allow for these - functionalities can no longer by used by HDF5. (MAM - 2011/07/08). - - Modified parallel tests to run with arbitrary number of processes. The - modified tests are testphdf5 (parallel dataset access), t_chunk_alloc - (chunk allocation), and t_posix_compliant (posix compliance). The rest of - the parallel tests already use in the code the number of processes - available in the communicator. (CMC - 2009/04/28) + - + Fortran Library: ---------------- - - - Added parallel routine H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) - - - Added for the C API the Fortran wrapper: - h5ocopy_f (MSB - 2012/03/22) - - - HDF5 Fortran library was enhanced to support Fortran 2003 standard. - The following features are available when the HDF5 library is configured - using --enable-fortran --enable-fortran2003 configure flags AND - if fortran compiler is Fortran2003 compliant: - - - Subroutines overloaded with the C_PTR derived type: - h5pget_f - h5pget_fill_value_f - h5pinsert_f - h5pregister_f - h5pset_f - h5pset_fill_value_f - h5rcreate_f - h5rderefrence_f - h5rget_name_f - h5rget_obj_type_f - - Subroutines overloaded with the C_PTR derived type - and simplified signatures: - h5aread_f - h5awrite_f - h5dread_f - h5dwrite_f - - New subroutines - h5dvlen_reclaim_f - h5literate_by_name_f - h5literate_f - h5ovisit_f - h5tconvert_f - - - Subroutines with additional optional parameters: - h5pcreate_class_f - (EIP - 2011/10/14) - - - Added for the C APIs the Fortran wrappers: - h5dget_access_plist_f - h5iis_valid_f - h5pset_chunk_cache_f - h5pget_chunk_cache_f - (MSB - 2009/04/17) - + - C++ Library: ------------ - - New member functions - + Overloaded CommonFG::getObjnameByIdx to take char* for name - + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*. - (BMR - 2010/05/02) - + DataSet::getInMemDataSize() to simplify getting the dataset's - data size in memory. (BMR - 2009/07/26) - - These member functions were added as wrapper for H5Rdereference to - replace the incorrect IdComponent::dereference(). - void H5Object::dereference(H5File& h5file, void* ref) - void H5Object::dereference(H5Object& obj, void* ref) - In addition, these constructors were added to create the associated - objects by way of dereference: - Attribute(H5Object& obj, void* ref); - Attribute(H5File& file, void* ref); - DataSet(H5Object& obj, void* ref); - DataSet(H5File& file, void* ref); - DataType(H5Object& obj, void* ref); - DataType(H5File& file, void* ref); - Group(H5Object& obj, void* ref); - Group(H5File& obj, void* ref); - (BMR - 2008/08/10) + - + Java Library: + ------------- + - + Tools: ------ - - h5repack: Added ability to use plugin filters. HDFFV-8345 (ADB - 2013/09/04). - - h5dump: Added option -N --any_path, which searches the file for paths that - match the search path. HDFFV-7989 (ADB - 2013/08/12). - - h5dump: Added optional arg 0 to -A, which excludes attributes from display. - HDFFV-8134 (ADB - 2013/08/01). - - h5dump: Fixed displaying compression ratio for unknown or user-defined - filters. HDFFV-8344 (XCAO 2013/03/19) - - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter. - HDFFV-8346 (XCAO 2013/03/19) - - h5dump: Added capability for "-a" option to show attributes containing "/" - by using an escape character. For example, for a dataset "/dset" - containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" - to show the content of the attribute. See details at HDFFV-7523 - (PC -- 2012/03/12) - - h5dump: Added ability to apply command options across multiple files using a - wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5". - HDFFV-7876 (ADB - 2012/03/12). - - h5repack: Improved performance for big chunked datasets (size > 128MB) - when used with layout (-l) or compression (-f) option. - It would perform much better prior to the improvement, - especially for cases that chunk dimentions looks like - "1024x5x1" (compare to "1x5x1024"). When bigger numbers - are toward front and smaller number is toward back in chunk - dimentions. HDFFV-7862 (JKM - 2012/03/01) - - h5dump: Added new option --no-compact-subset. This option will not - interpret the '[' character as starting the compact form of - subsetting. This is useful when the "h5dump error: unable to - open dataset "datset_name"" message is output because a dataset - name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31) - - h5dump: Corrected schema location: - <hdf5:HDF5-File - xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File" - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File - http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> - (ADB - 2011/08/10) - - h5diff: Added new level for -v (verbose) option. The new levels are - 1 and 2. So -v1 and -v2 can be specified to view more - information about attributes differences. - Bug#2121 (JKM 2011/3/23) - - h5dump: Added new option --enable-error-stack. This option will display - error stack information in the output stream. This is useful - when the "h5dump: Unable to print data" message is output. - (ADB - 2011/02/24) - - h5diff: Add a new flag --exclude-path. Specified path to an object will - be excluded from comparing the two files or two groups. If group - is specified all the member objects will be excluded. - (JKM - 2010/09/16). - - h5ls: Add new flag --no-dangling-links. (refer to --help for details) - (JKM - 2010/06/15) - - h5ls: Add new flag --follow-symlinks. (refer to --help for details) - (JKM - 2010/05/25) - - h5diff: Add new flag --no-dangling-links. (refer to --help for details) - (JKM - 2010/02/10) - - h5diff: Add new flag --follow-symlinks. (refer to --help for details) - (JKM - 2010/01/25) - - h5diff: fix for displaying garbage value on LE machine for BE data. - (JKM - 2009/11/20) - - h5dump: subsetting now allows default for count. Also trailing ; in short form - can be omitted after last specified value. - (ADB - 2009/09/04) - - h5dump/h5ls: now can display data in region references - using new -R, --region flag. - (ADB - 2009/09/04) - - h5diff: new flag, -c, --compare, list objects that are not comparable. - (PVN - 2009/4/10 - 1368) - - h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10) - - h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519) - - h5repack now handles group creation order. (PVN - 2009/4/2 - 1402) - - h5dump: added a printing of the compression ratio of uncompressed and compressed - sizes for cases where compression filters are present. (PVN - 2008/05/01) - - h5dump: added an option to allow a user defined formatting string for printf - regarding floating point numbers. (PVN - 2008/05/06) - - h5dump: support for external links, display the object that the external link - points to. (PVN - 2008/05/12) - - h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26) - - h5repack: add 2 options that call H5Pset_alignment in the repacked file. (PVN - 2008/08/29) - - h5ls: added capability to traverse through external links when the -r - (recursive) flag is given. (NAF - 2008/09/16) - - h5ls: added -E option to enable traversal of external links. h5ls will - not traverse external links without this flag being set. - (NAF - 2008/10/06) - - h5diff: added support for long double (PVN - 2008/10/28) - - h5dump: binary output defaults to NATIVE with -b optionally accepting - the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/10/30) - - h5diff: return 1 for file differences when both file graphs differ by any object. - Error return code was changed to 2 from -1. (PVN - 2008/10/30) - - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP - instead (PVN - 2008/10/30) - - h5repack: When user doesn't specify a chunk size, h5repack now defines a default - chunk size as the same size of the size of the hyperslab used to read the chunks. - The size of the hyperslabs are defined as the size of each dimension or a - predefined constant, whatever is smaller. This assures that the chunk - read fits in the chunk cache. (PVN - 2008/11/21) - - h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect) - before call ABS(...) at h5diff_array.c This will make that (INF==INF) is true - (INF is treated as an number instead of NaN) (PC -- 2009/07/28) - - h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON) - Change default to use strict equality (PC -- 2009/09/12) + - + - High-Level APIs: - ------ - - Table: In version 3.0 of Table, "NROWS" (used to store number of records) was - deprecated (PVN - 2008/11/24) - - - Added Fortran wrappers for Dimension Scale APIs. HDFFV-3797 - h5dsset_scale_f - h5dsattach_scale_f - h5dsdetach_scale_f - h5dsis_attached_f - h5dsis_scale_f - h5dsset_label_f - h5dsget_label_f - h5dsget_scale_name_f - h5dsget_num_scales_f - (EIP for SB - 2011/10/13) - - - New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks - if a path is correct and determines if a link resolves to a valid - object and checks that the link does not dangle. (MSB- 2012/3/15) - - - A new API function H5DOwrite_chunk. It writes a data chunk directly - into a file bypassing hyperslab selection, data conversion, and - filter pipeline. The user must be careful with the function and - clearly understand the I/O process of the library. - (SLU - 2013/2/11) - - Documentation - ------------- - -Support for new platforms, languages and compilers. -======================================= - - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) - - PathScale compilers are recognized and can build the HDF5 library - properly. AKC - 2009/7/28 - - - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and - Sun Fortran 95 8.6 compiler. (SLU - 2013/04/15) - -Bug Fixes since HDF5-1.8.0 release -================================== + ---------------- + - + + + C Packet Table API: + ------------------- + - + + + Internal header file: + --------------------- + - + + + Documentation: + -------------- + - Ported the existing VOL Connector Author Guide document to doxygen. + Added new dox file, VOLConnGuide.dox. + + (ADB - 2022/12/20) + + +Support for new platforms, languages and compilers +================================================== + - + +Bug Fixes since HDF5-1.13.3 release +=================================== Library ------- - - Incorrect usage of list in CMake COMPILE_DEFINITIONS set_property + - Seg fault on file close + + h5debug fails at file close with core dump on a file that has an + illegal file size in its cache image. In H5F_dest(), the library + performs all the closing operations for the file and keeps track of + the error encountered when reading the file cache image. + At the end of the routine, it frees the file's file structure and + returns error. Due to the error return, the file object is not removed + from the ID node table. This eventually causes assertion failure in + H5VL__native_file_close() when the library finally exits and tries to + access that file object in the table for closing. + + The closing routine, H5F_dest(), will not free the file structure if + there is error, keeping a valid file structure in the ID node table. + It will be freed later in H5VL__native_file_close() when the + library exits and terminates the file package. + + (VC - 2022/12/14, HDFFV-11052, CVE-2020-10812) + + - Fix CVE-2018-13867 / GHSA-j8jr-chrh-qfrf + + Validate location (offset) of the accumulated metadata when comparing. + + Initially, the accumulated metadata location is initialized to HADDR_UNDEF + - the highest available address. Bogus input files may provide a location + or size matching this value. Comparing this address against such bogus + values may provide false positives. Thus make sure, the value has been + initialized or fail the comparison early and let other parts of the + code deal with the bogus address/size. + Note: To avoid unnecessary checks, it is assumed that if the 'dirty' + member in the same structure is true the location is valid. + + (EFE - 2022/10/10 GH-2230) + + - Fix CVE-2018-16438 / GHSA-9xmm-cpf8-rgmx + + Make sure info block for external links has at least 3 bytes. - The CMake command, set_property with COMPILE_DEFINITIONS property - needs a quoted semi-colon separated list of values. CMake will - transform the list to a series of -D{value} for the compile. + According to the specification, the information block for external links + contains 1 byte of version/flag information and two 0 terminated strings + for the object linked to and the full path. + Although not very useful, the minimum string length for each (with + terminating 0) would be one byte. + Checking this helps to avoid SEGVs triggered by bogus files. + + (EFE - 2022/10/09 GH-2233) + + - CVE-2021-46244 / GHSA-vrxh-5gxg-rmhm + + Compound datatypes may not have members of size 0 + + A member size of 0 may lead to an FPE later on as reported in + CVE-2021-46244. To avoid this, check for this as soon as the + member is decoded. + + (EFE - 2022/10/05 GEH-2242) + + + - Fix CVE-2021-45830 / GHSA-5h2h-fjjr-x9m2 + + Make H5O__fsinfo_decode() more resilient to out-of-bound reads. + + When decoding a file space info message in H5O__fsinfo_decode() make + sure each element to be decoded is still within the message. Malformed + hdf5 files may have trunkated content which does not match the + expected size. Checking this will prevent attempting to decode + unrelated data and heap overflows. So far, only free space manager + address data was checked before decoding. + + (EFE - 2022/10/05 GH-2228) + + - Fix CVE-2021-46242 / GHSA-x9pw-hh7v-wjpf + + When evicting driver info block, NULL the corresponding entry. + + Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag + H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing + the pointer in f->shared->drvinfo will prevent use-after-free when it is + used in other functions (like H5F__dest()) - as other places will check + whether the pointer is initialized before using its value. + + (EFE - 2022/09/29 GH-2254) + + - Fix CVE-2021-45833 / GHSA-x57p-jwp6-4v79 + + Report error if dimensions of chunked storage in data layout < 2 + + For Data Layout Messages version 1 & 2 the specification state + that the value stored in the data field is 1 greater than the + number of dimensions in the dataspace. For version 3 this is + not explicitly stated but the implementation suggests it to be + the case. + Thus the set value needs to be at least 2. For dimensionality + < 2 an out-of-bounds access occurs. + + (EFE - 2022/09/28 GH-2240) - (ADB - 2014/12/09, HDFV-9041) - - - H5Z.c: H5Zfilter_avail(H5Z_filter_t id) - Added else block if the call to the internal H5Z_filter_avail(id) does not - fail and returns FALSE. This block calls the H5PL_load(H5PL_TYPE_FILTER, (int)id) - function to attempt to dynamically load the filter plugin. - (ADB - 2014/03/03 HDFFV-8629) - - Added const qualifier to source buffer parameters in H5Dgather and - H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/02) - - Fixed an error involving failure to write fill values to the user's - buffer when reading unallocated chunks from datasets that have a - fill value set to H5D_FILL_VALUE_DEFAULT. A consequence of this - was the reporting of spurious data values in h5dump and h5diff - output. - (HDFFV-8247; JP - 2013/05/03) - - Fixed an error that could occur when calling H5Ocopy within an - H5Literate callback (and possibly other situations). - (NAF - 2012/7/25 - HDFFV-5853) - - Fixed an error that would occur when copying an object with attribute - creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762) - - Fixed a bug in H5Ocopy(): When copying an opened object, call the - object's flush class action to ensure that cached data is flushed - so that H5Ocopy will get the correct data. - (VC - 2012/3/27 - HDFFV-7853) - - When an application tries to write or read many small data chunks and - runs out of memory, the library had a seg fault. The fix is to - return the error stack with proper information. (SLU - 2012/3/23. - Issue 7785) - - H5Pset_data_transform had seg fault in some cases like x*-100. It - works correctly now and handles other cases like 100-x or 2/x. - (SLU - 2012/3/15. Issue 7922) - - Fixed rare corruption bugs that could occur when using the new object - header format. (NAF - 2012/3/15 - HDFFV-7879) - - Creating a dataset in a read-only file caused seg fault when the file - is closed. It's fixed. The attemp to create a dataset will fail - with the error stack indicating the file is read-only. (SLU - - 2012/1/25. Issue 7756) - - Fixed a seg fault that could occur when shrinking a dataset with chunks - larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833) - - Fixed a bug that could cause file corruption when copying named - datatypes to a file using shared messages. (NAF - 2011/11/14) - - Fixed a bug that could cause H5Oget_info to return the wrong address - after copying a named datatype. (NAF - 2011/11/14) - - The library allowed the conversion of strings between ASCII and UTF8 - (Issue 7582). We have corrected it to report an error under this - situation. (SLU - 2011/11/8) - - The library had seg fault when it tried to shrink the size of compound type - through H5Tset_size immediately after the type was created (Issue - 7618). It's fixed now. (SLU - 2011/10/26) - - Fixed a bug that occurred when using H5Ocopy on a committed datatype - containing an attribute using that committed datatype. - (NAF - 2011/10/13 - Issue 5854) - - #ifdef _WIN32 instances changed to #ifdef H5_HAVE_WIN32_API and added - H5_HAVE_VISUAL_STUDIO checks where necessary. CMake only as configure - never set _WIN32. - - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - discovered 3 problems in tests and tools' library (Issue 7674): - 1. In dsets.c, left shifting an unsigned int for 32 bits or more - caused undefined behavior. - 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow - when the value is negative minimal and is being subtracted one. - 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits - or more caused undefined behavior. - All the problems have been corrected. (SLU - 2011/9/2) - - In v1.6 library, there was EOA for the whole MULTI file saved in the - super block. We took it out in v1.8 library because it's meaningless - for the MULTI file. v1.8 library saves the EOA for the metadata file, - instead. But this caused some backward compatibility problem. - v1.8 library couldn't open the file created with v1.6 library. We - fixed the problem by checking the EOA value to detect the file - created with v1.6 library. (SLU - 2011/6/22) - - When a dataset had filters and reading data failed, the error message - didn't say which filter isn't registered. It's fixed now. - (SLU - 2011/6/3) - - The datatype handler created with H5Tencode/decode used to have the - reference count 0 (zero). I have fixed it. It is 1 (one) now. - (SLU - 2011/2/18) - - Fixed a bug that caused big endian machines to generate corrupt files - when using the scale-offset filter with floating point data or - fill values. Note that such datasets will no longer be readable - by any machine after this patch. (NAF - 2010/02/02 - Bug 2131) - - Retrieving a link's name by index in the case where the link is - external and the file that the link refers to doesn't exist will - now fail gracefully rather than cause a segmentation fault. - (MAM - 2010/11/17) - - Modified library to always cache symbol table information. Libraries - version 1.6.3 have a bug which causes them to require this - information for some operations. (NAF - 2010/09/21 - 1864) - - Fixed a bug that could occur when getting information for a new-style - group that was previously opened through a file handle that was - later closed. (NAF - 2010/09/15) - - Added define check in H5public.h if stdint.h is supported by the C++ - compiler. This define is only available on Windows with VS2010 and - using CMake to build the library. (ADB - 2010/09/13 - Bug 1938) - - H5Eset_current_stack now also closes the error stack to be set as the - default. This is to avoid a potential problem (Bug 1799). - (SLU - 2010/9/7) - - Fixed the bug in the filter's public CAN_APPLY function. The return - value should be htri_t not herr_t (Bug #1239). (SLU - 2010/8/5) - - Fixed a bug in the direct I/O driver that could render files with - certain kinds of unaligned data unreadable or corrupt them. - (NAF - 2010/07/28) - - valgrind reported an error of copying data to itself when a new attribute - is written (Bug #1956). I fixed it by taking out the memcpy step in - the attribute code. (SLU - 2010/07/28) - - Fixed a bug that could cause file corruption when using non-default - sizes of addresses and/or lengths. This bug could also cause - uncorrupted files with this property to be unreadable. This bug - was introduced in 1.8.5. (NAF - 2010/07/16 - 1951) - - Fixed a file corruption bug that could happen when shrinking a - compressed dataset. (NAF - 2010/05/20) - - Fixed some memory leaks in VL datatype conversion when strings are - used as fill values. (MAM - 2010/05/12 - BZ# 1826) - - Fixed a bug when copying objects with NULL references with the - H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815) - - Files can now be concurrently opened more than once using the core file - driver, as long as the backing store is used. (NAF - 2010/03/09) - - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External - links will now be expanded if this flag is set. - (NAF - 2010/03/05 - 1733) - - Fixed a bug where the library, when traversing an external link, would - reopen the source file if nothing else worked. (NAF - 2010/03/05) - - Fixed an intermittent bug in the b-tree code which could be triggered - by expanding and shrinking chunked datasets in certain ways. - (NAF - 2010/02/16) - - H5Tdetect_class said a VL string is a string type. But when it's - in a compound type, it said it's a VL type (Bug #1584). I fixed it - to be consistent. It always return string type. (SLU - 2009/12/10) - - Fixed a bug where writing and deleting many global heap objects (i.e. - variable length data) would render the file unreadable. Previously - created files exhibiting this problem should now be readable. - (NAF - 2009/10/27 - 1483) - - Fixed incorrect return value for H5Pget_preserve. (AKC - 2009/10/08 - 1628) - - Fixed an assertion failure that occurred when H5Ocopy was called on a - dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597) - - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. - (NAF - 2009/09/25 - 1620) - - Fixed a bug where properties weren't being compared with the registered - compare callback. (NAF - 2009/09/25 - 1555) - - Fixed a bug where H5Pget_fitler_by_id would succeed when called for a - filter that wasn't present. (NAF - 2009/06/25 - 1250) - - Fixed an issue with committed compound datatypes containing a vlen. - Also fixed memory leaks involving committed datatypes. - (NAF - 2009/06/10 - 1593) - - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 - API. (NAF - 2009/04/20 - 1533) - - Fixed a problem with using data transforms with non-native types in the - file. (NAF - 2009/04/20 - 1548) - - Added direct.h include file to windows section of H5private.h - to fix _getcwd() warning. (ADB - 2009/04/14 - 1536) - - Fixed a bug that prevented external links from working after calling - H5close(). (NAF - 2009/04/10 - 1539) - - Modified library to write cached symbol table information to the - superblock, to allow library versions 1.3.0 to 1.6.3 to read files - created by this version. (NAF - 2009/04/08 - 1423) - - Changed skip lists to use a deterministic algorithm. The library should - now never call rand() or srand(). (NAF - 2009/04/08 - 503) - - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate - groups when that property was set. (NAF - 2009/04/07 - 1526) - - Fixed a bug that caused files with a user block to grow by the size of - the user block every time they were opened. - (NAF - 2009/03/26 - 1499) - - Fixed a rare problem that could occur with files using the old (pre 1.4) - array datatype. (NAF - 2009/03/23) - - Modified library to be able to open files with corrupt root group symbol - table messages, and correct these errors if they are found. Such - files can only be successfully opened with write access. - (NAF - 2009/03/23 - 1189) - - Removed the long_long #define and replaced all instances with - "long long". This caused problems with third party products. All - currently supported compliers support the type. (ADB - 2009/03/05) - - Fixed various bugs that could prevent the fill value from being written - in certain rare cases. (NAF - 2009/02/26 - 1469) - - Fixed a bug that prevented more than one dataset chunk from being cached - at a time. (NAF - 2009/02/12 - 1015) - - Fixed an assertion failure caused by opening an attribute multiple times - through multiple file handles. (NAF - 2009/02/12 - 1420) - - Fixed a problem that could prevent the user from adding attributes (or - any object header message) in some circumstances. - (NAF - 2009/02/12 - 1427) - - Fixed a bug that could cause problems when an attribute was added to a - committed datatype using the committed datatype's datatype. - (NAF - 2009/02/12) - - Fixed a bug that could cause problems when copying an object with a - shared message in its own object header. (NAF - 2009/01/29) - - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most - datatypes. (NAF - 2009/01/27 - 1443) - - Fixed a bug where H5Tpack wouldn't remove trailing space from an - otherwise packed compound type. (NAF - 2009/01/14) - - Fixed up some old v2 btree assertions that get run in debug mode that - were previously failing on compilation, and removed some of the - more heavily outdated and non-rewritable ones. (MAM - 2008/12/15) - - Fixed a bug that could cause problems when "automatically" unmounting - multiple files. (NAF - 2008/11/17) - - H5Ovisit and H5Ovisit_by_name will now properly terminate when the - callback function returns a positive value on the starting object. - (NAF - 2008/11/03) - - Fixed an error where a null message could be created that was larger - than could be written to the file. (NAF - 2008/10/23) - - Corrected error with family/split/multi VFD not updating driver info - when "latest" version of the file format used. (QAK - 2008/10/14) - - Corrected alignment+threshold errors to work correctly when metadata - aggregation is enabled. (QAK - 2008/10/06) - - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered - by the library for internal library use. (NAF - 2008/10/06) - - Fixed potential memory leak during compound conversion. - (NAF - 2008/10/06) - - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also - changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and - the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26) - - Fixed an issue that could cause data to be improperly overwritten - during compound type conversion. (NAF - 2008/09/19) - - Fixed pointer alignment violations that could occur during vlen - conversion. (NAF - 2008/09/16) - - Fixed problem where library could cause a segmentation fault when - an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) - - Fixed improper shutdown when objects have reference count > 1. The - library now tracks reference count due to the application separately - from that due to internal library routines. (NAF - 2008/08/19) - - Fixed assertion failure caused by incorrect array datatype version. - (NAF - 2008/08/08) - - Fixed an issue where mount point traversal would fail when using - multiple handles for the child. (NAF - 2008/08/07) - - Fixed an issue where mount points were inaccessible when using multiple - file handles for the parent. The mount table is now in the shared - file structure (the parent pointer is still in the top structure). - (NAF - 2008/08/07) - - when an attribute was opened twice and data was written with one of the handles, - the file didn't have the data. It happened because each handle had its own - object structure, and the empty one overwrote the data with fill value. This is - fixed by making some attribute information like the data be shared in the - attribute structure. SLU - 2008/07/22 - - Fixed issue where a group could have a file mounted on it twice. - (QAK - 2008/07/15) - - Fixed a Windows-specific issue in the ohdr test which was causing users - in some timezones to get false errors. This a deficiency in the Windows - mktime() function, and has been handled properly. SJW - 2008/06/19 - - Fixed the problem with the searching of target file for H5Lcreate_external(). - The searching pattern will depend on whether the target file's - pathname is an absolute or a relative path. Please see the description - in the RM for H5Lcreate_external(). (VC - 2008/04/08) - - Fixed possible file corruption bug when encoding datatype - descriptions for compound datatypes whose size was between - 256 & 511 bytes and the file was opened with the "use the - latest format" property enabled (with H5Pset_libver_bounds). - (QAK - 2008/03/13) - - Fixed bug in H5Aget_num_attrs() routine to handle invalid location - ID correctly. (QAK - 2008/03/11) - - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. - (PVN - 2009/01/8) - - Added code to maintain a min_clean_fraction in the metadata cache when - in serial mode. (MAM - 2009/01/9) + - Fix CVE-2018-14031 / GHSA-2xc7-724c-r36j + + Parent of enum datatype message must have the same size as the + enum datatype message itself. + Functions accessing the enumeration values use the size of the + enumeration datatype to determine the size of each element and + how much data to copy. + Thus the size of the enumeration and its parent need to match. + Check in H5O_dtype_decode_helper() to avoid unpleasant surprises + later. + + (EFE - 2022/09/28 GH-2236) + + - Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7 + + H5IMget_image_info(): Make sure to not exceed local array size + Malformed hdf5 files may provide more dimensions than the array dim[] in + H5IMget_image_info() is able to hold. Check number of elements first by calling + H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments. + This will cause the function to return only the number of dimensions. + The fix addresses a stack overflow on write. + + (EFE - 2022/09/27 HDFFV-10589, GH-2226) + + + Java Library + ------------ + - Configuration ------------- - - CMake: When CMake commands are executed individually on the command line - and the external filters are being built, the CMAKE_BUILD_TYPE define - must be set to the same value as the configuration - (-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed - by the the szip and zlib filter build commands. (ADB - HDFFV-8695) - - CMake: Remove use of XLATE_UTILITY program. (ADB - 2014/03/28 HDFFV-8640) - - CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the - MPI option. (ADB - 2014/02/27 HDFFV-8674) - - Modified H5detect.c to scan floating point types for padding bits before - analyzing the type further. This should fix problems with gcc 4.8 - (NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500) - - Fixed Makefile issue in which "-Wl," was not properly specified - prior to -rpath when building parallel fortran libraries with - an Intel compiler. (MAM - 2012/03/26) - - Makefiles generated by other packages using h5cc as the compiler - no longer error when 'make' is invoked more than once in order - to 'rebuild' after changes to source. (MAM - 2012/03/26) - - Added --enable-fortran2003 flag to enable Fortran2003 support - in the HDF5 Fortran library. The flag should be used along with the - --enable-fortran flag and takes affect only when Fortran compiler - is Fortran2003 compliant. (EIP - 2011/11/14) - - - In Windows platform, the default VFD, was Windows VFD, is restored back - to the SEC2, aka POSIX, VFD. The Windows VFD is deprecated. HDFFV-7740 - (AKC 2011/09/26) - - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file, - ibm-aix. (AKC - 2011/4/14) - - Shared C libraries are no longer disabled on Mac when Fortran - is enabled. Shared Fortran libraries are still not supported on Mac, - so configure will disable them by default, but this is overridable - with the new --enable-unsupported configure option. The configure - summary has been updated to reflect the fact that the shared-ness of - the C++/Fortran wrapper libraries may not align with the C library. - (MAM - 04/11/2011 - HDFFV-4353). - - Removed recognition of the parallel compilers of LAM(hcc) and - ChMPIon(cmpicc) since we have no access to these two MPI implementations - and cannot verify their correctness. (AKC - 2010/7/14 - Bug 1921) - - Removed the following config files, as we no longer support them: - config/dec-osf*, config/hpux11.00, config/irix5.x, - config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* - MAM - 2009/10/08 - - Modified configure and make process to properly preserve user's CFLAGS - (and company) environment variables. Build will now properly use - automake's AM_CFLAGS for any compiler flags set by the configure - process. Configure will no longer modify CFLAGS directly, nor will - setting CFLAGS during make completely replace what configure has set up. - MAM - 2009/10/08 - - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS - machine has long retired. AKC - 2009/10/06. - - Added $(EXEEXT) extension to H5detect when it's executed in the - src/Makfile to generate H5Tinit.c so it works correctly on platforms - that require the full extension when running executables. - MAM - 2009/10/01 - BZ #1613 - - Configure will now set FC and CXX to "no" when fortran and c++ - are not being compiled, respectively, so configure will not run - some of the compiler tests for these languages when they are not - being used. MAM - 2009/10/01 - - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to - recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - - - The --enable-static-exec flag will now properly place the -static flag - on the link line of all installed executables. This will force the - executable to link with static libraries over shared libraries, provided - the static libraries are available. MAM - 2009/08/31 - BZ #1583 - - The --includedir=DIR configuration option now works as intended, and can - be used to specify the location to install C header files. The default - location remains unchanged, residing at ${prefix}/include. - MAM - 2009/03/10 - BZ #1381 - - Configure no longer removes the '-g' flag from CFLAGS when in production - mode if it has been explicitly set in the CFLAGS environment variable - prior to configuration. MAM - 2009/03/09 - BZ #1401. - - Fixed error with 'make check install' failing due to h5dump - needing other tools built first. MAM - 2008/10/24. - - Wpen using shared szip, it is no longer necessary to specify - the path to the shared szip libraries in LD_LIBRARY_PATH. MAM - - 2008/10/24. - - The file libhdf5_fortran.settings is not installed since its content - is included in libhdf5.settings now. AKC - 2008/10/21 - - "make DESTDIR=xxx install" failed to install some tools and files - (e.g., h5cc and fortran modules). Fixed. AKC - 2008/10/8. - - Autotools: An export of LD_LIBRARY_PATH=<szip library location> was - removed from configure and make installcheck was revised to run - scripts installed in share/hdf5_examples to use the installed h5cc, etc. - to compile and run example source files also installed there. Make - installcheck will now fail when a shared szip or other external lib file - cannot be found in the same manner that executables compiled and linked - with h5cc will fail to run when those lib files cannot be found after - install. Make installcheck should pass after setting LD_LIBRARY_PATH to the - szip location. - (LRK - 2014/04/16) + - Remove Javadoc generation - Performance - ------------- - - Removed program perform/benchpar from the enable-build-all list. The - program will be retired or moved to another location. HDFFV-8156 - (AKC 2012/10/01) - - Retired program perform/mpi-perf. Its purpose has been incorporated - into h5perf before. (AKC 2012/09/20) - - ifdefs added to tests around include unistd.h and function to simulate - getlogin() on Windows. - (ADB - 2011/08/15) - - perf_serial test added to Windows projects and check batch file. - (ADB - 2009/06/11) - Fortran - -------- - - Fixed a typo in return value of the nh5dread_f_c function ( was 1 - instead of 0 on success); fixed the return value to make it consistent - with other Fortran functions; cleaned the code from debug statements. - (EIP - 2012/06/23) + The use of doxygen now supersedes the requirement to build javadocs. We do not + have the resources to continue to support two documentation methods and have + chosen doxygen as our standard. - - Fixed problem writing/reading control characters to a dataset; writing - a string containing: alerts, backspace, carriage_return, form_feed, - horizontal_tab, vertical_tab, new_line is now tested and working. - (MSB - 2012/09/01) + (ADB - 2022/12/19) - - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) + - Change the default for building the high-level tools + + The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed + in a future release. The default build setting for them have been changed from enabled + to disabled. A user can enable the build of these tools if needed. + autotools: --enable-hlgiftools + cmake: HDF5_BUILD_HL_GIF_TOOLS=ON + + (ADB - 2022/12/16) + + - Change the settings of the *pc files to use the correct format + + The pkg-config files generated by CMake uses incorrect syntax for the 'Requires' + settings. Changing the set to use 'lib-name = version' instead 'lib-name-version' + fixes the issue + + (ADB - 2022/12/06 HDFFV-11355) + + - Move MPI libraries link from PRIVATE to PUBLIC + + The install dependencies were not including the need for MPI libraries when + an application or library was built with the C library. Also updated the + CMake target link command to use the newer style MPI::MPI_C link variable. + + (ADB - 2022/10/27) - - Corrected the number of continuation lines in the src files - to be less then 32 lines for F95 compliance. (MSB - 2012/10/01) Tools ----- - - h5repack: h5repack would not attempt to remove UD filters. Added a - check to h5repack for UD filters that checks if the filter can - be dynamically loaded. This will require a change in the library to - add the H5PL_load() to the H5Zfilter_avail(). (ADB - 2014/03/03 HDFFV-8629) - - h5repack: Fixed failure for converting a layout of small chunked dataset - (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/18) - - h5diff: Fixed to return correct exit code 1 when detect unique extra - attribute. Prior to this fix, h5diff returned exit code 0 indicating - two files are identical. HDFFV-7643 (JKM 2013/02/15) - - h5diff: Improved speed when comparing HDF5 files with lots of - attributes. Much slower performance was identified with release - version from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19) - - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if - source file contains chunked dataset and a chunk dim is bigger than - the dataset dim. Another issue is that the command changed max dims - if chunk dim is smaller than the dataset dim. - These issue occurred when dataset size is smaller than 64k (compact - size limit) Fixed both. - HDFFV-8012 (JKM 2012/09/24) - - h5diff: Fixed not to accumulate attribute difference to dataset - difference in verbose mode (-v, -r), which caused incorrect - difference between dataset and group/datatype object if attribute - exist with any differences. This also lead to fix inconsistent - format indicating difference between dataset and group/datatype - object. HDFFV-5919 (JKM 2012/09/05) - - h5diff: Fixed the incorrect result when comparing attribute data - values and the data type has same class but different size. - HDFFV-7942 (JKM 2012/08/15) - - ph5diff: Fixed intermittent hang issue on a certain operation in - parallel mode. It was detected by daily test for comparing - non-comparable objects, but it could have occurred in other - operations depend on machine condition. HDFFV-8003 (JKM 2012/08/01) - - h5diff: Fixed test failure for "make check" due to failure of - copying test files when performed in HDF5 source tree. Also applied - to other tools. - HDFFV-8107 (JKM 2012/08/01) - - h5diff: Fixed the Function COPY_TESTFILES_TO_TESTDIR() of - testh5diff.sh to better report when there is an error in the file - copying. HDFFV-8105 (AKC -2012/07/22) - - h5diff: Fixed not to check and display dangling link status without - --follow-symlinks option. This also improved performance when - comparing lots of external links without the --follow-symlinks - option. HDFFV-7998 (JKM 2012/04/26) - - h5unjam: Fixed sefgault when used -V (show version) option. - HDFFV-8001 (JKM 2012/04/19) - - h5repack: Fixed a failure when change the chunk size of a specified - chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11) - - h5diff: Fixed failure for comparing same named object with different - object types in comparing groups. Prior to the fix, h5diff resulted - in error. After the fix, h5diff detects such case as non-comparable - and display messages accordingly. HDFFV-7664 (JKM 2012/03/28) - - h5diff: If unique objects exists only in one file and try to exclude - the unique objects with --exclude-path option, h5diff missed - excluding some objects. - Fixed to exclude objects correctly in such case. - HDFFV-7837 (JKM 2012/03/20) - - h5dump: Added tools library error stack to properly catch error - information generated within the library. - HDFFV-7958 (ADB 2012/03/12) - - h5dump: Dangling links no longer throw error message, change process - when open link fails. - HDFFV-7839 (ADB 2012/03/12) - - h5diff: When two symbolic dangling links are compared with - --follow-symlinks option, the result should be same. It worked for - comparing two files, but didn't work for comparing two objects. - HDFFV-7835 (JKM 2012/03/09) - - h5dump: Refactored code to remove duplicated functions. Split XML - functions from DDL functions. Corrected indentation and formatting - errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified - all tools call tools_init() in main. - HDFFV-7560 (ADB 2012/02/17) - - h5diff: fixed to prevent from displaying error stack message when - comparing the two dangling symlinks with follow-symlinks option. - HDFFV-7836 (JKM 2012/01/13) - - h5repack: fixed memory leak for handling variable length string in - attribute. HDFFV-7840 (JKM 2012/01/06) - - h5ls: fixed segfault when access region reference data in an - attribute. HDFFV-7838 (JKM 2011/12/29) - - h5diff: fixed segfault over non-comparable attribute with different - dimention or rank, along with '-c' option to display details. - HDFFV-7770 (JKM 2011/10/24) - - Fixed h5diff to display all the comparable object and attribute - regardless of non-comparables. HDFFV-7693 (JKM 2011/09/16) - - Fixed h5repack to update values of references(object and region) of - attributes in h5repack for 1) references, 2) ARRAY of references, - 3) VLEN of references, and 4) COMPOUND of references. - (JIRA HDF5 5932) PC -2011/09/14 - - h5diff: fixed segfault over dataset with container types - (array,lven) with multiple nested compound types. - (ex: compound->array->compound, compound->vlen->compound) - HDFFV-7712 JKM (2011/09/01) - - h5repack: added macro to handle failure in H5Dread/write when memory - allocation failed inside the library. (PC -- 2011/08/19) - - Fixed h5jam not to allow specifying an HDF5 formatted file as input - file for -u (user block file) option, because the original HDF5 file - will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15) - - Revised command help pages of h5jam and h5unjam. The descriptions - were not up to date and some were missing. - HDFFV-7515 (JKM 2011/08/15) - - h5repack: h5repack failed to copy dataset if the layout is changed - from chunked with unlimited dims to contiguous. HDFFV-7649 - (PC -- 2011/07/15) - - h5diff: "--delta" option considers two NaN of the same type are - different, which is wrong based on h5diff description in Reference - Manual. HDFFV-7656 (PC -- 2011/07/15) - - Fixed h5diff to display instructive error message and exit with 1 - when mutually exclusive options (-d, -p and --use-system-epsilon) - are used together. HDFFV-7600 (JKM 2011/07/07) - - Fixed h5dump to display the first line of each element into correct - position for multiple dimention array type. - Before this fix, the first line of each element in array were - displayed after the last line of previous element without - moving to the next line (+indentation). - Bug #HDFFV-5878 (JKM 2011/06/15) - - Fixed h5dump to display correct value for H5T_STD_I8LE dataset - on a system (ppc64, linux, Big-Endian, clustering). - Bug #HDFFV-7594 (ABERT & JKM 2011/05/12) - - Fixed h5diff to compare file itself correctly. Previously h5diff - reported either different or not compatible in certain cases even - comparing file itself. This fix also improve performance when - comparing same target objects through verifying the obj&file - addresses before comparing the details in the objects (ex: datasets - or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06) - - Updated h5dump test case script to prevent entire test failure upon - source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12) - - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in - attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type, - so h5dump is supposed to display -2 instead of 254. It worked - correctly on Little-Endian system , but not on Big-Endian system. - Bug #HDFFV-4358 (JKM 2011/04/08) - - Updated to unify option name to '--enable-error-stack' for printing - HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now. - For h5ls, this replaces "-e/--errors" option, which is deprecated. - Bug#2182 (JKM 2011/3/30) - - Fix h5diff for --use-system-epsilon option: the calculation changed - from ( |a - b| / b ) to ( |a - b| ). This was decided for better - performance. Bug#2184 (JKM 2011/3/24) - - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document - the output of a H5T_REFERENCE should be followed by the type; - <reference> ::= H5T_REFERENCE { <ref_type> } - <ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG - Previously this was only displayed if the -R option was used. - Bug#1725 (ADB 2011/3/28) - - Fix h5diff issues for #1: h5diff compared attributes correctly only - when two objects have the same number of attributes and attribute - names are identical, #2: didn't display useful information about - attribute difference. Bug#2121 (JKM 2011/3/17) - - Fixed memory leak for h5diff when accessing symbolic links with - --follow-symlink option. Bug#2214 (JKM 2011/3/18) - - Fixed memory leak for h5diff when access variable length string - data. Bug#2216 (JKM 2011/3/18) - - Fixed and improved help page for -a option of h5ls. - Bug#1904 (JKM 2011/3/11) - - Fixed h5dump not to include attribute values in the output file when - h5dump "-y -o output_file" options were used. The problem was introduced - in HDF5 1.8.6 by showing data pointed by region references. (XCAO 2011/3/9) - - Fixed h5copy to be able to copy any object into the same HDF5 file. - Previously h5copy displayed error message when target file is same - as source file. (XCAO 2011/3/8) - - Fixed h5dump for skipping some values for long array type dataset on - Windows. This issue only occurred on Windows due to the different - return behavior from _vsnprintf() funtion. Bug#2161 (JKM 2011/3/3) - - Fixed h5dump for skipping array indices every certain number - when the array type dataset is relatively big. The certain number - varies according to the size of array. Bug#2092 (JKM 2011/2/15). - - Fixed h5diff for the segfault when compares compound datasets - with combination of fixed length string types and vlen string types - in certain orders. bug#2089 (JKM 2010/12/28) - - Improve h5diff performance. 1) use HDmemcmp() before comparing each - elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype - information at dataset level not each element level for compound - datasets - - Fixed h5ls to display nested compound type with curly bracket - when -S (--simple) option is used with -l (--label), so it shows - which member (in curly bracket) belong to which nested compound type - and make the output make sense. bug#1979 (JKM 2010/11/09) - - Fixed h5diff to handle variable-length strings in a compound dataset - correctly. (also variable-length string array in a compound dataset) - Garbage values were displayed when h5diff compared multiple - variable-length strings in a compound type dataset. - Bug#1989 (JKM 2010/10/28) - - Fixed h5copy to fail gracefully when copying object to non-exist - group without -p option. Bug#2040 (JKM 2010/10/18) - - Fixed to compare member objects and groups recursively when two - files or groups are specified to be compared. Bug#1975 - (JKM 2010/9/16) - - Make h5repack be able to convert a layout to COMPACT for small size - dataset as default. bug#1896 (JKM 2010/09/15) - - Change h5ls not to manipulate special characters in object name or - attribute name for smart display. bug#1784 (JKM 2010/06/28) - - Fixed h5ls to return exit code 1 (error) when non-existent file is - specified. bug#1793. (JKM 2010/04/27) - - h5copy failed to copy dangling link when the link is specified - directly. bug#1817. (JKM 2010/04/22) - - h5repack lost attributes from a dataset of reference type. bug#1726. - (JKM 2010/3/25) - - h5repack sets NULL for object reference value for group or - named datatype. bug#1814. (JKM 2010/03/19) - - h5diff: fixed incorrect behavior (hang) in parallel mode when - specify invalid options (ex: -v and -q) (JKM 2010/02/17) - - h5dump/h5ls display buffer resize fixed in tools library. - (ADB - 2009/07/21 - 1520) - - Fixed many problems that could occur when using h5repack with named - datatypes. (NAF - 2009/4/20 - 1516/1466) - - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets - that have a datatype datum size greater than H5TOOLS_BUFSIZE, a - constant defined as 1024Kb, such as array types with large - dimensions (PVN - 2009/4/1 - 1501) - - h5import: By selecting a compression type, a big endian byte order was being - selected (PVN - 2009/3/11 - 1462) - - zip_perf.c had missing argument on one of the open() calls. Fixed. - (AKC - 2008/12/9) - - h5dump now checks for uniqueness of committed datatypes. - (NAF - 2008/10/15) - - Fixed unnecessary indentation of committed datatypes in h5dump. - (NAF - 2008/10/15) - - Fixed bugs in h5stat:segmemtation fault when printing groups and - print warning message when traversal of objects is unsuccessful. - (see bug #1253) (VC- 2008/10/13) - - Fixed bug in h5ls that prevented relative group listings (like - "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) - - Fixed bug in h5diff that prevented datasets & attributes with - variable-length string elements from comparing correctly. - (QAK - 2008/02/28) - - h5import bug on Windows w/binary datasets. fread in windows needs a - binary file to be open with 'rb' instead of 'r' otherwise it - terminates execution if an end of file character is found on the - input file. Besides that the binary file generated needs to be open - with 'wb' , otherwise an end of line character is read twice. - (PVN - 2008/02/19) - - Fixed bug in h5dump that caused binary output to be made only for the first - dataset, when several datasets were requested. (PVN - 2008/04/07) - - h5dump: when doing binary output (-b), the stdout printing of attributes - was done incorrectly. Removed printing of attributes when doing binary - output. PVN - 2008/06/05 - + - Fix h5repack to only print output when verbose option is selected - High-Level APIs: - ------ - - Fixed problem with H5DSget_scale_name including the NULL terminator in - the size calculation returned by the function. The API does not - include the NULL terminator in the size returned (MSB- 2013/2/10) - - - Fixed problem with H5TBdelete_record destroying all data following the deletion - of a row. (MSB- 2012/7/26) + When timing option was added to h5repack, the check for verbose was + incorrectly implemented. - - Fixed H5LTget_attribute_string not closing an object identifier when an - error occurs. (MSB- 2012/7/21) + (ADB - 2022/12/02, GH #2270) - - Fixed the H5LTdtype_to_text function. It had some memory problems when - dealing with some complicated data types. HDFFVI-7701 (SLU - 2011/10/19) - - Fixed a bug in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale - caused by using H5Tget_native_type function to determine the native - type for reading REFERENCE_LIST attribute. The bug was exposed - on Mac PPC. - (EIP - 2010/05/22 -1851) - - Fixed a bug in the H5DSdetach_scale function when 0 bytes - were allocated after the last reference to a dim. scale - was removed from the list of references in a VL element of the - DIMENSION_LIST attribute; modified the function to comply - with the Spec: DIMENSION_LIST attribute is deleted now when no - dimension scales left attached. - (EIP - 2010/05/14 -1822) - - Fixed a bug where the H5TB API would forget the order of fields when - added out of offset order. (NAF - 2009/10/27 - 1582) - - H5DSis_attached failed to account for different platform types. Added a - get native type call. (ADB - 2009/9/29 - 1562) - - Dimension scales: The scale index return value in H5DSiterate_scales was not always - incremented. (PVN - 2009/4/8 - 1538) + Performance + ------------- + - - Fortran High-Level APIs: - ------ - - Lite: The h5ltget_attribute_string_f used to return the C NULL character in the - returned character buffer. The returned Fortran charactor buffer now does - not return the C NULL character. (MSB - 2012/3/23) - - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) - was not correctly returning the dimension array. (PVN - 2009/3/23) - - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions - had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 + Fortran API + ----------- + - + High-Level Library + ------------------ + - + Fortran High-Level APIs + ----------------------- + - - Documentation - ------------- + Documentation + ------------- + - F90 APIs -------- - - Modified the h5open_f and h5close_f subroutines to not to call H5open - and H5close correspodningly. While the H5open call just adds overhead, - the H5close call called by an Fortran application shuts down the HDF5 - library making it unaccessible to the application. - HDFFV-915 (EIP & SB - 2011/10/13) - + - + C++ APIs -------- - - The constructor PropList::PropList(id) was fixed to act properly - according to the nature of 'id'. When 'id' is a property class id, - a new property list will be created. When 'id' id a property list id, - a copy of the property list will be made. (BMR - 2010/5/9) - - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and - CommonFG::getComment, respectively, now have default values for - user's convenience. (BMR - 2009/10/23) - - NULL pointer accessing was fixed, bugzilla 1061. (BMR - 2009/10/05) - - read/write methods of DataSet and Attribute classes were fixed - to handle string correctly. (BMR - 2009/07/26) - - Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20) - - Fixed bug in PropList::getClassName to use portable HDfree instead - of free. (BMR - 2008/04/20) - - Fixed a design bug which allowed an Attribute object to create/modify - attributes (bugzilla #1068). The API class hierarchy was revised - to address the problem. Classes AbstractDS and Attribute are moved - out of H5Object. Class Attribute now multiply inherits from - IdComponent and AbstractDs and class DataSet from H5Object and - AbstractDs. In addition, the data member IdComponent::id was - moved into subclasses: Attribute, DataSet, DataSpace, DataType, - H5File, Group, and PropList. (BMR - 2008/08/10) - - IdComponent::dereference was incorrect and replaced as described - in "New Features" section. - (BMR - 2008/08/10) + - + Testing ------- - - tools/h5diff/testh5diff.sh is run in every "make check", even after it - has passed in the previous run. It should not run again if there is no - code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392) - - In some Mac system, testlibinfo.sh failed with this error: - Check file ../src/.libs/libhdf5.7.dylib - strings: object: ../src/.libs/libhdf5.7.dylib malformed object \ - (unknown load command 15) - The strings command of Mac inspects library files and older - versions of strings may not know newer library format, resulting - in errors. Fixed by sending the library file as stdin to the strings - coommand to avoid this problem. (AKC - 2013/03/08 HDFFV-8305) - - - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation - faulted when used before. (AKC - 2013/02/12 HDFFV-8267) - - -Supported Platforms -=================== - AIX 6.1 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.2 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 13.7-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 14.0.2 (Build 20140120) - - Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.2 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 14.0.2 (Build 20140120) - - Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.8.2 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 13.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 14.0.2 (Build 20140120) - - Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers - ch5.x86_64 GNU/Linux Version 12.1.5.339 - (LLNL Aztec) - - IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 - (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 - XL Fortran for Blue Gene/P, bgxlf90 V11.1 - - SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc - (emu) Sun Fortran 95 8.6 SunOS_sparc - Sun C++ 5.12 SunOS_sparc - - Windows 7 Visual Studio 2008 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 - 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 - (duck) gfortran GNU Fortran (GCC) 4.6.2 - - Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 - (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 - gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 - g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 - gfortran GNU Fortran (GCC) 4.6.2 - - -Tested Configuration Features Summary -===================================== - - In the tables below - y = tested - n = not tested in this release - C = Cluster - W = Workstation - x = not working in this release - dna = does not apply - ( ) = footnote appears below second table - <blank> = testing incomplete on this feature or platform - -Platform C F90/ F90 C++ zlib SZIP - parallel F2003 parallel -Solaris2.11 32-bit n y/y n y y y -Solaris2.11 64-bit n y/n n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/n n y y y -Windows 7 x64 Cygwin n y/n n y y y -Windows 8 y y/y n y y y -Windows 8 x64 y y/y n y y y -Mac OS X Lion 10.7.3 32-bit n y/y n y y n -Mac OS X Lion 10.7.3 64-bit n y/y n y y y -Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y -Mac OS X Mavericks 10.9.1 64-bit n y/y n y y ? -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.11 32-bit y y y y -Solaris2.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y -Windows 8 y y y y -Windows 8 x64 y y y y -Mac OS X Lion 10.7.3 32-bit y n y y -Mac OS X Lion 10.7.3 64-bit y n y y -Mac OS X Mountain Lion 10.8.1 64-bit y n y y -Mac OS X Mavericks 10.9.1 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n -CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n -Linux 2.6.32-431.11.2.el6.ppc64 y y y n - -Compiler versions for each platform are listed in the preceding -"Supported Platforms" table. - - -More Tested Platforms -===================== -The following platforms are not supported but have been tested for this release. - - Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with - #1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1 - (jam) g95 (GCC 4.0.3 (g95 0.94!) - - Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with - #1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1 - (platypus) g95 (GCC 4.0.3 (g95 0.94!) - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - Debian7.5.0 3.2.0-4-686 #1 SMP Debian 3.2.51-1 i686 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.i6866 #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT i686 athlon i386 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 - hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai - + - -Known Problems -============== -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro DETECT_I - in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for - H5detect.c. In the future, we can separate flags for H5detect.c from the rest of - the library. (SLU - 2013/10/16) - -* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It - complains with this message: - "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. - - The reason is that __func__ is a predefined identifier in C99 standard. The - HDF5 C library uses it in H5private.h. The test ttypes.cpp includes - H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 - C++ compiler doesn't support __func__, thus fails to compile the C++ test. - But 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this - identifier, try to compile the following simple C++ program: - #include<stdio.h> - - int main(void) - { - printf("%s\n", __func__); - return 0; - } - (SLU - 2012/11/5) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The data conversion test dt_arith.c has failures (segmentation fault) from - "long double" to other datatypes during hard conversion when the library - is built with the default GCC 4.2.1 on Mac Lion system. It only happens - with optimization (-O3, -O2, and -O1). Some newer versions of GCC do not - have this problem. Users should disable optimization or try newer version - of GCC. (Issue 8017. SLU - 2012/6/12) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal - (3.2.2 on Fedora) doesn't have the problem. Users should lower down the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - It will overwrite the library's default optimization level. (Issue 7829. - SLU - 2012/2/7) - -* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or filesystems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - -* Parallel mode in AIX will fail some of the testcheck_version.sh tests where - it treats "exit(134) the same as if process 0 had received an abort signal. - This is fixed and will be available in the next release. AKC - 2009/11/3 - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not - existing. This is due to the MPI_File_open() call failing if the amode has - the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. (CMC - 2009/04/28) - -* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel - tests failed with MPI-IO file locking message. AKC - 2007/6/25. -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use - -mp -O1 compilation flags to build the libraries. Higher level of optimization - causes failures in several HDF5 library tests. -* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the - shared libraries (tested for 1.8.0-beta2) -* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass - and the parallel tests also pass with lots of non-fatal error messages. -* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test -* configuring with --enable-debug=all produces compiler errors on most - platforms. Users who want to run HDF5 in debug mode should use - --enable-debug rather than --enable-debug=all to enable debugging - information on most modules. -* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long - double to (unsigned) long long and from (unsigned)long long to long double. -* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3 - optimization flag. -* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to - HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard - for floating-point data. -* On Cray X1, a lone colon on the command line of h5dump --xml (as in - the testh5dumpxml.sh script) is misinterpereted by the operating system - and causes an error. -* On mpich 1.2.5 and 1.2.6, we found that if more than two processes - contribute no IO and the application asks to do IO with collective, we found - that when using 4 processors, a simple collective write will be hung - sometimes. This can be verified with t_mpi test under testpar. -* The dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is - enabled. There was a bug in the calculating code of the Fletcher32 - checksum in the library before v1.6.3. The checksum value wasn't consistent - between big-endian and little-endian systems. This bug was fixed in - Release 1.6.3. However, after fixing the bug, the checksum value is no - longer the same as before on little-endian system. The library release - after 1.6.4 can still read the dataset created or rewritten with the library - of v1.6.2 or before. SLU - 2005/6/30 -* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron - processor, there's a bug in the compiler for optimization(-O2). The library - failed in several tests but all related to multi driver. The problem has - been reported to the vendor. -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command poe. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - The tests may fail with messages like "The socket name is already - in use". HDF5 does not use sockets (except for stream-VFD). This is - due to problems of the poe command trying to set up the debug socket. - Check if there are many old /tmp/s.pedb.* staying around. These are - sockets used by the poe command and left behind due to failed commands. - Ask your system administrator to clean them out. Lastly, request IBM - to provide a mean to run poe without the debug socket. - -* The C++ library's tests fails when compiling with PGI C++ compiler. The - workaround until the problem is correctly handled is to use the - flag "--instantiate=local" prior to the configure and build steps, as: - setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher - - -* The stream-vfd test uses ip port 10007 for testing. If another - application is already using that port address, the test will hang - indefinitely and has to be terminated by the kill command. To try the - test again, change the port address in test/stream_test.c to one not - being used in the host. - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - -* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during - compilation. The ANSI version of the compiler complains about not being - able to handle the `long long' datatype with the warning: - - warning: ANSI C does not support `long long' - - This warning is innocuous and can be safely ignored. - -* Certain platforms give false negatives when testing h5ls: - - Cray J90 and Cray T90IEEE give errors during testing when displaying - some floating-point values. These are benign differences due to - the different precision in the values displayed and h5ls appears to - be dumping floating-point numbers correctly. - -* Not all platforms behave correctly with szip's shared libraries. Szip is - disabled in these cases, and a message is relayed at configure time. Static - libraries should be working on all systems that support szip, and should be - used when shared libraries are unavailable. There is also a configure error - on Altix machines that incorrectly reports when a version of szip without - an encoder is being used. - -* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library, - compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line - IF (total_error .ne. 0) CALL exit (total_error) - -* Information about building with PGI and Intel compilers is available in - INSTALL file sections 5.7 and 5.8 - -* On at least one system, (SDSC DataStar), the scheduler (in this case - LoadLeveler) sends job status updates to standard error when you run - any executable that was compiled with the parallel compilers. - - This causes problems when running "make check" on parallel builds, as - many of the tool tests function by saving the output from test runs, - and comparing it to an exemplar. - - The best solution is to reconfigure the target system so it no longer - inserts the extra text. However, this may not be practical. - - In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to - the configure and build. This will cause "make check" to continue after - detecting errors in the tool tests. However, in the case of SDSC DataStar, - it also leaves you with some 150 "failed" tests to examine by hand. - - A second solution is to write a script to run serial tests and filter - out the text added by the scheduler. A sample script used on SDSC - DataStar is given below, but you will probably have to customize it - for your installation. - - Observe that the basic idea is to insert the script as the first item - on the command line which executes the the test. The script then - executes the test and filters out the offending text before passing - it on. - - #!/bin/csh - - set STDOUT_FILE=~/bin/serial_filter.stdout - set STDERR_FILE=~/bin/serial_filter.stderr - - rm -f $STDOUT_FILE $STDERR_FILE - - ($* > $STDOUT_FILE) >& $STDERR_FILE - - set RETURN_VALUE=$status - - cat $STDOUT_FILE - - tail +3 $STDERR_FILE - - exit $RETURN_VALUE - You get the HDF make files and test scipts to execute your filter script - by setting the environment variable "RUNSERIAL" to the full path of the - script prior to running configure for parallel builds. Remember to - "unsetenv RUNSERIAL" before running configure for a serial build. +Platforms Tested +=================== - Note that the RUNSERIAL environment variable exists so that we can - can prefix serial runs as necessary on the target system. On DataStar, - no prefix is necessary. However on an MPICH system, the prefix might - have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to - get the serial tests to run at all. + Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16 + #1 SMP x86_64 GNU/Linux Cray clang 14.0.0 + (crusher) GCC 11.2.0 + (cmake) + + Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 + #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5) + (stria) GCC 7.2.0 (Spack GCC) + (cmake) + + Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1 + (vortex) GCC 8.3.1 + XL 16.1.1 + (cmake) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 + (lassen) GCC 8.3.1 + XL 16.1.1.2, 2021,09.22, 2022.08.05 + (cmake) + + Linux-4.12.14-197.99-default cray-mpich/7.7.14 + #1 SMP x86_64 GNU/Linux cce 12.0.3 + (theta) GCC 11.2.0 + llvm 9.0 + Intel 19.1.2 + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + (autotools and cmake) + + Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 19.0.4, 2022.2, oneapi.2022.2 + + Linux-3.10.0-1160.71.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (skybridge) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (attaway) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux Intel/19.1 + (chama) (cmake) + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2022 (cmake) + Visual Studio 2022 w/ clang 15.0.1 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2022 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) - In such cases, you will have to include the regular prefix in your - filter script. -* H5Ocopy() does not copy reg_ref attributes correctly when shared-message - is turn on. The value of the reference in the destination attriubte is - wrong. This H5Ocopy problem will affect h5copy tool +Known Problems +============== + ************************************************************ + * _ * + * (_) * + * __ ____ _ _ __ _ __ _ _ __ __ _ * + * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | * + * \ V V / (_| | | | | | | | | | | (_| | * + * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | * + * __/ | * + * |___/ * + * * + * Please refrain from running any program (including * + * HDF5 tests) which uses the subfiling VFD on Perlmutter * + * at the National Energy Research Scientific Computing * + * Center, NERSC. * + * Doing so may cause a system disruption due to subfiling * + * crashing Lustre. The sytem's Lustre bug is expected * + * to be resolved by 2023. * + * * + ************************************************************ + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Several tests currently fail on certain platforms: + MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. + + MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with + cray-mpich on theta and with XL compilers on ppc64le platforms. + + MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and are avoided by not building +the gif tool by default. Enable building the High-Level tools with these options: + autotools: --enable-hltools + cmake: HDF5_BUILD_HL_TOOLS=ON diff --git a/release_docs/USING_CMake_Examples.txt b/release_docs/USING_CMake_Examples.txt index db97ad2..853fa4f 100644 --- a/release_docs/USING_CMake_Examples.txt +++ b/release_docs/USING_CMake_Examples.txt @@ -2,38 +2,32 @@ * Build and Test HDF5 Examples with CMake * ************************************************************************ -Notes: This short instruction is written for users who want to quickly +Notes: This short instruction is written for users who want to quickly test the installation of HDF5 by using the CMake tools to build and test the HDF5 Examples. The following instructions will show the default usage and then present common changes for non-default installations. For more information, see the USING_HDF5_CMake.txt file. - - More information about using CMake can be found at the KitWare + + More information about using CMake can be found at the KitWare site, www.cmake.org. - + CMake uses the command line and these instructions use the script method of the ctest command. ======================================================================== -I. Preconditions +I. Preconditions ======================================================================== - 1. We suggest you obtain the latest CMake for windows from the Kitware - web site. The HDF5 1.8.x product requires a minimum CMake version - of 3.1.0. - - 2. You have installed the HDF5 library built with CMake, by executing - the HDF Install Utility (the *.exe file in the binary package for - Windows or the *.sh on Linux). If you are using a Windows platform, - you can obtain a pre-built Windows binary from The HDF Group's website - at www.hdfgroup.org. See Section "III. Common changes to the - HDF518_Examples.cmake file", for the line to change the location. - - 3. On Windows, you have installed the 7Zip package. See Section "III. - Common changes to the HDF518_Examples.cmake file", for the line to - change the command. + 1. We suggest you obtain the latest CMake for your platform from the Kitware + web site. The HDF5 1.13.x product requires a minimum CMake version + of 3.18. If you are using VS2022, the minimum version is 3.21. + + 2. You have installed the HDF5 library built with CMake, by executing + the HDF Install Utility (the *.msi file in the binary package for + Windows or the *.sh on Linux). You can obtain pre-built binaries + from The HDF Group's website at www.hdfgroup.org. @@ -42,42 +36,54 @@ II. Building HDF5 Examples with CMake ======================================================================== Files in the HDF5 install directory: - HDF5Examples-0.1.1-Source.zip (or HDF5Examples-0.1.1-Source.tar.gz) - HDF518_Examples.cmake - + HDF5Examples folder + CTestScript.cmake + HDF5_Examples.cmake + HDF5_Examples_options.cmake + Default installation process: Create a directory to run the examples, i.e. \test_hdf5. - Copy HDF5Examples-0.1.1-Source.zip(.tar.gz) to this directory, do NOT unzip. - Copy HDF518_Examples.cmake to this directory. - Edit line 8 of the HDF518_Examples.cmake file and change the INSTALLDIR - to the HDF5 install location. - - Execute from this directory: - ctest -S HDF518_Examples.cmake,HDF5Examples-0.1.1-Source -C Release -O test.log - -The script will uncompress the examples file HDF5Examples-0.1.1-Source.zip(.tar.gz), - and create a build directory inside the HDF5Examples-0.1.1-Source directory. - It will then configure, build, and execute the examples. All the log files - will be found under the build\Testing\Temporary directory, check these for - errors. - -The amount of script information can be increased by adding -V to the ctest - command. Even more information can be shown by adding -VV instead of -V. + Copy HDF5Examples folder to this directory. + Copy CTestScript.cmake to this directory. + Copy HDF5_Examples.cmake to this directory. + Copy HDF5_Examples_options.cmake to this directory. + The default source folder is defined as "HDF5Examples". It can be changed + with the CTEST_SOURCE_NAME script option. + The default installation folder is defined for the platform. + It can be changed with the INSTALLDIR script option. + (Note: Windows has issues with spaces and paths -The path will need to + be set correctly.) + The default ctest configuration is defined as "Release". It can be changed + with the CTEST_CONFIGURATION_TYPE script option. Note that this must + be the same as the value used with the -C command line option. + The default build configuration is defined to build and use static libraries. + + Shared libraries and other options can be changed by editing the + HDF5_Examples_options.cmake file. + + If the defaults are okay, execute from this directory: + ctest -S HDF5_Examples.cmake -C Release -V -O test.log + If the defaults need change, execute from this directory: + ctest -S HDF5_Examples.cmake,CTEST_SOURCE_NAME=MyExamples,INSTALLDIR=MyLocation -C Release -V -O test.log + + When executed, the ctest script will save the results to the log file, test.log, as + indicated by the ctest command. If you wish the to see more build and test information, + add "-VV" to the ctest command. The output should show; + 100% tests passed, 0 tests failed out of 156. ======================================================================== -III. Common changes to the HDF518_Examples.cmake file +III. Defaults in the HDF5_Examples_options.cmake file ======================================================================== -Line 8: change the INSTALLDIR to a different HDF5 install location. - -Line 14: uncomment to allow Mac machines to build shared examples. - -Line 15: uncomment to build and test Fortran examples. - -Line 16: uncomment to build and test Fortran examples with F2003 option. - -Line 17: comment to use an existing source directory. - -Line 71: change the CTEST_7Z_COMMAND to a different unzip program. +#### DEFAULT: ### +#### BUILD_SHARED_LIBS:BOOL=OFF ### +#### HDF_BUILD_C:BOOL=ON ### +#### HDF_BUILD_CXX:BOOL=OFF ### +#### HDF_BUILD_FORTRAN:BOOL=OFF ### +#### HDF_BUILD_JAVA:BOOL=OFF ### +#### HDF_BUILD_FILTERS:BOOL=OFF ### +#### BUILD_TESTING:BOOL=OFF ### +#### HDF_ENABLE_PARALLEL:BOOL=OFF ### +#### HDF_ENABLE_THREADSAFE:BOOL=OFF ### diff --git a/release_docs/USING_HDF5_CMake.txt b/release_docs/USING_HDF5_CMake.txt index 347876c..e8e50df 100644 --- a/release_docs/USING_HDF5_CMake.txt +++ b/release_docs/USING_HDF5_CMake.txt @@ -2,60 +2,80 @@ * Build and Install HDF5 Applications with CMake * ************************************************************************ -Notes: This short instruction is written for users who want to quickly - build HDF5 applications using the CMake tools. Users can adapt - these instructions for their own applications. For more information, +Notes: This short instruction is written for users who want to quickly + build HDF5 applications using the CMake tools. Users can adapt + these instructions for their own applications. For more information, see the "Minimum C Project Files for CMake" section. - - More information about using CMake can be found at the KitWare + + More information about using CMake can be found at the KitWare site, www.cmake.org. - - CMake uses the command line; however, the visual CMake tool is + + CMake uses the command line; however, the visual CMake tool is available for the configuration step. The steps are similar for all of the operating systems supported by CMake. - + NOTES: - 1. Using CMake for building and using HDF5 is under active - development. While we have attempted to provide error-free - files, please understand that development with CMake has not - been extensively tested outside of HDF. The CMake specific + 1. Using CMake for building and using HDF5 is under active + development. While we have attempted to provide error-free + files, please understand that development with CMake has not + been extensively tested outside of HDF. The CMake specific files may change before the next release. - - 2. CMake for HDF5 development should be usable on any system - where CMake is supported. Please send us any comments on how - CMake support can be improved on any system. - - 3. See the appendix at the bottom of this file for an example - of using a ctest script for building and testing. See + + 2. CMake for HDF5 development should be usable on any system + where CMake is supported. Please send us any comments on how + CMake support can be improved on any system. + + 3. See the appendix at the bottom of this file for an example + of using a ctest script for building and testing. See INSTALL_CMake.txt for more information. + 4. See https://cmake.org/cmake/help/latest/command/find_package.html + for more information on the CMake "Config Mode Search Procedure". ======================================================================== -I. Preconditions +I. Preconditions ======================================================================== - 1. We suggest you obtain the latest CMake for windows from the Kitware - web site. The HDF5 1.8.x product requires a minimum CMake version - of 3.1.0. - - 2. You have installed the HDF5 library built with CMake, by executing - the HDF Install Utility (the *.exe file in the binary package for - Windows). If you are using a Windows platform, you can obtain a - pre-built Windows binary from The HDF Group's website at - www.hdfgroup.org. - - 3. Set the environment variable HDF5_DIR to the installed location of - the config files for HDF5. On Windows: - HDF5_DIR=C:/Program Files/HDF_Group/HDF5/1.8.x/cmake/hdf5 - + 1. We suggest you obtain the latest CMake for your platform from the Kitware + web site. The HDF5 1.13.x product requires a minimum CMake version + of 3.18. If you are using VS2022, the minimum version is 3.21. + + 2. You have installed the HDF5 library built with CMake, by executing + the HDF Install Utility (the *.msi file in the binary package for + Windows or the *.sh on Linux). You can obtain pre-built binaries + from The HDF Group's website at www.hdfgroup.org. + + 3. Set the HDF5_ROOT CMake variable, -DHDF5_ROOT=<install_path> + or environment variable, set(ENV{HDF5_ROOT} "<install_path>") + to the installed location of HDF5. + On Windows: + HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/1.13.x/ + On unix: + HDF5_ROOT=<install root folder>/HDF_Group/HDF5/1.13.x/ + + If you are using shared libraries, you may need to add to the path + environment variable. Set the path environment variable to the + installed location of the library files for HDF5. + On Windows (*.dll): + PATH=%PATH%;C:/Program Files/HDF_Group/HDF5/1.13.x/bin + On unix (*.so): + LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<install root folder>/HDF_Group/HDF5/1.13.x/lib + + If you are using filter plugin libraries, you will need to set the + HDF5_PLUGIN_PATH environment variable. + On Windows: + HDF5_PLUGIN_PATH=C:/Program Files/HDF_Group/HDF5/1.13.x/lib/plugin + On unix: + HDF5_PLUGIN_PATH=<install root folder>/HDF_Group/HDF5/1.13.x/lib/plugin + (Note there are no quote characters used on Windows and all platforms use forward slashes) 4. Created separate source and build directories. (CMake commands are executed in the build directory) - 5. Created a CMakeLists.txt file(s) for your source. See Section III + 5. Created a CMakeLists.txt file(s) for your source. See Section III below. @@ -65,6 +85,7 @@ II. Building HDF5 Applications with CMake ======================================================================== Go through these steps to build HDF5 applications with CMake. + (The application must support building with CMake.) 1. Run CMake 2. Configure the cache settings @@ -79,95 +100,96 @@ These steps are described in more detail below. The visual CMake executable is named "cmake-gui.exe" on Windows and should be available in your Start menu. For Linux, UNIX, and Mac users the - executable is named "cmake-gui" and can be found where CMake was - installed. - - Specify the source and build directories. Make the build and source - directories different. For example on Windows, if the source is at - c:\MyHDFstuff\hdf5, then use c:\MyHDFstuff\hdf5\build or - c:\MyHDFstuff\build\hdf5 for the build directory. - + executable is named "cmake-gui" and can be found where CMake was + installed. + + Specify the source and build directories. Make the build and source + directories different. For example on Windows, if the source is at + c:\MyHDFstuff\hdf5, then use c:\MyHDFstuff\hdf5\build or + c:\MyHDFstuff\build\hdf5 for the build directory. + PREFERRED: - Users can perform the configuration step without using the visual - cmake-gui program. The following is an example command line + Users can perform the configuration step without using the visual + cmake-gui program. The following is an example command line configuration step executed within the build directory: - + cmake -G "<generator>" [-D<options>] <sourcepath> - - Where <generator> is + + Where <generator> is * MinGW Makefiles * NMake Makefiles * Unix Makefiles - * Visual Studio 12 - * Visual Studio 12 Win64 - * Visual Studio 11 - * Visual Studio 11 Win64 - * Visual Studio 10 - * Visual Studio 10 Win64 + * Visual Studio 14 2015 + * Visual Studio 14 2015 Win64 + * Visual Studio 15 2017 + * Visual Studio 15 2017 Win64 + * Visual Studio 16 2019 + * ... in addition VS2019 will need to set the "-A" option, + * ... [Win32, x64, ARM, ARM64] <options> is: * BUILD_TESTING:BOOL=ON - * USE_SHARED_LIBS:BOOL=[ON | OFF] + * BUILD_SHARED_LIBS:BOOL=[ON | OFF] 2. Configure the cache settings - 2.1 Visual CMake users, click the Configure button. If this is the first time you are - running cmake-gui in this directory, you will be prompted for the - generator you wish to use (for example on Windows, Visual Studio 10). - CMake will read in the CMakeLists.txt files from the source directory and - display options for the HDF5 project. After the first configure you + 2.1 Visual CMake users, click the Configure button. If this is the first time you are + running cmake-gui in this directory, you will be prompted for the + generator you wish to use (for example on Windows, Visual Studio 14 2015 Win64). + CMake will read in the CMakeLists.txt files from the source directory and + display options for the HDF5 project. After the first configure you can adjust the cache settings and/or specify locations of other programs. - + Any conflicts or new values will be highlighted by the configure - process in red. Once you are happy with all the settings and there are no - more values in red, click the Generate button to produce the appropriate - build files. - - On Windows, if you are using a Visual Studio generator, the solution and + process in red. Once you are happy with all the settings and there are no + more values in red, click the Generate button to produce the appropriate + build files. + + On Windows, if you are using a Visual Studio generator, the solution and project files will be created in the build folder. - + On linux, if you are using the Unix Makefiles generator, the Makefiles will be created in the build folder. 2.2 Alternative command line example on Windows in c:\MyHDFstuff\hdf5\build directory: - - cmake -G "Visual Studio 11" -DBUILD_TESTING:BOOL=ON -DUSE_SHARED_LIBS:BOOL=ON .. + + cmake -G "Visual Studio 14 2015 Win64" -DBUILD_TESTING:BOOL=ON .. 3. Build HDF5 Applications - - On Windows, you can build HDF5 applications using either the Visual Studio Environment + + On Windows, you can build HDF5 applications using either the Visual Studio Environment or the command line. The command line is normally used on linux, Unix, and Mac. To build from the command line, navigate to your build directory and execute the following: - - cmake --build . --config {Debug | Release} - + + cmake --build . --config {Debug | Release} + NOTE: "--config {Debug | Release}" may be optional on your platform. We recommend choosing either Debug or Release on Windows. If you are - using the pre-built binaries from HDF, use Release. - - 3.1 If you wish to use the Visual Studio environment, open the solution - file in your build directory. Be sure to select either Debug or + using the pre-built binaries from HDF, use Release. + + 3.1 If you wish to use the Visual Studio environment, open the solution + file in your build directory. Be sure to select either Debug or Release and build the solution. - + 4. Test HDF5 Applications To test the build, navigate to your build directory and execute: - + ctest . -C {Debug | Release} - + NOTE: "-C {Debug | Release}" may be optional on your platform. We recommend choosing either Debug or Release to match the build - step on Windows. + step on Windows. - 5. The files that support building with CMake are all of the files in the - config/cmake folder, the CMakeLists.txt files in each source folder, and - CTestConfig.cmake. CTestConfig.cmake is specific to the internal testing - performed by The HDF Group. It should be altered for the user's + 5. The files that support building with CMake are all of the files in the + config/cmake folder, the CMakeLists.txt files in each source folder, and + CTestConfig.cmake. CTestConfig.cmake is specific to the internal testing + performed by The HDF Group. It should be altered for the user's installation and needs. The cacheinit.cmake file settings are used by - The HDF Group for daily testing. It should be altered/ignored for the user's - installation and needs. + The HDF Group for daily testing. It should be altered/ignored for the user's + installation and needs. @@ -175,25 +197,28 @@ These steps are described in more detail below. III. Minimum C Project Files for CMake ======================================================================== -Create a CMakeLists.txt file at the source root. Include the -following text in the file: +Given the preconditions in section I, create a CMakeLists.txt file at the +source root. Include the following text in the file: ########################################################## -cmake_minimum_required (VERSION 3.1.0) -PROJECT (HDF5MyApp C CXX) +cmake_minimum_required (VERSION 3.18) +project (HDF5MyApp C CXX) + +set (LIB_TYPE STATIC) # or SHARED +string(TOLOWER ${LIB_TYPE} SEARCH_TYPE) -FIND_PACKAGE (HDF5 NAMES hdf5) -# FIND_PACKAGE (HDF5) # Find non-cmake built HDF5 -INCLUDE_DIRECTORIES (${HDF5_INCLUDE_DIR}) -set (LINK_LIBS ${LINK_LIBS} ${HDF5_LIBRARIES}) +find_package (HDF5 NAMES hdf5 COMPONENTS C ${SEARCH_TYPE}) +# find_package (HDF5) # Find non-cmake built HDF5 +set_directory_properties(PROPERTIES INCLUDE_DIRECTORIES "${HDF5_INCLUDE_DIR}") +set (LINK_LIBS ${LINK_LIBS} ${HDF5_C_${LIB_TYPE}_LIBRARY}) set (example hdf_example) add_executable (${example} ${PROJECT_SOURCE_DIR}/${example}.c) -TARGET_C_PROPERTIES (${example} " " " ") +TARGET_C_PROPERTIES (${example} PRIVATE ${LIB_TYPE}) target_link_libraries (${example} ${LINK_LIBS}) -ENABLE_TESTING () +enable_testing () include (CTest) add_test (NAME test_example COMMAND ${example}) @@ -205,67 +230,21 @@ add_test (NAME test_example COMMAND ${example}) IV. APPENDIX ======================================================================== -Below is an example of the ctest script used by The HDF Group. See the -Appendix in the INSTALL_CMake.txt file for the CTestScript.cmake file used -by this script. Adjust the values as necessary. Note that the source folder -is entered on the command line and the build folder is created as a sub-folder. -Windows should adjust the forward slash to double backslashes, except for -the HDF_DIR environment variable. - -NOTE: these files are available at the HDF web site: - http://www.hdfgroup.org/HDF5/release/cmakebuild.html - - CTestScript.cmake - - HDF518ExamplesWindowsbinaryCMake.cmake - - - -======================================================================== -ctest -======================================================================== - -############################################################################ -# Product specific script, HDF518Example.cmake, that uses the -# CTestScript.cmake file (see Appendix in the CMake.txt). Usage: -# "ctest -S HDF518Example.cmake,hdf518Examples -C Release -O hdf518EX.log" -# where hdf518Examples is the source folder relative to the location of these scripts -############################################################################ - -cmake_minimum_required(VERSION 3.1.0 FATAL_ERROR) - -set(CTEST_DASHBOARD_ROOT ${CTEST_SCRIPT_DIRECTORY}) -set(CTEST_SOURCE_NAME ${CTEST_SCRIPT_ARG}) -set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}/build) -set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_SOURCE_NAME}") -set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_BINARY_NAME}") -set(CTEST_BUILD_CONFIGURATION "Release") -set(MODEL "Experimental") - -# build generator name, see cmake generator list -set(CTEST_CMAKE_GENERATOR "Unix Makefiles") - -# machine description, can be removed on linux -set(CTEST_SITE "machine.domain") -set(SITE_OS_NAME "os name") -set(SITE_OS_VERSION "os version") -set(SITE_OS_BITS "os size") -set(SITE_COMPILER_NAME "compiler name") -set(SITE_COMPILER_VERSION "compiler version") - -# needed for source updates, change as required -set(REPOSITORY_URL "http://svn.${hdfgroup_url}/hdf5-examples/trunk/1_8") - -set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/hdf5Examples-1.8") - -# location of the installed hdf5 (cmake configuration folder) -set(ENV{HDF5_DIR} "/usr/share/cmake/hdf5") +Below is an example of a ctest script that can be used to build the examples. +Adjust the values as necessary. Note that the defaults can be entered on the +command line and the build folder is created as a sub-folder. Windows should +adjust the forward slash to double backslashes, except for the HDF_DIR +environment variable. -include(${CTEST_SCRIPT_DIRECTORY}/CTestScript.cmake) +NOTE: this file is available at the HDF web site: + https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake -message("DONE") -################################################################################# + HDF5_Examples.cmake + HDF5_Examples_options.cmake +Also available at the HDF web site is a CMake application framework template. +You can quickly add files to the framework and execute the script to compile +your application with an installed HDF5 binary. ======================================================================== diff --git a/release_docs/USING_HDF5_VS.txt b/release_docs/USING_HDF5_VS.txt index 9063ea6..5ec9996 100644 --- a/release_docs/USING_HDF5_VS.txt +++ b/release_docs/USING_HDF5_VS.txt @@ -6,29 +6,32 @@ These suggestions are for Visual Studio users. -Instructions for building and testing HDF5 applications using CMake can +Instructions for building and testing HDF5 applications using CMake can be found in the USING_HDF5_CMake.txt file found in this folder. -The following two sections are helpful if you do not use CMake to build +NOTE: Building applications with the dynamic/shared hdf5 libraries requires + that the "H5_BUILT_AS_DYNAMIC_LIB" compile definition be used. + +The following two sections are helpful if you do not use CMake to build your applications. - -======================================================================== -Using Visual Studio 2010 with HDF5 Libraries built with Visual Studio 2010 -======================================================================== + +============================================================================================== +Using Visual Studio 2010 and above with HDF5 Libraries built with Visual Studio 2010 and above +============================================================================================== 1. Set up path for external libraries and headers - The path settings will need to be in the project property sheets per project. - Go to "Project" and select "Properties", find "Configuration Properties", + The path settings will need to be in the project property sheets per project. + Go to "Project" and select "Properties", find "Configuration Properties", and then "VC++ Directories". - + 1.1 If you are building on 64-bit Windows, find the "Platform" dropdown and select "x64". - + 1.2 Add the header path to the "Include Directories" setting. - + 1.3 Add the library path to the "Library Directories" setting. - + 1.4 Select Linker->Input and beginning with the "Additional Dependencies" line, enter the library names. The external libraries should be listed first, followed by the HDF5 @@ -37,30 +40,30 @@ Using Visual Studio 2010 with HDF5 Libraries built with Visual Studio 2010 szip.lib zlib.lib hdf5.lib hdf5_cpp.lib - + ========================================================================== Using Visual Studio 2008 with HDF5 Libraries built with Visual Studio 2008 ========================================================================== 2. Set up the path for external libraries and headers - Invoke Microsoft Visual Studio and go to "Tools" and select "Options", + Invoke Microsoft Visual Studio and go to "Tools" and select "Options", find "Projects", and then "VC++ Directories". - + 2.1 If you are building on 64-bit Windows, find the "Platform" dropdown and select "x64". - 2.2 Find the box "Show directories for", choose "Include files", add the - header path (i.e. c:\Program Files\HDF_Group\HDF5\1.8.x\include) + 2.2 Find the box "Show directories for", choose "Include files", add the + header path (i.e. c:\Program Files\HDF_Group\HDF5\1.13.x\include) to the included directories. 2.3 Find the box "Show directories for", choose "Library files", add the - library path (i.e. c:\Program Files\HDF_Group\HDF5\1.8.x\lib) + library path (i.e. c:\Program Files\HDF_Group\HDF5\1.13.x\lib) to the library directories. - + 2.4 If using Fortran libraries, you will also need to setup the path for the Intel Fortran compiler. - + 2.5 Select Project->Properties->Linker->Input and beginning with the "Additional Dependencies" line, enter the library names. The external libraries should be listed first, followed by the HDF5 @@ -74,15 +77,11 @@ Using Visual Studio 2008 with HDF5 Libraries built with Visual Studio 2008 ======================================================================== 3.1 FAQ - + Many other common questions and hints are located online and being updated - in the HDF5 FAQ. For Windows-specific questions, please see: - - http://www.hdfgroup.org/HDF5/faq/windows.html - - For all other general questions, you can look in the general FAQ: - - http://hdfgroup.org/HDF5-FAQ.html - + in the HDF Knowledge Base, please see: + + https://portal.hdfgroup.org/display/knowledge/HDF+Knowledge+Base + ************************************************************************ Please send email to help@hdfgroup.org for further assistance. |