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authorLarry Knox <lrknox@hdfgroup.org>2019-03-07 18:51:27 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2019-03-07 18:51:27 (GMT)
commit8d2a047c25d2bd34c52c8d437802c309a9ae0985 (patch)
treef6e750cea1205d78f86a89ed6f3d0dbcafbe1f28
parentcdec6ca87f5485aa29679070908d4774127e8a78 (diff)
parent775e3740d64ca9a8a31ded673e93815d76387dad (diff)
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Merge pull request #1593 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '775e3740d64ca9a8a31ded673e93815d76387dad': Update documents following DHF5 1.10.5 release.
-rw-r--r--release_docs/HISTORY-1_10.txt1035
-rw-r--r--release_docs/README_HDF5_CMake23
-rw-r--r--release_docs/README_HPC285
3 files changed, 1264 insertions, 79 deletions
diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt
index 9887a54..ad8beb2 100644
--- a/release_docs/HISTORY-1_10.txt
+++ b/release_docs/HISTORY-1_10.txt
@@ -3,6 +3,8 @@ HDF5 History
This file contains development history of the HDF5 1.10 branch
+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
@@ -10,6 +12,1039 @@ This file contains development history of the HDF5 1.10 branch
[Search on the string '%%%%' for section breaks of each release.]
+%%%%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 specied 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
diff --git a/release_docs/README_HDF5_CMake b/release_docs/README_HDF5_CMake
new file mode 100644
index 0000000..a2e7dce
--- /dev/null
+++ b/release_docs/README_HDF5_CMake
@@ -0,0 +1,23 @@
+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
+ hdf5-1.11.4 HDF5 1.11.4 source
+ SZip.tar.gz source for building SZIP
+ ZLib.tar.gz source for building ZLIB
+
+For more information about building HDF5 with CMake, see USING_HDF5_CMake.txt in
+hdf5-1.11.4/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 hdf5-1.11.4/release_docs.
+
+
+
+
+
diff --git a/release_docs/README_HPC b/release_docs/README_HPC
index bdeab67..67a5d6c 100644
--- a/release_docs/README_HPC
+++ b/release_docs/README_HPC
@@ -1,79 +1,206 @@
-HDF5 version 1.11.4 currently under development
-
-HDF5 source tar files with the HPC prefix are intended for use on clusters where
-configuration and build steps will be done on a login node and executable and
-lib files that are built will be run on compute nodes.
-
-Note these differences from the regular CMake tar and zip files:
- - Test programs produced by this tar file will be run using batch scripts.
- - Serial and parallel HDF5options.cmake files, using parallel options by default.
-
-Note also that options are now available in HDF5 source to facilitate use of
-toolchain files for using cross compilers available on login nodes to compile
-HDF5 for compute nodes.
-
-Instructions to configure build and test HDF5 using CMake:
-
-1. The cmake version must be 3.10 or later (cmake --version).
-2. Load or switch modules and set CC, FC, CXX for compilers desired.
-3. run build-unix.sh to configure, build, test and package HDF5 with CMake.
-
-Contents:
-
-build-unix.sh Simple script for running CMake to configure, build,
- test, and package HDF5.
-CTestScript.cmake CMake script to configure, build, test and package
- HDF5.
-hdf5-<version> HDF5 source for <version>.
-HDF5config.cmake CMake script to configure, build, test and package
- HDF5.
-HDF5Examples Source for HDF5 Examples.
-HDF5options.cmake symlink to parallel or serial HDF5options.cmake files.
- Default is parallel file, which builds and tests both
- serial and parallel C and Fortran wrappers.
- To build serial only, C Fortran and C++ wrappers, delete
- The HDF5options.cmake link and run
- 'ln -s ser-HDF5options.cmake HDF5options.cmake' to switch.
-par-HDF5options.cmake Options file for HDF5 serial and parallel build and test.
-ser-HDF5options.cmake Options file for HDF5 serial only build and test.
-SZip.tar.gz Source for building SZip.
-ZLib.tar.gz Source for buildng Zlib.
-
-
-To cross compile with this HPC-CMake tar.gz HDF5 source file:
-On Cray XC40 haswell login node for knl compute nodes using CMake and Cray modules:
- 1. Uncomment line in HDF5options.txt to use a toolchain file - line 106 for
- config/toolchain/crayle.cmake.
- 2. Uncomment lines 110, 111, and 115 - 122 of HDF5options.cmake.
- Line 110 allows configuring to complete on the haswell node.
- Line 111 switches the compiler to build files for knl nodes.
- Lines 115 - 122 set up test files to use sbatch to run build tests
- in batch jobs on a knl compute node with 6 processes.
- 3. Compiler module may be the default PrgEnv-intel/6.0.4 to use
- intel/18.0.2 or other intel, PrgEnv-cray/6.0.4 to use cce/8.7.4,
- or PrgEnv-gnu/6.0.4 for GCC compilers. PrgEnv-pgi/6.0.4 is also
- available but has not been tested with this tar file.
- 4. These CMake options are set in config/toolchain/crayle.cmake:
- set(CMAKE_SYSTEM_NAME Linux)
- set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment")
- set(CMAKE_C_COMPILER cc)
- set(CMAKE_CXX_COMPILER c++)
- set(CMAKE_Fortran_COMPILER ftn)
- set(CMAKE_CROSSCOMPILING_EMULATOR "")
-
- 5. 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
- a. 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 options.
- b. 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.
--
+************************************************************************
+* 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 3.10 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://git@bitbucket.hdfgroup.org/scm/hdffv/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 "hdf5-1.11.4", or for the first hdf5_1_10_5 pre-release version,
+it should be renamed "hdf5-1.10.5-pre1".
+
+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
+ "hdf5-1.11.4".
+
+ 2. Three cmake script files need to be copied to the working directory, or
+ have symbolic links to them, created in the working directory:
+
+ hdf5-1.11.4/config/cmake/scripts/HDF5config.cmake
+ hdf5-1.11.4/config/cmake/scripts/CTestScript.cmake
+ hdf5-1.11.4/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
+ hdf5-1.11.4
+
+ 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 hdf5-1.11.4/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/3.10.2/bin/cmake"
+-C "<working directory>/hdf5-1.11.4/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/HDF5/1.11.4
+-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>/hdf5-1.11.4"
+
+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.