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* [svn-r21117] Issue 2763 - I added a new parameter of object access property ↵Raymond Lu2011-07-181-0/+4
| | | | | | list to the function H5Rdereference. It's called H5Rdereference2 now. H5Rdereference function has been deprecated to H5Rdereference1. I also added some test cases in trefer.c. Tested on jam, heiwa, and koala.
* [svn-r21105] Fixed two bugs:Peter Cao2011-07-151-0/+4
| | | | | | | - h5repack: h5repack failed to copy dataset if the layout is changed from chunked with unlimited dims to contiguous. (PC -- 2011/07/15) - h5diff: "--delta" option considers two NaN of the same type are different, which is wrong based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15)
* [svn-r21101] HDFFV-7639Mike McGreevy2011-07-141-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Remove H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS and H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS #defines from source. Description: Two advanced parallel functionalities, special collective IO and complex derived datatypes, are not supported by older implementations of mpi, and thus our code limits the use of these features with #ifdefs and has checks in configure to set them (or not). Unfortunately, configure can't actually run a parallel check to see if these features are working (nor not) so it resorts to looking in the config files where they are explicity enabled or disabled based on versions of mpi, sytems being built on, or for no documented reason at all (i.e. just set to on or off as some 'default'). Overriding these settings is easy if need be, provided it is known that it needs to be done to get improved performance, and oftentimes it is not. Most new MPI implementations successfully handle the functionality requested when these #defines are set, and many of the "turn these features off" cases in the config files are for old (> 5 years) versions of MPI and retired systems (such as NCSA's tungsten). Therefore, the decision has been made to remove the support for these old versions of MPI and systems that cannot handle these behaviors. The #ifdefs and supporting setup in the config/ files and configure script has been removed, and the code executed when these options were not set removed from the source. In passing, this commit also cleans up some whitespace issues in both t_mpi.c and H5Dmpio.c. Furthermore, in t_mpi.c, the special collective IO test was not getting regularly run due to it being written to work only with four processes (we regularly test with six, previously with three), and thus it failed when actually run due to an out of bounds data buffer assignment. It has been modified to run at any number of processes greater than four, and the memory problem has been fixed so the test passes. Tested: jam, h5committest, ember
* [svn-r21072] Purpose:Jonathan Kim2011-07-071-0/+3
| | | | | | | | | | | | Work for HDFFV-7600 - GMQS: h5diff - argument options -d, -p and --use-system-epsilon should be mutually exclusive. Description: Fixed h5diff to display instructive error message and exit with 1 when mutually exclusive options (-d, -p and --use-system-epsilon) are used together. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r21033] Snapshot version 1.9 release 84HDF Tester2011-06-261-1/+1
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* [svn-r21015] Bug fix for Issue 2598 - In v1.6 library, there was EOA for the ↵Raymond Lu2011-06-221-1/+9
| | | | | | | | | | | | | 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. I fixed the problem by checking the EOA value to detect the file created with v1.6 library. Tested on jam, koala, and heiwa.
* [svn-r21014] Purpose:Jonathan Kim2011-06-211-0/+6
| | | | | | | | | | | | | | HDFFV-5878 - GMQS: h5dump - incorrect output format for array type with multiple elements in an index Description: 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) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r21000] Snapshot version 1.9 release 83HDF Tester2011-06-191-1/+1
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* [svn-r20929] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-031-0/+3
| | | | | | say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output. Tested on jam, koala, and heiwa.
* [svn-r20922] Snapshot version 1.9 release 82HDF Tester2011-05-291-1/+1
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* [svn-r20913] Issue 7579 - The overflowing ENUM values are inconsistent. ↵Raymond Lu2011-05-271-0/+4
| | | | | | | | | | When no conversion is involved in reading or writing the data, overflowing values are retained. When conversion happens, the values become -1. The conversion function puts -1 when overflow happens. I added two new dataset transfer property to control whether to fill 0xff in the destination data or convert to the destination data when overflow happens. The two new functions are H5Pset(get)_enum_conv_overflow. I also added test cases in enum.c and dtypes.c. Tested on jam, koala, and heiwa.
* [svn-r20890] Snapshot version 1.9 release 82HDF Tester2011-05-231-1/+1
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* [svn-r20872] Issue 7564 - Allow H5Tcreat to create string type (fixed-length ↵Raymond Lu2011-05-201-0/+2
| | | | | | and variable-length). I also added a test case in dtypes.c. Tested on jam and linew - relatively simple.
* [svn-r20808] Add Using_CMake.txt file to docs and installAllen Byrne2011-05-131-0/+181
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* [svn-r20804] Purpose:Jonathan Kim2011-05-121-0/+3
| | | | | | | | | | | | HDFFV-7594 - GMQS: h5dump shows wrong values for H5T_STD_I8LE dataset on Blue-gene (ppc64 linux BE +@) Description: For the STD_I8 type data, updated to use 'signed char' instead of 'char' as 'char' could be defined as unsigned on a certain system, which cause h5dump to display data values incorrectly. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r20767] Purpose:Jonathan Kim2011-05-061-4/+10
| | | | | | | | | | | | HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Improved performance by eliminating duplicated action for getting object information in half from the previous fixe when comparing group vs group. This is addition to the previous commit r20676. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [svn-r20713] Packed Bits Merge:Allen Byrne2011-05-031-1/+0
| | | | | | | | | removed option defines and #ifdef/#endif refactored all printf to HDfprintf in h5dump.c formatted and indention improvements synched with 1.8 branch Tested: local linux
* [svn-r20689] Changed compiler name from xlf/mpxlf_r to xlf90/mpxlf90_r to avoidAlbert Cheng2011-04-291-2/+2
| | | | | misunderstanding. xlf/mpxlf_r are actually Fortran 77 compilers. HDF5 requires Fortran 90 or higher.
* [svn-r20646] Description:Quincey Koziol2011-04-261-14/+12
| | | | | | | | | | Small improvement to the core VFD's error reporting. Update FreeBSD information Tested on: FreeBSD/32 8.2 (loyalty) (too minor to require h5committest)
* [svn-r20639] Add missing entry for "Bug HDFFV-4358"Jonathan Kim2011-04-261-0/+5
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* [svn-r20520] Removed ibm-aix6.x file which just sourced ibm-aix file. ↵Albert Cheng2011-04-151-0/+2
| | | | | | | | | | Removed code in configure.in that tried to distinguish different versions of AIX. This is no longer needed. Tested: NCSA Blue-print. No h5committest since this affected AIX system only.
* [svn-r20502] Purpose:Mike McGreevy2011-04-141-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | Add "silent make" mode configure option. Description: Automake 1.11 has a new option available that allows for a silent make mode. This functionality needs to be explicitly enabled in configure.in via the use of the automake macro AM_SILENT_RULES, which is what this commit is adding. This introduces a new configure option: --{en|dis}able-silent-rules This option is on by default, and simplies compile and link line outputs when building the library. Disabling this option will print full "verbose" output (i.e., full compile and linking lines for each target). Tested: This was tested on jam & h5committested
* [svn-r20491] Rename H5Frelease_file_cache to H5Fclear_elink_file_cache.Neil Fortner2011-04-131-1/+1
| | | | Tested: Fedora (too minor for full committest)
* [svn-r20488] Purpose:Jonathan Kim2011-04-121-0/+2
| | | | | | | | | | | Fix HDFFV-4342 : GMQS: h5dump test fails when source directory is read-only Description: Updated h5dump test case script to prevent entire test failure upon source code directory is read-only. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20482] Larry Knox2011-04-121-2/+0
| | | | | | | | | | | | | | | | Fixed issue HDFFV-5866 (BZ 2156). Changed scripts to run examples to use specific names for compiled executable files instead of a.out, which did not work on Cywin as it produces a.exe by default. Removed issue from known problems section of RELEASE.txt. Tested with Cygwin 1.7.8 on Windows 7. This line, and those below, will be ignored-- M release_docs/RELEASE.txt M hl/c++/examples/run-hlc++-ex.sh.in M hl/fortran/examples/run-hlfortran-ex.sh.in M hl/examples/run-hlc-ex.sh.in M c++/examples/run-c++-ex.sh.in M fortran/examples/run-fortran-ex.sh.in M examples/run-c-ex.sh.in
* [svn-r20475] Purpose:Mike McGreevy2011-04-111-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Revise shared Fortran library disabling scenarios in configure - Improve configure output summary Description: Shared Fortran libraries are not supported on Mac, but were being disabled by configure in a way that also forced the C libraries to be static-only. This has been fixed, so now only shared Fortran is disabled while shared C can remain. This prompted two additional changes: 1. While working on the check that addresses whether or not shared Fortran libraries are allowed, removed old and no longer needed check(s) that disable shared Fortran libraries with HP, Intel 8, PGI, and Absoft compilers. (Essentially, Mac is the only situation in which Fortran shared are disabled by configure.) 2. Having two different states of libraries (i.e. shared C library with static-only Fortran library) was not apparent in the configure summary, which labeled all libraries as either shared and/or static. I've added lines to both the C++ and Fortran output sections to list shared/static-ness of these libraries specifically. Additionally, I've made sure that the new --enable-unsupported configure option correctly overrides configure if it tries to disable a shared library. Tested: jam, fred, & h5committest
* [svn-r20410] Corrected text in INSTALL file: there is no --enable-szlib ↵Larry Knox2011-04-041-1/+1
| | | | configure option, it should be --with-szlib=.
* [svn-r20405] Description:Quincey Koziol2011-04-041-1/+1
| | | | Bump patch release number, after giving out private snapshots.
* [svn-r20384] Purpose:Jonathan Kim2011-03-311-0/+3
| | | | | | | | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Merged from HDF5 1.8 branch r20369. Fixed h5diff for --use-system-epsilon option: the calculation changed from ( |a - b| / b ) to ( |a - b| ). This was decided for better performance and was corrected only in HDF5 trunk, so 1.8 got updated. Also comments for equal_XXX() function were updated correctly. Also help page and RM got updated correctly. Also add test cases for testing the differences w/wo the option. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r20378] Purpose:Jonathan Kim2011-03-301-0/+4
| | | | | | | | | | | | | | | | | | | Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions Description: Decided to use --enable-error-stack long option name only to display error stack messages from HDF5 lib among tools. 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. For h5dump, remove -E from help page and RM , which was added by mistake before release1.8.7. Help page and RM got updated. Updated test case. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r20358] added notation for BZ 1725Allen Byrne2011-03-281-0/+6
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* [svn-r20334] Purpose:Jonathan Kim2011-03-251-0/+4
| | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: This is related to previous checkin r20294. Add help page update for verbose option level feature, which displays useful information about attribute difference with -v1, --verbose=1 -v2 or --verbose=2 option. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20315] brought revisions 19868:20300 from the 1.8.6_vms branch to the ↵Raymond Lu2011-03-241-2/+2
| | | | trunk for VMS work
* [svn-r20294] Purpose:Jonathan Kim2011-03-221-0/+4
| | | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: Previously h5diff compared attributes correctly only when two objects have the same number of attributes and attribute names are identical. This fix covers all other cases. Also didn't display useful information about attribute difference. This fixes both issues. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20274] Purpose:Jonathan Kim2011-03-181-0/+2
| | | | | | | | | | | | | | Fixed Bug 2214 - GMQS: h5diff - memory leak in diff() Description: Memory leaks occurred when accessing symbolic links with --follow-symlink option. Test cases are in testing script. (400 - 456, 501 - 518) An example test : valgrind --leak-check=full h5diff --follow-symlinks -v h5diff_softlinks.h5 h5diff_softlinks.h5 Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20270] Purpose:Jonathan Kim2011-03-181-0/+2
| | | | | | | | | | | | | | | | Improve the previous fix for Bug 2216 - GMQS: h5diff - memory leak when compares vlen string in dataset or attributes Description: Improve the fix along with the previous checkin r20266. Add a new function to tool lib, h5tools_detect_vlen_data() which return TRUE if include any kind of vlen data all at once, either VLEN-data or VLEN-string and so on. Also updated h5ls and h5dump code accordingly. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20243] Update CMake version to 2.8.4Allen Byrne2011-03-141-1/+1
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* [svn-r20231] Purpose:Jonathan Kim2011-03-111-0/+2
| | | | | | | | | | Fixed Bug 1904 - h5ls : usage of '-a' option is not clear to display expected output Description: Fixed incorrect content and improved help page for -a option of h5ls. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Cmake (jam)
* [svn-r20226] Entered known problem of --with-mpe does not work with mpich2.Albert Cheng2011-03-101-0/+2
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* [svn-r20224] Add enable-error-stack option to new features-tools section.Allen Byrne2011-03-101-7/+13
| | | | Enable h5stat tests for valgrind testing.
* [svn-r20223] Adding notes for fixing h5dump bug on -y -o options.Peter Cao2011-03-101-0/+3
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* [svn-r20203] Purpose:Jonathan Kim2011-03-081-0/+3
| | | | | | | | | | | | | Fix Bug 2120 - h5copy: improve to copy an object into same HDF file Description: Before the fix users can't copy an object (dataset or group) with different name if input file (-i) and output file (-o) is same. This feature would be useful to clone any object with different name and reuse contents. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r20188] Purpose:Jonathan Kim2011-03-041-0/+3
| | | | | | | | | | | | Fixing Bug 2161 - GMQS: h5dump - only on Windows, skip displaying a data value every a certain lines in array type dataset Description: 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. Tested: Windows, jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20141] Bring 1.8 r20139 cmake and windows changes to trunkAllen Byrne2011-02-221-72/+102
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* [svn-r20121] Bug 1586 - the datatype handler created with H5Tencode/decode ↵Raymond Lu2011-02-181-0/+3
| | | | | | had the reference count 0. I fixed it by changing the APP_REF parameter of H5I_register from FALSE to TRUE and added a test case in dtypes.c. Tested on jam, heiwa, and amani.
* [svn-r20113] Add note to RELEASE.txt about external file cache.Neil Fortner2011-02-171-0/+4
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* [svn-r20108] Purpose:Jonathan Kim2011-02-151-0/+3
| | | | | | | | | | | | | | Fixing Bug 2092 - h5dump does not display index for a dataset Description: h5dump skip displaying array indices every certain number when the array type dataset is relatively big. The certain number varies according to the size of each array. This checkin fix the skipping array indices problem. This fix also correct indentation of the dataset data output. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20095] Removed AIX 5.3 and Cray xt3, added AIX 6.1 as supported platforms.Albert Cheng2011-02-131-13/+8
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* [svn-r20089] Add note to known problems section of RELEASE.txt about ↵Neil Fortner2011-02-111-0/+2
| | | | | | run-all-ex.sh on Cygwin. Tested: kwrite
* [svn-r20076] Updated for the adding of mpicc/mpif90 as default parallel ↵Albert Cheng2011-02-091-0/+3
| | | | | | compiler commands for linux systems.
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