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* [svn-r21872] Update a comment to make clear from the previous commit ↵Jonathan Kim2012-01-111-2/+3
| | | | (r21869) for HDFFV-7840.
* [svn-r21869] Purpose:Jonathan Kim2012-01-094-57/+86
| | | | | | | | | | | | | | Fix for HDFFV-7840 h5repack: memory leak over one of the h5diff test file Description: Turned out that there were two causes of memory leaks. 1. for handling variable length string in attribute. 2. for handling compound type with non-reference members. The first issue is fixed in copy_attr() which is updated to use h5tools_detect_vlen to take care of vlen string as well as vlen data. The second is fixed in copy_refs_attr() of compound handling code. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE), Cmake (jam)
* [svn-r21804] Update CMake Required version in all folders to match current ↵Allen Byrne2011-12-051-1/+1
| | | | standard 2.8.6
* [svn-r21667] Update FOLDER solution option for target properties. Added ↵Allen Byrne2011-10-251-4/+3
| | | | | | OPTION command for solution folder and no packaging. Tested: local linux
* [svn-r21664] Added solution folders for most of the projects. This still ↵Dana Robinson2011-10-251-0/+4
| | | | | | needs some polish - the solution folder assignment should go closer to the target declaration and not all projects are grouped (parallel, c++, fortran, hl, and a few others). Tested on Windows.
* [svn-r21586] Description:Jonathan Kim2011-10-143-0/+6
| | | | | | | | | Added a funtion to reset dataset & hyperslab buffer size for h5repack from an environment variable. This is performance debugging purpose for now. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE), cmake
* [svn-r21489] Bug:Albert Cheng2011-10-071-4/+4
| | | | | | | | | | | h5dump was used in test script but was not invoked by RUNSERIAL. THis does not work in batch machines like Blue Gene in LLNL. Solution: Added $RUNSERIAL to invoke $H5DUMP_BIN. Tested: LLNL BlueGene (udawn)
* [svn-r21389] Test case added for HDFFV-5932 - h5repack breaks files with ↵Jonathan Kim2011-09-141-4/+2
| | | | | | | dimension scales. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r21386] Fixed a void pointer (need to cast it to char*) because it ↵Peter Cao2011-09-141-4/+4
| | | | causes problem on Windows.
* [svn-r21382] Update values of references(object and region) of attributes in ↵Peter Cao2011-09-142-160/+324
| | | | h5repack for 1) references, 2) ARRAY of references, 3) VLEN of references, and 4) COMPOUND of references.
* [svn-r21297] Move all tests into DEPENDS structure so that clear-all-objects ↵Allen Byrne2011-08-231-311/+318
| | | | | | is first. Also preface all tests with H5REPACK.
* [svn-r21283] H5Eget_major() is depreciated. use the H5Eget_msg() instead.Peter Cao2011-08-221-6/+3
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* [svn-r21265] h5repack: added macro to handle failure in H5Dread/write when ↵Peter Cao2011-08-191-11/+37
| | | | memory allocation failed inside the library
* [svn-r21249] Description: Part II of F2003 branch merge into the trunk.Scot Breitenfeld2011-08-181-0/+3
| | | | | | Ran bin/reconfigure to update the Makefile.in in directories not part of the fortran directory check=in. Updates Makefile.in due to changes made in configure.in for the Fortran 2003 additions. Tested on all platforms run under daily tests.
* [svn-r21125] Description:Quincey Koziol2011-07-191-31/+31
| | | | | | | | | | | | Correct char arrays that were too small for strings defined. Also, change cleanup to work correctly. Tested on: Mac OS X/32 10.6.8 (amazon) w/debug FreeBSD/32 8.2 (loyalty) w/debug FreeBSD/64 8.2 (freedom) w/debug Linux/64 2.6 (heiwa) w/debug Linux/64 2.6 (ember) w/parallel
* [svn-r21121] Description:Quincey Koziol2011-07-181-4/+4
| | | | | | | | | Switch from H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for calls to H5Rdereference2(). Tested on: Mac OS X/32 10.6.8 (amazon) w/debug (too minor to require h5committest)
* [svn-r21117] Issue 2763 - I added a new parameter of object access property ↵Raymond Lu2011-07-181-4/+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 Cao2011-07-152-0/+5
| | | | | | | - 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-r21057] [hdf5 Trunk ] TODOJonathan Kim2011-06-301-134/+200
| | | | | | | | | | | Purpose: Work for HDFFV-7602 - HDF5 command tools: Provide framework for reusable test files among tools Description: Provide framework to share test files among tools for tools test. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20504] Purpose:Mike McGreevy2011-04-141-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | General shared library improvements for CYGWIN / AIX Description: Shared libraries are disabled on both CYGWIN and AIX due to inability to build them correctly. Part of the problem in both of these situations is the lack of the libtool flag -no-undefined, which tells libtool that all needed symbols are defined at link time (a requirement on these systems) and that it's okay to build shared libraries. Another problem are lack of dependencies between wrapper libraries and core C HDF5 library. This patch addresses both of these by fixing configure to add in -no-undefined flag for libtool during linking and adds automake dependencies in the Makefile.am files. After testing, both CYGWIN and AIX now generate shared libraries, but there are still some test failures in each. (cache_api, dt_arith, and testerror.sh on CYGWIN, and fortran tests on AIX). Even though the shared libraries are not quite perfect, this is a general improvement to what we had before, so I'm applying the patch anyways. Note that default behavior of shared libraries on these systems being disabled has NOT been changed and requires the use of the --enable-unsupported to attempt to build them. We will need to address the test failures in each architecture prior to formally supporting shared libraries on each. Tested: h5committested & CYGWIN tested (on bangan) (AIX tested by Albert on bp-login2)
* [svn-r20502] Purpose:Mike McGreevy2011-04-141-18/+38
| | | | | | | | | | | | | | | | | | | | | | | | 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-r20475] Purpose:Mike McGreevy2011-04-111-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - 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-r20249] Add test properties to H5LS for expected failAllen Byrne2011-03-151-12/+18
| | | | Add SKIPPED to test name if test skipped, also do not run skipped tests if doing memcheck
* [svn-r20171] Add HDF5_USING_MEMCHECKER guards around script mode ADD_TEST. ↵Allen Byrne2011-03-011-56/+63
| | | | | | This will replace the list of ignore tests in CTestCustom.cmake file. Tested: local linux
* [svn-r20161] Correct test properties for test orderAllen Byrne2011-02-251-3/+7
| | | | Tested: local linux
* [svn-r20153] Move ext lib handling for ext project building to a common ↵Allen Byrne2011-02-241-3/+3
| | | | | | macro. Update HDF5 project to use HDFMacros.cmake file. Add test properties for test ordering. Tested: local linux, windows
* [svn-r20141] Bring 1.8 r20139 cmake and windows changes to trunkAllen Byrne2011-02-221-0/+18
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* [svn-r20103] Purpose:Jonathan Kim2011-02-147-87/+66
| | | | | | | | | | | | Change to use HDxxx macros. Description: Originally this started for fixing incorrect pointer usage. But that got fixed through coverity merge. So this is mainly changing to use HDxxx macros and clean up some related code. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20061] Description:Quincey Koziol2011-02-081-41/+45
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity branch to trunk: r19930: Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in copy_attr and diff_attr were not checked for the presence of a vlen before being freed, and vlen storage was never reclaimed. Added checks and calls to H5D_vlen_reclaim(). r19933: Purpose: Fix memory leak in H5L_move_cb() Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using H5FL_MALLOC, this causes the link to be allocated from the free list but is never put back on the free list when it is freed. This prevents the link free list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb() to free the link properly using H5O_msg_free(). r19973: Fix resource leaks by freeing string created by HD5f2string r19974: Issue #345: Inialize buf variable to null Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r20052] Description:Quincey Koziol2011-02-061-27/+30
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up Coverity warnings, and fix some style issues: r19735: Fix for memory leak in test/mf found by valgrind. r19736: Fix memory leak in h5repack. The buffer in copy_objects, when copying the entire dataset at once, was not checked for the presence of a vlen, and vlen storage was never reclaimed. Added check and call to H5D_vlen_reclaim(). r19772: Change H5assert() to if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype") r19774: removed unused priv. r19775: removed unused variables r19778: Fix memory leak comparing for variable length data types. r19834: Fixed memory leaks found by valgrind. Memory errors remain for another day. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on branch)
* [svn-r20012] Use "if...else" to exclude the use when travt is null.Peter Cao2011-01-271-9/+8
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* [svn-r20011] make sure that travt is nor nullPeter Cao2011-01-271-1/+1
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* [svn-r20005] Purpose:Jonathan Kim2011-01-262-2/+0
| | | | | | | | Clean up tool code. Remove "h5test.h" from tool code. Currently only in h5repack. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE)
* [svn-r19907] Windows: Correct how fortran links in CRT library. Also correct ↵Allen Byrne2011-01-041-3/+3
| | | | | | macro use for checking libtype. bring r19906 from 1.8 branch
* [svn-r19895] Remove use of /MT compile flag for building static libs and ↵Allen Byrne2010-12-291-3/+0
| | | | programs. Added BUILT_AS_STATIC_LIBRARY define to set the windows import/export defines correctly for static libraries.
* [svn-r19839] Updated to libtool v 2.4, autoconf 2.68 and m4-1.4.15.Larry Knox2010-11-231-0/+3
| | | | Tested with h5committest on amani, heiwa, and jam.
* [svn-r19818] Purpose:Jonathan Kim2010-11-181-3/+9
| | | | | | | Change to skip copying when a dataset is not allocated. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r19706] Added VFD test options.Allen Byrne2010-11-011-0/+36
| | | | Bring r19705 from branch
* [svn-r19527] Add clear generated objects commands to test blocks.Allen Byrne2010-10-061-0/+66
| | | | | | Add configurefile command to copy CTestCustom to build folder. Tested: local linux
* [svn-r19506] Bring changes from revisions 19408, 19421, and 19442 from ↵Larry Knox2010-10-041-5/+15
| | | | | | branches/hdf5_1_8 to trunk. These revisions reorganize the compile scripts using h5cc.in, h5fc.in, and h5c++.in, add checks for installed examples to the scripts that run them after installation, and add DESTDIR for install as needed for RPMs. Tested on amani, heiwa and jam by h5committest and with CYGWIN.
* [svn-r19434] Correct use of lib, include, bin in INSTALL commands to use ↵Allen Byrne2010-09-201-1/+1
| | | | | | proper variables. Tested: local linux
* [svn-r19403] Update to H5REPACK tests for layout info required a grep script ↵Allen Byrne2010-09-161-3/+74
| | | | | | | | like runTest.cmake. Update CMakeLists.txt for new h5repack layout tests. Tested: local linux
* [svn-r19392] Purpose:Jonathan Kim2010-09-151-3/+0
| | | | | | | | | | Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed to Description: Remove unnecessary lopping code, which only lowers performance. Tested: jam, amani, heiwa
* [svn-r19389] Purpose:Jonathan Kim2010-09-154-22/+261
| | | | | | | | | | Fix for Bug1896 h5repack - changing layout to COMPACT does not work Description: Make h5repack be able to convert a layout to COMPACT for small size dataset as default. Also add verifying layout changes in our test script. Tested: jam, amani, heiwa
* [svn-r19366] Updated autoconf to version 2.6.7, libtool to version 2.2.10, ↵Larry Knox2010-09-101-1/+1
| | | | | | and m4 to version 1.4.14. Also added m4 directory for m4 macros according to autoconf suggestion. Tested with h5committest on amani, jam, and heiwa, and on linew.
* [svn-r19361] Move Windows specific compile and link flags to macrosAllen Byrne2010-09-091-30/+3
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* [svn-r19325] Added parallel build commands.Allen Byrne2010-08-311-4/+4
| | | | | | | Corrected use/name of source folder aliases. Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work). Tested: local linux with mpich
* [svn-r19300] BZ 1958: Add h5dump xml tests to CMake supportAllen Byrne2010-08-251-29/+55
| | | | Tetsed: local linux
* [svn-r19237] Description:Quincey Koziol2010-08-121-16/+11
| | | | | | | | | | Clean up misc. compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
* [svn-r19183] Corrected h5repack verbose test for windowsAllen Byrne2010-08-061-3/+3
| | | | | | Updated tools/lib source dir variable for source list Tested: local linux
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