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* [svn-r19375] [BZ1938] - VS2010 on windows requires stdint.h to compile C++ ↵Allen Byrne2010-09-131-2/+6
| | | | | | library. CMake will check if c++ compiler supports stdint.h and set the H5_HAVE_STDINT_H_CXX define. Tested: windows and local linux
* [svn-r19373] Add copies of m4 macros that were erroneously links.Larry Knox2010-09-115-0/+8050
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* [svn-r19372] Remove symbolic links that should be copies.Larry Knox2010-09-115-5/+0
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* [svn-r19371] Updated autoconf to version 2.6.7, libtool to version 2.2.10, ↵Larry Knox2010-09-1052-3228/+3307
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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. -This line, and those below, will be ignored-- M hdf5_1_8/test/Makefile.in A hdf5_1_8/m4 AM hdf5_1_8/m4/ltsugar.m4 AM hdf5_1_8/m4/libtool.m4 AM hdf5_1_8/m4/ltversion.m4 AM hdf5_1_8/m4/lt~obsolete.m4 AM hdf5_1_8/m4/ltoptions.m4 M hdf5_1_8/configure M hdf5_1_8/Makefile.in M hdf5_1_8/testpar/Makefile.in M hdf5_1_8/configure.in M hdf5_1_8/src/Makefile.in M hdf5_1_8/tools/Makefile.in M hdf5_1_8/tools/misc/Makefile.in M hdf5_1_8/tools/h5dump/Makefile.in M hdf5_1_8/tools/h5repack/Makefile.in M hdf5_1_8/tools/h5jam/Makefile.in M hdf5_1_8/tools/h5diff/Makefile.in M hdf5_1_8/tools/lib/Makefile.in M hdf5_1_8/tools/h5copy/Makefile.in M hdf5_1_8/tools/h5import/Makefile.in M hdf5_1_8/tools/h5stat/Makefile.in M hdf5_1_8/tools/h5ls/Makefile.in M hdf5_1_8/hl/test/Makefile.in M hdf5_1_8/hl/tools/Makefile.in M hdf5_1_8/hl/tools/gif2h5/Makefile.in M hdf5_1_8/hl/Makefile.in M hdf5_1_8/hl/src/Makefile.in M hdf5_1_8/hl/c++/test/Makefile.in M hdf5_1_8/hl/c++/Makefile.in M hdf5_1_8/hl/c++/src/Makefile.in M hdf5_1_8/hl/c++/examples/Makefile.in M hdf5_1_8/hl/fortran/test/Makefile.in M hdf5_1_8/hl/fortran/Makefile.in M hdf5_1_8/hl/fortran/src/Makefile.in M hdf5_1_8/hl/fortran/examples/Makefile.in M hdf5_1_8/hl/examples/Makefile.in M hdf5_1_8/config/commence.am M hdf5_1_8/MANIFEST M hdf5_1_8/c++/test/Makefile.in M hdf5_1_8/c++/Makefile.in M hdf5_1_8/c++/src/Makefile.in M hdf5_1_8/c++/examples/Makefile.in M hdf5_1_8/bin/ltmain.sh M hdf5_1_8/bin/reconfigure M hdf5_1_8/perform/Makefile.in M hdf5_1_8/fortran/test/Makefile.in M hdf5_1_8/fortran/testpar/Makefile.in M hdf5_1_8/fortran/Makefile.in M hdf5_1_8/fortran/src/Makefile.in M hdf5_1_8/fortran/examples/Makefile.in M hdf5_1_8/aclocal.m4 M hdf5_1_8/examples/Makefile.in
* [svn-r19368] Purpose:Mike McGreevy2010-09-1013-83/+251
| | | | | | | | | | | | | | | | | | | Add windows threads support to HDF5. Description: Added calls to the windows threads library to the H5TS layer, and wrapped most calls to either pthreads or windows threads library with portable H5TS-style defines. Modified tests to use portable function definitions as well. This can be configured via CMake with the HDF5_ENABLE_THREADSAFE option, and should work on windows vista and later operating systems. Tested: h5committest, plus threadsafe with pthreads on jam and amani, and tested on a Windows Vista VM with threadsafe using windows threads.
* [svn-r19365] Bug Fix: ID 2019Albert Cheng2010-09-101-3/+9
| | | | | | | | | | | | | | | | | | | | | Description: The development (--disable-production) mode ran a long time, especially on the testhdf5 (select) that exceeded the wall clock 10 minutes limits and was terminated. It turned out the development had DEBUG_CFLAG set to "-g -xildoff".\ The -xildoff was added back when h5detect had errors when -g only was used. But that bug does not exist any more since when only -g is used to build, h5detect did not fail and all tests passed. Therefore -xildoff is removed. Furthermore, when "-g -O" is used to build the library, debuggers such as dbx can still use the executable, though some debugging ability like displaying local variables is not available in optimized code. But overall execution time shorten. Therefore, the C, Fortran aand CXX DEBUG flags are all set to "-g -O" by default. Tested: in Linew using the default development mode because the changes affect only the Sun platform.
* [svn-r19362] Move Windows specific compile and link flags to macrosAllen Byrne2010-09-0929-702/+171
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* [svn-r19359] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-0841-175/+589
| | | | | | | couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. Tested with h5committest - jam, heiwa, amani.
* [svn-r19358] Add POSIX warning to report ignore list.Allen Byrne2010-09-081-0/+1
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* [svn-r19356] Bug fix: ID 2026Albert Cheng2010-09-082-2/+2
| | | | | | | | | | | | | | | | Description: testhdf5/select runs very slow when in --disable-production mode using pgcc compiler. This was caused by the -Mchkfpstk compiler switch added to the DEBUG_FLAGS in config/pgi-flags file. Solution: Removed -Mchkfpstk from both pgi-flags and pgi-fflags. See Bug 2026 for dettails. Tested: (no h5committest test since they don't use PGI compilers.) Jam (linux32): using pgcc/pgf90/pgCC using default and --enable-production. Amani (linux64): using pgcc/pgf90/pgCC (32 bits mode by "-tp k8-32"), using default and --enable-production.
* [svn-r19355] Quincey and I made H5Eset_current_stack also close the stack to ↵Raymond Lu2010-09-073-1/+82
| | | | | | | | | | | be set. This is to avoid H5Eclose_stack clearing the default stack. Please see bug 1799. Tested on jam - simple change. The changes to configure.in, tools/lib, config, c++/test, Makefile.am, and fortran are only property changes from the merge.
* [svn-r19353] Description:Quincey Koziol2010-09-042-39/+14
| | | | | | | | | | Bring r19352 from trunk to 1.8 branch: Align w/changes on revise_chunks branch Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19349] Description:Quincey Koziol2010-09-041-25/+20
| | | | | | | | Bring r19348 from trunk to 1.8 branch Tested on: Linux/64 2.6 (abe) w/parallel (too unusual to require h5committest)
* [svn-r19345] Description:Quincey Koziol2010-09-031-0/+3
| | | | | Add note about bugfix that requires H5Pset_chunk for all chunked datasets now.
* [svn-r19344] Corrected long long printf test.Allen Byrne2010-09-023-30/+102
| | | | | | | | | Added CMake commands to allow the install of the extlibs on windows. Updated ctest warning exception regex for VS2010 Bring r19343 from trunk Tested: windows
* [svn-r19341] Added cmake tests for c++ examplesAllen Byrne2010-09-022-0/+8
| | | | Tetsed: local linux
* [svn-r19337] Change #ifndef _WIN32 to #ifdef H5_HAVE_UNISTD_HAllen Byrne2010-09-011-3/+3
| | | | Tested: windows, heiwa and local linux
* [svn-r19335] Update CMake referenceAllen Byrne2010-09-011-9/+9
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* [svn-r19332] Removed extranous string from list of ddl files.Allen Byrne2010-09-011-1/+1
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* [svn-r19329] Description:Quincey Koziol2010-08-313-13/+44
| | | | | | | | | | | | | | | Bring r19328 from trunk to 1.8 branch: Add some extra range checking for invalid chunk sizes. Tweak default chunk sizes to be zero, so that it's more likely that application developers will be forced to set them correctly. Add a few tests to verify these checks. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19326] Added parallel build commands.Allen Byrne2010-08-3133-230/+887
| | | | | | | | Corrected use/name of source folder aliases. Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work). Bring r19325 from trunk Tested: local linux with mpich
* [svn-r19321] Added correction to check for existence of H5PRINTF_LL in ↵Allen Byrne2010-08-271-37/+39
| | | | | | PRINTF_LL test. Tested: local linux
* [svn-r19319] Correct ENDIF text (non-executable) to match IF parameterAllen Byrne2010-08-271-1/+1
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* [svn-r19314] Description:Quincey Koziol2010-08-264-157/+191
| | | | | | | | | | Bring r19313 from trunk to 1.8 branch: Clean up a few compiler warnings and style issues in/near recent changes. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19311] Description:Quincey Koziol2010-08-261-1/+1
| | | | | | | | Bump optimization down for Intel 10.* compilers, due to apparent bad code generation. Tested on: Linux/64 2.6 (cobalt) w/debug & production & Intel 11.1 compilers (h5committest not appropriate)
* [svn-r19310] Description:Quincey Koziol2010-08-263-12/+174
| | | | | | | | | | | | | | | | | | | | | Bring r19309 from trunk to 1.8 branch: Bring revisions from Coverity branch back to trunk: r19191: Fix coverity items 104 and 105. Added calls to H5HF_sect_indirect_free to H5HF_sect_indirect_reduce and H5HF_sect_indirect_reduce_row if there is an errorbefore "peer_sect" is linked into the main free space structure via its direct sections. Also delayed call to H5HF_sect_indirect_first to prevent peer_sect from being left in an inconsistent state. r19268: Added fix to disallow extendible compact dataset. This was the same check as in H5D_contig_construct() in H5Dcontig.c. Added test to verify the creation of extendible dataset with various layouts. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (h5committested on branch)
* [svn-r19308] Correct test for H5_LONE_COLON - added NOTAllen Byrne2010-08-261-1/+1
| | | | | | Bring r19307 from trunk Tested: windows
* [svn-r19303] bug 1678: temporary fix.Albert Cheng2010-08-251-0/+5
| | | | | | | | | | | | | | | | Description: aix -q32 default to a memory limit that some HDF5 tests would fail in malloc. Solution: Temporary hardset RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA"} to bypass this problem until the test programs are fixed. Though -q64 binary has a higher default memory limit and does not need this patch, it is applied the same for the sake of simplicity since it is a temporary fix. Tested: in uP, tested 32 and -q64 modes. No h5committest since this applies to the AIX platform only.
* [svn-r19301] BZ 1958: Add h5dump xml tests to CMake supportAllen Byrne2010-08-2514-127/+596
| | | | | | Bring r19300 from trunk Tetsed: local linux
* [svn-r19298] Description:Quincey Koziol2010-08-257-13/+77
| | | | | | | | | | | | Bring r19297 from trunk to 1.8 branch: Whack a few more memory errors exposed by valgrind. Make the debugging dump output a little bit prettier. Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committested on trunk)
* [svn-r19291] Description:Quincey Koziol2010-08-245-44/+52
| | | | | | | | | Avoid getting object information for soft/external links if we aren't going to traverse across the link itself. Tested on: Linux/64 2.6 (chicago) w/debug & production (h5committest coming up)
* [svn-r19290] Description:Quincey Koziol2010-08-241-27/+43
| | | | | | | | | Correct another error in metadata accumulator dirty region calculations (this time with a corner case when freeing data in the file). Tested on: Linux/32 2.6 (talwit) w/debug (following up with h5committest)
* [svn-r19289] bug 1678: temporary fix.Albert Cheng2010-08-241-0/+5
| | | | | | | | | | | | | | | | Description: aix -q32 default to a memory limit that some HDF5 tests would fail in malloc. Solution: Temporary hardset RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA"} to bypass this problem until the test programs are fixed. Though -q64 binary has a higher default memory limit and does not need this patch, it is applied the same for the sake of simplicity since it is a temporary fix. Tested: in BP, both -q32 and -q64 modes. No h5committest since this applies to the AIX platform only.
* [svn-r19287] Corrected name of file appearing in expected output.Allen Byrne2010-08-241-1/+1
| | | | (Missed edit from local test)
* [svn-r19284] Description:Quincey Koziol2010-08-241-0/+1
| | | | Add note about correcting valgrind issues.
* [svn-r19283] Description:Quincey Koziol2010-08-249-183/+198
| | | | | | | | | | | | | | | | | | | | | | | | Bring r19278 from trunk to 1.8 branch: More fixes to memory allocation, etc. exposed by valgrind. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.4 (amazon) 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-r19281] Fix test scripts changed extension of fileAllen Byrne2010-08-231-1/+1
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* [svn-r19280] Fix test scripts (Cmake needs to capture output yet)Allen Byrne2010-08-234-22/+54
| | | | | | linux script needed -R and double compare: Tested: local linux
* [svn-r19279] Bug 1934 - I added support of all data types for H5Tget_order. ↵Raymond Lu2010-08-234-35/+105
| | | | | | | | | I added a new byte order H5T_ORDER_MIXED specifically for compound types and its derived types. They report mixed orders if they have members of different orders. Tested on heiwa, jam, and amani.
* [svn-r19277] Description:Quincey Koziol2010-08-221-1/+1
| | | | | | | | | | Bring r19276 from trunk to 1.8 branch: Correct calculation of end of dirty information in metadata accumulator Tested on: FreeBSD/32 6.3 (duty) in debug mode (h5committested on trunk)
* [svn-r19274] Description:Quincey Koziol2010-08-2030-494/+677
| | | | | | | | | | | | | | | | | | | | Bring r19272 & 19273 from trunk to 1.8 branch: Close out various resource leaks and usages of uninitialized memory that were flagged by valgrind. [There's still some more valgrind warnings, but it's better now... :-/ ] Also clean up warnings and code formatting. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Mac OS X/32 10.6.4 (amazon) 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-r19270] Add warning exceptions.Allen Byrne2010-08-201-0/+16
| | | | Add memcheck ignore.
* [svn-r19266] Remove configuration of cmake zlib config filed which has been ↵Allen Byrne2010-08-202-2/+1
| | | | | | | deleted. Correct naming of SKIP test Tested: local linux
* [svn-r19263] Undo r19258Allen Byrne2010-08-201-0/+7
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* [svn-r19259] Correct formatting and endif labelsAllen Byrne2010-08-202-28/+28
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* [svn-r19258] Remove unused variables and allocationAllen Byrne2010-08-201-7/+0
| | | | Tested: local linux
* [svn-r19257] Change Cmake to allow a local zlib header to be used in ↵Allen Byrne2010-08-209-96/+211
| | | | | | | | | | | H5Zdelate module. Corrected use of "SKIP" message in cmake. Corrections to cmake configuration files (for cmake external projects). Community suggested changes. Tested: local linux
* [svn-r19256] Description:Quincey Koziol2010-08-201-0/+1
| | | | | | | | | Bring r19255 from trunk to 1.8 branch: Add missing include file from r19252. Tested on: (Eyeballed only, too simple to require h5committest)
* [svn-r19254] Description:Quincey Koziol2010-08-1930-462/+510
| | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19252 & 19253 from trunk to 1.8 branch: Bring Coverity changes from branch to trunk: r19161: Fixed the part for matching the subset info with dataset r19189: BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump. Changed all references to use new data structure. Added tests for each subset parameter. r19190: Added new h5dump ddl files Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r19250] New feature(bug #1934): I made H5Tset_order support all data ↵Raymond Lu2010-08-185-39/+197
| | | | | | | | | | | | | | | types with some restictions: 1. For enum type, members shouldn't be defined yet. 2. H5T_ORDER_NONE only works for reference and fixed-length string. 3. For opaque type, the order will be ignored. 4. For compound type, all restrictions above apply to the members. I'll change H5Tget_order and do another commit. Tested on jam, heiwa, and amani.
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