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* [svn-r19451] Update version of 1.8 branch to HDF5 1.8.7-snap0Mike McGreevy2010-09-2114-29/+29
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* [svn-r19449] Undo previous commit:Albert Cheng2010-09-211-208/+117
| | | | Big.c was included by mistake.
* [svn-r19448] Fix for legacy Windows test added for 1890 h5diff exclude-pathJonathan Kim2010-09-211-2/+2
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* [svn-r19446] Update for previous checkin r19444Jonathan Kim2010-09-201-0/+1
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* [svn-r19444] Purpose:Jonathan Kim2010-09-205-10/+35
| | | | | | | | | | | Fix for group comparison with exclude-path case. Use relative path. Description: Merge from hdf5 trunk (r19443) Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19407) Tested: jam, amani
* [svn-r19442] Move $LIBS to just after $lib_objs in the link command line. ↵Larry Knox2010-09-203-21/+29
| | | | | | Otherwise the linker doesn't find the functions called by the program being compiled. $LIBS is ofr libraries specified by the compile script user. We don't currently have any tests checked in to do this. Tested with netCDF-4 and hdf5 on jam.
* [svn-r19441] Bug fix for 1707 - in a hurry, explain later.Raymond Lu2010-09-2022-89/+332
| | | | tested on jam and amani, heiwa hasn't finished yet.
* [svn-r19440] Description:Mike McGreevy2010-09-201-3/+3
| | | | | | | Update bin/chkconfigure to reflect version 2.67 of Autoconf Tested: ran bin/chkconfigure on jam
* [svn-r19438] Correct use of lib, include, bin in INSTALL commands to use ↵Allen Byrne2010-09-2017-37/+50
| | | | | | proper variables. Tested: local linux
* [svn-r19436] remove source package command - not neededAllen Byrne2010-09-201-2/+1
| | | | add missing -C options
* [svn-r19433] Description:Binh-Minh Ribler2010-09-201-0/+1
| | | | Added ./config/ibm-aix6.x
* [svn-r19432] Updated configuration section with optional command line usage. ↵Allen Byrne2010-09-201-24/+100
| | | | Also added section on CPack.
* [svn-r19429] Update to H5REPACK tests for layout info required a new ↵Allen Byrne2010-09-201-23/+161
| | | | | | function in batch file Tested: Windows
* [svn-r19428] Updates for cmake tests from the h5diff group recursive updates.Jonathan Kim2010-09-201-4/+4
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* [svn-r19426] Fix for legay Windows test for h5diff exclude-path updatesJonathan Kim2010-09-201-8/+10
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* [svn-r19424] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Albert Cheng2010-09-201-1/+4
| | | | | | | | | | | | | | | | | | Description: In an AIX 6.1 system, configure --enable-shared could not build a shared HDF5 library. The problem was because the version of config.guess was too old to recongnize AIX 6.X and also configure.in had a local fix which did not recognize AIX 6.X. Solution: 1. Mike McGreevy updated bin/config.guess to handle AIX 6.X. 2 Albert fixed configure.in to recognize AIX 6.X. Note that though HDF5 can build shared lib for AIX 6.X systems but it still could not install the proper library as in AIX 5.X systems. Also, bin/config.sub should be updated too. Tested: BP which is the AIX 6.1 system that exposed this problem.
* [svn-r19423] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Albert Cheng2010-09-204-136/+306
| | | | | | | | | | | | | | | | | | | Description: In an AIX 6.1 system, configure --enable-shared could not build a shared HDF5 library. The problem was because the version of config.guess was too old to recongnize AIX 6.X and also configure.in had a local fix which did not recognize AIX 6.X. Solution: 1. Mike McGreevy updated bin/config.guess to handle AIX 6.X. 2 Albert fixed configure.in to recognize AIX 6.X. Note that though HDF5 can build shared lib for AIX 6.X systems but it still could not install the proper library as in AIX 5.X systems. Also, bin/config.sub should be updated too. Tested: BP which is the AIX 6.1 system that exposed this problem.
* [svn-r19421] Reorganize compile scripts h5cc.in, h5fc.in and h5c++.in to put ↵Larry Knox2010-09-173-20/+169
| | | | | | LDFLAGS in the correct place and to enable the script user to set and override CFLAGS, CPPFLAGS, CXXFLAGS, FFLAGS, LDFLAGS, and LIBS that take pprecedence over the library paths and compile flags from the hdf5 build. Tested with h5committest on amani, heiwa, and jam.
* [svn-r19420] Ported recent checkin on trunk to the 1.8 branch -- trunk checkinJohn Mainzer2010-09-171-48/+570
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | log entry reproduced below: -------------------------------------------------------------- Modified shape same tests to deal with the performance problem on Abe. Problem appears to have been caused by file system contention. In the chunked dataset case, reshaping the chunks so that only one process would touch each chunk and setting the alignment equal to the default Lustre block size more or less dealt with the problem. For contiguous datasets, the problem was a bit more difficult, as re-working the test to avoid contention would have been very time consuming. Instead, I added code to time one execution of each type of shape same test, and skip additional tests of that type if the duration of the test exceeded some threshold In all cases, I set up code to turn off the above fixes if express test is 0. Tested on Abe and commit tested. On the commit test, the configure test failed -- probably because I was h5committest from heiwa due to some ssh wierdness. In any case a manual reconfigure run on jam seemed to work fine. Also, in h5committest, I ran into some data conversion warnings. I didn't worry about them as the only code I changed was in testpar.
* [svn-r19419] On windows, an include bypassed the WIN32_LEAN_AND_MEAN define. ↵Allen Byrne2010-09-172-2/+2
| | | | | | Moved the define up. Moved the h5dif.h to after the h5private include Tested: Windows
* [svn-r19416] Fix for Cmake test. Merged from hdf5 trunk (r19415).Jonathan Kim2010-09-171-22/+28
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* [svn-r19414] Error return value was FAIL. Should be NULL.Albert Cheng2010-09-171-1/+1
| | | | Tested: LLNL up which this was flagged.
* [svn-r19411] Purpose: Jonathan Kim2010-09-1713-1/+503
| | | | | | | | | | | | Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Merged from hdf5 trunk (r19409) Additional tests for combination of group recursive and --follow-symlinks with multi-linked external links with several files (same name/strucure). Tested: jam, amani, heiwa
* [svn-r19408] In this revision the '/' after ${DESTDIR} wherever it occursLarry Knox2010-09-1660-244/+684
| | | | | | | | | | | | | | | | | | | | has been removed. According to the official description of DESTDIR by Gnu at http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is prepended to the normal and complete install path that it precedes for the purpose of installing in a temporary directory which is useful for building rpms and other packages. The '/' after ${DESTDIR} will be followed by another '/' at the beginning of the normal install path. When DESTDIR is empty the path then begins with '//', which is incorrect and causes problems at least for Cygwin. The change made in config/commence.am affects many Makefile.*s when bin/reconfigure is run. EXAMPLEDIRs had to be corrected individually. Also the scripts to run examples after they are installed have checks added to see that the fortran and c++ directories are present before trying to run the scripts in them. Tested with h5committest on amani, heiwa and jam.
* [svn-r19407] Purpose:Jonathan Kim2010-09-1617-18/+659
| | | | | | | | | | | | Add --exclude-path option Description: Merged from hdf5 trunk (r19406). Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded. Related to "1890: h5diff excluding object for file comparison via command line" Tested: jam, amani
* [svn-r19405] Description:Quincey Koziol2010-09-165-8/+69
| | | | | | | | | | | | | | | | | | | | | | Bring r19402 from trunk to 1.8 branch: Correct Bz#1968 (Problem when opening new format file with H5F_LIBVER_EARLIEST) by initializing symbol table leaf information in a more universal way. Also cleaned up other superblock initialization a little bit while I'm here. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production 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-r19404] Update to H5REPACK tests for layout info required a grep script ↵Allen Byrne2010-09-164-6/+139
| | | | | | | | like runTest.cmake. Update CMakeLists.txt for new h5repack layout tests. Tested: local linux
* [svn-r19401] Purpose:Jonathan Kim2010-09-1656-664/+2444
| | | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Merged from hdf5 trunk (r19400). Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani
* [svn-r19399] Description:Quincey Koziol2010-09-1635-439/+369
| | | | | | | | | | | | | | Bring r19398 from trunk to 1.8 branch: Clean up the internal usage H5I_dec_ref() to eliminate the sequence of flags that has been creeping in. 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 Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* [svn-r19397] Description:Quincey Koziol2010-09-1611-140/+61
| | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19396 from trunk to 1.8 branch: Bring back various modifications to the v2 B-trees that were introduced in the revise_chunks branch but aren't dependent on any file format or API changes. 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-r19394] Purpose: Fixed bug 1903Binh-Minh Ribler2010-09-167-28/+14
| | | | | | | | | | | Description: After a C++ API object is closed, its id should be reset regardless of the reference count of the underlying HDF5 object. User reported the bug for Group, but it's applicable to all other objects. Fixed. Platforms tested: Linux/32 2.6 (jam) FreeBSD/64 6.3 (liberty) SunOS 5.10 (linew)
* [svn-r19393] Purpose:Jonathan Kim2010-09-151-3/+0
| | | | | | | | | | | Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed to Description: Merged from hdf5 trunk (r19392) Remove unnecessary lopping code, which only lowers performance. Tested: jam, amani
* [svn-r19391] Purpose:Jonathan Kim2010-09-156-22/+264
| | | | | | | | | | | Fix for Bug1896 h5repack - changing layout to COMPACT does not work Description: Merged from hdf5 trunk (r19389) 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
* [svn-r19388] Purpose: Fix build errorNeil Fortner2010-09-151-8/+0
| | | | | | | | Description: When merging r19386 from the trunk calls to H5AC_ignore_tags were not removed. This has been corrected. Tested: Fedora
* [svn-r19387] Purpose: Fix assertion failure caused by fractal heap header ↵Neil Fortner2010-09-154-4/+147
| | | | | | | | | | | | | | file pointer Description: The fractal heap header structure keeps a pointer to the file associated with it. However, it is possible for that file pointer to be closed while the header is still in cache (through the shared file pointer). Previously, the header's file pointer was not updated and subsequently pointed to an invalid file structure. Modified fractal heap code to update the file pointer every time the header is accessed. Tested: jam, linew, amani (h5committest)
* [svn-r19385] Description:Quincey Koziol2010-09-153-53/+50
| | | | | | | | | | | | Bring r19384 from trunk to 1.8 branch: Correct an error I convinced Mike to introduce with the phread_once() code, :-( along with another one that wasn't my fault. Also, clean up warnings and restructure code in the pthread side of the thread-safe code a bit. Tested on: Mac OS X/32 10.6.4 (amazon) w/production + thread-safe (not a configuration that h5committest tests)
* [svn-r19376] Added bug 1938 resolutionAllen Byrne2010-09-131-8/+11
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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)
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