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* [svn-r19458] Add CMake tests for check-vfd; includes new vfdTest.cmake ↵Allen Byrne2010-09-213-0/+79
| | | | | | script and OPTION HDF5_TEST_VFD Tested: local linux
* [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-2123-89/+335
| | | | | | | | | | | | | application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a document for it. Tested on heiwa, jam, and amani. The property change in configure.in, config, and Makefile.am came from the merge of the 1.8 library change.
* [svn-r19447] Fix for Windows legacy test added for 1890 h5diff exclude-pathJonathan Kim2010-09-211-2/+2
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* [svn-r19445] Update for previous checkin r19443Jonathan Kim2010-09-201-0/+1
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* [svn-r19443] Purpose:Jonathan Kim2010-09-205-10/+35
| | | | | | | | | | Fix for group comparison with exclude-path case. Use relative path. Description: Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406) Tested: jam, amani and heiwa
* [svn-r19439] Description:Mike McGreevy2010-09-201-3/+3
| | | | | | | Update bin/chkconfigure to reflect version 2.67 of Autoconf Tested: ran bin/chkconfigure on jam
* [svn-r19437] add missing -C optionsAllen Byrne2010-09-201-1/+1
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* [svn-r19435] remove source package command - not neededAllen Byrne2010-09-201-1/+0
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* [svn-r19434] Correct use of lib, include, bin in INSTALL commands to use ↵Allen Byrne2010-09-2017-37/+50
| | | | | | proper variables. Tested: local linux
* [svn-r19431] Updated configuration section with optional command line usage. ↵Allen Byrne2010-09-201-24/+100
| | | | Also added section on CPack.
* [svn-r19430] Update to H5REPACK tests for layout info required a new ↵Allen Byrne2010-09-201-23/+161
| | | | | | function in batch file Tested: Windows
* [svn-r19427] Updates for cmake tests from the h5diff group recursive updates.Jonathan Kim2010-09-201-4/+4
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* [svn-r19425] Fix for legay Windows test for h5diff updates.Jonathan Kim2010-09-201-8/+10
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* [svn-r19418] 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-r19417] Error return value was FAIL. Should be NULL.Albert Cheng2010-09-171-1/+1
| | | | Tested: LLNL up which this was flagged.
* [svn-r19415] Fix for Cmake test.Jonathan Kim2010-09-171-22/+28
| | | | | Tested: jam
* [svn-r19412] Modified shape same tests to deal with the performance problem ↵John Mainzer2010-09-171-48/+570
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r19410] Purpose: Jonathan Kim2010-09-174-0/+0
| | | | | Add missing files from the previous checkin. (Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object)
* [svn-r19409] Purpose: Jonathan Kim2010-09-169-1/+503
| | | | | | | | | | | Add extra test cases for bug1975 h5diff - support recursive comparison on group when specified as an object. Description: 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-r19406] Purpose:Jonathan Kim2010-09-1617-18/+659
| | | | | | | | | | | Add --exclude-path option Description: 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 and heiwa
* [svn-r19403] 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-r19402] Description:Quincey Koziol2010-09-164-12/+65
| | | | | | | | | | | | | | | | | | | | | | | | | 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 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-r19400] Purpose:Jonathan Kim2010-09-1656-663/+2442
| | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: 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, heiwa
* [svn-r19398] Descriptino:Quincey Koziol2010-09-1635-439/+369
| | | | | | | | | | | | | | | | | | | | | | | 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/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-r19396] Description:Quincey Koziol2010-09-1611-140/+61
| | | | | | | | | | | | | | | | | | | | | | | | 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-r19395] 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-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 Kim2010-09-156-22/+264
| | | | | | | | | | 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-r19386] Purpose: Fix assertion failure caused by fractal heap header ↵Neil Fortner2010-09-154-7/+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-r19384] Description:Quincey Koziol2010-09-153-53/+50
| | | | | | | | | | 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 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-r19377] Added bug 1938 resolutionAllen Byrne2010-09-131-0/+3
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* [svn-r19374] [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-r19370] Removed entry for m4 directory.Larry Knox2010-09-101-1/+0
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* [svn-r19369] Update MANIFEST for new m4 directory and macros. Directory and ↵Larry Knox2010-09-101-0/+6
| | | | | | files are for reconfigure and therefore marked _DO_NOT_DISTRIBUTE_. Tested on jam.
* [svn-r19367] 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-r19366] Updated autoconf to version 2.6.7, libtool to version 2.2.10, ↵Larry Knox2010-09-1051-3224/+11344
| | | | | | 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-r19364] 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-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-0941-163/+577
| | | | | | | 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-r19361] Move Windows specific compile and link flags to macrosAllen Byrne2010-09-0929-712/+172
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* [svn-r19360] 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-r19357] Add POSIX warning to report ignore list.Allen Byrne2010-09-081-0/+1
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* [svn-r19354] 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.
* [svn-r19352] Description:Quincey Koziol2010-09-042-39/+14
| | | | | | | | 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-r19348] Description:Quincey Koziol2010-09-031-25/+20
| | | | | | | | Clean up warnings, etc. Tested on: Linux/64 2.6 (abe) w/parallel (to specific to need h5committest)
* [svn-r19343] 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 Tested: windows
* [svn-r19342] Added cmake tests for c++ examplesAllen Byrne2010-09-022-0/+8
| | | | Tetsed: local linux
* [svn-r19336] Change #ifndef _WIN32 to #ifdef H5_HAVE_UNISTD_HAllen Byrne2010-09-011-3/+3
| | | | Tested: windows and local linux
* [svn-r19334] Update CMake referenceAllen Byrne2010-09-011-6/+6
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* [svn-r19331] Correct list of h5 files needed for testsAllen Byrne2010-09-011-1/+3
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* [svn-r19328] Description:Quincey Koziol2010-08-313-13/+44
| | | | | | | | | | | | | 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)
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