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* [svn-r19795] Cleaned up some part of the code. It now works on all Unix and ↵Albert Cheng2010-11-161-36/+26
| | | | | | Windows 7 platforms.
* [svn-r19790] CMake: Correct Error tests. Add Deprecated Symbols option.Allen Byrne2010-11-161-16/+36
| | | | Tested: local linux
* [svn-r19783] Fix to the checkin for bug #1930.Vailin Choi2010-11-151-1/+6
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* [svn-r19782] Fix CMake testing for links_env test which requires an ↵Allen Byrne2010-11-152-4/+45
| | | | | | | | environment variable at test run-time. Modified runTest.cmake file to allow optional ENV_VAR and ENV_VALUE to be passed. runTest.cmake requires a reference file, added links_env.out to testfiles folder. Also updated root CMakeLists.txt to output a message when unsopported options are configured with the PARALLEL option. CMake will still generate files. Tested: windows and local linux
* [svn-r19781] Fix for bug #1930:Vailin Choi2010-11-156-117/+261
| | | | | | 1) Move the test for H5D_EXT_PREFIX in links.c to a separate file: links_env.c 2) links_env.c will be used by testlinks_env.sh to test for the environmental variable H5D_EXT_PREFIX in searching for the external linked file.
* [svn-r19764] Updated NPROCS default value from 3 to 6.Albert Cheng2010-11-111-121/+223
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* [svn-r19706] Added VFD test options.Allen Byrne2010-11-011-3/+68
| | | | Bring r19705 from branch
* [svn-r19702] Removed special fheap timeout - replaced by timeout set in ↵Allen Byrne2010-11-011-4/+0
| | | | | | | CTestConfig.ctest Added MemCheck Ignore tests for repeated tools tests Added Debug flag for windows
* [svn-r19697] Description:Quincey Koziol2010-10-291-0/+129
| | | | | | | | | Add another test for shutting down open object IDs without using the standard "close" routines. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19696] Bug 2008 - IBM Power6 Linux uses special conversion algorithms ↵Raymond Lu2010-10-281-0/+32
| | | | | | | | | | | to convert some values from long double to (unsigned) long and from (unsigned) long to long double. I added tests in configure.in to detect these algorithms. Before I can figure out them, I disable the tests in dt_arith.c. There are property changes to tools/misc, config, and Makefile.am when I brought the fix from 1.8. Tested on jam, heiwa, amani, IBM Power6 Linux machine in Holland (huygens.sara.nl).
* [svn-r19668] Description:Quincey Koziol2010-10-261-0/+19
| | | | | | | | | | Do some extra range-checking on H5Pset_elink_acc_flags() calls. Clean up some minor compiler warnings also. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19654] Description:Quincey Koziol2010-10-212-191/+191
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity revisions from branch back to trunk, and clean up some other misc. compiler warnings also. r19500: Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in ohdr.c so the test never tries to close uninitialized locations. r19501: Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c. r19502: Fixed coverity issue 579 and some additional warnings in the file as well. r19503: Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26 r19504: minor mods to try to keep coverity from flagging false positives. r19505: Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel (h5committested on trunk)
* [svn-r19650] Put back deleted library check in configure.Allen Byrne2010-10-201-5/+3
| | | | | | Remove shared library check around ws2_32.lib linking in test library. Issue on windows static builds. Tested: windows
* [svn-r19623] Purpose:Mike McGreevy2010-10-181-6/+6
| | | | | | | | | | | | | | - Fix a bug in each of the metadata accumulator source and test code Description: - In accum.c test file, switch dxpl_id used in H5F_accum_* function calls to H5P_DATASET_XFER_DEFAULT (instead of H5AC_dxpl_id), to fix compilation on windows. - Changed boundary checking from <= to < when checking if a read from disk with overlapping dirty metadata in the accumulator has the read ending such that it aligns exactly with the dirty accumulator (line 234 of H5Faccum.c). Tested: - h5committested
* [svn-r19617] Purpose:Mike McGreevy2010-10-154-32/+1851
| | | | | | | | | | Merge accum_tests branch back to the trunk. Description: Changes consist of addition of tests for H5Faccum.c source code, as well as some fixes that address some discovered bugs in the metadata accumulator on several corner cases. Tested: h5committested
* [svn-r19587] Description:Quincey Koziol2010-10-131-7/+168
| | | | | | | | | | | | | | | | | | | | | | | | | Address issue with object headers being created getting evicted from the metadata cache cache before they are completely initialized. This is done by pinning the object header in the cache until it is completely initialized and attached to a group. 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-r19578] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-10-113-82/+354
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | 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 structure H5E_auto_t. I added a IS_DEDAULT flag in it. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function. Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2. 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-r19507] Fix for bug 1707 - I changed the design from the previous fix ↵Raymond Lu2010-10-042-121/+251
| | | | | | | | | | | | | | | | | | | | as Quincey suggested. I added a flag IS_DEDAULT in the H5E_auto_t structure. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function. Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2. Tested on jam, heiwa, and amani.
* | [svn-r19527] Add clear generated objects commands to test blocks.Allen Byrne2010-10-061-0/+72
| | | | | | | | | | | | Add configurefile command to copy CTestCustom to build folder. Tested: local linux
* | [svn-r19523] I added another test case - disabling chunk cache. H5Dwrite ↵Raymond Lu2010-10-051-31/+58
| | | | | | | | | | | | | | | | will fail instead of H5Dclose when the chunk cache is disabled and the mandatory filter fails. Tested on jam - simple change.
* | [svn-r19520] Move 'int nerrors = 0' declaration out of '#ifdef' block to ↵Allen Byrne2010-10-051-1/+1
| | | | | | | | match return.
* | [svn-r19509] Improve CMake support for CYGWIN.Allen Byrne2010-10-041-0/+1
| | | | | | | | | | | | Correct script comment in testh5diff.sh Tested: Windows Cygwin
* | [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-r19481] I'm backing out my fix for bug 1707 because there're some ↵Raymond Lu2010-09-2710-240/+49
|/ | | | | | | | | | | unresolved issues - r19441 and 19467. Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with the 1.8 library to compile. I created a branch off the trunk called set_auto to continue working on the problem. Tested on jam - backing out, simple.
* [svn-r19472] Description:Quincey Koziol2010-09-232-111/+111
| | | | | | | | | | | | | | | | | | | | | | Create a new, more streamlined method of generating I/O sequences when there is only a single block defined by a hyperslab. This improves the performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%. 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 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-r19471] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Albert Cheng2010-09-221-0/+5
| | | | | | | | | | Description: The AIX platform does not install the lib*.so for some reason but libhdf5.a acts like a shared library. Until we can find out how to fix this, patch up tetlibinfo.sh to not look for an lib*.so in AIX. (Note the test results look wierd as it says libhdf5.a passed and skipped.) Tested: NCSA BP for both enable and disable-shared.
* [svn-r19458] Add CMake tests for check-vfd; includes new vfdTest.cmake ↵Allen Byrne2010-09-211-0/+37
| | | | | | script and OPTION HDF5_TEST_VFD Tested: local linux
* [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-2110-49/+240
| | | | | | | | | | | | | 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-r19402] Description:Quincey Koziol2010-09-163-2/+63
| | | | | | | | | | | | | | | | | | | | | | | | | 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-r19398] Descriptino:Quincey Koziol2010-09-161-2/+2
| | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2010-09-162-111/+28
| | | | | | | | | | | | | | | | | | | | | | | | 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-r19386] Purpose: Fix assertion failure caused by fractal heap header ↵Neil Fortner2010-09-151-1/+141
| | | | | | | | | | | | | | 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-r19367] Purpose:Mike McGreevy2010-09-106-44/+39
| | | | | | | | | | | | | | | | | | | 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 Knox2010-09-101-1/+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-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-094-23/+413
| | | | | | | 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 Byrne2010-09-091-70/+7
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* [svn-r19354] Quincey and I made H5Eset_current_stack also close the stack to ↵Raymond Lu2010-09-071-0/+65
| | | | | | | | 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 Koziol2010-09-041-21/+10
| | | | | | | | 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-r19331] Correct list of h5 files needed for testsAllen Byrne2010-09-011-1/+3
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* [svn-r19328] Description:Quincey Koziol2010-08-311-11/+33
| | | | | | | | | | | | | 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-r19325] Added parallel build commands.Allen Byrne2010-08-311-79/+142
| | | | | | | 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-r19313] Description:Quincey Koziol2010-08-262-57/+49
| | | | | | | | 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-r19309] Description:Quincey Koziol2010-08-261-0/+126
| | | | | | | | | | | | | | | | | | | 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-r19297] Description:Quincey Koziol2010-08-254-6/+65
| | | | | | | | | | Whack a few more memory errors exposed by valgrind. Make the debugging dump output a little bit prettier. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug (h5committest forthcoming)
* [svn-r19288] Bug 1934 - I added support of all data types for H5Tget_order. ↵Raymond Lu2010-08-241-19/+51
| | | | | | | | | | | | 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. There is no change to configure.in, config, and Makefile.am in the top directory. They have some property changes when I merged the code from 1.8. Tested on jam. I tested the same change for 1.8 with h5committest.
* [svn-r19278] Description:Quincey Koziol2010-08-233-149/+136
| | | | | | | | | | | | | | | | | | | | | | 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-r19272] Description:Quincey Koziol2010-08-2013-330/+538
| | | | | | | | | | | | 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: Mac OS X/32 10.6.4 (amazon) w/debug & valgrind (h5committest forthcoming)
* [svn-r19251] New feature(bug #1934): I made H5Tset_order support all data ↵Raymond Lu2010-08-192-27/+124
| | | | | | | | | | | | | | | | | | 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. There is no change to configure.in, config, and Makefile.am. There is some property change for these files when I did a merge from 1.8. Tested on jam. But I tested the 1.8 on heiwa, and amani.
* [svn-r19242] Description:Quincey Koziol2010-08-162-4/+22
| | | | | | | | | Add in override for testing timeout alarm to allow "HDF5_ALARM_SECONDS" environment variable to change the timeout value from the default value. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (Too minor to require h5committest)
* [svn-r19237] Description:Quincey Koziol2010-08-122-27/+22
| | | | | | | | | | 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
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