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* [svn-r19654] Description:Quincey Koziol2010-10-211-34/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r19637] Purpose:Jonathan Kim2010-10-191-291/+290
| | | | | | | | | | | | | | Fix nightly build error on non-linux platforms related to the Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. (r19633) Description: - Updated to use standard C functions instead of strndup() due to failure on non-linux platforms. - Changed to Use HDxxx macros for future reference. - Correct indentation. Tested: jam, amani, heiwa, linew
* [svn-r19633] Purpose:Jonathan Kim2010-10-183-26/+113
| | | | | | | | | | Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. Description: Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed. Tested: jam, amani, heiwa
* [svn-r19605] Purpose:Jonathan Kim2010-10-153-107/+21
| | | | | | | | | | | Backout the previous changes (r19598): (Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.) Description: Some failure occurred on talwit, so backout the changes and will put it back after the fix. (Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed. Merged from hdf5 trunk r19598.)
* [svn-r19598] Purpose:Jonathan Kim2010-10-143-21/+107
| | | | | | | | | | Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. Description: Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. Expected to be failed. Tested: jam, amani, heiwa
* [svn-r19587] Description:Quincey Koziol2010-10-134-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | 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-r19548] Remove reference files from clearall commandAllen Byrne2010-10-081-3/+0
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* [svn-r19527] Add clear generated objects commands to test blocks.Allen Byrne2010-10-068-49/+939
| | | | | | Add configurefile command to copy CTestCustom to build folder. Tested: local linux
* [svn-r19509] Improve CMake support for CYGWIN.Allen Byrne2010-10-043-8/+8
| | | | | | Correct script comment in testh5diff.sh Tested: Windows Cygwin
* [svn-r19506] Bring changes from revisions 19408, 19421, and 19442 from ↵Larry Knox2010-10-0412-63/+230
| | | | | | 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-r19491] Purpose:Jonathan Kim2010-09-2911-0/+264
| | | | | | | | | | Update help page for exclude-path feature. Description: Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406) Tested: jam, amani, heiwa
* [svn-r19481] I'm backing out my fix for bug 1707 because there're some ↵Raymond Lu2010-09-277-53/+17
| | | | | | | | | | | 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-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-217-17/+53
| | | | | | | | | | | | | 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-r19443] Purpose:Jonathan Kim2010-09-204-10/+31
| | | | | | | | | | 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-r19434] Correct use of lib, include, bin in INSTALL commands to use ↵Allen Byrne2010-09-2010-13/+13
| | | | | | proper variables. Tested: local linux
* [svn-r19427] Updates for cmake tests from the h5diff group recursive updates.Jonathan Kim2010-09-201-4/+4
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* [svn-r19418] On windows, an include bypassed the WIN32_LEAN_AND_MEAN define. ↵Allen Byrne2010-09-171-1/+1
| | | | | | Moved the define up. Moved the h5dif.h to after the h5private include Tested: Windows
* [svn-r19415] Fix for Cmake test.Jonathan Kim2010-09-171-22/+28
| | | | | Tested: jam
* [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 Kim2010-09-167-1/+468
| | | | | | | | | | | 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 Kim2010-09-1614-17/+612
| | | | | | | | | | | 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 Byrne2010-09-161-3/+74
| | | | | | | | like runTest.cmake. Update CMakeLists.txt for new h5repack layout tests. Tested: local linux
* [svn-r19400] Purpose:Jonathan Kim2010-09-1653-633/+2328
| | | | | | | | | | 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-r19396] Description:Quincey Koziol2010-09-161-4/+7
| | | | | | | | | | | | | | | | | | | | | | | | 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-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 Knox2010-09-1011-11/+11
| | | | | | 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 Byrne2010-09-099-228/+24
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* [svn-r19325] Added parallel build commands.Allen Byrne2010-08-3110-36/+50
| | | | | | | 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-r19324] Description:Quincey Koziol2010-08-311-17/+30
| | | | | | | | | | | | | | | | | | | | | | | Bring recent tweaks to extensible and fixed array file formats from revise_chunks branch back to trunk. 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-r19318] Correct ENDIF text (non-executable) to match IF parameterAllen Byrne2010-08-271-1/+1
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* [svn-r19307] Correct test for H5_LONE_COLON - added NOTAllen Byrne2010-08-261-1/+1
| | | | Tested: windows
* [svn-r19300] BZ 1958: Add h5dump xml tests to CMake supportAllen Byrne2010-08-2510-106/+562
| | | | Tetsed: local linux
* [svn-r19292] Description:Quincey Koziol2010-08-245-44/+52
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Merge r19290 & r19291 from 1.8 branch to trunk: r19290: Correct another error in metadata accumulator dirty region calculations (this time with a corner case when freeing data in the file). r19291: Avoid getting object information for soft/external links if we aren't going to traverse across the link itself. 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-r19286] Corrected name of file appearing in expected output.Allen Byrne2010-08-241-1/+1
| | | | (Missed edit from local test)
* [svn-r19282] Fix test scripts (Cmake needs to capture output yet)Allen Byrne2010-08-234-22/+43
| | | | | | linux script needed -R and double compare: Tested: local linux
* [svn-r19265] Correct naming of SKIP testAllen Byrne2010-08-201-1/+4
| | | | Tested: local linux
* [svn-r19262] Undo r19261.Allen Byrne2010-08-201-0/+7
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* [svn-r19261] Remove unused variables and allocationAllen Byrne2010-08-201-7/+0
| | | | Tested: local linux
* [svn-r19255] Description:Quincey Koziol2010-08-201-0/+1
| | | | | | | | | | | | | | | | | | | | | | Add missing include file from r19252. 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-r19252] Description:Quincey Koziol2010-08-1915-223/+267
| | | | | | | | | | | | | | | | | | | | | | | 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 branch)
* [svn-r19237] Description:Quincey Koziol2010-08-125-75/+59
| | | | | | | | | | 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-r19228] File read/write happens at configure time, so moved windows ↵Allen Byrne2010-08-111-10/+11
| | | | | | specific copy from test macro to where the expected file is copied. Tested: windows
* [svn-r19214] Test for compare of output text to expected needed to account ↵Allen Byrne2010-08-101-9/+17
| | | | | | | | for windows line endings. Moved ADD_TEST commands to macro. Tested: local linux, windows
* [svn-r19202] [BZ1953]implementation for the proposed changes suggested by ↵Allen Byrne2010-08-094-19/+404
| | | | | | | the "h5dump_output_option" RFC. This required that the region reference code be duplicated and reduced to allow the do_bin_output() function to understand region references. The container type-id also needed to be propagated into the do_bin_output() function and functions referenced (render_bin_output*). Existing tests tested the binary function, so only one test was added to test the region reference generated file. Tested: local linux
* [svn-r19183] Corrected h5repack verbose test for windowsAllen Byrne2010-08-062-21/+21
| | | | | | Updated tools/lib source dir variable for source list Tested: local linux
* [svn-r19181] Added new h5repack test for bug1797 to CMakeLists.txt. Added ↵Allen Byrne2010-08-062-8/+26
| | | | | | corrected changes to test script for verbose filters Tested: local linux
* [svn-r19179] Description:Quincey Koziol2010-08-057-12/+161
| | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity branch back to trunk: r19079 & 19080: [BZ1942] h5dump -u to generate XML, it does not respect the -m option xml version of dump_data function didn't check for use of fp_format variable. Added new test expected file for committed bug 1942 r19103, 19104 & 19105: [BZ1821] h5repack -v did not display correct output for a selected compression. Needed new test for comparing output of -v option. Added new test file for solution to BZ1821 BZ1821 - Bring test changes from the shell script actually used. Tested on: Mac OS X/32 10.6.4 (amazon) debug & production (h5committested on branch)
* [svn-r19173] Took out several redundant lines when object IDs are closed.Raymond Lu2010-08-051-9/+0
| | | | Tested on jam.
* [svn-r19156] Description:Quincey Koziol2010-07-301-142/+168
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring revisions from Coverity branch back to trunk: r19044: Coverity #449 - Line 1560 called function H5O_chunk_protect for 2 pointers to allocate. But when there's failure on the second one, the first wasn't freed (H5O_chunk_unprotect). We fixed it by freeing the pointers when an error happens. r19045: Fixed coverity issue # 319. Free sec_node in done if it is not NULL. r19046: Add intended but missing assignments to initialize pointers to NULL (coverity issue fixes). r19049: Hdf5_1_8_coverity branch was recreated from hdf5_1_8 branch in revision 18839 without fix for Coverity issue #84 having been propagated to the hdf5_1_8 branch. This revision adds the fix again. r19060: added parentheses to see if they will keep subversion from getting confused r19061: Fix coverity item 139. Fixed incorrect condition for freeing buffer on error. Fix coverity items 20 and 21. Removed unused NTESTS facility from dtypes.c. Cleanup in H5Shyper.c. r19062: Fix coverity item 450. Check to see if chk_proxy has been allocated before attempting to free it. Fix coverity item 454. Check to see if allocation of buf failed in H5D_fill_refill_vl. Fix coverity items 455-457. Initilize hid_t's to -1, check their value before attempting to close them, and check if the close failed. r19063: New fix to address coverity issue #84. Check that pointers in H5Z_xform_find_type are not NULL before passing them to H5T_cmp. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (Too minor to require h5committest)
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