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* [svn-r23305] HDFFV-8257: szip still used even if headers are not found. ↵Allen Byrne2013-02-181-1/+1
| | | | | | Change configure to test the result of the CHECK HEADERS call before checking for the library. Tested: local linux, h5committest
* [svn-r23260] Bug fix: HDFFV-8267Albert Cheng2013-02-121-1/+1
| | | | | | | | | | The ERROR macro had a typo of missing a separator comma. When used, it seg. fault. Added the comma back in. Fix is reviewed in Crucible HDF5-107. Tested: h5committest passed. Also tested using the ERROR macro in the Mac (Owl) platform. Before fix, it seg. fault. After fix, it prints the message as intended.
* [svn-r23237] Purpose: Implement H5Dscatter and H5DgatherNeil Fortner2013-02-081-1/+17
| | | | | | | | | | | Description: Adds 2 new API functions, H5Dscatter and H5Dgather. H5Dscatter retrieves data from a specified callback function and scatters it into a selection, defined by a supplied dataspace, within a supplied memory buffer. H5Dgather gathers data from a selection within a supplied memory buffer and passes it in a contiguous form to a supplied callback function. Added tests for these functions Tested: jam, ostrich, koala (h5committest); ummon
* [svn-r23234] Fix out-of-bounds errors on pgcc for H5Dscatter and H5Dgather ↵Neil Fortner2013-02-071-10/+10
| | | | | | tests. Tested: jam (pgcc), ummon (gcc)
* [svn-r23230] Purpose: Implement H5Dscatter and H5DgatherNeil Fortner2013-02-051-0/+1012
| | | | | | | | | | | Description: Adds 2 new API functions, H5Dscatter and H5Dgather. H5Dscatter retrieves data from a specified callback function and scatters it into a selection, defined by a supplied dataspace, within a supplied memory buffer. H5Dgather gathers data from a selection within a supplied memory buffer and passes it in a contiguous form to a supplied callback function. Added tests for these functions Tested: jam, ostrich, koala (h5committest); ummon
* [svn-r23219] Description:Quincey Koziol2013-02-023-111/+139
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring reviewed changes from Coverity branch back to trunk (QK & JK): r20457: Coverity issue 691: return of H5duo could be negative. Fixed by using STDOUT_FILENO and redesign parse_command_line and main to cleanup file allocations. The output_file var is null when using stdout. In cleanup do not close output_file if NULL. r20510: Initialize ufid = -1 and predicate HDclose call on ufid != -1 r20511: Purpose: Fix coverity issue 1715 Description: Free "file" and nested data on failure in H5FD_core_open. r20512: Initialize ifid = -1 and predicate HDclose call on ifid != -1 r20514: Initialize h5fid = -1 and predicate HDclose call on h5fid != -1 r20516: Added else branch to the if (ret_value < 0) check. r20522: Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor potential buffer overwrite bugs, or coverity errors. Fixed by replacing strcpy and sprintf with strncpy and snprintf. r20523: fixed coverity issues 68, 1120, 1116i r20524: Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence. r20601: Purpose: Fix coverity issues 1703-1705 Description: Modified the cleanup code in test_free in accum.c to reset allocated buffers to NULL after they are freed, and modified the error cleanup code to check if these buffers are NULL before freeing them. Also fixed some unrelated warnings in accum.c. r20602: Use HDsnprintf and HDstrncat r20603: Purpose: Fix coverity issues 808-809 Description: Modified test_core in vfd.c to check the returns from malloc, and keep track of whether points and check are allocated by setting them to NULL when they are not. Added code to free points and check on error if they are not NULL. Also fixed unrelated warnings in vfd.c. r20604: Use HDstrncpy. r20605: Use HDstrncpy and HDstrncat. r20606: Purpose: Fix coverity issue 807 Description: Modified long_compact in stab.c to keep track of whether objname is allocated by setting it to NULL when it is not. Added code to free objname on error if it is not NULL. r20607: Changed string function calls to use versions that specify the string length to fix coverity issues 832 and 839. Tested on: Mac OSX/64 10.8.2 (amazon) (Too minor to require h5committest)
* [svn-r23161] ported revisions 23146:23160 from the trunkRaymond Lu2013-01-142-3/+3
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* [svn-r23152] I took out the obsolete function H5PSIwrite_chunk and its ↵Raymond Lu2013-01-113-359/+23
| | | | | | related test and performance test. Tested on koala.
* [svn-r23149] I put more condition checks with macro when DEFLATE filter is ↵Raymond Lu2013-01-101-1/+17
| | | | | | disabled. Tested on koala.
* [svn-r23147] ported revisions 23081:23145 from the trunkRaymond Lu2013-01-094-4/+4
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* [svn-r23097] I changed H5Dopen to H5Dopen2 in test/dectris_tst.c and ↵Raymond Lu2012-12-131-2/+2
| | | | | | | | | | hl/test/test_dset_opt.c. I added hl/test/dectris_hl_perf.c perform/dectris_perf.c test/dectris_tst.c Tested on koala.
* [svn-r23017] I added a prototype function H5DOwrite_chunk in HL library for ↵Raymond Lu2012-11-071-1/+4
| | | | | | | | | Dectris people to test performance. The library's API function H5PSIdirect_write is still in. I reorganized the internal library by adding H5D__pre_write function. Tested on koala.
* [svn-r22987] ported revisions from 22742 to 22986 from the trunkRaymond Lu2012-10-2939-157/+1465
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* [svn-r22739] ported revisions 22615 to 22737 from the trunkRaymond Lu2012-09-0521-338/+583
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| * [svn-r22709] HDFFV-8129: reconfigured on jam, Remove overloading of ↵Allen Byrne2012-08-235-30/+25
| | | | | | | | | | | | autotools TESTS var, rename configure.in to configure.ac, convert test scripts from hard *.sh to configure managed *sh.in files. Tested: h5committest
| * [svn-r22706] Updated autotools: autoconf 2.69, automake 1.12.3, m4 1.4.16, ↵Larry Knox2012-08-221-124/+177
| | | | | | | | | | | | libtool 2.4.2 Tested THG machines.
| * [svn-r22676] Changes needed to make the default free-list mapping from ↵Vailin Choi2012-08-133-125/+306
| | | | | | | | H5FD_FLMAP_SINGLE to H5FD_FLMAP_DICHOTOMY.
| * [svn-r22668] Description:Quincey Koziol2012-08-111-4/+4
| | | | | | | | | | | | | | | | | | Have free space manager use temporary address space for storing the section info, until the file is flushed or closed. Tested on: Mac OSX/64 10.7.4 (amazon) w/debug, gcc 4.7.x, C++, FORTRAN & threadsafe (h5committest forthcoming)
| * [svn-r22646] Description:Quincey Koziol2012-08-0813-54/+70
| | | | | | | | | | | | | | | | | | Changes resulting from Klocwork static analysis tool, from Mark Miller @ LLNL (miller86@llnl.gov). Tested on: Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x (too minor to require h5committest)
* | [svn-r22655] Dectris project - I changed the rank of the offset for ↵Raymond Lu2012-08-091-1/+1
| | | | | | | | | | | | | | | | H5PSIdirect_write from RANK+1 to RANK. But internally, it expands to RANK+1 as the library requires it to terminate with a zero. Tested on koala.
* | [svn-r22653] Dectris project: I revised the code per Quincey's suggestion.Raymond Lu2012-08-094-567/+29
| | | | | | | | Tested on koala.
* | [svn-r22641] Dectris project: I revised the code per Quincey's and Neil's ↵Raymond Lu2012-08-084-25/+640
| | | | | | | | | | | | comments. I added a performance benchmark program dectris_perf.c in the test/ directory. Tested on koala and jam.
* | [svn-r22616] The code for H5PSIdirect_write and its test dectris_tst.c.Raymond Lu2012-07-303-25/+268
|/ | | | Tested on koala and jam.
* [svn-r22601] Purpose: Fix HDFFV-5853Neil Fortner2012-07-251-0/+99
| | | | | | | | | | | | | | Description: When jumping out from between H5_BEGIN_TAG and H5_END_TAG macros using HGOTO_ERROR or HGOTO_DONE, the previous metadata tag is not reset on the dxpl. This could cause problems when, for example, calling H5Ocopy within an H5Literate callback. Added new HGOTO_ERROR_TAG and HGOTO_DONE_TAG macros which must be used in place of the above between H5_BEGIN_TAG and H5_END_TAG. Tested: jam, koala, ostrich (h5committest), durandal
* [svn-r22582] Description:Quincey Koziol2012-07-161-9/+9
| | | | | | | | | Refactor ID class registration to be more like how other "class"s in the library are registered, and clean up compiler warnings. Tested on: Mac OSX/64 10.7.4 (amazon) w/debug (Too minor to require h5comittest)
* [svn-r22487] Snapshot version 1.9 release 122HDF Tester2012-06-241-15/+17
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* [svn-r22486] Description:Quincey Koziol2012-06-231-3/+4
| | | | Fix typo with last change and reformat a little bit
* [svn-r22484] Description:Quincey Koziol2012-06-232-18/+19
| | | | | | | | | | | | Copy the file image test file from the source directory to the build directory, instead of trying to open the [in-memory] file R/W. Also, clean up a few other test files that were left lying around from other tests. Tested on: MacOSX/64 10.7.4 (amazon) w/debug Too minor to require h5committest
* [svn-r22444] (1) fix for making MEM_GHEAP as MEM_DRAWVailin Choi2012-06-071-9/+41
| | | | | | | (2) fix to extend into the aggregator based on threshold (3) fix for the "flavor" logging problem (4) fix for test failures due to the above fixes (5) bug fix for h5stat when h5stat against a non-existing file
* [svn-r22411] reduce compiler warnings by removing unreferenced variables and ↵Allen Byrne2012-05-251-2/+1
| | | | | | adding cast Tested: local linux
* [svn-r22393] I forgot to close a few datatypes in test_str_create. I fixed ↵Raymond Lu2012-05-231-0/+5
| | | | | | them in this commit. Tested on jam - very simple change.
* [svn-r22375] add a test to expose a memory leak when adding/removing the ↵Mohamad Chaarawi2012-05-181-0/+42
| | | | | | | | same property in property list multiple times. fix that bug. test with h5committest
* [svn-r22287] Description:Quincey Koziol2012-04-166-156/+160
| | | | | | | | Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r22263] Use correct index for inserting null terminatorAllen Byrne2012-04-091-9/+9
| | | | Tested: windows under debug
* [svn-r22247] Added new files and tests to CMakeLists.txtAllen Byrne2012-04-041-0/+3
| | | | Tested: local linux
* [svn-r22233] Description:Quincey Koziol2012-04-011-4/+128
| | | | | | | | | | | | | | | | | Correct several errors in fractal heap code: root indirect block was getting pinned/protected more than once, "single" free space sections weren't getting "re-parented" correctly when the heap transitioned between having a root indirect block and a root direct block, and several related issues. Also cleaned up some warnings in library/tests. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Mac OSX/64 10.7.3 (amazon) w/debug
* [svn-r22229] Description:Quincey Koziol2012-04-011-21/+22
| | | | | | | | | | | | | Add 'H5O_mcdt_search_cb_t' to bin/trace script and re-run the bin/reconfigure script. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode
* [svn-r22219] Description:Quincey Koziol2012-03-315-22/+1466
| | | | | | | | Merge "file image" changes from feature branch back to trunk. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest upcoming)
* [svn-r22173] Purpose: Fix HDFFV-7762Neil Fortner2012-03-281-1/+169
| | | | | | | | | | | | | | | | Description: When copying an object with attribute creation order tracked, the attribute creation order was not copied correctly to the destination file, causing an error if the creation order was also indexed (due to attempting to insert duplicate keys) or incorrect creation orders otherwise. Fixed to copy the creation order correctly. Also fixed the attribute character set not being copied, and fixed an issue where an attribute opened with H5Aopen (or similar, but not by_idx), from an object using the latest format but without creation order being tracked, would always report the creation order as 0 (and marked as valid). Tested: jam, koala, ostrich (h5committest), durandal
* [svn-r22171] Description:Quincey Koziol2012-03-281-1/+3220
| | | | | | | | | Bring "merge committed datatypes during H5Ocopy" feature from branch to trunk. (Also has some minor bugfixes with it) Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest coming up)
* [svn-r22164] Fixed a bug in H5Ocopy(): When copying an opened object, call ↵Vailin Choi2012-03-281-0/+314
| | | | | | | the object's flush class action to ensure that cached data is flushed so that H5Ocopy will get the correct data. (HDFFV-7853)
* [svn-r22161] Added a message when the time-consuming test is skipped due to ↵Dana Robinson2012-03-271-0/+2
| | | | | | a lack of sparse file support. Minor change: tested on 64-bit Windows 7
* [svn-r22152] Added a "skipped" message to the istore sparse test function.Dana Robinson2012-03-261-9/+16
| | | | | Minor change: tested on jam (test not skipped) and Mac OS-X Lion (test skipped due to HFS not supporting sparse files).
* [svn-r22112] Description:Quincey Koziol2012-03-211-3/+10
| | | | | | | | Minor code safety issue in test/fheap.c and whitespace in other files. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (Too minor to require h5committest)
* [svn-r22111] Removed incorrect 'executable' svn properties.Dana Robinson2012-03-211-0/+0
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* [svn-r22110] Removed incorrect 'executable' svn properties.Dana Robinson2012-03-215-0/+0
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* [svn-r22103] Fix for HDFFV-7769 (HDF5 tests time out on Windows when core ↵Dana Robinson2012-03-201-1/+47
| | | | | | | | | | | | | | | | | | | | | | | VFD is set). This occurs due to the istore test creating very large files on systems which do not have POSIX-like sparse file semantics. The large amount of I/O causes the test to run for a very long period of time. The fix was to copy the "big" test's sparse file check and only run the largest sparse file test when POSIX-like sparse file semantics are found. Tested on: jam (nfs) ostrich (nfs) loyalty (ufs) 64-bit linux VM (ext4) 64-bit OS-X Lion (hfs, detected as not POSIX sparse) 64-bit Windows 7 (NTFS, detected as not POSIX sparse) The OS-X failure to pass the sparse check is likely an error and will be entered as a new bug.
* [svn-r22076] #Issue 7922 - H5Pset_data_transform had seg fault with some ↵Raymond Lu2012-03-151-4/+176
| | | | | | | | | operations like x*-100. The parser mistaked "-" as substraction. I fixed it and also fixed another problem with some special cases like 100-x and 2/x. Tested on jam, koala, and ostrich.
* [svn-r22072] Purpose: Fix rare corruption bug (HDFFV-7879)Neil Fortner2012-03-151-0/+135
| | | | | | | | | | | | | | Description: When using the new object header format, it was possible for corruption to occur if the first object header chunk changed size such that the lenght of the "chunk 0 size" field changed. This only occurred if there were messages that had not been decoded. The original algorithm that changed the object header chunk size marked all messages as dirty, causing those that had not been decoded to have both the raw and native form invalidated. Changed the algorithm to avoid marking messages dirty and added assertions to catch the case where messages are dirtied without being decoded (or recently created) first. Tested: jam, koala, ostrich (h5committest), durandal
* [svn-r22070] Purpose: Fix rare corruption bugNeil Fortner2012-03-151-1/+206
| | | | | | | | | | Description: When using the new object header format and adding an attribute with a size near 64K, it was possible for file corruption to occur. This happened only if the first object header chunk was smaller than 256 bytes and then grew to larger than 64K after the attribute was added. Tested: ostrich, jam, koala (h5committest), durandal
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