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* [svn-r29659] Added fixed array chunk indexing from revise_chunks.Dana Robinson2016-04-071-0/+406
| | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 Autotools serial w/ Java, Fortran, & C++
* [svn-r29635] Description:Quincey Koziol2016-04-051-3/+22
| | | | | | | | | Bring support for earray and v2 B-trees from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29607] Description:Quincey Koziol2016-04-021-18/+209
| | | | | | | | | Bring "don't filter partial edge chunks" capability from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/debug, production & parallel (h5committest forthcoming)
* [svn-r29548] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-21/+18
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r28710] Description:Quincey Koziol2015-12-191-33/+34
| | | | | | | | | | | | Bring r28708 from revise_chunks branch: Fix earray, farray and btree2 use of incorrect file pointer when two files are opened and used to access the data structure. Misc. minor code cleanups as well. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel h5committest forthcoming
* [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-10-201-1/+1
| | | | | | | | | | | | | | available Fix tests accordingly and fix misuse of hbool_t in various places Fix initialization of H5Pgcpl/ocpl structs in property decoding routines Tested on: Linux/32 (jam) Linux/64 (platypus) Linux/PPC64 (ostrich) MacOSX/64 10.11
* [svn-r27810] Description:Quincey Koziol2015-09-161-6/+39
| | | | | | | Clean up resources on failure Tested on: Linux/32 2.6.x (jam) w/Purify
* [svn-r27807] Description:Quincey Koziol2015-09-161-0/+2
| | | | | | | Close memory leak on failure. Tested on: Linux/32 2.6.x (jam) w/purify
* [svn-r27800] Minor warning fixes in the library tests.Dana Robinson2015-09-161-43/+55
| | | | Tested on: jam (too minor for h5committest)
* [svn-r27768] Description:Quincey Koziol2015-09-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r27626] Various minor warning fixes before major SWMR and VDS merges.Dana Robinson2015-08-311-1/+1
| | | | | | | | | | | gcc 4.9.2 was used to create the warning list - implicit casts - shadowed variables - various enum issues - other minor fixes (comments, unused macros, etc.) Tested on: h5committest
* [svn-r27548] Revert r27545Jerome Soumagne2015-08-211-1/+1
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* [svn-r27545] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-08-211-1/+1
| | | | | | available Fix tests accordingly
* [svn-r27204] Description:Quincey Koziol2015-06-151-10/+10
| | | | | | | | | Clean up compiler warnings before merging in v3 metadata cache changes from branch. Tested on: MacOSX/64 10.10.3 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-21/+21
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r26757] Description:Quincey Koziol2015-04-071-7/+7
| | | | | | | | Minor typos & code cleanups Tested on: MacOSX/64 10.10.2 (amazon) w/serial & parallel (Too minor to require h5committest)
* [svn-r26333] Eliminates gcc warnings due to -Wunsuffixed-float-constants.Dana Robinson2015-03-011-37/+49
| | | | | | | | | | | | - Adds 'F' suffixes for most float constants. - A few constants MUST be of type double. These now receive the long double L suffix and are then cast to double. I do this via a new H5_DOUBLE() macro which was added to H5private.h. Fixes: HDFFV-9148 Tested on: h5committest
* [svn-r26329] Merge of r26069, r26070, and r26072 from the ↵Dana Robinson2015-02-271-325/+39
| | | | | | | | | | | | | | | | | | features/autotools_rework branch. Removed the configure option that allows selective disabling of individual internal filters (fletcher32, shuffle, etc.). This feature mucked up the code with a lot of #ifdefs, saved very little space, and was not scalable to a general scheme for library size reduction. We've decided to remove the feature while we investigate a more general scheme for decreasing the library size. Part of: HDFFV-9086 Tested on: h5committest
* [svn-r25496] Description:Quincey Koziol2014-07-301-1/+1
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r25401] add serial and parallel regression tests for zero dset ↵Mohamad Chaarawi2014-07-091-0/+76
| | | | read/write bug.
* [svn-r24995] Description:Quincey Koziol2014-04-091-1/+10
| | | | | | | Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls. Tested on: Linux/32 2.4.x (jam) w/gcc
* [svn-r24416] Fixed some compiler warnings in the dsets test.Dana Robinson2013-11-071-17/+19
| | | | | | | | Tested on: 32-bit LE linux (jam) (These are just minor casting changes in the tests, hence the minimal testing.)
* [svn-r24376] Updated all code to use HDmalloc, HDcalloc, and HDfree.Dana Robinson2013-10-311-5/+5
| | | | | | | | | | | | | Prep work for adding a memory free function, part of HDFFV-8551. Tested on: 32-bit LE linux (jam) * with C++, Fortran * with thread safety on These are minor changes (almost entirely renaming foo functions to HDfoo) that don't change functionality. This should not require a full commit test.
* [svn-r24101] Description:Quincey Koziol2013-09-051-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up warnings, enable new compiler warning flag(s) and bring back changes from Coverity branch: r20813: Remove the dead code as listed for coverity bug #1722. h5committested. r20814: Issue 69: Check return value and throw error if negative return. Also free datatype id on error r20815: Use HDstrncpy. --gh r20816: Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832. r20817: Use HDstrncpy and HDstrncat. --gh r20818: Purpose: Fix valgrind issues with h5jam Description: Modified h5jam to free strings strdup'd in parse_command_line before exit. Note that they may still not be freed in case of error, due to the widespread use of exit(). r20819: Issue 80: change loop to use int as loop index. r20820: Maintenance: Fixed the bug found by coverity CID 788 There were two problems with this function: 1) it tried to unnecessary free NULL pointer 2) it tried to allocate c_name buffer that is done by H5Pget_class_name Tested on: Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN (too minor to require h5committest)
* [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-r23117] Changed extension of hdf5 files from .hdf5 to .h5 for consistancy.Scot Breitenfeld2012-12-211-2/+2
| | | | | | HDFFV-422: Change extention of the binary files from hdf5 to h5 Tested: jam (gnu)
* [svn-r22646] Description:Quincey Koziol2012-08-081-8/+6
| | | | | | | | | 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-r21801] Remove unintentional change to dsets.c from r21793.Neil Fortner2011-12-051-115/+0
| | | | Tested: durandal
* [svn-r21793] Add RELEASE.txt note for r21789Neil Fortner2011-12-011-0/+115
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* [svn-r21792] Add ^L marker to test introduced in r21789Neil Fortner2011-12-011-1/+1
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* [svn-r21789] Purpose: Fix HDFFV-7833Neil Fortner2011-12-011-0/+116
| | | | | | | | | | | | Description: When shrinking a chunked dataset, the library fills in the unused parts of chunks that have been shrunk. The fill value buffer allocated for this purpose had a maximum size of 1 MB, but the fill was performed in a single operation. Therefore, if the amount of unused space in a chunk after being shrunk was greater than 1 MB, the library would read off the end of the fill value buffer. Changed the maximum fill buffer size to be equal to the chunk size. Tested: durandal; jam, koala, heiwa (h5committest)
* [svn-r21220] The original code Raymond Lu2011-08-121-1/+12
| | | | | | | | | i_mask = ~((unsigned)~0 << (precision[0] + offset[0])) & ((unsigned)~0 << offset[0]); in line 3680 left shifted a 32-bit integer for 32-bit. The result is undefined by C language. A user discovered it using clang compiler with -fcatch-undefined-behavior option (see Issue 7674 in Jira). So I changed it in a funny way to avoid it. Tested on jam, koala, and heiwa.
* [svn-r20529] Purpose: Add testing for bug 1864Neil Fortner2011-04-151-0/+3
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r20480] Description:Quincey Koziol2011-04-121-4/+4
| | | | | | | | | | | Remove global variable for the path name in the group traversal code. Also clean up a bunch of compiler warnings. Tested on: Mac OS X/32 10.6.7 (amazon) w/debug & production FreeBSD/32 6.3 (duty) w/debug FreeBSD/64 6.3 (liberty) w/debug Solaris/32 2.7 (linew) w/debug
* [svn-r19833] Bug fix - In the code of N-bit filter, one line (the last line ↵Raymond Lu2010-11-191-0/+383
| | | | | | | | | | | of H5Znbit.c in H5Z_nbit_compress - "*buffer_size = j + 1;" was mistakenly taken out by someone. It is necessary to update the new size. I put it back and made 2 test cases for integer and float to verify the correct dataset size. I'm bringing the fix from 1.8 branch. The changes to configure.in, tools/misc, config, Makefile.am are only property changes. Tested on jam. But I tested 1.8 on jam, heiwa, and amani.
* [svn-r19396] Description:Quincey Koziol2010-09-161-110/+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-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-r19313] Description:Quincey Koziol2010-08-261-11/+11
| | | | | | | | 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-r19272] Description:Quincey Koziol2010-08-201-10/+17
| | | | | | | | | | | | 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 Lu2010-08-191-10/+6
| | | | | | | | | | | | | | | | | | 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-r19175] Bug fix for #1239 - The filter's public function CAN_APPLY ↵Raymond Lu2010-08-051-6/+213
| | | | | | | | | | | | should return htri_t not herr_t. To minimize the change of the library's behavior, in the function H5Z_prelude_callback of H5Z.c, if the return value of can_apply is FALSE and the filter is MANDATE, this function returns a FAILURE. If the return value is FALSE but the filter is OPTIONAL, this function returns a SUCCEED. During the IO, the filter will fail and return a size of zero. But the pipeline will skip this filter. Tested the same change for 1.8 on jam, linew, and amani. Tested on jam with szip.
* [svn-r18419] Description:Quincey Koziol2010-03-181-0/+1
| | | | | | | | | Clean up srcdir querying code more, extracting it into single header file, to avoid compiler warnings. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & prod Linux/32 2.6 (jam)
* [svn-r18413] Description:Quincey Koziol2010-03-171-25/+3
| | | | | | | | | | | | | | Unify srcdir handling for test executables and allow them to use the srcdir setting from configure time without requiring the 'srcdir' environment variable be set (although you still can, to override the built in setting). Attempted to get this right for Windows builds also. Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so that the test/testcheck_version.sh script works correctly. Tested on: Linux/32 2.6 (jam) Mac OS X/32 10.6.2 (amazon)
* [svn-r18388] Description:Quincey Koziol2010-03-061-8/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity session from branch into trunk: r18378: Fixed coverity issues 207 and 322. Pointer hdr was checked for NULL after being asserted and dereferenced. Check was removed. r18379: Fix coverity issues # 88 and # 435. r18380: Fixed Coverity issue # 85. Added check of returned pointer for NULL before use. r18381: Resolve coverity issues # 214 and # 215 r18382: Issue 131: Add null checks to allocations and check for free in error handling r18383: Issue 421: Reorganized code to make intention clearer. Also, set local variable fl to NULL after transfer to tail. Heap->freelist will take care of all allocations r18384: Coverity #249 and #250 - STRING_ATT_CHECK wasn't allocated before being used and freed in function test_write_vl_string_attribute and test_read_vl_string_attribute. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & prod (h5committested in daily tests)
* [svn-r18346] Description:Quincey Koziol2010-02-271-56/+66
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity fixes back from branch to trunk: r18336: Fix coverity issues 275, 276, 277, 323, 432, 433, and 434 r18337: Fix Coverity issue #106: release free space section node on error r18338: Fixed Coverity #94 - In H5P_register, new_class wasn't closed when there's an error after it's created. r18339: Fix Coverity #185 - In test_conv_str_1, BUF wasn't freed when there's an error in this function. r18340: Correct error in r18337 that wasn't releasing indirect fractal heap block early enough. r18341: Close nodes if any failed in the middle of allocating new nodes. Coverity 140 and 141 r18342: Correct [another] problem w/r18337. r18343: Fix coverity items 185, 20, and 21. r18344: Fix Coverity 213 - In H5FD_family_close, the double pointer file->memb was dereferenced without NULL checking (We believe). r18345: Fix Coverity issue # 210; removed NULL check after pointer dereferenced in H5HFdblock.c. Also assigned NULL to pointer in H5Pint.c to fix segmentation fault. 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18197] Description:Quincey Koziol2010-01-301-28/+28
| | | | | | | | | Trim trailing whitespace from source code files with this command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r18193] I added a test for copying an existing DCPL and using the copy ↵Raymond Lu2010-01-291-0/+137
| | | | | | | | | to create a new dataset. There's a bug report (#1608) saying h5repack failed to do that sometimes. But I couldn't reproduce it. So I added this test and closed the report. The test is in the function test_copy_dcpl in dsets.c. Tested on jam. But I tested the same change in 1.8 on jam, amani, and linew.
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