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* [svn-r25233] Snapshot version 1.8 release 14 (snap5)HDF Tester2014-06-022-5/+5
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* [svn-r25225] Description:Quincey Koziol2014-05-292-0/+6
| | | | | | | | | | | | | | | | Bring r25215 from trunk to 1.8 branch: Bring changes from Coverity branch back to trunk: r20914: Use HDstrncpy and HDstrncat! --gh r20915: Use HDstrncpy and HDstrncat! --gh Tested on: MacOSX/64 10.9.3 (amazon) w/gcc 4.9, FORTRAN, C++, multi-threads & parallel (h5committested on the trunk)
* [svn-r25222] Merge cmake_ext_mod into 1.8Allen Byrne2014-05-271-21/+38
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* [svn-r25217] Snapshot version 1.8 release 14 (snap4)HDF Tester2014-05-251-2/+2
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* [svn-r25200] Snapshot version 1.8 release 14 (snap3)HDF Tester2014-05-181-2/+2
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* [svn-r25198] Description:Quincey Koziol2014-05-182-5/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r25197 from trunk to 1.8 branch: Bring changes from hdf5_1_8_coverity branch back to trunk: r20878: Issue 76: Check if H5Tget_nmembers(type) fails and simply return(FALSE). Also move printf to after check. r20880: Issue 192: Create ret_val var set to -1. Add out label for failures to jump to, return ret_val at bottom. r20882: Fixes for coverity: 1) bug #1679: remove dead code in test/mf.c 2) bug #1680: remove dead code in tools/lib/h5diff_dset.c r20883: Fix coverity issue 585 Description: Changed variable "c" in processStrData in h5import.c to an int, to match fgetc return value, and removed call to feof, instead checking if c == EOF. Tested on: MacOSX/64 10.9.3 (amazon) w/C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r25159] Snapshot version 1.8 release 14 (snap2)HDF Tester2014-05-041-2/+2
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* [svn-r25140] Commit Joel's fix to this branch.Albert Cheng2014-05-011-5/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix: HDFFV-8247 Description: Failure to write fill values to the user's buffer when reading unallocated chunks from datasets that have a fill value set to H5D_FILL_VALUE_DEFAULT. A consequence of this was the reporting of spurious data values in h5dump and h5diff output. Solution: Added check for fill value of H5D_FILL_VALUE_DEFAULT whenever fill value setting was checked to decide whether or not to fill. This effectively treats H5D_FILL_VALUE_DEFAULT the same as H5D_FILL_VALUE_USER rather than H5D_FILL_VALUE_UNDEFINED. Tested: h5committest (platypus, ostrich, jam-pp, koala) ran successfully (fillval test was modified to reveal and check for this error) H5Dchunk.c: fix in library code. fillval.c: Added test_partalloc to expose potential fill value issues.
* [svn-r25127] Snapshot version 1.8 release 14 (snap1)HDF Tester2014-04-271-2/+2
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* [svn-r25111] Changed Subeversion EOL and executable properties. No code changes.Dana Robinson2014-04-251-49/+49
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* [svn-r25109] Description:Quincey Koziol2014-04-2542-707/+927
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r25084, 25088, 25092, 25097 from trunk to 1.8 branch: r25084: Begin process of migrating from using property list IDs internally to the library to using the internal generic property list data structure. r25088: Introduce "file I/O info" struct, to hold file & dxpl pointers, and start propagating up through library. r25092: More migration to using H5F_io_info_t pointers and away from using property list IDs internally. Also, clean up some compiler warnings in the cache code. r25097: Make progress toward moving from DXPL IDs to property list structures within the library. Also move the signature location code from the H5F package to the H5FD package, where it's a better fit. Also, clean up some more compiler warnings along the way. Tested: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (h5committested on trunk)
* [svn-r25106] Removed LT_ADD_LIBHDF5_DEPENDENCY configure conditional to roll ↵Larry Knox2014-04-251-1/+0
| | | | | | | | back fix for removing rpaths from lib files. The fix also removed dependencies on libhdf5, etc. when the --disable-sharedlib-rpath configure option was invoked. Added instead configure variable hardcode_into_lib=no. This removes rpath from lib files on Linux and solaris machines. Tested with h5committest on jam, koala, ostrich and platypus (cmake), and on emu and kite.
* [svn-r25071] Snapshot version 1.8 release 14 (snap0)HDF Tester2014-04-201-2/+2
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* [svn-r25050] Description:Quincey Koziol2014-04-1625-86/+347
| | | | | | | | | | | | | | | Bring r24995 and r24998 from the trunk to the 1.8 branch: r24995: Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls. r24998: Check in Neil's changes for correctly handling case where library is reinitialized through a deprecated routine. Tested on: Mac OSX/64 10.9.2 (amazon) w/serial & paralle (change has baked on trunk for >7 days)
* [svn-r25036] Maintenance before creating 1_8_13 branch: changed version ↵Elena Pourmal2014-04-142-4/+4
| | | | number to 1.8.14-snap0
* [svn-r25035] Snapshot version 1.8 release 13 (snap8)HDF Tester2014-04-131-2/+2
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* [svn-r25033] Purpose:Dana Robinson2014-04-124-40/+447
| | | | | | | | | | | | | | | | | | Merged r24993 from the trunk. Adds core VFD write tracking functionality. When enabled, the core VFD will track dirty regions of the file and only write out the changed regions. The new H5Pget/set_core_write_tracking() API call controls this feature. A new "core_paged" VFD target was added to the check-vfd target in test/Makefile.am that runs all tests with the new write tracking functionality. Tested on: 32-bit LE linux (jam) 64-bit LE linux (koala) 64-bit BE linux (ostrich) Each platform was tested with HDF5_DRIVER set to "core" and "core_paged". Jam was also tested with the standard sec2 driver.
* [svn-r25018] Purpose:Dana Robinson2014-04-116-114/+330
| | | | | | | | | Merged r24893, r24961, r24965 from trunk. Fix for thread-local storage resource leaks on Windows with Win32 threads. Prohibits thread-safe + C++/Fortran/static library in CMake. Tested on: 64-bit Windows 7 w/ Visual Studio 2012
* [svn-r25014] Purpose:Dana Robinson2014-04-112-0/+26
| | | | | | | | | | | | | | | | | Merge of r24937 from the trunk Adds H5free_memory to the API. This function should be used to free memory allocated by the library (e.g., returned values from H5Tget_tag, H5Pget_class_name, etc.). This is mainly to help Windows applications deal with multiple CRT instances, but can also be helpful when a debug memory manager is being used or when the HDF5 API is being wrapped for managed languages like Python and Java. Tested on: 32-bit LE linux (jam) with fortran and C++ 64-bit BE linux (ostrich) 64-bit LE linux (koala)
* [svn-r24980] HDFFV-8290: Merge automake 1.14.1 changes from trunkAllen Byrne2014-04-071-67/+420
| | | | Tested: h5committest
* [svn-r24968] Snapshot version 1.8 release 13 (snap7)HDF Tester2014-04-061-2/+2
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* [svn-r24927] Snapshot version 1.8 release 13 (snap6)HDF Tester2014-03-301-2/+2
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* [svn-r24921] Add MINGW checkAllen Byrne2014-03-271-4/+4
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* [svn-r24906] Merge latest CMake changes from trunk.Allen Byrne2014-03-261-106/+119
| | | | Tested: local linux
* [svn-r24894] Description:Quincey Koziol2014-03-254-9/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24869 & r24875 from trunk to 1.8 branch: Clean up more compiler warnings, plus merge a few Coverity bug fixes from the hdf5_1_8_coverity branch back to the trunk: r20877: Purpose: Fix coverity issue 1723 Description: Modified test_generate in hl/test_image to close file "f" before exit, even if an error occurs. r20879: Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go futher if call fails as well as empty. r20881: Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the condition check in the print statement. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel (daily tested on trunk)
* [svn-r24878] Description:Quincey Koziol2014-03-2418-1678/+116
| | | | | | | | | | | | | | | | | | | | | Bring r24864 from trunk to 1.8 branch: Remove all traces of MPI-POSIX VFD and GPFS detection/code. Remove remaining traces of stream VFD. Remove testpar/t_posix_compliant test (it's not actually verifying anything). Clean up H5D__mpio_opt_possible() further. Moved environment variable that disables MPI collective operations into MPI-IO VFD (instead of it being in src/H5S.c). A few other small code cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (daily tested on trunk)
* [svn-r24871] Snapshot version 1.8 release 13 (snap5)HDF Tester2014-03-231-2/+2
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* [svn-r24810] Description:Quincey Koziol2014-03-173-73/+75
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24803 & r24804 from trunk to 1.8 branch: r24804: Brought changes from Coverity branch back to trunk, and cleaned up misc. other warnings & formatting issues: r20833: Fixed Coverity 667 and 668 with real integer overflow tests this time. r20834: Use HDstrncpy and HDstrncat. --gh r20835: Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159 r20836: Fixed coverity 585 by casting output of fgetc() to a char. r20837: Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967. r24803: Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t in DIAG_OFF(long-long) macros. Clean up a bunch of "macro '-' is unused" warnings. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r24794] Port r24757 from trunk to 1.8 branch.Neil Fortner2014-03-132-3/+5
| | | | | | | | | | | | Tested: ostrich, platypus (h5committest, apparent system issue on jam and koala) Log from r24635: Change assertion to condition check/error return. Should fix periodic assertion failure in fheap test (in test that is expected to fail cleanly). Fix typo in H5detect.c Tested: ostrich, platypus (h5committest - jam and koala having issues)
* [svn-r24785] Description:Quincey Koziol2014-03-1213-167/+637
| | | | | | | | | | | | | Bring r24769 & r24772 from trunk to 1.8 branch: Check in Mohamad's changes to support collective I/O on point selections, along with some other minor cleanups. Correct some dynamically sized arrays that fail on Windows. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel (And has been through the daily test regime on the trunk)
* [svn-r24771] Snapshot version 1.8 release 13 (snap4)HDF Tester2014-03-091-2/+2
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* [svn-r24754] Snapshot version 1.8 release 13 (snap3)HDF Tester2014-03-021-2/+2
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* [svn-r24746] Merge trunk revision 24744 from cmake branch includes;Allen Byrne2014-02-271-1/+7
| | | | | | HDFFV-8505: UD filter changes to remove filters in h5repack. Tested: local linux
* [svn-r24735] Port r24635 from trunk to 1.8 branch.Neil Fortner2014-02-241-2/+4
| | | | | | | | | | | | | | Note: despite the log from r24635, it was decided that this is the actual fix for the error described in HDFFV-8647 that is not specific to BSD. This does not address the BSD issue, which is apparently unrelated. Tested: jam, ostrich, platypus (h5committest, apparent system issue on koala) Log from r24635: Change some range check assertions to errors in H5HF_man_remove in an attempt to aid in diagnosing issue HDFFV-8647. Tested: ummon
* [svn-r24732] Fix for reconfigure, which fails because ↵Larry Knox2014-02-221-0/+1
| | | | | | LT_ADD_LIBHDF5_DEPENDENCY is used in Makefiles but the declaration in configure.ac is missing. Copied declaration from trunk. Tested with h5committest on jam ostrich koala and platypus(cmake).
* [svn-r24728] Description:Quincey Koziol2014-02-216-75/+92
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24726 & r24727 from trunk to 1.8 branch: Description: Revert some earlier usage of strncpy, which was incorrect. Bring Coverity changes from branch back to trunk: r20821: Use HDstrncpy. --gh (Fixed already, with strdup) r20822: (Not merged, incorrect use of HDstrncpy()) r20823: (Not merged, incorrect use of HDstrncpy()) r20824: Maintenance: Bug fix: addressed CID 666. Value stored at *expression_len should be used in the call to HD5packFstring to avoid overflow (and unnecessary arithmetic calculation and casting) r20825: Issue 642: Added check for error and handler with print to stderr and exit. r20826: Undo revision 20818, as that issue has already been fixed in the 1.8 branch and trunk (but not coverity branch) r20827: (Not merged, incorrect use of HDstrncpy()) r20828: Use HDstrncpy. --gh (Corrected use of strncpy()) r20829: Check return of H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0. Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &objname) was successful and allow print. Otherwise filename and objname are not created. (init those to NULL) r20830: resolved coverity issues 939, 940, 941, 944, and 947. all were complaints about use of sprintf, and in all cases, the buffers used were large enough for all eventualities. Resolved issue by replacing calls to sprintf with calls to snprintf. r20831: Maintenance: Addressed CID 852 Replaced sprintf with snprintf r20832: Purpose: Fix valgrind issues with hl/examples/ex_image2 Description: Modified hl/examples/ex_image2 to free global "gbuf" before exit. Tested on: Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety (too minor to require h5committest)
* [svn-r24720] bring r24709 from trunk:Mohamad Chaarawi2014-02-1837-311/+371
| | | | | | | rename H5V to H5VM since H5V is needed in the fastforward project for view objects. The addition of view objects in the fastforward project is expected to be brough into the trunk sometimes in the future, which is why we need to make this change.
* [svn-r24699] Port r24463 from trunk to 1.8 branch.Neil Fortner2014-02-101-1/+1
| | | | | | | | | Tested: jam, ostrich, platypus (h5committest, apparent system issue on koala) Log from r24463: Issue 8484 - Segfault during H5Fopen of corrupt file. I put a condition check to make sure a pointer isn't NULL. Tested on jam - very simple change.
* [svn-r24684] Add IF SHARED block around Windows PDB file generation command.Allen Byrne2014-02-041-2/+3
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* [svn-r24599] Merged /trunk:r24598 Mohamad Chaarawi2013-12-301-48/+42
| | | | | | | | | | | allocate and use the H5AC_aux_t struct even if num_procs == 1. This was a bug exposed by running a single process with a program that generates lots of dirty metadata that needs to be flushed. --This line, and those below, will be ignored-- _M . M src/H5AC.c
* [svn-r24477] Description:Quincey Koziol2013-11-307-26/+25
| | | | | | | | | | | Bring r24476 from trunk to 1.8 branch: Remove duplicate "intent" flags from top & shared file structures, leaving them only in the shared file structure. Tested on: Mac OSX/64 10.9.0 (amazon) w/gcc 4.8, both parallel & serial (too minor to require h5committest)
* [svn-r24466] Snapshot version 1.8 release 13 (snap2)HDF Tester2013-11-251-2/+2
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* [svn-r24464] Changed an H5FL_MALLOC call to H5MM_calloc to fix a very small ↵Dana Robinson2013-11-231-1/+1
| | | | | | | | | | | | memory leak when the thread-safe version of the library is built. Part of HDFFV-8518. Tested on: 32-bit LE linux (jam) with threadsafe and callstack enabled. (very minor change)
* [svn-r24438] Issue 8147 - clang's -fcatch-undefined-behavior exposed ↵Raymond Lu2013-11-131-4/+43
| | | | | | undefined behavior in the alignment detection algorithm for integers in H5detect.c. Quincey decided to solve it in two steps. First, catch illegal instruction signal in the original algorithm. Second, use POSIX __alignof function to detect alignment if it's available. This checkin is the first step. I merged the change from the trunk. Tested on wren, jam, ostrich, platypas, and koala.
* [svn-r24391] Issue 8528 - H5F_get_objects overfilled the list for object ↵Raymond Lu2013-11-011-66/+73
| | | | | | IDs. I merged the fix the trunk. I put the safeguard in both H5F_get_objects and H5F_get_objects_cb to prevent overfill the list. I also added test cases in tfile.c. Tested with h5committest on jam, koala, ostrich, and platypus.
* [svn-r24379] Merged r24333 from trunk.Dana Robinson2013-10-312-3/+3
| | | | | | | Added volatile keyword to find_bias() function in H5detect. Fixes HDFFV-8547. Change to H5win32defs.h fixes a minor typo. Tested on 64-bit Visual Studio 2010 / 64-bit Windows 7 (Visual Studio warning)
* [svn-r24377] - Added uint32_t to the list of traceable types.Dana Robinson2013-10-311-1/+1
| | | | | | | | - Fixed a couple of commenting typos in configure.ac. Tested on: 32-bit LE linux (jam) w/ parallel and Fortran These are minor changes, hence the limited testing.
* [svn-r24335] Snapshot version 1.8 release 13 (snap1)HDF Tester2013-10-211-2/+2
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* [svn-r24288] Snapshot version 1.8 release 13 (snap0)HDF Tester2013-10-141-2/+2
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* [svn-r24262] Description:Quincey Koziol2013-10-0718-506/+516
| | | | | | | | | | | | | | | | | | | Bring r24256 & r24261 from trunk to 1.8 branch: Switch H5I internal data structure from using hash table to skip lists. Also, a few misc. cleanups. 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 Solaris/32 2.11 (emu) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode
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