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* [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
* [svn-r24259] Maintenance: Updated version number to 1.8.13-snap0; cleaned up ↵Elena Pourmal2013-10-072-4/+4
| | | | | | RELEASE.txt for new info. The 1.8 branch is open now for code changes.
* [svn-r24257] Snapshot version 1.8 release 12 (snap19)HDF Tester2013-10-061-2/+2
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* [svn-r24231] Issue 1264: CYGWIN had long double rounding problem from ↵Raymond Lu2013-09-301-4/+0
| | | | | | | | unsigned long long. Allen confirmed the problem is gone. So I took out the macro CYGWIN_ULLONG_TO_LDOUBLE_ROUND_PROBLEM. It skipped the test related to this issue. Tested with h5committest.
* [svn-r24228] HDFFV-8529: Space separate define stringsAllen Byrne2013-09-301-1/+1
| | | | Tested: local linux
* [svn-r24219] Snapshot version 1.8 release 12 (snap18)HDF Tester2013-09-291-2/+2
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* [svn-r24209] Port r24171 from trunk to 1.8 branch.Neil Fortner2013-09-274-122/+125
| | | | | | | | | | | | | | | | | | | Tested: jam, koala, ostrich, platypus (h5committest) Log from r24171: Purpose: Fix problem with gcc 4.8 Description: With optimization enabled, gcc 4.8 inserts garbage into the padding bytes of floating point types when assigning from a literal constant. This caused problems when H5detect.c scanned the bits in floating point types to determine their properties. Modified H5detect.c to scan for padding before further analyzing the type, and to ignore all information in the padding areas. Also removed code that temporarily disabled optimization. Tested: jam, koala, ostrich, platypus (h5committest)
* [svn-r24205] Merge HDFFV-8513/8522 from trunk (via cmake branch), h5repack ↵Allen Byrne2013-09-263-8/+10
| | | | | | | | UD plugins. Also warning session fixes. Tested: CMake local linux
* [svn-r24204] Port r24140 from trunk to 1.8 branch.Neil Fortner2013-09-263-36/+41
| | | | | | | | | | | | | | | | | | | | Tested: jam, koala, ostrich, platypus (h5committest) Log from r24140: Purpose: Remove problematic abandonment of error stack Description: H5Fis_hdf5 uses H5F_locate_signature to check if the file is hdf5. If it does not locate the signature, H5F_locate_signature would issue an error and return HADDR_UNDEF. H5Fis_hdf5 does not consider it an error if the signature is not found, so it does not issue an error or clear the stack. The filled stack could then cause issues later on. Changed H5F_locate_signature to return herr_t, not issue an error if the signature is not found, and added a parameter for a pointer to the signature address that the function fills in. Tested: jam, koala, ostrich (h5committest)
* [svn-r24203] Port r24139 from trunk to 1.8 branch.Neil Fortner2013-09-261-42/+74
| | | | | | | | | Tested: jam, koala, ostrich, platypus (h5committest) Log from r24139: Remove "will never be exectued" warnings in H5detect.c Tested: jam, koala, ostrich (h5committest)
* [svn-r24187] Snapshot version 1.8 release 12 (snap17)HDF Tester2013-09-221-2/+2
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* [svn-r24156] Port r23987 from trunk to 1.8 branch.Neil Fortner2013-09-1810-181/+177
| | | | | | | | | | | | | | | | Tested: jam, koala, ostrich, platypus (h5committest) Log from r23987: Merge r23939 from reduce_warning branch to trunk Tested: jam, koala, ostrich (h5committest) Log from r23939: Fix unused variables warnings in trunk Rename static functions in H5Adense.c, H5B2cache.c, H5Bcache.c Switch these functions to use FUNC_ENTER_STATIC* macros Tested: koala
* [svn-r24117] Description:Quincey Koziol2013-09-093-26/+5
| | | | | | | | Revert accidental checkin of a patch that disables file truncation for parallel I/O. Tested on: MacOSX/64 10.8.4 (amazon)
* [svn-r24112] Description:Quincey Koziol2013-09-068-53/+144
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24101 & 24111 from trunk to 1.8 branch: r24101: ======= Description: 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 r24111: ======= Description: Restrict GCC diagnostic pragmas to only gcc 4.6+ Tested on: Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN (too minor to require h5committest)
* [svn-r24106] Add help text tests for h5dump and h5repack to the linux ↵Allen Byrne2013-09-062-2/+2
| | | | | | scripts. HDFFV-8498 merge from trunk. Tested: local linux - cmake and autotools
* [svn-r24093] Snapshot version 1.8 release 12 (snap16)HDF Tester2013-09-011-2/+2
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* [svn-r24080] Since dtransform.c uses H5T_conv_i_f and H5T_conv_f_i, I added ↵Raymond Lu2013-08-281-3/+2
| | | | | | them back for OpenVMS. But I took out the test case in dtransform.c which has problem. See Jira issue VMS-8. Tested on jam.
* [svn-r24074] I took out the soft conversion functions H5T__conv_i_f and ↵Raymond Lu2013-08-261-1/+4
| | | | | | | | | H5T__conv_f_i for OpenVMS because they have problem to convert between integers and floating numbers. I also commented out the test case in dt_arith.c for OpenVMS. Tested on jam - simple change.
* [svn-r24072] Merge trunk cmake changes to 1.8 branch. Allen Byrne2013-08-261-1/+6
| | | | | | | Also add default switch blocks to h5import. Merge h5dump any_path option from trunk. Tested: local linux
* [svn-r24069] Snapshot version 1.8 release 12 (snap15)HDF Tester2013-08-251-2/+2
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