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* [svn-r25321] Reworked and enhanced extreme sanity check in H5C.c, fixing an John Mainzer2014-06-189-90/+1938
| | | | | | | | | | | | | | | | | | | | | | | | | uninitialized variable bug in passing. Added the H5C_get_entry_ptr_from_addr() and H5C_verify_entry_type() in H5C.c, along with their pass through functions in H5AC.c. Note that H5C_get_entry_ptr_from_addr() is quite slimey, and should be avoided if possible. Updated fractal heap to use flush ordering to force children in the hdr / iblock / dblock tree to be flushed prior to parents. This is part of a port of the fractal heap to the V3 cache, although I gather that it will also be useful for SWMR. Added sanity checking code to the fractal heap to verify that direct blocks are flushed before their parent indirect blocks, child indirect block are flushed prior to their parent indirect blocks, and that the root iblock or dblock is flushed prior to the header Tested on: Jam: Serial and parallel Phoenix (Debian): serial, debug and production amazon (MacOS): serial
* [svn-r25302] Add nounistd option to flex command for windows caompatibilityAllen Byrne2014-06-171-1/+1
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* [svn-r25285] Snapshot version 1.9 release 184HDF Tester2014-06-156-857/+857
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* [svn-r25283] Description:Quincey Koziol2014-06-142-12/+12
| | | | | | | | | | Correct error in new hyperslab selection test to use the right # of dimensions for start/stride/count/block arrays. Also, switch H5Sselect_select to H5Smodify_select. Tested on: MacOSX/64 10.9.3 (amazon) w/gcc 4.9.1, OpenMPI, C++, FORTRAN & threadsafe (Too minor to require h5committest)
* [svn-r25274] Adds #defines that ensures that DllMain is only compiled in ↵Dana Robinson2014-06-131-2/+6
| | | | | | | | when the thread-safe shared library is built on Windows. Fixes HDFFV-8837. Tested on 64-bit Windows 7 with VS2012.
* [svn-r25273] Description:Quincey Koziol2014-06-1332-2734/+3611
| | | | | | | | | | | Bring in Chao/Neil/my changes to optimize hyperslab selection operations further, along with 3 new public API routines: H5Scombine_hyperslab(), H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to the code and fixing a few compiler warnings. Tested on: Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI (h5commttest forthcoming)
* [svn-r25241] Snapshot version 1.9 release 183HDF Tester2014-06-082-3/+3
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* [svn-r25216] Snapshot version 1.9 release 182HDF Tester2014-05-253-6/+6
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* [svn-r25215] Description:Quincey Koziol2014-05-252-0/+6
| | | | | | | | | | | | | | Bring changes from Coverity branch back to trunk: r20914: Use HDstrncpy and HDstrncat! --gh 20915: Use HDstrncpy and HDstrncat! --gh Tested on: Mac OSX/64 10.9.3 (amazon) w/gcc 4.9.0, C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r25208] Make the header generation optional and depend on finding perl ↵Allen Byrne2014-05-211-31/+37
| | | | executable. Needed because window does not have perl.
* [svn-r25205] Fix CMP0040 Policy cmake usageAllen Byrne2014-05-201-7/+18
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* [svn-r25199] Snapshot version 1.9 release 181HDF Tester2014-05-182-3/+3
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* [svn-r25197] Description:Quincey Koziol2014-05-172-5/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | 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-r25188] Implement change to cmake_ext_mod config folderAllen Byrne2014-05-141-3/+11
| | | | Tested: local linux
* [svn-r25181] Snapshot version 1.9 release 180HDF Tester2014-05-112-3/+3
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* [svn-r25161] Removed some C++-style comments from H5FDcore.c.Dana Robinson2014-05-051-8/+0
| | | | | | | Tested on: 32-bit LE linux (jam) Tested with HDF5_DRIVER set to "core_paged".
* [svn-r25158] Snapshot version 1.9 release 179HDF Tester2014-05-042-3/+3
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* [svn-r25126] Snapshot version 1.9 release 178HDF Tester2014-04-272-3/+3
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* [svn-r25117] Removed LT_ADD_LIBHDF5_DEPENDENCY configure conditional to roll ↵Larry Knox2014-04-251-1/+0
| | | | | | | | | | | back fix for removing rpaths from l ib files. The fix also removed dependencies on libhdf5, etc. when the --disable-sharedlib-rpath co nfigure 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 with configure option --disable-sharedlib-rpath on emu, platypus and quail.
* [svn-r25097] Description:Quincey Koziol2014-04-258-122/+129
| | | | | | | | | | | 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 on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (h5committest forthcoming)
* [svn-r25092] Description:Quincey Koziol2014-04-246-232/+241
| | | | | | | | | | 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. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (h5committest forthcoming)
* [svn-r25088] Description:Quincey Koziol2014-04-235-63/+93
| | | | | | | | | Introduce "file I/O info" struct, to hold file & dxpl pointers, and start propagating up through library. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (h5committest coming)
* [svn-r25084] Description:Quincey Koziol2014-04-2338-359/+537
| | | | | | | | | Begin process of migrating from using property list IDs internally to the library to using the internal generic property list data structure. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (h5committest forthcoming)
* [svn-r25045] Fixed a few missing lines of code that were not merged when theDana Robinson2014-04-141-5/+15
| | | | | | | | | | | core VFD paging changes were brought over. Tested on: 32-bit LE linux (jam) 64-bit LE linux (koala) 64-bit BE linux (ostrich) All were tested with HDF5_DRIVER set to "core_paged".
* [svn-r25034] Snapshot version 1.9 release 177HDF Tester2014-04-132-3/+3
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* [svn-r24998] Description:Quincey Koziol2014-04-0926-56/+338
| | | | | | | | Check in Neil's changes for correctly handling case where library is reinitialized through a deprecated routine. Tested on: Linux 2.4.x/32 (jam)
* [svn-r24995] Description:Quincey Koziol2014-04-091-36/+43
| | | | | | | Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls. Tested on: Linux/32 2.4.x (jam) w/gcc
* [svn-r24993] Purpose:Dana Robinson2014-04-094-41/+453
| | | | | | | | | | | | | | | Adds write tracking to the core VFD, which can be configured via the H5Pset/get_core_write_tracking() API call. When enabled and writing to the backing store is enabled, this feature will track writes and only write out the changed bytes on flush/close. Tested on: 32-bit LE linux (jam) w/ Fortran and C++ 64-bit BE linux (ostrich) 64-bit Darwin 12.5.0 (kite) All were tested using the core VFD w/ paging on (core_paged in the VFD list). Make check-vfd was also tested on jam.
* [svn-r24966] Snapshot version 1.9 release 176HDF Tester2014-04-062-3/+3
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* [svn-r24965] Fixed a typo in the thread-safe code.Dana Robinson2014-04-051-1/+1
| | | | | Tested on: 32-bit LE linux w/ thread-safe (jam)
* [svn-r24961] Updates to Win32 thread-local storage cleanup when the ↵Dana Robinson2014-04-046-77/+254
| | | | | | | | | | | thread-safe library is built on Windows. Previously, thread-local storage was not cleaned up, causing resource leaks. Fixes HDFFV-8518, HDFFV-8699 As a part of these changes, the thread-safe + static library options are declared unsupported since the solution relies on DllMain. A solution for the static library is probably doable, but requires much more complicated surgery and has been deferred to HDF5 1.8.14. Tested on: 64-bit Windows 7 using VS 2012 (changes only affect Windows)
* [svn-r24937] Adds an H5free_memory() function to the library for use withDana Robinson2014-03-312-0/+26
| | | | | | | | | | | | functions that return library-allocated memory. The test and tool code were modified to use this new function where it's appropriate. Fixes HDFFV-7710, HDFFV-8519, and HDFFV-8551 Tested on: 64-bit Windows 7 w/ VS2012 32-bit LE linux w/ parallel and fortran (jam) 32-bit LE linux w/ fortran and C++ (jam)
* [svn-r24932] HDFFV-8290: Remove unnecessary $(srcdir) and use AM_CPPFLAGS ↵Allen Byrne2014-03-311-67/+420
| | | | | | instead of INCLUDES. Update automake to 1.14.1 h5committest
* [svn-r24924] Snapshot version 1.9 release 175HDF Tester2014-03-302-3/+3
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* [svn-r24919] Add MINGW checkAllen Byrne2014-03-271-4/+4
| | | | Tested: MinGW on Windows 7
* [svn-r24886] Fix fortran mod file handling and packingAllen Byrne2014-03-241-0/+3
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* [svn-r24869] Description:Quincey Koziol2014-03-235-16/+19
| | | | | | | | | | | | | | | | | | | | | | | | | 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 (too minor to require h5committest)
* [svn-r24864] Description:Quincey Koziol2014-03-2117-1702/+139
| | | | | | | | | | | | | | | | | | 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
* [svn-r24803] Description:Quincey Koziol2014-03-163-73/+75
| | | | | | | | | | | | 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/gcc 4.8.2, C++, FORTRAN, parallel (too minor to require h5committest)
* [svn-r24789] Bump up the minimum cmake versionAllen Byrne2014-03-131-1/+1
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* [svn-r24781] HDFFV-8700 -Allen Byrne2014-03-111-133/+143
| | | | | | | KitWare recommendations: Change CMake commands to lower case. Remove INCLUDE_DIRECTORIES in src for target level includes. Change ADD_DEFINITIONS package debug defines into CMake option. Remove -DNDEBUG
* [svn-r24770] Snapshot version 1.9 release 174HDF Tester2014-03-092-3/+3
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* [svn-r24769] Description:Quincey Koziol2014-03-0713-165/+632
| | | | | | | | | Check in Mohamad's changes to support collective I/O on point selections, along with some other minor cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (h5committest forthcoming)
* [svn-r24757] Change assertion to condition check/error return. Should fix ↵Neil Fortner2014-03-032-3/+5
| | | | | | | | | | periodic assertion failure in fheap test (in test that is expected to fail cleanly). Fix type in H5detect.c Tested: ostrich, platypus (h5committest - jam and koala having issues)
* [svn-r24753] Snapshot version 1.9 release 173HDF Tester2014-03-022-3/+3
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* [svn-r24726] Description:Quincey Koziol2014-02-206-75/+92
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r24725] HDFFV-8629: h5repack will not attempt to remove UD filters. ↵Allen Byrne2014-02-201-17/+21
| | | | | | h5repack requires a check for UD filters that also must check if the filter can be dynamically loaded. This require a change in the library that checks for this. Tested: locally and reviewed
* [svn-r24716] Snapshot version 1.9 release 172HDF Tester2014-02-162-3/+3
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* [svn-r24709] rename H5V to H5VM since H5V is needed in the fastforward ↵Mohamad Chaarawi2014-02-1357-385/+385
| | | | | | | | | | | | 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. Tested Manually on Jam and Ostrich. Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes. error on Koala: error while loading shared libraries: libirng.so
* [svn-r24698] Snapshot version 1.9 release 171HDF Tester2014-02-092-3/+3
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