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* Merge pull request #1133 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop ↵Binh-Minh Ribler2018-07-141-2/+2
|\ | | | | | | | | | | | | | | | | to develop Fixed HDFFV-10404 * commit 'ec31438afdaf575368938e930eb3af0865a342b3': Fixed HDFFV-10404 Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
| * Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-2/+2
| | | | | | | | | | | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
| * Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-7/+6
| | | | | | | | | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
| * Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-61/+55
| |\
| * | Fix for daily test failures.Vailin Choi2017-12-071-2/+2
| | |
| * | Fix for HDFFV-9947 H5SencodeVailin Choi2017-11-281-4/+5
| | | | | | | | | | | | Modifications to fix H5Sencode bug when num points selected is > 2^32.
| * | Change copyright headers to replace url referring to file to be removedlrknox2017-04-141-6/+4
| | | | | | | | | | | | | | | | | | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* | | Fix for HDFFV-10333:Vailin Choi2018-07-111-1/+1
| |/ |/| | | | | | | | | | | | | | | 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
* | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-6/+4
|\ \ | | | | | | | | | merge_hyperslab_updates
| * | Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| |/ | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* | Further minor cleanupsQuincey Koziol2017-03-281-34/+30
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* | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-33/+31
|/ | | | improvements.
* [svn-r30189] Description:Quincey Koziol2016-07-181-29/+82
| | | | | | | | | Clean up more warnings: drop the warning count from ~1310 down to ~940, with only 31 types of warnings in 148 files (down from 38 types in 167 files). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27946] Brought VDS branch in sync with trunk (up to r27945).Dana Robinson2015-10-041-11/+19
|\ | | | | | | | | | | | | | | Tested on Ubuntu 15.04 (Linux 3.19 x86_64), gcc 4.9.2, MPICH 3.1.4 and CMake 3.3.2. - Autotools serial w/ Fortran, C++ - Autotools parallel w/ Fortran - CMake serial w/ Fortran, C++
| * [svn-r27939] Remove H5D__iterate and use H5S_select_iterate directlyJerome Soumagne2015-10-021-11/+19
| | | | | | | | | | Add internal library callback to H5S_select_iterate to avoid having to pass hid_t objects internally
| * [svn-r27851] Description:Quincey Koziol2015-09-221-2/+7
| | | | | | | | | | | | | | | | | | Normalization changes that wouldn't otherwise be necessary if the VDS branch wasn't coming in shortly. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest forthcoming)
* | [svn-r27850] Description:Quincey Koziol2015-09-221-1/+1
|\ \ | |/ | | | | | | | | | | | | Sync w/trunk Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
| * [svn-r27849] Description:Quincey Koziol2015-09-221-1/+1
| | | | | | | | | | | | | | | | Normalize against incoming changes on VDS branch. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest forthcoming)
* | [svn-r27848] Description:Quincey Koziol2015-09-221-1/+1
| | | | | | | | | | | | | | | | Clean up warnings and some normalization against trunk. Tested: McaOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
* | [svn-r27835] Description:Quincey Koziol2015-09-211-26/+26
|\ \ | |/ | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-24/+24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r27701] RM offset initialization that is no longer necessary with the ↵Neil Fortner2015-09-081-4/+0
| | | | | | | | | | | | | | | | recent fix to H5Screate(). Tested: ummon
* | [svn-r27632] Description:Quincey Koziol2015-08-311-14/+11
| | | | | | | | | | | | | | | | | | | | Revert changes to pass file pointer to selection serialize/deserialize routines. Also patch back in some changes that were merged out in the previous merge w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
* | [svn-r27538] Add tests to cover remaining code coverage assertions in src ↵Neil Fortner2015-08-201-1/+0
| | | | | | | | | | | | | | | | directory except for those in H5Doh.c and H5Shyper.c. Tested: ummon
* | [svn-r27479] Add checking for invalid inputs to H5Dset_virtual: point ↵Neil Fortner2015-08-071-4/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | selections, incorrect numbers of elements selected, incorrect "slice" through limited dimensions, incorrect number of printf substitutions. Patch source selection space extent with bounds of selection if extent is unknown before returning via H5Pget_virtual_srcspace. Write updated VDS dataspace to file when it changes due to unlimited selections. Other minor fixes/cleanup. Tested: ummon
* | [svn-r27450] Add descriptions for all non-public functions.Neil Fortner2015-07-311-6/+19
| | | | | | | | | | | | | | Other comments. Add some input checking. Tested: ummon
* | [svn-r27246] Remove "clipped" status from unlimited selections, decoupling ↵Neil Fortner2015-06-181-6/+0
| | | | | | | | | | | | | | | | | | | | | | them from the extent. Improve algorithm for calculation of VDS extent by removing the need for a temporary copy of a dataspace. Other minor fixes/cleanup. Tested: ummon
* | [svn-r27153] Implement fill value support for VDS.Neil Fortner2015-06-051-0/+89
| | | | | | | | | | | | | | | | | | Add testing for this. Fix bug in printf string parsing. Add test for this. Other minor fixes/cleanup. Tested: ummon
* | [svn-r27103] Merge revisions 26780 through 27102 from trunk to vds branch.Neil Fortner2015-05-211-2/+2
|\ \ | |/ | | | | Tested: ummon
| * [svn-r27045] Renamed H5_ASSIGN_OVERFLOW() to H5_CHECKED_ASSIGN() and re-orderedDana Robinson2015-05-101-2/+2
| | | | | | | | | | | | the arguments to be in a more logical order. Tested on: h5committest
* | [svn-r26962] Add support for unlimited selections to VDS code.Neil Fortner2015-04-291-1/+39
| | | | | | | | | | | | | | | | Not tested (except for percival-unlim example) Fix percival-unlim example Other bug fixes/cleanup Tested: Fedora 64
* | [svn-r26878] Fix errors in unlimited selection serialize/deserializeNeil Fortner2015-04-211-4/+9
| | | | | | | | | | | | Other minor fixes Tested: jam
* | [svn-r26828] Implement support for unlimited selections (not supported by ↵Neil Fortner2015-04-161-11/+37
| | | | | | | | | | | | | | | | | | VDS code yet). Add tests for unlimited selections. Various other minor changes. Tested: ummon
* | [svn-r26680] Implement minor suggestions from 3/26/15 code review.Neil Fortner2015-03-311-3/+1
| | | | | | | | | | | | Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
* | [svn-r26476] Add support for I/O in all cases with fixed size datasets and ↵Neil Fortner2015-03-181-17/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | no point selections. Add source dataspace extent patching (should allow closing the source file). Note fill values and various other features are not yet supported. Note there are still some code coverage assertions in the selection matching algorithm - if you hit these try taking them out. Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
* | [svn-r26469] INCOMPLETE, UNWORKING CODENeil Fortner2015-03-171-35/+39
| | | | | | | | Commit progress through 3/17/15
* | [svn-r26411] Add support for I/O in very simple cases (virtual mapping and ↵Neil Fortner2015-03-091-0/+93
|/ | | | | | | | | file space are both H5S_ALL). Note make check fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26302] Description:Quincey Koziol2015-02-251-18/+63
| | | | | | | | | Revise dataspace encode/decode routines to make them work better with future virtual dataset feature. Tested on: Mac OSX/64 10.10.2 (amazon) w/serial (h5committest forthcoming)
* [svn-r25766] Description:Quincey Koziol2014-11-031-108/+39
| | | | | | | | | | Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They are buggy and it's taking me a long time to correct the problem. I'll check in a revised form of the changes when I've got them straightened out. Tested on: Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN Linux 2.6.x (jam) w/parallel
* [svn-r25273] Description:Quincey Koziol2014-06-131-39/+108
| | | | | | | | | | | 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-r24769] Description:Quincey Koziol2014-03-071-25/+28
| | | | | | | | | 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-r24709] rename H5V to H5VM since H5V is needed in the fastforward ↵Mohamad Chaarawi2014-02-131-4/+4
| | | | | | | | | | | | 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-r23713] Description:Quincey Koziol2013-05-211-26/+26
| | | | | | | | | | Clean up warnings, switch library code to use Standard C/POSIX wrapper macros, remove internal calls to API routines, update checkapi and checkposix scripts. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN Big-Endian Linux/64 (ostrich)
* [svn-r22646] Description:Quincey Koziol2012-08-081-1/+1
| | | | | | | | | 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-r21919] Description:Quincey Koziol2012-02-091-34/+34
| | | | | | | | Refactor function name macros and simplify the FUNC_ENTER macros, to clear away the cruft and prepare for further cleanups. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r20536] Description:Quincey Koziol2011-04-171-5/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up various warnings & code formatting issues. Bring changes from Coverity branch to trunk: r20085: Purpose: Fix coverity issue 793 Description: Modified H5S_hyper_project_simple_higher() to free the entire span list in new_space on failure. r20091: This is a fix for coverity bug #1683. Changed the two printfs to use %lu (unsigned long) for printing "dset_size". r20162: Purpose: Fix coverity issue 785 Description: Modified H5T_enum_nameof() to free "name" on failure if it was allocated. Also clarified some code in H5S_hyper_rebuild_helper(). r20189: Addressed coverity defect 783. H5SL_new_node() in H5SL.c was failing to free space allocated in its first alloc if the second alloc failed. Added a call to H5FL_FREE to address this issue. This is purely to keep coverity happy -- if this code is ever triggered, we have much larger problems. Note that this fix will trigger an unused return value complaint from coverity next week. r20190: Fixed Coverity issues 1561 1565 and 1678 (UNUSED_VALUES) by moving checks of return values to after the function call. r20191: Fixed coverity issues 643 644 and 1678 (CHECKED_RETURN). r20232: Addressed coverity issues 923-925. Replaced calls to sprintf with calls to HDsnprintf. r20233: Fix coverity issue 662. Don't try to sort 0 attributes in H5Aint.c. r20234: Fix coverity issue 664. Check for NULL before dereferencing in H5Gdeprec.c. r20271: Purpose: Fix coverity issue 784 Description: Modified H5_debug_mask() to keep a list of files opened for use as a debugging output stream, and modified H5_term_library to close these files on exit. r20272: addressed coverity issues 838 & 955. Issue was use of strcpy() -- existing code was safe, but modified to use strncpy() to keep coverity happy. r20273: Addresed coverity issues 1388 and 1389. Initialized sel_iter->type to NULL in H5S_select_iter_init. r20275: Purpose: Fix valgrind issue in mf.c Description: Fixed bug (incomplete if statement) in test_mf_fs_alloc_free() so the retrieved node gets freed. 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
* [svn-r19472] Description:Quincey Koziol2010-09-231-2/+2
| | | | | | | | | | | | | | | | | | | | | | Create a new, more streamlined method of generating I/O sequences when there is only a single block defined by a hyperslab. This improves the performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%. 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 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-r19099] Description:Quincey Koziol2010-07-191-2/+2
| | | | | | | | | | Fix const pointer issues for projection construction routine and also bump time before alarm kicks in to terminate a test from 20 minutes to 30 minutes, to give the PGI compiler tests w/debugging enabled a chance to finish. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug Linux/32 2.6.18 (jam) w/PGI & debug
* [svn-r19092] Description:Quincey Koziol2010-07-191-135/+605
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring "shape same" changes from LBL branch to trunk. These changes allow shapes that are the same, but projected into dataspaces with different ranks to be detected correctly, and also contains code to project a dataspace into greater/lesser number of dimensions, so the I/O can proceed in a faster way. These changes also contain several bug fixes and _lots_ of code cleanups to the MPI datatype creation code. Many other misc. code cleanup are included as well... 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r16279] Description:Quincey Koziol2009-01-081-13/+13
| | | | | | | | | | | | | | Bring revision 16278 back from revise_chunks branch: Update layout information in DCPL to unify all information in one underlying property and switch to using H5O_layout_t for storing it, which simplifies things considerably. Also, fix many compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode (Original patch tested on many machines)
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