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* H5TRACE3 macro change for hdf5 1 12 (#656)Larry Knox2021-05-181-1/+1
| | | | | | | | | * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual from PR #448 Various clang tidy warning fixes, to maintain binary compatibility in hdf5_1_12. * Commit H5Trace3 macro change for code change merged from develop. * Enable maintainer mode.
* Update version to 1.12.2-1.Larry Knox2021-05-181-1/+1
| | | | Update so numbers according to compatibility rules for 1.12.1 release.
* Brings the thread-safety recursive writer locks to 1.12 (#466)Dana Robinson2021-05-141-2/+46
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * First cut at replaceing the existing mutex with a recursive R/W lock. This implementation has the following issues: 1) pthreads implementation only -- we still need a windows version. 2) must investigate thread cancelation issues 3) Error reporting is very poor. I followed the error reporting on the existing thread safe code, but this should be re-visited and improved. Code is currently setup to use the new recursive R/W lock instead of the global mutex to control entry to the library in threadsafe builds. To revert to the global mutex, set H5TS__USE_REC_RW_LOCK_FOR_GLOBAL_MUTEX in H5TSprivate.h to FALSE. Added a reasonably robust regression test for the reursive R/W lock in test/ttsafe_rec_rw_lock.c Note that the change to hl/src/H5LTanalyse.c is an artifact of clang-format. Tested serial threadsafe debug and production on jelly, and also regular serial / debug. On Windows builds, the new recursive R/W lock should not be built and we should use the existing global mutex -- however this is not tested at this time. * Updates CMake to build recursive RW lock test * Updates to allow building on Windows * Moves #if statements to better protect non-RW lock code * Adds configure and CMake options for the recursive RW locks * Committing clang-format changes * Updates RELEASE.txt and the build options * Renames H5TS RW lock things * Makes struct members platform independent Also removes _ptr from identifiers * Partial thread-safety RW locks platform independence * Committing clang-format changes * Pthreads side of things is platform-independent now * Formatted source * Added Windows equivalents for some Pthreads calls * Rename H5TS takedown call to destroy * Reorg of RW lock code * Committing clang-format changes * Changes to Pthreads code after development on Visual Studio * Moves stats macros to static inline functions and tidies memory allocs * Converts RW lock print stats call to use C99 formatting * Fixes typos * Formatted source * Updates the RELEASE.txt note to indicate no Win32 threads support Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 12 doxygen merge (#615)Allen Byrne2021-05-041-4/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * Some Javadoc warning fixes * Committing clang-format changes * Updated javadoc fixes * HDFFV-11228/9 merges from develop * remove obsolete debug comment * Fix conflict * HDFFV-11229 merge changes from develop * HDFFV-11229 merge second compare from develop * HDFFV-11229 fix reference file * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update with changes from develop * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Whitespace changes * Rework CMake add_custom to use the BYPRODUCTS argument * Revert CMake configure checks for round defines * With VS 2015 minimum strdup is supported * Doxygen comments merged from develop * doxygen build updates * Correct version string for map functions Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 12 merge java copyright header changes (#391)Allen Byrne2021-03-011-8/+39
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - files not in src or test.
* 1 12 merges from develop (#319)Allen Byrne2021-02-081-0/+45
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop
* Warnings merge 112 (#299)Allen Byrne2021-02-041-8/+39
| | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Merge dev warnings changes from develop
* Stat st blocks fix 112 (#248)Larry Knox2021-01-111-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fixes Autotools detection of the st_blocks field in stat (#246) * Fixes Autotools detection of the st_blocks field in stat The Autotools and CMake will now both correctly determine if the stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS appropriately. * Fixes a typo in configure.ac Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. (#116)Larry Knox2020-11-231-1/+1
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* Manual sync with develop (#95)Dana Robinson2020-11-171-0/+51
| | | | Brings all features from develop. Note that RELEASE.txt has not been updated (will be done in a future PR).
* Add doxygen framework for CMake and autotoolsAllen Byrne2020-11-131-4/+70
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* Merge changes from developAllen Byrne2020-10-081-1/+2
| | | | | Comments and whitespace Skip file-locking and cache changes
* Snapshot version 1.12 release 1-2. Update version to 1.12.1-3Larry Knox2020-09-181-1/+1
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* 1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] afterLarry Knox2020-08-171-6/+6
| | | | | | | | AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
* Sync with developDana Robinson2020-08-011-0/+47
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* Snapshot version 1.12.1-1hdftest2020-07-191-1/+1
| | | | Update version to 1.12.1-2
* Merge pull request #2686 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-131-1/+4
| | | | | * commit '800f93f7c994f88dfa716746153ded4b1e690e3a': Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
* Merge pull request #2670 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-061-3/+4
| | | | | * commit 'fc69de0e8ae30e80c1c3c542b156226a75444525': Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
* Squashed commit of the following:Larry Knox2020-06-211-1/+58
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit 45b0cbc71929930a874e1c09e0770aa64d0ae697 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Apr 23 13:14:56 2020 -0500 Add C++ warnings treated as error for autotools builds. commit 6debcddcc766601799d5bd661bd60946f951a07e Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jun 19 16:50:03 2020 -0500 Remove tests for develop branch from testh5cc.sh.in. Add @H5_ECXXFLAGS@ to AM_CXXFLAGS. commit fed497e7f207313b2a133d3b68c942b7d7104b90 Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jun 12 15:06:39 2020 -0500 Merge pull request #2646 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit '998c6470d78e14228695419c3b514c35ecf3d69e': Remove unnecessary version conditions for Clang compilers. commit 92e52ce5c211bd1d3991a3b8bb67287ac7b652aa Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jun 10 18:53:45 2020 -0500 Merge pull request #2639 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit 'a33667faf226f5d8c9633bf537893e8fce1bf1f6': Add c++ to --enable-sanitize-checks option. commit 2e802534fb997b81fa98fdd1c7d97d4310898e0d Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jun 10 15:18:36 2020 -0500 Merge pull request #2633 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit '20eab963899841c9a003baebead8e3bc07d9e127': Remove duplicate entries in MANIFEST. Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers. Update new clang files to not pick up clang as vendor for pgCC. Add new files to MANIFEST Temporary demotion of 2 -Werror warning flags that fail on macos 10.12 Remove Production flag unknown to Apple clang. commit 96ef60a58a23847a7da89a891f2415055ec2ab60 Author: Larry Knox <lrknox@hdfgroup.org> Date: Mon Jun 8 16:24:49 2020 -0500 Merge pull request #2631 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit 'b942a4d8a3e27317cac50ce37ff5302d477664d8': Clean up code to get clang version in config/linux-gnulibc1 commit 8a7c687da568e8b50b38fa53da1ca63759be6ec4 Author: Larry Knox <lrknox@hdfgroup.org> Date: Mon Jun 8 11:42:37 2020 -0500 Merge pull request #2623 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit 'c7626f79fdee4eee13925e240ef41e61f3367eab': Add flags from config/clang-warnings/*general files to H5 C and CXX flags for all versions of Clang and Clang++ compilers. Switched from cut to awk in testcheck_version.sh.in to avoid dependence on tab vs. " " in version definitions in H5public.h. Add files for adding warning flags for clang compilers in autotools configure. commit db3ef7ff3c1ed79167cecef831501411cff8291f Merge: 5a0f8d7 f9f1310 Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jun 19 14:46:22 2020 -0500 Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12 commit 5a0f8d7940ae57b445f545a0abd7e303ce6924ee Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jun 10 20:15:41 2020 -0500 Merge pull request #2636 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:HDFFV-11000-update-testh5cc.sh.in-for-version to develop * commit '5c0bd670d6e9919c463fbc05de99e2ba55b0761e': Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags. HDFFV-11000: update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop.
* Snapshot version 1.12 release 1 (snap0)hdftest2020-04-271-1/+1
| | | | Update version to 1.12.1-1
* TRILAB-192 merging warnings changes from developAllen Byrne2020-03-301-0/+4
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* Update version to 1.12.1-snap0 for hdf5_1_12 branch.Larry Knox2020-01-281-1/+1
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* Let us override the examples directory using --with-examplesdir=DIR.David Young2019-12-191-0/+22
| | | | | | | | | This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Place hdf5_examples/ under ${datarootdir} which on most systems will be ${prefix}/share/, anyway.
* Make the HDF5 configure script grok NetBSD.David Young2019-12-191-0/+3
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* Update version to 1.12.0-alpha1.Larry Knox2019-12-121-1/+1
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* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-091-38/+4
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-061-4/+38
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* Update RELEASE.txt and add HISTORY-1_10_0-1_12_0.txt file.Larry Knox2019-10-211-1/+1
| | | | Set version to 1.12.0-alpha0 for snapshot release.
* Cleanup whitespace and comments compared to developAllen Byrne2019-10-021-1/+1
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* Set versions in initial hdf5_1_12 revision.hdf5_1_12-initialLarry Knox2019-09-251-1/+1
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* Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package."Dana Robinson2019-09-241-2/+2
| | | | This reverts commit 431123503d387bce30b1f6db7dc4ad3a33bc51bb.
* Moved NDEBUG guards to H5EA_DEBUG in H5EA package.Dana Robinson2019-09-171-2/+2
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* Untangle #ifdef mess in ROS3 code.Dana Robinson2019-08-201-0/+5
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+26
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* Squashed commit of the following:Larry Knox2019-07-251-0/+125
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* Fixed libhdf5 settings file for both autotools & CMakeDhvanil Popat2019-06-251-1/+1
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* Moved h5cc.in and h5redeploy.in from tools/misc to bin directory. TheyLarry Knox2019-06-141-1/+2
| | | | | | | should always be built and installed whether tools are enabled or disabled. Also added Makefile.am to bin to build h5redeploy and to install and uninstall them. h5cc is created from h5cc.in by configure.
* Modified Makefile.ams for h5repack, h5watch and gif2h5 to allowLarry Knox2019-06-121-2/+2
| | | | | | | disabling tests. Moved h5cc.in from tools/src/misc to src directory to always create h5cc whether or not tools are enabled. Added configuration status of tools and tests to libhdf5.settings.
* Add options to enable or disable building tools and tests. The defaultLarry Knox2019-06-061-4/+50
| | | | is enabled for each.
* Snapshot version 1.11 release 5.hdftest2019-05-021-1/+1
| | | | Update version to 1.11.6.
* Merge branch 'develop' of ↵Songyu Lu2019-04-041-2/+2
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * Snapshot version 1.11 release 4.hdftest2019-04-011-2/+2
| | | | | | | | Update version to 1.11.5.
* | This commit basically has the following changes:Songyu Lu2019-04-041-0/+2
|/ | | | | | 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get.
* Updated sec2, log, and core VFDs to use pread/pwrite whenDana Robinson2019-01-311-2/+44
| | | | available (can be controlled via a configure/CMake option)
* Merge pull request #1450 in HDFFV/hdf5 from ↵Ray Lu2019-01-081-0/+24
|\ | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:TRILAB-98-dt_arith-and-cpp_testhdf5-tests to develop * commit 'b02de315b93ac29d2483a91d526b110a25073505': NNSA Tri-LabsTRILAB-98: Another two test cases out. NNSA Tri-Labs TRILAB-98: Taking out a few more test cases. NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on sierra.llnl.gov: According to the group decision, simply provide a macro to disable some failing test cases on sierra (IBM power9 cpu). All failing cases involve long double data type.
| * NNSA Tri-Labs TRILAB-98: Taking out a few more test cases.Songyu Lu2019-01-081-3/+3
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| * NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on ↵Songyu Lu2019-01-081-0/+24
| | | | | | | | sierra.llnl.gov: According to the group decision, simply provide a macro to disable some failing test cases on sierra (IBM power9 cpu). All failing cases involve long double data type.
* | HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs.Scot Breitenfeld2019-01-081-0/+9
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Vailin Choi2019-01-021-0/+2
|\ | | | | | | | | | | | | | | develop Resolve conflicts: Conflicts: test/Makefile.am
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