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* Add an option to disable doxygen warn as error (#3708)Allen Byrne2023-10-191-0/+7
| | | | | | | | | | | | Add for both CMake and the Autotools * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON) * --enable-doxygen-errors: enable/disable (Default: enable) The default will fail compile if the doxygen parsing generates warnings. The option can be disabled if certain versions of doxygen have parsing issues. i.e. 1.9.5, 1.9.8. Fixes #3398
* Some corrections and fix for plugins (#3712)Allen Byrne2023-10-191-0/+7
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* Fixes GH#1027 compilation error (#3654)Scot Breitenfeld2023-10-101-0/+6
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* Drop MPI-2 support (#3643)Scot Breitenfeld2023-10-081-0/+6
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* Split out test logic to separate file (#3639)Allen Byrne2023-10-061-94/+1
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* Fail CMake on Windows when sub-filing VFD is enabled (#3636)H. Joe Lee2023-10-061-1/+4
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* Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624)Allen Byrne2023-10-041-7/+0
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* Disable static + thread-safe on Windows w/ CMake (#3622)Dana Robinson2023-10-031-2/+3
| | | | | | | | | The thread-safety feature on Windows requires a hook in DllMain() and thus is only available when HDF5 is built as a shared library. This was previously a warning, but has now been elevated to a fatal error that cannot be overridden with ALLOW_UNSUPPORTED. Fixes GitHub #3613
* Develop tools move (#3580)Allen Byrne2023-09-261-0/+1
| | | Reorganizes the tools files to support the VOL tests
* Update DEFAULT_API_VERSION documentation for CMake (#3255)Allen Byrne2023-07-181-3/+3
| | | | | | | | | * Update DEFAULT_API_VERSION documentation for CMake * Fix hint --------- Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Subfiling VFD source cleanup (#3241)jhendersonHDF2023-07-131-1/+15
| | | | | | | | | | | | | | | | * Subfiling VFD source cleanup Modularize Subfiling CMake code into separate CMakeLists.txt file Update Mercury util code to latest version and update Copyright Generate mercury_util_config.h header file instead of using pre-generated file Remove unnecessary Mercury functionality Fix minor warning in Subfiling VFD code * Remove Mercury headers from Autotools publicly-distributed header list
* Remove H5detect and H5make_libsettings (#3104)Dana Robinson2023-06-131-6/+0
| | | | | | | | Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
* Fix the default for API_VERSION to only allow one default (#3107)Allen Byrne2023-06-131-6/+0
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* API test updates (#3018)jhendersonHDF2023-05-261-0/+5
| | | | | | | | | | | | | | | | | | | | | | | | | * Remove macros from api tests (#2929) * Remove macros and undefined callbacks (#2959) * Remove remaining macros from H5_api_tests_disabled.h (#2968) * Put some vol capability checks in testpar tests and remove remaining warnings (#2995) * API tests datatype generation cleanup * Clean up API tests' random datatype generation and fix bug with enum datatype generation * Init parallel API tests with MPI_THREAD_MULTIPLE * HDF5 API tests - Check VOL connector registration * Determine whether a VOL connector failed to load before running API tests * Cleanup some usages of H5VL_CAP_FLAG_CREATION_ORDER in API tests * Remove some now-unused macros from H5_api_tests_disabled.h * Enable HDF5 API tests by default * Implement CMake option to install HDF5 API tests * Check for invalid AAPL from H5Acreate * Enable building of VOL connectors alongside HDF5 in CMake * Prepend CMake VOL URL option indices with 0s so they come in order * Don't turn on API tests by default yet * Document VOL connector FetchContent functionality * Add release note for API test updates * Only install testing library if API tests are installed * Fix grammar
* Fix multiConfig variable usage and remove unused CMake vars (#3013)Allen Byrne2023-05-251-10/+0
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* Add initial version of HDF5 API tests (#2877)jhendersonHDF2023-05-021-16/+38
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* Update java logger version (#2643)Allen Byrne2023-04-031-3/+3
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* CMake - Match Autotools behavior for library instrumentation (#2648)jhendersonHDF2023-04-011-1/+7
| | | Enable library instrumentation by default for parallel debug builds
* Fix minor things noted when doing 1.10 merges (#2610)Dana Robinson2023-03-241-1/+1
| | | | * Duplicated HDF_RESOURCES_DIR from cmake_ext_mod merge * Typos in comments
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2544)Allen Byrne2023-03-131-13/+15
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* Add fetchcontent for compression libs and fix cmake config (#2487)Allen Byrne2023-02-261-13/+5
| | | | | | | | | | | | | * Add fetchcontent for compression libs and fix cmake config * MSDOS is a reserved define name * Add release note and update install doc for FetchContent * Add CI test for FetchContent * Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends * Use general link
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-211-0/+11
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
* Removes dmalloc support (#2239)Dana Robinson2022-11-091-9/+0
| | | | | | | | | | This has not been used to debug the library in a very long time. Most developers use valgrind, -fsanitize=address, or some other memory checker instead of this library. This removes: * dmalloc.h include from H5private.h * --with-dmalloc= Autotools configure option * HDF5_ENABLE_USING_DMALLOC CMake option
* Removes the memory allocation sanity checks feature (#2218)Dana Robinson2022-11-031-8/+0
| | | | | | | | | | | | | | | * Removes the memory allocation sanity checks feature * Committing clang-format changes * Removes zero size checks for H5MM_(c|m)alloc() * Explicitly return NULL when size == 0 in H5allocate_memory() * Committing clang-format changes * Format fix Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Subfiling Fortran wrapper work. (#2143)Scot Breitenfeld2022-10-061-0/+1
| | | | | | | | | | | | | | | | | * added C ref. for Fortran constants * added C ref. for Fortran constants * move constant paramters to H5* module listing * added back comment * Fortran subfiling and ioc FD with tests. H5Pset/get_mpi_params wrappers with tests, misc.. parallel test clean-up. * misc. fixes * fixed CMake testpar issues, formatted, misc. updates * updated tests
* Subfiling VFD updates (#2106)jhendersonHDF2022-09-161-0/+6
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* develop Merge doxygen from 1.12 branch (#2095)Allen Byrne2022-09-141-0/+5
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* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-031-60/+18
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* [WIP] Add Developer build mode to CMake (#1659)jhendersonHDF2022-08-201-0/+7
| | | | | | | | | | | | | | | | * Add Developer build mode to CMake * Set a few CMake variables for Developer build modes * Refactor enabling of debug and developer-level compile definitions * Convert cache debugging macros to normal ifdef style Normal ifdef-style instead of if-style allows build system to define macros without warning about redefining macros with different values (0 vs. 1) * Add HDF5 Developer compile definitions to testing files * Temporarily disable -fanalyzer flag for GCC 12+ Developer builds
* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-191-5/+4
| | | | At one time this content was a git submodule shared between several projects but that time has long passed.
* Subfiling VFD misc fixes (#1938)jhendersonHDF2022-07-261-0/+12
| | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built
* Subfiling VFD (#1883)jhendersonHDF2022-07-221-0/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added support for vector I/O calls to the VFD layer, and associated test code. Note that this includes the optimization to allow shortened sizes and types arrays to allow more space efficient representations of vectors in which all entries are of the same size and/or type. See the Selection I/o RFC for further details. Tested serial and parallel, debug and production on Charis. serial and parallel debug only on Jelly. * ran code formatter quick serial build and test on jelly * Add H5FD_read_selection() and H5FD_write_selection(). Currently only translate to scalar calls. Fix const buf in H5FD_write_vector(). * Format source * Fix comments * Add selection I/O to chunk code, used when: not using chunk cache, no datatype conversion, no I/O filters, no page buffer, not using collective I/O. Requires global variable H5_use_selection_io_g be set to TRUE. Implemented selection to vector I/O transaltion at the file driver layer. * Fix formatting unrelated to previous change to stop github from complaining. * Add full API support for selection I/O. Add tests for this. * Implement selection I/O for contiguous datasets. Fix bug in selection I/O translation. Add const qualifiers to some internal selection I/O routines to maintain const-correctness while avoiding memcpys. * Added vector read / write support to the MPIO VFD, with associated test code (see testpar/t_vfd.c). Note that this implementation does NOT support vector entries of size greater than 2 GB. This must be repaired before release, but it should be good enough for correctness testing. As MPIO requires vector I/O requests to be sorted in increasing address order, also added a vector sort utility in H5FDint.c This function is tested in passing by the MPIO vector I/O extension. In passing, repaired a bug in size / type vector extension management in H5FD_read/write_vector() Tested parallel debug and production on charis and Jelly. * Ran source code formatter * Add support for independent parallel I/O with selection I/O. Add HDF5_USE_SELECTION_IO env var to control selection I/O (default off). * Implement parallel collective support for selection I/O. * Fix comments and run formatter. * Update selection IO branch with develop (#1215) Merged branch 'develop' into selection_io * Sync with develop (#1262) Updated the branch with develop changes. * Implement big I/O support for vector I/O requests in the MPIO file driver. * Free arrays in H5FD__mpio_read/write_vector() as soon as they're not needed, to cut down on memory usage during I/O. * Address comments from code review. Fix const warnings with H5S_SEL_ITER_INIT(). * Committing clang-format changes * Feature/subfiling (#1464) * Initial checkin of merged sub-filing VFD. Passes regression tests (debug/shared/paralle) on Jelly. However, bugs and many compiler warnings remain -- not suitable for merge to develop. * Minor mods to src/H5FDsubfile_mpi.c to address errors reported by autogen.sh * Code formatting run -- no test * Merged my subfiling code fixes into the new selection_io_branch * Forgot to add the FindMERCURY.cmake file. This will probably disappear soon * attempting to make a more reliable subfile file open which doesn't return errors. For some unknown reason, the regular posix open will occasionally fail to create a subfile. Some better error handling for file close has been added. * added NULL option for H5FD_subfiling_config_t in H5Pset_fapl_subfiling (#1034) * NULL option automatically stacks IOC VFD for subfiling and returns a valid fapl. * added doxygen subfiling APIs * Various fixes which allow the IOR benchmark to run correctly * Lots of updates including the packaging up of the mercury_util source files to enable easier builds for our Benchmarking * Interim checkin of selection_io_with_subfiling_vfd branch Moddified testpar/t_vfd.c to test the subfiling vfd with default configuration. Must update this code to run with a variety of configurations -- most particularly multiple IO concentrators, and stripe depth small enough to test the other IO concentrators. testpar/t_vfd.c exposed a large number of race condidtions -- symtoms included: 1) Crashes (usually seg faults) 2) Heap corruption 3) Stack corruption 4) Double frees of heap space 5) Hangs 6) Out of order execution of I/O requests / violations of POSIX semantics 7) Swapped write requests Items 1 - 4 turned out to be primarily caused by file close issues -- specifically, the main I/O concentrator thread and its pool of worker threads were not being shut down properly on file close. Addressing this issue in combination with some other minor fixes seems to have addressed these issues. Items 5 & 6 appear to have been caused by issue of I/O requests to the thread pool in an order that did not maintain POSIX semantics. A rewrite of the I/O request dispatch code appears to have solved these issues. Item 7 seems to have been caused by multiple write requests from a given rank being read by the wrong worker thread. Code to issue "unique" tags for each write request via the ACK message appears to have cleaned this up. Note that the code is still in poor condtition. A partial list of known defects includes: a) Race condiditon on file close that allows superblock writes to arrive at the I/O concentrator after it has been shutdown. This defect is most evident when testpar/t_subfiling_vfd is run with 8 ranks. b) No error reporting from I/O concentrators -- must design and implement this. For now, mostly just asserts, which suggests that it should be run in debug mode. c) Much commented out and/or un-used code. d) Code orgnaization e) Build system with bits of Mercury is awkward -- think of shifting to pthreads with our own thread pool code. f) Need to add native support for vector and selection I/O to the subfiling VFD. g) Need to review, and posibly rework configuration code. h) Need to store subfile configuration data in a superblock extension message, and add code to use this data on file open. i) Test code is inadequate -- expect more issues as it is extended. In particular, there is no unit test code for the I/O request dispatch code. While I think it is correct at present, we need test code to verify this. Similarly, we need to test with multiple I/O concentrators and much smaller stripe depth. My actual code changes were limited to: src/H5FDioc.c src/H5FDioc_threads.c src/H5FDsubfile_int.c src/H5FDsubfile_mpi.c src/H5FDsubfiling.c src/H5FDsubfiling.h src/H5FDsubfiling_priv.h testpar/t_subfiling_vfd.c testpar/t_vfd.c I'm not sure what is going on with the deletions in src/mercury/src/util. Tested parallel/debug on Charis and Jelly * subfiling with selection IO (#1219) Merged branch 'selection_io' into subfiling branch. * Subfile name fixes (#1250) * fixed subfiling naming convention, and added leading zero to rank names. * Merge branch 'selection_io' into selection_io_with_subfiling_vfd (#1265) * Added script to join subfiles into a single HDF5 file (#1350) * Modified H5FD__subfiling_query() to report that the sub-filing VFD supports MPI This exposed issues with truncate and get EOF in the sub-filing VFD. I believe I have addressed these issues (get EOF not as fully tested as it should be), howeer, it exposed race conditions resulting in hangs. As of this writing, I have not been able to chase these down. Note that the tests that expose these race conditions are in testpar/t_subfiling_vfd.c, and are currently skipped. Unskip these tests to reproduce the race conditions. tested (to the extent possible) debug/parallel on charis and jelly. * Committing clang-format changes * fixed H5MM_free Co-authored-by: mainzer <mainzer#hdfgroup.org> Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com> Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Move Subfiling VFD components into H5FDsubfiling source directory * Update Autotools build and add H5_HAVE_SUBFILING_VFD macro to H5pubconf.h * Tidy up CMake build of subfiling sources * Merge branch 'develop' into feature/subfiling (#1539) Merge branch 'develop' into feature/subfiling * Add VFD interface version field to Subfiling and IOC VFDs * Merge branch 'develop' into feature/subfiling (#1557) Merge branch 'develop' into feature/subfiling * Merge branch 'develop' into feature/subfiling (#1563) Merge branch 'develop' into feature/subfiling * Tidy up merge artifacts after rebase on develop * Fix incorrect variable in mirror VFD utils CMake * Ensure VFD values are always defined * Add subfiling to CMake VFD_LIST if built * Mark MPI I/O driver self-initialization global as static * Add Subfiling VFD to predefined VFDs for HDF5_DRIVER env. variable * Initial progress towards separating private vs. public subfiling code * include libgen.h in t_vfd tests for correct dirname/basename * Committing clang-format changes * removed mercury option, included subfiling header path (#1577) Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests. * added check for stdatomic.h (#1578) * added check for stdatomic.h with subfiling * added H5_HAVE_SUBFILING_VFD for cmake * fix old-style-definition warning (#1582) * fix old-style-definition warning * added test for enable parallel with subfiling VFD (#1586) Fails if subfiling VFD is not used with parallel support. * Subfiling/IOC VFD fixes and tidying (#1619) * Rename CMake option for Subfiling VFD to be consistent with other VFDs * Miscellaneous Subfiling fixes Add error message for unset MPI communicator Support dynamic loading of subfiling VFD with default configuration * Temporary fix for subfile name issue * Added subfile checks (#1634) * added subfile checks * Feature/subfiling (#1655) * Subfiling/IOC VFD cleanup Fix misuse of MPI_COMM_WORLD in IOC VFD Propagate Subfiling FAPL MPI settings down to IOC FAPL in default configuration case Cleanup IOC VFD debugging code Change sprintf to snprintf in a few places * Major work on separating Subfiling and IOC VFDs from each other * Re-write async_completion func to not overuse stack * Replace usage of MPI_COMM_WORLD with file's actual MPI communicator * Refactor H5FDsubfile_mpi.c * Remove empty file H5FDsubfile_mpi.c * Separate IOC VFD errors to its own error stack * Committing clang-format changes * Remove H5TRACE macros from H5FDioc.c * Integrate H5FDioc_threads.c with IOC error stack * Fix for subfile name generation Use number of I/O concentrators from existing subfiling configuration file, if one exists * Add temporary barrier in "Get EOF" operation to prevent races on EOF Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix for retrieval of machine Host ID * Default to MPI_COMM_WORLD if no MPI params set * added libs rt and pthreads (#1673) * added libs rt and pthreads * Feature/subfiling (#1689) * More tidying of IOC VFD and subfiling debug code * Remove old unused log file code * Clear FID from active file map on failure * Fix bug in generation of subfile names when truncating file * Change subfile names to start from 1 instead of 0 * Use long long for user-specified stripe size from environment variable * Skip 0-sized I/Os in low-level IOC I/O routines * Don't update EOF on read * Convert printed warning about data size mismatch to assertion * Don't add base file address to I/O addresses twice Base address should already be applied as part of H5FDwrite/read_vector calls * Account for 0-sized I/O vector entries in subfile write/read functions * Rewrite init_indep_io for clarity * Correction for IOC wraparound calculations * Some corrections to iovec calculations * Remove temporary barrier on EOF retrieval * Complete work request queue entry on error instead of skipping over * Account for stripe size wraparound for sf_col_offset calculation * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Re-write and fix bugs in I/O vector filling routines (#1703) * Rewrite I/O vector filling routines for clarity * Fix bug with iovec_fill_last when last I/O size is 0 * added subfiling_dir line read (#1714) * added subfiling_dir line read and use it * shellcheck fixes * I/O request dispatch logic update (#1731) Short-circuit I/O request dispatch when head of I/O queue is an in-progress get EOF or truncate operation. This prevents an issue where a write operation can be dispatched alongside a get EOF/truncate operation, whereas all I/O requests are supposed to be ineligible for dispatch until the get EOF/truncate is completed * h5fuse.sh.in clean-up (#1757) * Added command-line options * Committing clang-format changes * Align with changes from develop * Mimic MPI I/O VFD for EOF handling * Initialize context_id field for work request objects * Use logfile for some debugging information * Use atomic store to set IOC ready flag * Use separate communicator for sending file EOF data Minor IOC cleanup * Use H5_subfile_fid_to_context to get context ID for file in Subfiling VFD * IOVEC calculation fixes * Updates for debugging code * Minor fixes for threaded code * Committing clang-format changes * Use separate MPI communicator for barrier operations * Committing clang-format changes * Rewrite EOF routine to use nonblocking MPI communication * Committing clang-format changes * Always dispatch I/O work requests in IOC main loop * Return distinct MPI communicator to library when requested * Minor warning cleanup * Committing clang-format changes * Generate h5fuse.sh from h5fuse.sh.in in CMake * Send truncate messages to correct IOC rank * Committing clang-format changes * Miscellaneous cleanup Post some MPI receives before sends Free some duplicated MPI communicator/Info objects Remove unnecessary extra MPI_Barrier * Warning cleanup * Fix for leaked MPI communicator * Retrieve file EOF on single rank and bcast it * Fixes for a few failure paths * Cleanup of IOC file opens * Committing clang-format changes * Use plan MPI_Send for send of EOF messages * Always check MPI thread support level during Subfiling init * Committing clang-format changes * Handle a hang on failure when IOCs can't open subfiles * Committing clang-format changes * Refactor file open status consensus check * Committing clang-format changes * Fix for MPI_Comm_free being called after MPI_Finalize * Fix VFD test by setting MPI params before setting subfiling on FAPL * Update Subfiling VFD error handling and error stack usage * Improvements for Subfiling logfiles * Remove prototypes for currently unused routines * Disable I/O queue stat collecting by default * Remove unused serialization mutex variable * Update VFD testing to take subfiling VFD into account * Fix usage of global subfiling application layout object * Minor fixes for failure pathways * Keep track of the number of failures in an IOC I/O queue * Make sure not to exceed MPI_TAG_UB value for data communication messages * Committing clang-format changes * Update for rename of some H5FD 'ctl' opcodes * Always include Subfiling's public header files in hdf5.h * Remove old unused code and comments * Implement support for per-file I/O queues Allows the subfiling VFD to have multiple HDF5 files open simultaneously * Use simple MPI_Iprobe over unnecessary MPI_Improbe * Committing clang-format changes * Update HDF5 testing to query driver for H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag * Fix a few bugs related to file multi-opens * Avoid calling MPI routines if subfiling gets reinitialized * Fix issue when files are closed in a random order * Update HDF5 testing to query VFD for "using MPI" feature flag * Register atexit handler in subfiling VFD to call MPI_Finalize after HDF5 closes * Fail for collective I/O requests until support is implemented * Correct VOL test function prototypes * Minor cleanup of old code and comments * Update mercury dependency * Cleanup of subfiling configuration structure * Committing clang-format changes * Build system updates for Subfiling VFD * Fix possible hang on failure in t_vfd tests caused by mismatched MPI_Barrier calls * Copy subfiling IOC fapl in "fapl get" method * Mirror subfiling superblock writes to stub file for legacy POSIX-y HDF5 applications * Allow collective I/O for MPI_BYTE types and rank 0 bcast strategy * Committing clang-format changes * Use different scheme for subfiling write message MPI tag calculations * Committing clang-format changes * Avoid performing fstat calls on all MPI ranks * Add MPI_Barrier before finalizing IOC threads * Use try_lock in I/O queue dispatch to minimize contention from worker threads * Use simple Waitall for nonblocking I/O waits * Add configurable IOC main thread delay and try_lock option to I/O queue dispatch * Fix bug that could cause serialization of non-overlapping I/O requests * Temporarily treat collective subfiling vector I/O calls as independent * Removed unused mercury bits * Add stubs for subfiling and IOC file delete callback * Update VFD testing for Subfiling VFD * Work around HDF5 metadata cache bug for Subfiling VFD when MPI Comm size = 1 * Committing clang-format changes Co-authored-by: mainzer <mainzer#hdfgroup.org> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com> Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
* Develop sync (#1793)Allen Byrne2022-06-091-0/+3
| | | | | * Synch update * Branch sync changes
* Set default level to minimum time (#1722)Allen Byrne2022-05-171-1/+6
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* Allows parallel + thread-safe combination in Autotools and CMake (#1760)Dana Robinson2022-05-131-9/+0
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* Parallel Compression improvements (#1302)jhendersonHDF2022-02-241-4/+8
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* Add SZ filter and adjust compression file names to avoid conflicts (#1434)Allen Byrne2022-02-171-2/+2
| | | | | | | | | * Updated plugins project required adjustments * Updated plugins need to distinguish external libs * Fix missed rename * Use same name for windows as linux - avoid name clash
* Update the java slf4j logging jars to latest 1.7.33 (#1369)Allen Byrne2022-01-181-3/+3
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* Add support for parallel tools based on the 3rd party library mpiFileUtils ↵rawarren2021-11-291-0/+25
| | | | | | | | | | (libMFU) … (#1177) Adds tool h5dwalk and configure options to enable building it. Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Consolidate VFD create list macro (#1132)Allen Byrne2021-10-261-0/+3
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-201-4/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* Fix various warnings and issues in doxygen doc generation (#994)Allen Byrne2021-09-101-14/+15
| | | | | * Fix various warnings and issues in doxygen doc generation * Add new file to list
* C++ warning and build fixes (#707)Dana Robinson2021-06-011-1/+0
| | | | | | | | | | | | * Committing clang-format changes * C++ build and warning updates * Fixes all warnings on C++ (with gcc 9.3) * Updates CMake and Autotools C++ builds * Undo warning clobber Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake advanced options for clang needs an OPTION command #556 (#557)Allen Byrne2021-04-201-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake no longer builds the C++ library by default (#555)Dana Robinson2021-04-201-1/+1
| | | | | | | * Committing clang-format changes * CMake no longer builds C++ library by default Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cleanup CMake code for doxygen and perl shell scripts (#552)Allen Byrne2021-04-191-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge pr7 (#516)Larry Knox2021-03-251-14/+21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Add cmake variable HDF5_LIB_INFIX (#7) * Add cmake variable HDF5_LIB_INFIX This infix is added to all library names after 'hdf5'. e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' This name is used in packages on debian based systems. (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) This option is useful when testing projects on debian based systems with custom builds of hdf5 while trying to minimize differences between the custom setup and the environment created by installing system packages. * Added RELEASE.txt entry for HDF5_LIB_INFIX. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
* Removed checks/workarounds for pre-C++89 compatibility (#449)Sean McBride2021-03-101-3/+0
| | | | | | | | After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool
* Fix cmake syntax error with regex escaping (#336)Sean2021-02-151-1/+1
| | | | | | | | | | | | | Fixes: Syntax error in cmake code at /some/path/hdf5/CMakeLists.txt:240 when parsing string .*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._\-]*)\".*$ Invalid escape sequence \-
* Small fixes (#285)Allen Byrne2021-01-271-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Small changes plus merge of tools arg parse from 1.12