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* Strip HD prefix from string/char C API calls (#3540)Dana Robinson2023-09-151-30/+30
| | | | | | | | | | | | | | | | | | | | | * Strip HD prefix from string/char C API calls * HD(f)(put|get)(s|c) * HDstr* * HDv*printf * HD(s)(print|scan)f * HDperror But NOT: * HDstrcase* * HDvasprintf * HDstrtok_r * HDstrndup As those are not C99 and have portability work-around implementations. They will be handled later. * Fix th5_system.c screwup
* Consistent initialization of hid_t in the tests (#3521)Scot Breitenfeld2023-09-081-1/+1
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* Convert hbool_t --> bool in test (#3494)Dana Robinson2023-09-051-8/+8
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* Remove HD from HDmem* calls (#3211)Dana Robinson2023-06-291-7/+7
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* Remove programmer/date from comments (#3210)Dana Robinson2023-06-291-6/+0
| | | | * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work
* Remove HD from memory allocate/free calls (#3195)Dana Robinson2023-06-281-2/+2
| | | | | | * HDcalloc * HDfree * HDmalloc * HDrealloc
* Many fixes to various compiler warnings (#3124)Sean McBride2023-06-191-1/+1
| | | | | | | | | | | * Fixed various -Wmissing-variable-declarations by adding static keyword * In a few cases, renamed the variable suffix from _g to _s. * Fixed some -Wmissing-variable-declarations by using different declaration macros * Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero * Fixed various -Wcomma warnings * Fixed clang -Wstrict-prototypes warnings * Fixed various -Wunused-variable warnings * Updated some casts to fix the only 3 -Wcast-qual warnings * Fixed the only -Wsometimes-uninitialized warning
* Many clang -Wextra-semi-stmt fixes (#2537)Sean McBride2023-06-161-4/+4
| | | | | * Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Subfiling VFD (#1883)jhendersonHDF2022-07-221-5/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* h5test.h testing macros get enclosed in do..while loops (#1721)Dana Robinson2022-05-041-926/+926
| | | | | | | * h5test.h testing macros get enclosed in do..while loops * Adds missed macro in hl C++ code * Fixes macro in Windows code
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* VFD plugins (#602)jhendersonHDF2021-09-291-2/+6
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* Update clang config (#473)Quincey Koziol2021-03-171-1/+4
| | | | | | | * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)Sean McBride2021-03-101-5/+5
| | | | | | | | | * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* HD prefix updates in src/ and test/Dana Robinson2020-10-241-2/+2
| | | | | | | Adds missing HD prefixes to API calls in src and test. Adds some extra processing to bin/checkposix to keep the noise levels down when running the script (not comprehensive).
* Clang-format of source filesAllen Byrne2020-09-301-1294/+2075
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* Removes staff email addresses from the repositoryDana Robinson2020-08-071-1/+1
| | | | Removes redundant C library headers from hl library
* Trim trailing whitespaceQuincey Koziol2020-04-201-2/+2
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* So that I can use PASSED(); anywhere a statement can go, #define PASSED() withDavid Young2020-02-281-14/+14
| | | | a do-while wrapper.
* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-5/+5
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* Small changes from the token_refactoring branch, to reduce the delta to developQuincey Koziol2020-01-041-4/+4
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Vailin Choi2018-05-311-2/+2
|\ | | | | | | | | * commit 'e8ece625f223032db0d26cfffafc045e4ccdf37d': Normalize with vol_integration.
| * Normalize with vol_integration.Dana Robinson2018-05-291-2/+2
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* | Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-1/+1
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* | Fix for HDFFV-10180 Performance issues with H5Oget_info.Vailin Choi2018-04-241-1/+1
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* 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.
* [svn-r30189] Description:Quincey Koziol2016-07-181-44/+45
| | | | | | | | | 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-r27768] Description:Quincey Koziol2015-09-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | 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-r27572] Removed VMS-specific code from the library.Dana Robinson2015-08-241-2/+0
| | | | | | | | | The only remaining code consists of a few floating-point tests that rely on pre-generated and checked-in VMS files. These have been left alone, even though they will not be possible to recreate, since testing VMS float behavior is still important. Tested on: h5committest
* [svn-r26772] Fixed wrong fapl for H5Fopen when testing H5Iget_name with ↵Scot Breitenfeld2015-04-091-1/+1
| | | | | | anonymously created datatype. Tested: jam (using split virtual driver)
* [svn-r26767] Added test to address HDFFV-3065:Scot Breitenfeld2015-04-081-2/+57
| | | | | | H5Iget_name on datatype that is not named returns no error Tested: h5committest
* [svn-r25496] Description:Quincey Koziol2014-07-301-8/+8
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r24681] Description:Scot Breitenfeld2014-02-041-1/+14
| | | | | | | | | Fix for HDF5/HDFFV-8620 H5Rget_name with NULL name parameter fails. The name parameter now excepts NULL, in which case the length of then name is returned. Tested: jam (intel and gnu)
* [svn-r21923] Description:Quincey Koziol2012-02-101-1/+1
| | | | | | | | | Add FUNC_ENTER macros for package-private routines and begin process of switching package routines to use them. All H5G routines are currently finished. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r21121] Description:Quincey Koziol2011-07-181-12/+12
| | | | | | | | | Switch from H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for calls to H5Rdereference2(). Tested on: Mac OS X/32 10.6.8 (amazon) w/debug (too minor to require h5committest)
* [svn-r21117] Issue 2763 - I added a new parameter of object access property ↵Raymond Lu2011-07-181-12/+12
| | | | | | list to the function H5Rdereference. It's called H5Rdereference2 now. H5Rdereference function has been deprecated to H5Rdereference1. I also added some test cases in trefer.c. Tested on jam, heiwa, and koala.
* [svn-r20529] Purpose: Add testing for bug 1864Neil Fortner2011-04-151-0/+3
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r20315] brought revisions 19868:20300 from the 1.8.6_vms branch to the ↵Raymond Lu2011-03-241-0/+2
| | | | trunk for VMS work
* [svn-r19237] Description:Quincey Koziol2010-08-121-1/+0
| | | | | | | | | | Clean up misc. compiler warnings. Tested on: FreeBSD/32 6.3 (duty) 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-r19133] Description:Quincey Koziol2010-07-281-5/+104
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Correct traversal of user-defined links (including external links) to retain path information of object, allowing H5Iget_name() queries to work quickly (without searching entire destination file). This required some refactoring and addition of a mechanism to detect if a "fast" query was performed (for the tests). Minor code cleanups, etc. 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 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-r16560] Description:Quincey Koziol2009-03-101-18/+17
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r15800] Description:Quincey Koziol2008-10-071-1/+1
| | | | | | | | | | | | | | | | | | | | | | | Bring file free space branch changes through r15795 into trunk, which includes a fair bit of code cleanup & rearrangement along with a couple of bug fixes also. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15628] Description:Quincey Koziol2008-09-161-30/+30
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r14420] Description:Quincey Koziol2008-01-151-1/+1
| | | | | | | | Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for the coordinates, instead of 'hsize_t **'. Tested on: Mac OS X/32 10.5.1 (amazon)
* [svn-r14284] Description:Quincey Koziol2007-11-241-32/+59
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add H5Lvisit_by_name() API routine to library. Eliminated all (five!) other group traversal routines and changed them all to use the new API routine. Cleaned up output of h5ls & h5stat: - Issue error when requesting recursive traversal of a file with the "group info" flag, but no group given - Print info about root group in all(?) appropriate situations - Don't print "verbose" information about root group until the root group is in the list of objects to display (mostly because h5ls & h5stat had a different twist on traversing the groups in a file that the other utilities) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14199] Description:Quincey Koziol2007-10-111-27/+27
| | | | | | | | | | | | | | | | | | | | | Add H5Dcreate to API versioned routines, replacing internal usage with H5Dcreate2 Fix thread-safe error stack initialization for API versioned error stack printing routines. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14193] Description:Quincey Koziol2007-10-081-27/+27
| | | | | | | | | | | | | | | | | | | Make H5Dopen versioned and change all internal usage to use H5Dopen2 Add simple regression test for H5Dopen1 Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14160] Description:Quincey Koziol2007-09-271-58/+57
| | | | | | | | | | | | | | | | Make H5Topen versioned, and add regression test for H5Topen1. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64 2.6 (smirom) 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 AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
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