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* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-212-8/+9
| | | | | | | | | | | | | | | * 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
* Update develop branch version to 1.13.4-1 (#2189)Larry Knox2022-10-261-7/+7
| | | | | | * Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3 release. Added new version to exceptions in lines 74-5 of src/H5.c
* Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)Larry Knox2022-08-121-7/+7
| | | | release. Added new version to exceptions in line 75 of src/H5.c.
* Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for ↵Larry Knox2022-08-121-7/+7
| | | | | | | | release" This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95. H5TEST-tcheck_version-release failed.
* Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for releaseLarry Knox2022-08-121-7/+7
| | | | of HDF5 1.13.2.
* Onion VFD (#1953)Dana Robinson2022-08-023-0/+53
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Onion VFD feature * Fixes onion VFD errors with non-sec2 backing store VFDs * Disables the onion VFD tests w/ ph5diff * Disables non-sec2 VFDs as onion VFD backing stores * Committing clang-format changes * Formatted source * Typo * Adds onion VFD tools tests to CMake * Fixes for v16 API compatibility * Memset structs to avoid bad frees on errors * H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE * Properly decodes checksums on BE machines * Be more careful about uint64_t to haddr_t/hsize_t conversions * Another fix for BE data comparison * Removed double underscores from onion constants * Replace hard-coded onion header string w/ constant * Fixes cleanup paths in H5FD__onion_ingest_history() * Fixed use of size_t revision numbers * Fix h5dump revision count format string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move error-stack text to top of usage display (#1564)Allen Byrne2022-04-011-2/+3
| | | | | | | | | * Move error-stack text to top of usage display * Add optional tag ti list * format changes * Revert incorrect change
* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-011-7/+7
| | | | | | to MANIFEST (#1460)
* 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>
* Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236)Larry Knox2021-11-301-7/+7
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* Add option for h5repack timing (#1142)Allen Byrne2021-11-081-1/+2
| | | | | | | | | | | | | | | | | * Add timing option to h5repack * Adjust help text * fix format * fix typos * Correct spacing * Change timing to use H5Timer * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD plugins (#602)jhendersonHDF2021-09-291-0/+12
| | | | | | | | | | | | | | | | | * 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
* Bmr dev hdffv 11223 (#640)bmribler2021-05-122-0/+0
| | | | | | | | | | | | | | | | | | | * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 11099 Add help text line (#259)Allen Byrne2021-01-151-0/+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
* Bring async branch to develop (#166)Quincey Koziol2020-12-141-14/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add H5Fwait, H5Dwait, and other changes for async vol connector * Revert temporary testing changes * Add H5Fwait to header file * Add H5VLreset_lib_state() routine. * Correct VOL wrap context when retrieving library state for file open & create. * Manage the API context's VOL connector state as part of the library state. * Set the 'VOL connector property valid' flag when restoring the library state. * Don't push new API context on stack when retrieving "current" one. * Check for NULL VOL wrap context before decrementing refcount on it, when freeing the API context state. * Manage recount of underlying connector for VOL wrap context. * Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and release the global lock on the HDF5 library. * Update library with new functions related to library global lock * Add asynchronous token API * Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the threadsafety (H5TS*) routines. * Sync w/develop * Initial event set code framework. * Elaborate on the H5ES routines, starting to add API routines. Update the "close ID" callbacks to allow asynchronous request tokens to be passed in from an asynchronous close API call. Refactor current asynchronous API routines (H5Fopen/H5Fclose and H5Dread/H5Dread) to use event sets instead of directly working with request tokens from the application. Clean up a few other minor warnings & code style issues. * Implement H5EScreate, H5ESget_count, and H5ESclose. It should be possible to write a simple application that creates an event set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and H5Fclose_async, then calls H5ESclose (which waits for all async events to complete). * Add source file for event set test. * Refactor sync & async API routines to call common routine. Move dataset API read / write routines to src/H5D.c, along with all the other API routines. Progress on "fake" async VOL connector, for testing. * Modify async implementation to wrap async requests in a H5VL_object_t struct so the VOL layer can find the connector when accessing the request at a later point. * Free the requests is H5ESclose. Remove comments implying that request wait, notify, and cancel callbacks should free the request. * Fix bug in error handling in H5Fclose. * Fix bugs in async file routines. Rename H5VL_create_object_generic to H5VL_create_object. * Add explicit async version of H5Fcreate. * Add more _async routines * Correct typo for return value from H5Awrite changes * Add H5EStest and H5ESwait routines * Updated with API tracing info * Fix NULL pointer dereference in H5ES__wait * Add H5is_library_terminating() routine, so that VOL connectors can detect when the library is shutting down. * Fix typo * Remove event from event set's linked list * Move block of code so that vol_obj is valid * Avoid setting properties in the DXPL when reseting the library state (and in the test code). * Refactor argument tracing to implement new capability for tracing arguments of non-API routines, with the H5ARG_TRACE macro. This macro is updated automatically with the bin/trace script that runs as part of the autogen.sh process. Major changes were in src/H5trace.c and bin/trace, with the other changes being cleanups to the argument lists, to improve their presentation in the tracing output. Also - added the "managed string" routines, which can dynamically allocate strings, appending printf-formatted output to the string efficiently. * Release memory for managed strings * Fix printf() formats. * More printf() format fixes. * Add H5Eappend_stack routine and regression tests * Clean up a few missed merge conflicts and update the error stacks. * Remove unnecessary fork() operations and ten second sleep(). * Restore commented out attribute out, to better enable tracking down the previous failure * Allow multiple H5ARG_TRACE macros within a routine to be updated * Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert. * Merge "managed" string routines into "ref-counted" strings, and refactor code to use them. * Add missing file. * Add caller's name and arguments to event, for error reporting * Refactor event set setup for "API common" internal routines * Checkin async API routines for H5A* and H5G* modules as listed in ID-283. Fix couple h5dump expected output files due to the changes. * Add some of the error query routines needed for event sets. * Refactor to make async setup / teardown and "common" routines cleaner * (1) Add async APIs to H5L, H5F, and H5D modules (2) Fix errors in previous checkins of async APIs in H5A and H5G modules (3) h5dump expected output changes * Enhance event info, for better error handling * Change name of temporary vol_obj variable, to help reduce coding errors * Fix oversight with vol_obj pointer * Minor code cleanup * Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state * Run source formatter * Change H5TSmutex lock and release to include a lock count * Update error reporting ideas * Minor updates to improve sanity checking for retrieving / restoring library state * Updated with feedback from h5py team members * Refactor internal event set list and event handling, add implementation for H5ESget_err_info * Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines. * Update API tracing for new H5VL_request_status_t typedef * Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure * Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation * Remove 'canceled' event status from Java constants * Be safer about releasing resources when inserting a newly opened/created object or file into an event set * Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate". * Remove H5ES_STATUS_CANCELED from Java wrappers also * (a) Add async APIs for H5O module as listed in jira issue ID-283. (b) Remove verification of name parameter in async related routines for H55A and H5L modules because it is checked in H5VL_setup* routine. (c) Modify h5dump expected output due to the async changes. * Corrections based on PR feedback. * Further changes to make based on PR feedback. * Fix missed merge marker, and reformatted line * Clean up some warnings * Correct level of indirection * Relocate prototype (and doxygen info) for H5Aclose * Change non-static function declarations to be static * Ensure that H5TSpublic.h header gets installed (#129) * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c. * Add H5Iregister_future routine and tests. * Correct return value for H5Lexists_async * Add H5_DLL macro to public H5ES API routines * Update supported -> flags parameter for introspect_query callback * Remove my email address. Update passthrough VOL connector ID. * Fix comment for post_open_api_common * Remove unused non-blocking VOL connector * Minor cleanup in async branch in preparation for merge to develop * Update CMake and the Autotools to use the new pass-through VOL ID * Fix for SWMR daily test failures (#160) The H5I_register_using_existing_id() call did not initialize the future ID callbacks, causing the library to segfault when it tried to resolve those function pointers. * Added selective async APIs (#150) * Added selective async APIs Description: Added the following APIs: H5Ropen_attr_async H5Ropen_object_async H5Ropen_region_async H5Mcreate_async H5Mopen_async H5Mput_async H5Mget_async H5Mclose_async H5Tcommit_async H5Topen_async H5Tcopy_async H5Tclose_async - Updated an expected output file to include a new internal function in the error stack for the failure case. * Updated async APIs per reviews, including removing async version of H5Tcopy. * Removed statements that were added by mistake in the previous commit. * Fix compile issues in H5M and warnings elsewhere * Reformat code * Brings VOL_LIST changes from develop. (#163) Co-authored-by: Houjun Tang <htang4@lbl.gov> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <derobins@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-1/+1
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Miscellaneous updateBinh-Minh Ribler2020-11-111-0/+0
| | | | | - added test for CMake - renamed new input file to conform to the existing files
* Added test for the fix HDFFV-10590Binh-Minh Ribler2020-10-281-0/+0
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* HDFFV-9984 - correct name of ref filesAllen Byrne2020-08-145-0/+0
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* HDFFV-9984 add missing ref fileAllen Byrne2020-08-141-0/+28
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* HDFFV-9984 - add missing ref filesAllen Byrne2020-08-145-0/+523
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* HDFFV-9984 Add options to merge/prune external links during repackAllen Byrne2020-08-1421-0/+1006
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* Changed identifiers and command-line options from "id" to "value" in toolsDana Robinson2020-04-141-4/+4
| | | | code to be in agreement with H5VL API terminology.
* Updated test ddl files so CMake passes after h5dump failures.Dana Robinson2020-04-061-1/+1
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* Update Tools library to be better compatible with VOL connectorsJordan Henderson2020-03-171-0/+12
| | | | | | | | | | | | | | | | | | | | | Modify h5repack to integrate with VOL connectors Update tools library to accomodate VOL connectors Update logic in h5tools_fopen for VOL connectors Add command-line options to h5repack for specifying in/out VOL connectors Implement h5tools_set_vol_fapl Fix library shutdown issue Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme Avoid H5Ocopy in h5repack when using different VOL connectors Update h5tools_test_utils.c for ROS3 and HDFS integration
* Clean up tools warnings introduced by H5TOOLS_ERR_INIT macroJordan Henderson2019-12-311-1/+1
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* HDFFV-10876 Update dump to match DDL specAllen Byrne2019-12-052-0/+88
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* HDFFV-10919 merge synchingAllen Byrne2019-10-021-5/+5
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* Update versioning to next major versionAllen Byrne2019-09-251-1/+2
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* Update develop branch version to 1.13.0 after creation of hdf5_1_12Larry Knox2019-09-251-7/+7
| | | | branch.
* Merge branch 'develop' of ↵Jacob Smith2019-09-231-1/+2
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Update libvers usageAllen Byrne2019-07-281-1/+2
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* | Refactor h5repackgentest to have more modular internals, for easierJacob Smith2019-09-2319-0/+1
| | | | | | | | | | addition of new tests. Update manifest and test script for new hdf5 external-storage .h5 files.
* | Merge branch 'develop' of ↵Jacob Smith2019-07-222-5/+5
|\ \ | |/ | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Checkin for new shutting down free-space manager.Vailin Choi2019-06-202-5/+5
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* | Minor formatting adjustments.Jacob Smith2019-07-221-4/+4
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* | Fix failing automated reporting.Jacob Smith2019-06-1912-0/+3
| | | | | | | | Add 8-bit big-endian testfile.
* | Add initial failing test for h5repack copying external data into new file.Jacob Smith2019-05-303-0/+0
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* | Fit help message to 80 character width and clarify some details.Jacob Smith2019-05-141-27/+44
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* Snapshot version 1.11 release 5.hdftest2019-05-021-7/+7
| | | | Update version to 1.11.6.
* Snapshot version 1.11 release 4.hdftest2019-04-011-7/+7
| | | | Update version to 1.11.5.
* Switch tool error output to match VOL changes within libraryQuincey Koziol2018-11-121-13/+16
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-071-7/+7
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| * Commit version changes for additional files for 1.11.3 snapshot release.Larry Knox2018-11-061-7/+7
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* | Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-1/+1
|/ | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-101-10/+16
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* Snapshot version 1.11 release 2.hdftest2018-09-201-7/+7
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* Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-7/+7
| | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-5/+5
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-185-13/+28
| |\ | | | | | | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
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