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* 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.
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-19/+19
| | | | | * Update format source to clang 13 * More format changes
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Combo set of async and other changes (#161)Quincey Koziol2021-06-021-13/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Apply patch for dynamically registering optional VOL operations * (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. * Remove H5Dwait & H5Fwait (moved to the async connector). Added H5atclose routine. Updated 'optional op' operations. * Fix missed merge marker, and reformatted line * Update API tracing infrastructure for H5atclose callback * Clean up some warnings * Normalize against develop branch * Correct level of indirection * Add doxygen info for H5is_library_terminating and regression tests for it and H5atclose * Relocate prototype (and doxygen info) for H5Aclose * Align w/changes on develop * Move group package initialization code to H5Gint.c, and update tracing macros * Change non-static function declarations to be static * Correct GCC diagnostic macro * Ensure that H5TSpublic.h header gets installed (#129) * Finish moving API routines that invoke VOL framework to main source files. * Fix position of H5Fmount and H5Funmount * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Add wrappers for dynamically registered optional operations * Fix typo * Update doxygen comment for H5atclose with additional detail. * Add H5VL\*_vararg versions of H5VL routines that use va_list parameters * Implement and test H5S_BLOCK * 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 * Finish another iteration on public H5ES routines, along with running the code reformatter * Another round of reformatting * 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) * Remove H5Dwait and H5Fwait calls, which were incorrectly brought back in * Tiny cleanup of H5Lcreate_hard_async * Run source formatter * Allow for canceled operation in wait_cb * Attempt to fix switch on string value * Re-run source formatter * Add H5S_BLOCK testfile to CMake clean target * Add H5Pset_vol_async API routine and 'get_cap_flags' VOL introspection callback * Clean up warnings * Add H5P(set\|get)_vol_implicit_async API routines to allow \/ disallow implicit asynchronous operations (default is disallowed) * Run formatting script * Remove H5VL_REQUEST_WAIT\* * Warning cleanup * Eliminate strdup()s on statically allocated strings * Warning cleanup * Split H5VLrestore_lib_state into H5VLstart_lib_state and H5VLrestore_lib_state, and rename H5VLreset_lib_state to H5VLfinish_lib_state. * Duplicate strings when building err_info to return to applicatin * Move connector author routines into seperate header files, all included in the new hdf5dev.h header * Run bin/trace to add TRACE macros * Allow H5ES_NONE as a valid, but no-op, parameter to all H5ES API routines that accept an event set ID * Clean up formatting * Remove H5Pset/get_vol_implicit_async * Clean up warning * Remove H5Pget_vol_async and replace with more generic H5Pget_vol_cap_flags * Clean up warnings * Add H5ESfree_err_info convenience routine * Fix typo * Correct matching for cached VOL plugins * Add developer header file * Update for C99 compatibility * Add missing trace macro * Stop clang-format from messing with the trace macros. Don't set up VOL wrappers for 'infrastructure' objects like requests and blobs * Fix warning about formatting a directory * Clean up formatting for H5E_BEGIN_TRY / H5E_END_TRY * Reduce scope of H5ES__close * Enable CMake checks for various types on MacOS * Clean up properly when H5CX_retrieve_state() fails. Also clean up many compiler warnings. * Committing clang-format changes * Merge from develop * Fix mis-placed assert * Remove commented-out code * Re-add macro for unsetenv on Windows (I think it accidentally was merged out) * Strengthen sanity check from error report to assertion * Committing clang-format changes * Add units to the comments for a few fields * Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it. * Committing clang-format changes * Remove H5ESget_time_estimate * Committing clang-format changes * Create developer header for datatype routines and move type conversion register/unregister routines there. * Simplify internal H5VL_setup_name_args and H5VL_setup_idx_args routines * Add H5VLlink_optional_op, allowing dynamicly registered optional operations for the link VOL subclass, also added H5VL_loc_params argument to the link 'optional' callback to allow them to work correctly. * Run bin/format_source on current code * Add H5VLobject_optional_op, allowing dynamicly registered optional operations for the object VOL subclass, also added H5VL_loc_params argument to the object 'optional' callback to allow them to work correctly. * Run bin/format_source on current code * Committing clang-format changes * Revert "Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it." This reverts commit 5ac92014da2682bdba62d7a2524b8d90e38f6b19. * Committing clang-format changes * Convert attribute 'get' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Update tracing macros * Convert attribute 'specific' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert dataset 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to attribute 'get' and 'specific' operation parameters. * Convert datatype 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to H5O_refresh_metadata arguments. * Reduce warnings * Reduce warnings * Track change to datatype 'get' callback * Fix bug with file pointer getting invalidated when object closed * Reformat source * Convert file and group VOL classes 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also small cleanup to the attribute get name operation. Also moved 'mount' and 'unmount' operations to be group specific operations, instead of file specific, to better align with their behavior (mounted files are on groups, so a group is what is operated on). * Remove remainder of merge conflict marking * Convert link VOL class 'create' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Remove some unused local variables * Convert link VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor 'get name by idx' routines to return actual length of name with a parameter instead of the return value, and move some callback context structs for the link interface from the private header file into the source code module, to reduce their visibility scope. * Update tracing macros * Convert link VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert object VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert object VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor H5G_loc_exists, et al, to return 'exists' flag in a parameter and errors with the function return value, instead of overloading both into the return value. And, corrected logic error in test/links.c around non-existant objects in a file. * Convert request VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert blob VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also removes the H5VL_BLOB_GETSIZE operation, as it's unused in the library and the blob ID size for a container is now returned with H5VL_FILE_GET_CONT_INFO. * Add 'const' to several parameters that are only queried. * Convert all VOL classes' 'optional' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Convert several 'get' routines to return the length of an array in a parameter instead of combining it into the return value. Move several routines to be in less public namespace. Correct direct_chunk test to verify that parameters aren't modified on error. * Switch get/specific/optional VOL callback argument structures to be 'async-friendly'. Also other minor cleanups and bug-fixes. * Add H5Pset_dataset_io_hyperslab_selection / H5S_PLIST feature, to allow skipping H5Dget_space + H5Sselect_hyperslab for async operation * Add dynamic optional operations for request objects * Update dynamic operation test for optional request operations * Update a comment for an operation argument * Run trace and format_source scripts * Committing clang-format changes * Committing clang-format changes 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> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Align with "parallel fence" changes (#479)Quincey Koziol2021-03-241-1/+0
| | | | | | | | | * Small code updates and simplifications * Committing clang-format changes * Fix 'make installcheck' for parallel builds Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-231-3/+3
| | | | | | | | | | | | | | | | * Fixed many -Wreserved-id-macro warnings by fixing header guard spelling Removed leading underscore(s) from header guard spelling. Used 2 regexes: ` _H5(.*)_H` ` __H5(.*)_H` Applied case-insensitively to only .h files. * Modified scripts that generate header files to not use underscore prefix Interestingly, there was already no leading underscore in the trailing comment at the end of the file * Fixed remaining -Wreserved-id-macro warning not caught by regex
* 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.
* Clang-format of source filesAllen Byrne2020-09-301-250/+248
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* Moves lock flag to H5F_shared_t and adds test.Dana Robinson2020-08-171-1/+1
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* Adds fix for H5Fstart_swmr_write lock issueDana Robinson2020-08-171-0/+1
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* Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01Quincey Koziol2020-08-071-0/+7
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| * Squash merge of file locking fixesDana Robinson2020-08-031-0/+7
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* | Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-1/+1
|/ | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Trim trailing whitespaceQuincey Koziol2020-04-201-13/+13
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-1/+0
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* Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILEJerome Soumagne2019-11-271-1/+0
| | | | Remove H5F__get_file_id() and use only private routine instead
* Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-0/+2
| | | | | | | | | | | location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
* Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.Quincey Koziol2019-10-081-0/+1
| | | | Remove "by address" location for VOL operations. (Switching to "by token")
* Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-081-3/+1
| | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
* Move ext_path field in H5F_t to H5F_shared_t.Vailin Choi2019-08-311-1/+2
| | | | Remove unused routine H5F_set_coll_md_read().
* Move coll_md_read and coll_md_write fields in H5F_t to H5F_shared_t.Vailin Choi2019-08-311-4/+6
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* Add a 'closing' flag on the shared file struct, and switch several of theQuincey Koziol2019-08-261-0/+1
| | | | "internal" data structures to use it.
* Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to matchQuincey Koziol2019-08-221-18/+18
| | | | naming convention for shared structs in rest of library data structures.
* Rest of changes for 'top' file pointer to 'shared' file pointer for H5F__accumQuincey Koziol2019-08-191-2/+2
| | | | routines.
* Partial H5F__accum_* routines.Quincey Koziol2019-08-191-3/+3
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* Fix H5F_get_file_id and H5F__get_file_id to take app_ref parameterJerome Soumagne2019-08-141-1/+1
| | | | Fix app_ref_count from being incremented when private routines are used
* Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-8/+8
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* Merge branch 'develop' of ↵Vailin Choi2019-06-261-0/+3
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~vchoi/my_third_fork into bugfix/new_shutdown_fsm
| * Fix for HDFFV-10808 H5Pset_file_space_strategy succeeds when using ↵Vailin Choi2019-06-241-0/+3
| | | | | | | | | | | | | | H5Pset_libver_bounds v18,v18. Fails file creation when non-default free-space info is set in fcpl and the library version high bound is less than v110 because free-space info message is introduced in library release v110.
* | Checkin for new shutting down free-space manager.Vailin Choi2019-06-201-8/+3
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* Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-181-32/+0
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| * Remove H5VL_FILE_CACHE_VOL_CONN from file specific callbacks, as it turns outQuincey Koziol2018-12-171-1/+0
| | | | | | | | | | | | not to be necessary. Also, correct _MSC_VER #ifdef
| * Moved the native VOL connector's optional enums to theDana Robinson2018-12-151-29/+0
| | | | | | | | | | public headers and renamed to include native/NATIVE in the name.
* | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-121-24/+55
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| * Revert some of the changes to support the original property list value ofQuincey Koziol2018-11-181-1/+0
| | | | | | | | metadata read attempts.
| * Add VOL connector info to the flie access property list returned fromQuincey Koziol2018-11-181-15/+7
| | | | | | | | H5Fget_access_plist(). Also, other misc. cleanups, etc.
| * Remove most debugging shims & scaffolding.Quincey Koziol2018-11-041-7/+9
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-041-1/+1
| |\ | | | | | | | | | stackable_vol
| | * Makes the installed header files the same between the autotoolsDana Robinson2018-10-271-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | and CMake. * CMake will no longer install private generated headers and tools library headers. * Several empty public header files (which represent internal packages) were removed. These were only installed by CMake. * Autotools installs will install H5FDwindows.h. Fixes HDFFV-10614.
| * | Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-6/+8
| |/ | | | | | | modified: test/dsets.c
| * Fixed a C++ style commenting issue and removed an unused fieldDana Robinson2018-10-121-1/+0
| | | | | | | | from H5F_trav_obj_ids_t.
| * VOL FEATUREDana Robinson2018-10-101-3/+33
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| * Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-8/+19
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| * Normalization with vol_integration (test code and H5Xtest.c)Dana Robinson2018-09-201-5/+5
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| * Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-09-181-6/+1
| | | | | | | | orginally intended to support the full SWMR feature.
* | Stash work on object header reduction code and tests.Jacob Smith2018-09-111-0/+1
|/ | | | CMake stuff is not verified.
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-1/+1
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Normalization with vol_integration branch.Dana Robinson2018-06-071-36/+26
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* Merge remote-tracking branch 'origin/develop' into merge_func_enter_volQuincey Koziol2018-04-011-0/+1
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* \ Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-13/+18
|\ \ | |/ | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
generated by cgit v0.12 at 2024-11-18 05:03:55 (GMT)