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* Misc clang production warning fixes (#1932)Dana Robinson2022-07-271-11/+14
| | | | | | | * Misc clang production warning fixes * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-17/+17
| | | | | * Update format source to clang 13 * More format changes
* Fix some const cast and stack/static object size warnings (#1700)jhendersonHDF2022-05-011-0/+9
| | | | | | | | | * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now
* Warnings fixes (#1680)jhendersonHDF2022-04-251-2/+2
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* Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-081-17/+17
| | | | | * Removes the STATIC flavor of FUNC_ENTER macros
* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-081-12/+12
| | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Combo set of async and other changes (#161)Quincey Koziol2021-06-021-32/+93
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* 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.
* Jan ws changes (#282)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 * Whitespace fixes except for H5Tprivate.h typo fix
* Fix problems with vlens and refs inside compound using H5VLget_file_type() ↵hdf5-1_13_0-rc5Neil Fortner2021-01-221-1/+12
| | | | | | | | | | | | (#274) * Fixed problems with vlens and refs inside compound using H5VLget_file_type() * Fix date in RELEASE.txt * Add assertions * Move some manipulation of H5VL_object_t struct fields into the H5VL package.
* Reformat source (#244)Quincey Koziol2021-01-071-4/+4
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* Avoid aligned access for references by decoding into temporary buffer and ↵Quincey Koziol2020-12-191-6/+11
| | | | then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* Replaces C std library calls with H5MM equivalentsDana Robinson2020-10-301-2/+2
| | | | Mostly H5MM_memcpy in newer VFDs
* Removes -Wimplicit-fallthrough=5 from the gcc warningsDana Robinson2020-10-221-0/+1
| | | | | | | | | | | | -Wimplicit-fallthrough=3 is added by -Wextra, which we already set. Bumping the warning level only changes how fall-through comments are parsed, with level 5 turning off fall-through comments entirely. This is unnecessary and results in having to do extra work to squash warnings when included external code uses fall-through. This change also adds /* FALLTHROUGH */ comments where H5_ATTR_FALLTHROUGH is used so compilers that don't use attributes but do respect fall-through comments don't raise spurious warnings.
* Clang-format of source filesAllen Byrne2020-09-301-302/+302
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-4/+4
| | | | | | 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.
* H5R: fix encoding of references that are part of compound typesJerome Soumagne2020-07-281-0/+31
| | | | Add corresponding test and some debug information
* H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-161-23/+40
| | | | Update trefer.c with vlen test case
* Replaced a few calls to HDmemcpy with H5MM_memcpy, which does overlapDana Robinson2020-05-151-2/+2
| | | | checking.
* merge and fixkmu2020-01-211-3/+3
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| * Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-3/+3
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* | merge and fix conflictkmu2020-01-191-3/+4
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| * H5R: set app ref when incrementing ref_count on location held by referenceJerome Soumagne2020-01-101-2/+3
| | | | | | | | (fix HDFFV-10992)
* | merge and fix conflictskmu2020-01-141-84/+185
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| * Cleanups from PR reviewsQuincey Koziol2019-12-201-77/+77
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| * Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-90/+191
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Added a new VOL sub-class called "introspect" where callbacks that report information about the connector or container can be placed. Added an 'opt_query' callback to this sub-class, for a connector to report back to the library whether a particular optional callback operation is supported. Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or the terminal connector, H5VL_GET_CONN_LVL_TERM). Moved the "post open" operation from a file 'specific' operation to a file 'optional' operation, now that it's possible to detect (with the 'opt_query' introspection callback) whether a VOL connector implements an optional operation, without just returning an error. Added new internal VOL helper routines: H5VL_object_is_native, to determine if an object is in (or is a) native file, and H5VL_file_is_same, to determine if two objects are in (or are) the same terminal VOL connector's container. (And moved the special handling for FILE_IS_EQUAL operation out of internal VOL callback routine into H5VL_file_is_same) Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better with other 'get' operations in API. Fixed several issues with pass-through connectors, which are now passing the 'make check-passthrough-vol' tests again. A bunch of warning and style cleanups as well.
* | fix unused related warningskmu2020-01-131-1/+7
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* Merge pull request #2063 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:vol_file_cmp ↵Neil Fortner2019-12-011-30/+71
|\ | | | | | | | | | | | | | | | | to develop * commit '40b2658b4b266b4dc65ec3db2897e0aaf54f8e42': Fix missing free in H5T__ref_mem_read() Fix bugs in H5VL file comparison code. Add short circuit success to H5VL_cmp_connector_cls(). Implement file comparison VOL callback. Other changes to allow references to work with non-native connectors. There is a bug somewhere.
| * Fix missing free in H5T__ref_mem_read()Neil Fortner2019-11-291-0/+2
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| * Fix bugs in H5VL file comparison code. Add short circuit success toNeil Fortner2019-11-281-6/+6
| | | | | | | | H5VL_cmp_connector_cls().
| * Implement file comparison VOL callback. Other changes to allowNeil Fortner2019-11-271-30/+69
| | | | | | | | | | references to work with non-native connectors. There is a bug somewhere.
* | Merge pull request #2059 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:topic_nullref to ↵Jerome Soumagne2019-11-281-12/+252
|\ \ | |/ |/| | | | | | | | | develop * commit '6b68cc352ffabb5fe997db1eb52216b3ee80e669': H5R: fix H5Tconv to check for null references
| * H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-11-261-12/+252
| | | | | | | | | | | | Valid for both deprecated and non-deprecated references Update test
* | Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILEJerome Soumagne2019-11-271-1/+1
|/ | | | Remove H5F__get_file_id() and use only private routine instead
* Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-87/+148
| | | | | | | | | | | 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.
* Merge pull request #2000 in HDFFV/hdf5 from ↵Jerome Soumagne2019-10-111-14/+21
|\ | | | | | | | | | | | | ~JSOUMAGNE/hdf5:fix_endian_develop to develop * commit '294e4faab724c26985867fe8ede684967da8a698': Fix encode and decode of tokens in H5VLnative
| * Fix encode and decode of tokens in H5VLnativeJerome Soumagne2019-10-111-14/+21
| | | | | | | | | | | | | | | | Fix encode and decode of deprecated object reference addresses Make H5Rdeprec.c use tokens instead of haddr_t Fix H5Oopen_by_addr() to serialize addr to token
* | Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-0/+761
Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
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