| Commit message (Collapse) | Author | Age | Files | Lines |
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* Also brings over the apostrophe fix
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Cherry pick of
ea7dfcd (Change Powershell to PowerShell in docs)
to
4497feb (Update H5Dget_space_status bug note to reference 1.14.0)
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* Merge doxygen plist tables changes from develop
* Doxy corrections
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b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)
70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320)
8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319)
784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321)
6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315)
10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html
0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303)
a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295)
502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293)
a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
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* 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.
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* Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean.
* format fixes
* fixed DOXYGEN_PREDEFINED
* Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args
* format fixes
* Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN
* reordered multidataset declarations
* alt. for H5Aclose_async and H5Acreate_async
* made doxgyen API into seperate blocks
* updated codespell
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fix bug with cross platform compatibility of references within vlens.
No testing yet.
* Merge from multi_rd_wd_coll_io to a more recent branch from develop.
Untested, probably does not work yet.
* Committing clang-format changes
* Committing clang-format changes
* Fix many bugs in multi dataset branch. Mostly works, some issues in
SWMR tests.
* Committing clang-format changes
* Disable test in swmr.c that was failing due to bug in HDF5 unrelated to
multi dataset.
* Committing clang-format changes
* Fixed fortran multi-dataset tests
* Fixed xlf errors
* Added benchmark code for multi-datasets
* loops over datasets
* added missing error arg.
* Added gnuplot formatting
* Jonathan Kim original MD benchmarking code
* updated MD benchmarking code
* code clean-up
* Only make files in feature test mode
* misc clean-up
* removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option
* Committing clang-format changes
* Change multi dataset API to use arrays of individual parameters instead
of the parameter struct.
* Committing clang-format changes
* Update to new multi dataset Fortran API and tests. (#1724)
* Update to new multi dataset Fortran API and tests.
* Sync Fortran with develop.
* skipping h5pget_mpio_actual_io_mode_f for now
* Fixed issue with dxpl_id, changed to variable size dim. (#1770)
* Remove "is_coll_broken" field from H5D_io_info_t struct
* Committing clang-format changes
* Minor cleanup in multi dataset code.
* Committing clang-format changes
* Clean up in multi dataset code.
* Committing clang-format changes
* Committing clang-format changes
* Fix speeling
* Fix bug in parallel compression. Switch base_maddr in io_info to be a
union.
* Committing clang-format changes
* Implement selection I/O support with multi dataset. Will be broken in
parallel until PR 1803 is merged to develop then the MDS branch.
* Committing clang-format changes
* Spelling
* Fix bug in multi dataset that could cause errors when only some of the
datasets in the multi dataset I/O used type conversion.
* Committing clang-format changes
* Integrate multi dataset APIs with VOL layer. Add async versions of
multi dataset APIs.
* Committing clang-format changes
* Spelling fixes
* Fix bug in non-parallel HDF5 compilation.
* Committing clang-format changes
* Fix potential memory/free list error. Minor performance fix. Other minor
changes.
* Committing clang-format changes
* Fix memory leak with memory dataspace for I/O.
* Committing clang-format changes
* Fix stack variables too large. Rename H5D_dset_info_t to
H5D_dset_io_info_t.
* Committing clang-format changes
* Remove mem_space_alloc field from H5D_dset_io_info_t. Each function is
now responsible for freeing any spaces it adds to dset_info.
* Committing clang-format changes
* fixed _multi Fortran declaration
* Refactor various things in (mostly) the serial I/O code path to make
things more maintainable.
* Committing clang-format changes
* updated to array based, doxygen, and examples
* Reinstate H5D_chunk_map_t, stored (via pointer) inside
H5D_dset_io_info_t.
* Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t.
Switch temporary dset_infos to be local stack variables.
* Committing clang-format changes
* format cleanup
* format cleanup
* added coll and ind
* Modify all parallel I/O paths to take dset_info instead of assuming
dset_info[0].
* Committing clang-format changes
* fixed output
* Rework parallel I/O code to work properly with multi dataset in more
cases. Fix bug in parallel compression.
* Committing clang-format changes
* Prevent H5D__multi_chunk_collective_io() from messing up collective opt
property for other datasets in I/O. Other minor cleanup. Add new test
case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now
due to failures apparently unrelated to multi dataset code.
* Fix spelling
* Committing clang-format changes
* Replace N log N algorithm for finding chunk in
H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of
io_info->sel_pieces in that function.
* Committing clang-format changes
* Replace sel_pieces skiplist in io_info with flat array of pointers, use
qsort in I/O routine only when necessary.
* Committing clang-format changes
* Add new test case to mdset.c
* Committing clang-format changes
* Fix spelling
* Very minor fix in H5VL__native_dataset_read()
* Fix bug that could affect filtered parallel multi-dataset I/O.
* Add RM entries for H5Dread_multi(), H5Dread_multi_async(),
H5Dwrite_multi(), and H5Dwrite_multi_async()
* Unskip test in swmr.c
* Committing clang-format changes
* Eliminate H5D__pre_read and H5D__pre_write
* Remove examples/ph5mdsettest.c. Will fix and re-add as a test.
* Enable hyperslab combinations in mdset test
* Committing clang-format changes
* Clarify H5Dread/write_multi documentation.
* Fix bugs in multi-dataset I/O. Expand serial multi dataset test.
Update macro in parallel multi dataset test.
* Committing clang-format changes
* Spelling
* Remove obsolete entry in bin/trace
* Rework type conversion buffer allocation. Only one buffer is shared
between datasets in mdset mode, and it is malloced instead of calloced.
* Committing clang-format changes
* Fix bug in error handling in H5D__read/write
* added multi-dataset fortran check with optional dataset creation id (#2150)
* removed dup. dll entry
* Address comments from code review.
* Remove spurious changes in H5Fmpi.c
* Fix issue with reading unallocated datasets in multi-dataset mode.
Address other comments from code review.
* Committing clang-format changes
* Delay chunk index lookup from io_init to mdio_init so it doesn't add
overhead to single dataset I/O.
* Committing clang-format changes
* Fix inappropriate use of piece_count
* updated copyright on new file, removed benchmark from testing dir.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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* H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419
* Update docs for H5Dchunk_iter, H5Dget_chunk_info*
Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following
* offset Logical position of the chunk’s first element in units of dataset elements
* filter_mask Bitmask indicating the filters used when the chunk was written
* size Chunk size in bytes, 0 if the chunk does not exist
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* Sketch of the H5S life cycle.
* Committing clang-format changes
* Fix H5S_UNLIMITED snafu.
* Updated RM template and RM page.
* Added H5S life cycle.
* Committing clang-format changes
* Added H5T life cycle.
* Committing clang-format changes
* Cleaner layout (?)
* Cleaned the H5F life cycle. Called out unfinished biz.
* Committing clang-format changes
* Remaining life cycle skeletons.
* Committing clang-format changes
* Committing clang-format changes
* Added H5Z life cycle.
* Committing clang-format changes
* Added H5G life cycle.
* Committing clang-format changes
* H5 and H5I life cycle updates.
* Committing clang-format changes
* Added H5PL life cycle.
* Committing clang-format changes
* Added H5L life cycle.
* Committing clang-format changes
* Fix for Chris' comment.
* Add a variable for Doxygen pre-processor definitions.
* Forgot to add the H5M API.
* Clarify the H5Z life cycle.
* Committing clang-format changes
* Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle.
* Committing clang-format changes
* Clarified introduction and fixed missing label declaration.
* Added H5O life cycle.
* Committing clang-format changes
* H5O cleanup, part 1.
* Committing clang-format changes
* Cleaned up some of the endless repetition in H5O.
* Committing clang-format changes
* Cookbook & RFC draft layouts.
* Updated manifest.
* Updated the manifest, the example paths, and sketched the 1st recipe.
* Committing clang-format changes
* Outlined two more recipes.
* Committing clang-format changes
* More recipes and RFCs.
* Committing clang-format changes
* Draft of templatized RFC references.
* Another batch of RFC changes.
* Another batch of RFCs.
* Fixed reference.
* RFCs in reverse chronological order.
* First cut of RFCs.
* Fixed reference.
* Updated recipes.
* Updated recipes.
* More RFCs.
* Updated D*PL comments.
* Added H5P descriptions.
* Committing clang-format changes
* H5R life-cycle snapshot.
* Committing clang-format changes
* H5R life-cycle. Added line numbers to life-cycle examples.
* Committing clang-format changes
* Fixed formatting for H5Dchunk_iter().
* Added comment on collective mode requirement w/ compression.
* Simplified API compat. macro dox.
* More API vers. updates.
* Hide the async macro entrails.
* Latest VFD SWMR RFC.
* Create a tag file for permalinks.
* Added TODOs for metadoc.
* Removed duplication.
* Revised RM landing page.
* Trimmed more duplication.
* Committing clang-format changes
* Revised H5D.
* Committing clang-format changes
* Updated survey link.
* Added Doxygen RM entry template link.
* Added the "Multi-Thread HDF5" RFC.
* Added DOXYGEN_TAG_FILE.
* Added selection I/O RFC.
* Added the VFD Sub-filing RFC.
* Updated meta-documentation and added two old presentations.
* Added a few more RFCs (4).
* Fixed MANIFEST.
* Updated meta-documentation.
* Added Filters technical note.
* Fixed MANIFEST.
* Restore the path stripper.
* Experimental full-text search via Google.
* Better full-text search integration.
* Whoops. Forgot this one.
* Oh boy.
* Make CMake happy.
* Added "Debugging HDF5 Applications" technical note.
* Another batch of RFCs.
* Fixes for #1221.
* Updated overview.
* Fixed image dependencies.
* CMake updates.
* Fixed SET.
* Better?
* Update doxygen/dox/Overview.dox
* Fixed documentation errors. Added missing version info.
* Callback documentation updates.
* Fixed indexing errors in the outline.
* Doxygen-ized the HDF5 glossary.
* Fix a few minor typos
.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* 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>
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* Fix various warnings and issues in doxygen doc generation
* Add new file to list
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* Create a tag file for permalinks.
* Added DOXYGEN_TAG_FILE.
* Added Doxygen life-cycle examples for different modules.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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>
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* Add H5Dchunk_iter method for iterating over chunks
This method iterates over all chunks in dataset, calling a user-supplied
callback with the chunk information and optional user supplied data.
The iterator is stopped when ITER_STOP is returned by the user-supplied
callback or the iterator is exhausted.
Existing methods to get chunk_info performs an iteration each time, so
to get many or all chunks causes SUM(i) for i = 0 -> N operations for N
chunks, as opposed to N operations when using this iterator for this use case.
* H5Dchunk_iter: test iterating all chunks, some chunks and failing iteration.
* H5D: move H5Dchunk_iter private methods to specific
* trace: add H5D_chunk_iter_op_t and trace H5D.c
* chunks-iter: document chunk_iter
* chunk-iter: chunk add FUNC_ENTER/FUNC_LEAVE macros
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Committing clang-format changes
* Fixes overly pedantic casting in public headers
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fixed warnings and started H5Epublic.h.
* Include H5FD* headers to correctly resolve references.
* Doxygen2 (#330)
* H5Eauto_is_v2.
* Added a few more calls.
* Added a few more H5E calls.
* First cut of H5E v2.
* Added the deprecated v1 calls.
* Updated spacing.
* Once more.
* Taking some inspiration from Eigen3.
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.
* doxygen work. fixs format by using clang-format.
* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.
* added documentation for H5P APIs (#350)
* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios
* format corrections
* fixed grammer
* fixed herr_t
* Better name.
* A fresh look.
* add doxygen to H5Ppublic.h
* use attention instead of warning
* Add doxygen comments in H5Ppublic.h (#375)
* Add doxygen comments in H5Ppublic.h
* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops
* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt
* Fix clang-format errors
* Fix filenames in doxygen/examples
* add doxygen to H5Ppublic.h (#378)
* add doxygen to H5Ppublic.h
* use attention instead of warning
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
* Revert "add doxygen to H5Ppublic.h (#378)"
This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2.
* Updated Doxygen variables.
* I forgot to copy two images.
* Enable desktop search by default.
* Add my assigned Doxygen documentation.
* Remove whitespace at EOL. Appease clang-format.
* Addressed Chris' comments.
* Added an alias for asynchronous functions.
* One space is enough for all of us.
* Slightly restructured RM page.
* address some issues
* reformatting
* Style external links.
* reformatting
* reformatting
* Added "Metadata Caching in HDF5" as a technical note example.
* Revise this soon!
* Added specification examples.
* Fixed references.
* Added H5AC cache image stuff and file format study.
* Added older FMT versions. Where did 1.0 go?
* Updated C/C++ note and replaced ambiguous labels.
* Reformat source with clang v10.0.1.
* Added the VFL technical note.
* Added what I believe might be called version 1.0 of the format.
* Added the remaining specs.
* Added H5Z callback documentation and fixed a few mistakes.
* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.
* clang-format happy?
* Ok?
* Bonus track: Deprecated H5D functions.
* Carry over the more detailed group description.
* Added documentation for the missing and deprecated H5R calls.
* Life is easier and less repetitive w/ snippets. Use them!
* Eliminate the snippet block ID artifacts in the HTML rendering.
* Fixed snippet HTML artifacts and added a few missing calls.
* Under 20 H5Ps to go!
* Almost complete!
* "This is a form of pedantry up with which I will not put." (Churchill)
* Let's not waste as much space on bulleted lists!
* First complete (?) draft of the Doxygen-based RM.
* Completeness check and minor fixes along the way.
* Pedantry.
* Adding missing H5FD calls checkpoint.
* Pedantry.
* More pedantry.
* Added H5Pset_fapl_log.
* First draft of H5ES.
* Fixed warnings.
* Prep. for map module.
* First cut of the map module.
* Pedantry.
* Possible H5F introduction.
* Fix the indentation.
* Pedantry.
* Ditto.
* Thanks to the reviewers for their comments.
* Added missing images.
* Line numbers are a distraction here.
* More examples, references, and clean-up. Don't repeat yourself!
* Clang pedantry.
* Ditto.
* More reviewer comments...
* Templatized references and cleaned up \todos.
* Committing clang-format changes
* Fixed MANIFEST.
* Addressed Quincey's comments. (OCPLs)
* Fixed a few more \todo items.
* Fixed more \todo items.
* Added attribute life cycle.
* Forgot the examples file.
* Committing clang-format changes
* Pedantry.
* Live and learn!
* Added a sample H5D life cycle.
* Committing clang-format changes
* Pedantry.
Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* 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
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* 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.
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* Transferred RM blocks in H5D and H5G to develop
* Added RM blocks to H5R and added new aliases.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* 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>
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* 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
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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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Description:
- Added functions to query chunk information:
H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
Gets the number of written chunks that intersect with the given
dataspace. However, in this version, the intersection is not
yet completed. Thus, the number of all written chunks will be
returned.
H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size)
Given a chunk's logical coordinates, returns the chunk's filter,
address, and size.
H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size)
Given a chunk's index, returns the chunk's logical coordinates, filter,
address, and size. The chunk belongs to a set of chunks that have
nonempty intersection with the specified dataspace. However, in
this version, the intersection is not yet completed, and the index
is of all the written chunks.
These functions comply with VOL.
- Fixed some oversights found in the library for the tests in chunk_info.c
to work correctly. The returned value from a callback function was not
checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate().
This oversight caused a callback function to continue iterating even though
it's supposed to stop.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
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typedef and a set of #defines.
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public headers and renamed to include native/NATIVE in the
name.
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* Changed the offset copy to use an array on the stack.
* Yanked some unused #defines.
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them H5D calls.
* Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*.
* Moved the hl/test/test_dset_opt test to test/ and renamed to
direct_chunk.
* Moved the hl/test/dectris_hl_perf test to tools/test/perform
and renamed to direct_write_perf.
* Updated autotools and CMake files.
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This is the same patch that had already been integrated to 1.8 branch (pull request #387).
Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
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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.
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Bring object/dataset/group/named datatype features from revise_chunks
branch to trunk. Also CMake support for h5format_convert and a bunch of
misc. cleanups.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Bring h5format_convert tool from revise_chunks branch to trunk.
Tested on:
MacoSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Bring H5DOappend(), H5P[s|g]et_object_flush_cb, and H5P[s|g]et_append_flush
from revise_chunks branch to trunk. Brings along updated metadata cache
entry tagging, and the internal object flush routine.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Bring 'none' chunk index from revise_chunks branch to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd)
(h5committest forthcoming)
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Bring "single" chunk index from revise_chunks branch to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd)
(h5committest forthcoming)
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Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
Autotools serial w/ Java, Fortran, & C++
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Tested on: 64-bit Ubuntu 15.10 (build only, not used in existing code)
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Bring support for earray and v2 B-trees from revise_chunks branch to
trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Bring "don't filter partial edge chunks" capability from revise_chunks
to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/debug, production & parallel
(h5committest forthcoming)
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