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* [1.12 Merge] Fix serial to parallel chunked dataset file space allocation ↵jhendersonHDF2023-09-011-10/+24
| | | | bug (#3394) (#3476)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-151-0/+27
| | | | (#2726)
* Update Copyright headers. (#2534)Larry Knox2023-03-131-1/+0
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* Persist dataset access properties when using H5Fstart_swmr_write - merge to ↵Neil Fortner2022-08-221-15/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1.12 branch (#2031) * Merge GitHub #1862 (HDFFV-11308) to 1.12 branch Persist dataset access properties when using H5Fstart_swmr_write (#1862) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix bug in swmr.c introduced with recent merge (double_t) (#1913) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes * Replace accidental use of double_t in swmr.c with double. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for HDFFV-11308 (#2029) * Add note to RELEASE.txt for HDFFV-11308 * Fix formatting error in RELEASE.txt * Committing clang-format changes * Fix inappropriate use of HGOTO_ERROR (#2055) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Spelling fixes for codespell (#2038)Dana Robinson2022-08-181-1/+1
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* clang 13 format #1933 (#1939)Allen Byrne2022-07-271-49/+49
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* [1.12 Merge]Hdf5 1 12 warnings fixes (#1715)jhendersonHDF2022-05-031-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in ntypes (#1695) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * 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 * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.12 Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12: Last round of normalizations for 1.12.2 (#1621)Dana Robinson2022-04-081-3/+3
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* Commit codespell spelling corrections.Larry Knox2022-04-071-4/+4
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* Hdf5 1 12 parallel compression merge (#1529)jhendersonHDF2022-03-281-34/+21
| | | | | | | | | | | | | | | | * Fix the function cast error in H5Dchunk.c and activate (#1170) `-Werror=cast-function-type`. Again. * Parallel Compression improvements (#1302) * Fix for parallel compression examples on Windows (#1459) * Parallel compression adjustments for HDF5 1.12 * Committing clang-format changes Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - src and test directories.
* 1 12 Whitespace changes after clang-format run (#288)Allen Byrne2021-01-291-4/+4
| | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version
* Basic alignment with async branch (#115) (#137)Quincey Koziol2020-11-301-9/+4
| | | | | | | * 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
* Manual sync with develop (#95)Dana Robinson2020-11-171-13/+21
| | | | Brings all features from develop. Note that RELEASE.txt has not been updated (will be done in a future PR).
* Source formattedAllen Byrne2020-10-011-941/+939
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* Src file format preventive updatesAllen Byrne2020-09-281-51/+51
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* Switch H5VM inline routines back to single underscope and put a comment in ↵Quincey Koziol2020-08-221-3/+3
| | | | their header about this naming
* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-8/+10
| | | | | | 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.
* Sync with developDana Robinson2020-08-011-14/+20
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* Whitespace cleanupAllen Byrne2020-05-131-0/+2
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* Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-041-1/+1
| | | | the dataset is extended.
* Fix according to PR feedback.vchoi2020-04-071-1/+1
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* Fix error in previous merge: should use NULL instead of FAIL.vchoi2020-04-071-4/+2
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* Merge pull request #2461 in HDFFV/hdf5 from ↵Vailin Choi2020-04-021-2/+12
| | | | | | | ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop * commit 'afdcac28b85d690eebc80ab568fa5266081baaaa': A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
* Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to developDavid Young2020-02-251-2/+2
| | | | | | | | | | | Merged per discussion with Elena. * commit '3f903a441ad84001ea66589728bd8b036b6fdfca': Take out the temporary performance tests. Make calls through a function pointer. Use the same number of arguments, always. Increase iterations, provide a baseline for no-op, simplify the overhead case a bit. Temporarily add some code that measures the time to run the simplest possible H5T__copy_all()-like routine 10 million times and then measures the version with FUNC_ENTER_STATIC/_LEAVE_NOAPI and a HGOTO_ERROR() statement. H5T_copy() constification plus Quincey's contributions.
* Squashed commit of the following:David Young2020-01-311-3/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit ff7a9a34de2fcd78f5d32a1532f3d0e224b20d94 Author: Kimmy Mu <kmu@hdfgroup.org> Date: Wed Jan 29 14:12:18 2020 -0600 Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12 * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop commit 9f3d808c05d2a3b308f32c958c6671fcac0a432c Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 11:43:55 2020 -0600 testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings. commit 43a4b80b21c0329fbc1f9a0e2854795189f0bb50 Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 10:47:30 2020 -0600 Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required. Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c. commit 035bfa0769a4012881fc659b673bacf44d146537 Author: David Young <dyoung@hdfgroup.org> Date: Tue Jan 28 20:35:28 2020 -0600 Reduce differences between my -Werror branch and `develop`: Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-281-4/+3
| | | | | | | | | | | * commit '145ef3ceee20c28a443bd11507c58858bea3f889': more cleanup change it back pick up missing piece fix unused related warnings removed unused parameter more fix and address comments remove unsed var,function,macro, etc
* Remove unnecessary H5CX callQuincey Koziol2020-01-041-4/+0
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* Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-01-041-26/+219
| | | | generic fallback for VOL connectors that don't implement operation
* Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-01-041-40/+142
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* Implement support for using H5Dvlen_get_buf_size withNeil Fortner2019-12-061-1/+1
| | | | non-native VOL connectors.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-061-2/+2
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* Add changes from PR 2049 to hdf5_1_12 branchChris Hogan2019-12-031-15/+62
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-45/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Progress toward moving the dataset routines to using the 'shared' file pointerQuincey Koziol2019-08-211-1/+1
| | | | instead of the 'top' file pointer.
* Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-2/+3
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-21/+21
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Updated H5Tcopy() to get the dataset's datatype through the VOL whenDana Robinson2019-06-241-24/+0
| | | | that is passed in as the object ID.
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-1/+0
| | | | clean up warnings.
* Merge pull request #1600 in HDFFV/hdf5 from ↵Ray Lu2019-04-181-28/+38
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:HDFFV-10658-performance-drop-from-1-8 to develop * commit 'b5ef82a1786605ae86502bc82086047720b7d4ca': (21 commits) Moving the handling of null prefix into H5_combine_path. Changing the prefix of external file and VDS from empty string to null for performance improvement. Improving the condition checking of empty string. Replacing string operation strdup with assignment for empty string. Adding back links_env.out which I accidentally removed in my previous commit. Taking out two unnecessary diff output files. Taking out unnecessary diff files for output. Adding some comments. Some coding style changes. Adding the standard output files for the external_env.c and vds_env.c tests. Small correction for my previous commit. Forgot to add external_common.c and external_common.h. Updated CMake for the splitting of external.c and vds.c. Minor fix: removal of unnecessary enum values. Minor fixes: updating the test vds_env.c according to the set up of vds.c. Left out this file in previous commit. HDFFV-10658 - setting and getting properties in API context: 1. switched to use the existing H5F_prefix_open_t for enum type; 2. put the common private function used by external.c and external_env.c into external_common.c This commit basically has the following changes: 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get. HDFFV-10658: I left out this file in my previous commit. HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work. ...
| * Changing the prefix of external file and VDS from empty string to null for ↵Songyu Lu2019-04-171-19/+16
| | | | | | | | performance improvement.
| * Improving the condition checking of empty string.Songyu Lu2019-04-171-8/+8
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| * Replacing string operation strdup with assignment for empty string.Songyu Lu2019-04-171-11/+18
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| * HDFFV-10658 - setting and getting properties in API context:Songyu Lu2019-04-091-14/+8
| | | | | | | | | | 1. switched to use the existing H5F_prefix_open_t for enum type; 2. put the common private function used by external.c and external_env.c into external_common.c
| * Merge branch 'develop' of ↵Songyu Lu2019-04-041-8/+9
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * | This commit basically has the following changes:Songyu Lu2019-04-041-4/+4
| | | | | | | | | | | | | | | | | | 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get.
| * | HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce ↵Songyu Lu2019-03-221-14/+26
| | | | | | | | | | | | the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work.
| * | HDFFV-10658: setting and getting properties in API context:Songyu Lu2019-03-131-18/+18
| | | | | | | | | | | | | | | 1. external file prefix and VDS prefix. 2. the datatype, dataspace, and LCPL of the dataset for VOL connector.
* | | Correct set extent operation on VDS to iterate over # of used sub-datasetsQuincey Koziol2019-04-161-1/+1
| |/ |/| | | | | instead of # of allocated sub-datasets.
* | Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-7/+7
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