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* Comment cleanup (#2689)Quincey Koziol2023-04-1155-910/+3
| | | * Clean up content and redundant logging in comments.
* Remove dead code hidden behind #ifdef LATER (#2686)Dana Robinson2023-04-102-38/+4
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* Synchronize HDF5 tests with VOL tests (#2628)jhendersonHDF2023-04-0315-226/+779
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* chore: make comment consistent (#2654)H. Joe Lee2023-04-011-1/+1
| | | Use a 3rd person verb to match "Does not" in the next sentence.
* Fix test script names in cleanup code (#2590)Dana Robinson2023-03-201-6/+9
| | | | When the test scripts were renamed, DISTCLEANFILES in Makefile.am was not updated.
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2544)Allen Byrne2023-03-132-3/+3
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* HDFFV-10368 (OESS-319): Making two useful macros (H5L_EXT_FLAGS_ALL and ↵raylu-hdf2023-02-212-2/+109
| | | | | | | | | | | | | | | | | | | | | H5L_EXT_VERSION) public (#2386) * HDFFV-10368 (OESS-319): Move two useful macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from H5Lpkg.h to H5Lpublic.h for public usage. The test in vol.c only envokes H5Lcreate_external using the passthru VOL. To test if the macros are public, one can use them in the link creation of the passthru VOL, such as printing out their values. * Committing clang-format changes * Moved the test for the external link public macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from vol.c to links.c. * Committing clang-format changes * Minor change: changed a pointer variable to an integer. * Committing clang-format changes * Moved two macros (H5L_EXT_VERSION and H5L_EXT_FLAGS_ALL) to H5Ldevelop.h for only developers to use. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove duplicated "help@hdfgroup.org" lines in file headers. (#2441)Larry Knox2023-02-113-3/+0
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* Add szip/libaec to GitHub CI and fix warnings (#2438)Dana Robinson2023-02-092-8/+4
| | | | | | | | szip (or libaec) is currently not tested in CI. This adds szip to the the Autotools GitHub CI actions on Linux when building with the Autotools. This PR also cleans up a few warnings that remained in the szip- related code so the -Werror check will pass.
* HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a ↵raylu-hdf2023-01-101-0/+80
| | | | | | | | | | | | | | | committed datatype (#2398) * HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a committed datatype. Added a test case for the fix that Quincey checked in. * Committing clang-format changes * Fixed a typo in a comment. * Fixed a typo in a comment. * Minor change: changed H5Tcommit to H5Tcommit2. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Pass-through connector testing flexibility (#2399)Quincey Koziol2023-01-091-7/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths * Use API routine to determine if native connector is terminal. * Committing clang-format changes * Make string size larger, to allow for connectors with longer names. * Be more flexible about testing external pass through connectors, especially if they have registered new optional operations. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Play nice with existing plugin paths (#2394)Quincey Koziol2023-01-061-1/+1
| | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-214-6/+13
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
* Fix up the H5Pencode2 test for virtual layout. (#2325)vchoi-hdfgroup2022-12-211-91/+87
| | | | | | | | | | * Fix up the H5Pencode2 test for virtual layout. * Committing clang-format changes * Remove VERIFY and use TEST_ERROR. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)Mark Kittisopikul2022-12-191-9/+9
| | | | | | | * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info * Modify chunk_info test to for unsigned / hsize_t types * Fix types in test
* Hdffv 11052 (#2315)vchoi-hdfgroup2022-12-161-3/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes * Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291. * Committing clang-format changes * Add the test file to Cmake. * Skip test_misc37() for drivers that is not default compatible as it is using a pre-generated file. * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdffv 11052 (#2303)vchoi-hdfgroup2022-12-153-0/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes * Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291. * Committing clang-format changes * Add the test file to Cmake. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Bug Fix: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called ↵raylu-hdf2022-11-171-0/+76
| | | | | | | | | | | | | | | | from an application (#2248) * Jira HDFFV-10881: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application. A quick and simple fix to make it fail with a relevant error message. * Format changes. * Committing clang-format changes * Minor change: split one condition check into two for clarity. * Adding doxygen comment for H5VLwrap_register. * Minor change: adding a little more detail to the Doxygen comment for H5VLwrap_register.
* Bug fix: the previous checkin only supported the native connector (#2211)raylu-hdf2022-11-051-5/+21
| | | | | | | * Bug fix: make sure the test case supports the pass_through connector. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the memory allocation sanity checks feature (#2218)Dana Robinson2022-11-031-46/+11
| | | | | | | | | | | | | | | * Removes the memory allocation sanity checks feature * Committing clang-format changes * Removes zero size checks for H5MM_(c|m)alloc() * Explicitly return NULL when size == 0 in H5allocate_memory() * Committing clang-format changes * Format fix Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update copyright headers (#2184)Larry Knox2022-11-01171-183/+22
| | | | | * 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.
* Added a test case for H5VLget_connector_name (#2195)raylu-hdf2022-10-281-0/+58
| | | | | | | * Added a test case for H5VLget_connector_name. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added a test case to verify the VOL capacity flags work correctly. (#2178)raylu-hdf2022-10-251-10/+112
| | | | | | | * Added a test case to verify the VOL capacity flags work correctly. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-10-251-1/+78
| | | | | | | | | | | file handles (#2181) * Fix bug with variable length attributes being accessed through multiple file handles. * Committing clang-format changes Co-authored-by: Neil Fortner <nfortne2@localhost.localdomain> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Multi Dataset (#2120)Neil Fortner2022-10-194-3/+718
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Fix mostly java warnings, and cpp cast (#2134)Allen Byrne2022-10-031-1/+1
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* Fixed an issue that could occur when combining hyperslab selections (#2122)Neil Fortner2022-09-271-0/+52
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* Use case-insensitive comparison for headers fix #2100 (#2101)Frank Berghaus2022-09-211-0/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use case-inseneitive comparison for headers HTTP headers should be case-insensitive. Use case-insensitive string comparisons when working with HTTP header responses to ensure compatibility. * Revert "Use case-inseneitive comparison for headers" This reverts commit a02f591723506b62b7208449be6eef7122120398 * Ignore case when searching HTTP header responses Looking up the Content-Length in the header returned by S3 storage endpoints should ignore case. To guarantee portability implement a function for case-insensitive string search, because it is non-standard. * Add an _ after H5 for the strcasestr implementation It is a private function and should sport that underscore. * Remove author comment from the doc comment * Use search function defined by system if available Check whether the system provides a function implementing case insensitive string searches. Only use the custom implementation if the system does not provide the functionality. * Add tests for case-insensitive search Basic tests: - Search for empty string - Search with exact match - Search with case-insensitive match - search with no match * Enforce clang-format style Some variable definitions in the th5_system tests did not conform to clang-format's expectations. Updated the offending lines. * Correct comment describing test case * Added some spaces to please clang-format * Ignore discarding const Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
* Updates VOL capabilities flags (#2105)Dana Robinson2022-09-172-23/+23
| | | | | | | | | | | | | | | * Added feature/vol_cap_flags branch to GitHub actions * Convert unsigned cap flag field to uint64_t and add flags * Committing clang-format changes * Convert unsigned cap flag field to uint64_t and add flags * Committing clang-format changes * Updates the VOL struct version number Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-031-1/+1
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Address review comments from downstream merge of #2016 (#2073)Neil Fortner2022-08-311-1/+1
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* GitHub workflow cleanup (#2047)Dana Robinson2022-08-221-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up main GitHub workflow(s) * Combines main.yml and pr-check.yml, which differed trivially * Reduces config redundancy via proper use of the matrix scheme * Adds build-only configs for: - Version 1.6 default API - No deprecated symbols - Parallel HDF5 * The -Werror config was converted to build-only * Makes the naming scheme more uniform * Spaces out the code and adds comments * Typo fix * Fix mirror VFD CMake configure typo * Debugging hack * Undo debug hack and fix CMake build mode * Set CC=mpicc for parallel builds * Another attempt to fix parallel builds * Updates comments in main.yml * Fixes a v16 API bug in the mirror VFD test code * Committing clang-format changes * Added checks for v1.8 - 1.12 APIs * Manually specify Windows configs Java debug builds time out when running tests on Windows. We'll disable them in debub mode while we investigate. * Revert "Manually specify Windows configs" This reverts commit d710d8d21990a57084841e82bd9f7e7d9f53a244. * Skip Debug Windows configs while we investigate Java H5L timeouts Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* [WIP] Add Developer build mode to CMake (#1659)jhendersonHDF2022-08-203-7/+64
| | | | | | | | | | | | | | | | * Add Developer build mode to CMake * Set a few CMake variables for Developer build modes * Refactor enabling of debug and developer-level compile definitions * Convert cache debugging macros to normal ifdef style Normal ifdef-style instead of if-style allows build system to define macros without warning about redefining macros with different values (0 vs. 1) * Add HDF5 Developer compile definitions to testing files * Temporarily disable -fanalyzer flag for GCC 12+ Developer builds
* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-191-11/+11
| | | | At one time this content was a git submodule shared between several projects but that time has long passed.
* Fixes codespell issues (#2032)Dana Robinson2022-08-173-7/+7
| | | | | * Fixes codespell issues * Fixed another typo
* Fix bug in attribute type conversion wiith compound types (#2016)Neil Fortner2022-08-161-0/+131
| | | | | | | | | | | | | * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix typos found in the rest of the hdf5 code-base (#1985)luzpaz2022-08-1018-36/+35
| | | | | | | | | | | * Fix typos found in the rest of the hdf5 code-base * Typo in tool.cmake * Revert "Typo in tool.cmake" This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b. * Fix clang-format styling
* Remove stray files, incorrect vds and mpi clean files (#1979)Allen Byrne2022-08-091-13/+0
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* Revert for older cmake versions (#1974)Allen Byrne2022-08-081-2/+2
| | | | | * Revert for older cmake versions * Remove unneeded clear/clean tests because of changes to test macro
* Develop cmake clean (#1971)Allen Byrne2022-08-071-207/+202
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* H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969)Mark Kittisopikul2022-08-071-2/+2
| | | | | | | | | | | * 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
* Adds platform-independent basename and dirname (#1951)Dana Robinson2022-08-055-1/+510
| | | | | | | | | | | | | | | | | | | | * Adds platform-independent basename and dirname * Tidy up H5_dirname and H5_basename implementations and add tests * Committing clang-format changes * Fix misspelling * Several fixes for H5_dirname/H5_basename from review * Committing clang-format changes * Add reason to VERIFY_STR macros in th5_system.c * Use H5MM_free instead of HDfree in H5_dirname/H5_basename tests Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD (#1953)Dana Robinson2022-08-023-1/+4969
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Onion VFD feature * Fixes onion VFD errors with non-sec2 backing store VFDs * Disables the onion VFD tests w/ ph5diff * Disables non-sec2 VFDs as onion VFD backing stores * Committing clang-format changes * Formatted source * Typo * Adds onion VFD tools tests to CMake * Fixes for v16 API compatibility * Memset structs to avoid bad frees on errors * H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE * Properly decodes checksums on BE machines * Be more careful about uint64_t to haddr_t/hsize_t conversions * Another fix for BE data comparison * Removed double underscores from onion constants * Replace hard-coded onion header string w/ constant * Fixes cleanup paths in H5FD__onion_ingest_history() * Fixed use of size_t revision numbers * Fix h5dump revision count format string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes format string warnings in tselect w/ clang 14 (#1955)Dana Robinson2022-07-311-11/+11
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* Cleanup of mirror VFD test code (#1949)Dana Robinson2022-07-302-1545/+1269
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* Misc clang production warning fixes (#1932)Dana Robinson2022-07-272-0/+12
| | | | | | | * 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 Byrne2022-07-26107-1317/+1319
| | | | | * Update format source to clang 13 * More format changes
* Subfiling VFD (#1883)jhendersonHDF2022-07-2229-289/+544
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added support for vector I/O calls to the VFD layer, and associated test code. Note that this includes the optimization to allow shortened sizes and types arrays to allow more space efficient representations of vectors in which all entries are of the same size and/or type. See the Selection I/o RFC for further details. Tested serial and parallel, debug and production on Charis. serial and parallel debug only on Jelly. * ran code formatter quick serial build and test on jelly * Add H5FD_read_selection() and H5FD_write_selection(). Currently only translate to scalar calls. Fix const buf in H5FD_write_vector(). * Format source * Fix comments * Add selection I/O to chunk code, used when: not using chunk cache, no datatype conversion, no I/O filters, no page buffer, not using collective I/O. Requires global variable H5_use_selection_io_g be set to TRUE. Implemented selection to vector I/O transaltion at the file driver layer. * Fix formatting unrelated to previous change to stop github from complaining. * Add full API support for selection I/O. Add tests for this. * Implement selection I/O for contiguous datasets. Fix bug in selection I/O translation. Add const qualifiers to some internal selection I/O routines to maintain const-correctness while avoiding memcpys. * Added vector read / write support to the MPIO VFD, with associated test code (see testpar/t_vfd.c). Note that this implementation does NOT support vector entries of size greater than 2 GB. This must be repaired before release, but it should be good enough for correctness testing. As MPIO requires vector I/O requests to be sorted in increasing address order, also added a vector sort utility in H5FDint.c This function is tested in passing by the MPIO vector I/O extension. In passing, repaired a bug in size / type vector extension management in H5FD_read/write_vector() Tested parallel debug and production on charis and Jelly. * Ran source code formatter * Add support for independent parallel I/O with selection I/O. Add HDF5_USE_SELECTION_IO env var to control selection I/O (default off). * Implement parallel collective support for selection I/O. * Fix comments and run formatter. * Update selection IO branch with develop (#1215) Merged branch 'develop' into selection_io * Sync with develop (#1262) Updated the branch with develop changes. * Implement big I/O support for vector I/O requests in the MPIO file driver. * Free arrays in H5FD__mpio_read/write_vector() as soon as they're not needed, to cut down on memory usage during I/O. * Address comments from code review. Fix const warnings with H5S_SEL_ITER_INIT(). * Committing clang-format changes * Feature/subfiling (#1464) * Initial checkin of merged sub-filing VFD. Passes regression tests (debug/shared/paralle) on Jelly. However, bugs and many compiler warnings remain -- not suitable for merge to develop. * Minor mods to src/H5FDsubfile_mpi.c to address errors reported by autogen.sh * Code formatting run -- no test * Merged my subfiling code fixes into the new selection_io_branch * Forgot to add the FindMERCURY.cmake file. This will probably disappear soon * attempting to make a more reliable subfile file open which doesn't return errors. For some unknown reason, the regular posix open will occasionally fail to create a subfile. Some better error handling for file close has been added. * added NULL option for H5FD_subfiling_config_t in H5Pset_fapl_subfiling (#1034) * NULL option automatically stacks IOC VFD for subfiling and returns a valid fapl. * added doxygen subfiling APIs * Various fixes which allow the IOR benchmark to run correctly * Lots of updates including the packaging up of the mercury_util source files to enable easier builds for our Benchmarking * Interim checkin of selection_io_with_subfiling_vfd branch Moddified testpar/t_vfd.c to test the subfiling vfd with default configuration. Must update this code to run with a variety of configurations -- most particularly multiple IO concentrators, and stripe depth small enough to test the other IO concentrators. testpar/t_vfd.c exposed a large number of race condidtions -- symtoms included: 1) Crashes (usually seg faults) 2) Heap corruption 3) Stack corruption 4) Double frees of heap space 5) Hangs 6) Out of order execution of I/O requests / violations of POSIX semantics 7) Swapped write requests Items 1 - 4 turned out to be primarily caused by file close issues -- specifically, the main I/O concentrator thread and its pool of worker threads were not being shut down properly on file close. Addressing this issue in combination with some other minor fixes seems to have addressed these issues. Items 5 & 6 appear to have been caused by issue of I/O requests to the thread pool in an order that did not maintain POSIX semantics. A rewrite of the I/O request dispatch code appears to have solved these issues. Item 7 seems to have been caused by multiple write requests from a given rank being read by the wrong worker thread. Code to issue "unique" tags for each write request via the ACK message appears to have cleaned this up. Note that the code is still in poor condtition. A partial list of known defects includes: a) Race condiditon on file close that allows superblock writes to arrive at the I/O concentrator after it has been shutdown. This defect is most evident when testpar/t_subfiling_vfd is run with 8 ranks. b) No error reporting from I/O concentrators -- must design and implement this. For now, mostly just asserts, which suggests that it should be run in debug mode. c) Much commented out and/or un-used code. d) Code orgnaization e) Build system with bits of Mercury is awkward -- think of shifting to pthreads with our own thread pool code. f) Need to add native support for vector and selection I/O to the subfiling VFD. g) Need to review, and posibly rework configuration code. h) Need to store subfile configuration data in a superblock extension message, and add code to use this data on file open. i) Test code is inadequate -- expect more issues as it is extended. In particular, there is no unit test code for the I/O request dispatch code. While I think it is correct at present, we need test code to verify this. Similarly, we need to test with multiple I/O concentrators and much smaller stripe depth. My actual code changes were limited to: src/H5FDioc.c src/H5FDioc_threads.c src/H5FDsubfile_int.c src/H5FDsubfile_mpi.c src/H5FDsubfiling.c src/H5FDsubfiling.h src/H5FDsubfiling_priv.h testpar/t_subfiling_vfd.c testpar/t_vfd.c I'm not sure what is going on with the deletions in src/mercury/src/util. Tested parallel/debug on Charis and Jelly * subfiling with selection IO (#1219) Merged branch 'selection_io' into subfiling branch. * Subfile name fixes (#1250) * fixed subfiling naming convention, and added leading zero to rank names. * Merge branch 'selection_io' into selection_io_with_subfiling_vfd (#1265) * Added script to join subfiles into a single HDF5 file (#1350) * Modified H5FD__subfiling_query() to report that the sub-filing VFD supports MPI This exposed issues with truncate and get EOF in the sub-filing VFD. I believe I have addressed these issues (get EOF not as fully tested as it should be), howeer, it exposed race conditions resulting in hangs. As of this writing, I have not been able to chase these down. Note that the tests that expose these race conditions are in testpar/t_subfiling_vfd.c, and are currently skipped. Unskip these tests to reproduce the race conditions. tested (to the extent possible) debug/parallel on charis and jelly. * Committing clang-format changes * fixed H5MM_free Co-authored-by: mainzer <mainzer#hdfgroup.org> Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com> Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Move Subfiling VFD components into H5FDsubfiling source directory * Update Autotools build and add H5_HAVE_SUBFILING_VFD macro to H5pubconf.h * Tidy up CMake build of subfiling sources * Merge branch 'develop' into feature/subfiling (#1539) Merge branch 'develop' into feature/subfiling * Add VFD interface version field to Subfiling and IOC VFDs * Merge branch 'develop' into feature/subfiling (#1557) Merge branch 'develop' into feature/subfiling * Merge branch 'develop' into feature/subfiling (#1563) Merge branch 'develop' into feature/subfiling * Tidy up merge artifacts after rebase on develop * Fix incorrect variable in mirror VFD utils CMake * Ensure VFD values are always defined * Add subfiling to CMake VFD_LIST if built * Mark MPI I/O driver self-initialization global as static * Add Subfiling VFD to predefined VFDs for HDF5_DRIVER env. variable * Initial progress towards separating private vs. public subfiling code * include libgen.h in t_vfd tests for correct dirname/basename * Committing clang-format changes * removed mercury option, included subfiling header path (#1577) Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests. * added check for stdatomic.h (#1578) * added check for stdatomic.h with subfiling * added H5_HAVE_SUBFILING_VFD for cmake * fix old-style-definition warning (#1582) * fix old-style-definition warning * added test for enable parallel with subfiling VFD (#1586) Fails if subfiling VFD is not used with parallel support. * Subfiling/IOC VFD fixes and tidying (#1619) * Rename CMake option for Subfiling VFD to be consistent with other VFDs * Miscellaneous Subfiling fixes Add error message for unset MPI communicator Support dynamic loading of subfiling VFD with default configuration * Temporary fix for subfile name issue * Added subfile checks (#1634) * added subfile checks * Feature/subfiling (#1655) * Subfiling/IOC VFD cleanup Fix misuse of MPI_COMM_WORLD in IOC VFD Propagate Subfiling FAPL MPI settings down to IOC FAPL in default configuration case Cleanup IOC VFD debugging code Change sprintf to snprintf in a few places * Major work on separating Subfiling and IOC VFDs from each other * Re-write async_completion func to not overuse stack * Replace usage of MPI_COMM_WORLD with file's actual MPI communicator * Refactor H5FDsubfile_mpi.c * Remove empty file H5FDsubfile_mpi.c * Separate IOC VFD errors to its own error stack * Committing clang-format changes * Remove H5TRACE macros from H5FDioc.c * Integrate H5FDioc_threads.c with IOC error stack * Fix for subfile name generation Use number of I/O concentrators from existing subfiling configuration file, if one exists * Add temporary barrier in "Get EOF" operation to prevent races on EOF Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix for retrieval of machine Host ID * Default to MPI_COMM_WORLD if no MPI params set * added libs rt and pthreads (#1673) * added libs rt and pthreads * Feature/subfiling (#1689) * More tidying of IOC VFD and subfiling debug code * Remove old unused log file code * Clear FID from active file map on failure * Fix bug in generation of subfile names when truncating file * Change subfile names to start from 1 instead of 0 * Use long long for user-specified stripe size from environment variable * Skip 0-sized I/Os in low-level IOC I/O routines * Don't update EOF on read * Convert printed warning about data size mismatch to assertion * Don't add base file address to I/O addresses twice Base address should already be applied as part of H5FDwrite/read_vector calls * Account for 0-sized I/O vector entries in subfile write/read functions * Rewrite init_indep_io for clarity * Correction for IOC wraparound calculations * Some corrections to iovec calculations * Remove temporary barrier on EOF retrieval * Complete work request queue entry on error instead of skipping over * Account for stripe size wraparound for sf_col_offset calculation * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Re-write and fix bugs in I/O vector filling routines (#1703) * Rewrite I/O vector filling routines for clarity * Fix bug with iovec_fill_last when last I/O size is 0 * added subfiling_dir line read (#1714) * added subfiling_dir line read and use it * shellcheck fixes * I/O request dispatch logic update (#1731) Short-circuit I/O request dispatch when head of I/O queue is an in-progress get EOF or truncate operation. This prevents an issue where a write operation can be dispatched alongside a get EOF/truncate operation, whereas all I/O requests are supposed to be ineligible for dispatch until the get EOF/truncate is completed * h5fuse.sh.in clean-up (#1757) * Added command-line options * Committing clang-format changes * Align with changes from develop * Mimic MPI I/O VFD for EOF handling * Initialize context_id field for work request objects * Use logfile for some debugging information * Use atomic store to set IOC ready flag * Use separate communicator for sending file EOF data Minor IOC cleanup * Use H5_subfile_fid_to_context to get context ID for file in Subfiling VFD * IOVEC calculation fixes * Updates for debugging code * Minor fixes for threaded code * Committing clang-format changes * Use separate MPI communicator for barrier operations * Committing clang-format changes * Rewrite EOF routine to use nonblocking MPI communication * Committing clang-format changes * Always dispatch I/O work requests in IOC main loop * Return distinct MPI communicator to library when requested * Minor warning cleanup * Committing clang-format changes * Generate h5fuse.sh from h5fuse.sh.in in CMake * Send truncate messages to correct IOC rank * Committing clang-format changes * Miscellaneous cleanup Post some MPI receives before sends Free some duplicated MPI communicator/Info objects Remove unnecessary extra MPI_Barrier * Warning cleanup * Fix for leaked MPI communicator * Retrieve file EOF on single rank and bcast it * Fixes for a few failure paths * Cleanup of IOC file opens * Committing clang-format changes * Use plan MPI_Send for send of EOF messages * Always check MPI thread support level during Subfiling init * Committing clang-format changes * Handle a hang on failure when IOCs can't open subfiles * Committing clang-format changes * Refactor file open status consensus check * Committing clang-format changes * Fix for MPI_Comm_free being called after MPI_Finalize * Fix VFD test by setting MPI params before setting subfiling on FAPL * Update Subfiling VFD error handling and error stack usage * Improvements for Subfiling logfiles * Remove prototypes for currently unused routines * Disable I/O queue stat collecting by default * Remove unused serialization mutex variable * Update VFD testing to take subfiling VFD into account * Fix usage of global subfiling application layout object * Minor fixes for failure pathways * Keep track of the number of failures in an IOC I/O queue * Make sure not to exceed MPI_TAG_UB value for data communication messages * Committing clang-format changes * Update for rename of some H5FD 'ctl' opcodes * Always include Subfiling's public header files in hdf5.h * Remove old unused code and comments * Implement support for per-file I/O queues Allows the subfiling VFD to have multiple HDF5 files open simultaneously * Use simple MPI_Iprobe over unnecessary MPI_Improbe * Committing clang-format changes * Update HDF5 testing to query driver for H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag * Fix a few bugs related to file multi-opens * Avoid calling MPI routines if subfiling gets reinitialized * Fix issue when files are closed in a random order * Update HDF5 testing to query VFD for "using MPI" feature flag * Register atexit handler in subfiling VFD to call MPI_Finalize after HDF5 closes * Fail for collective I/O requests until support is implemented * Correct VOL test function prototypes * Minor cleanup of old code and comments * Update mercury dependency * Cleanup of subfiling configuration structure * Committing clang-format changes * Build system updates for Subfiling VFD * Fix possible hang on failure in t_vfd tests caused by mismatched MPI_Barrier calls * Copy subfiling IOC fapl in "fapl get" method * Mirror subfiling superblock writes to stub file for legacy POSIX-y HDF5 applications * Allow collective I/O for MPI_BYTE types and rank 0 bcast strategy * Committing clang-format changes * Use different scheme for subfiling write message MPI tag calculations * Committing clang-format changes * Avoid performing fstat calls on all MPI ranks * Add MPI_Barrier before finalizing IOC threads * Use try_lock in I/O queue dispatch to minimize contention from worker threads * Use simple Waitall for nonblocking I/O waits * Add configurable IOC main thread delay and try_lock option to I/O queue dispatch * Fix bug that could cause serialization of non-overlapping I/O requests * Temporarily treat collective subfiling vector I/O calls as independent * Removed unused mercury bits * Add stubs for subfiling and IOC file delete callback * Update VFD testing for Subfiling VFD * Work around HDF5 metadata cache bug for Subfiling VFD when MPI Comm size = 1 * Committing clang-format changes Co-authored-by: mainzer <mainzer#hdfgroup.org> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com> Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
* Fix bug in swmr.c introduced with recent merge (double_t) (#1913)Neil Fortner2022-07-191-3/+3
| | | | | | | | | | | | | | | * 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>
* Persist dataset access properties when using H5Fstart_swmr_write (#1862)Neil Fortner2022-07-191-0/+373
| | | | | | | | | | | | | * 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>
generated by cgit v0.12 at 2024-11-09 10:50:49 (GMT)