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* fixed buf definition in h5dfill_f (#1465)Scot Breitenfeld2022-03-011-8/+4
| | | | | | | * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * fixed buf definition in h5dfill_f
* Remove targets PERMISSIONS setting (#1462)Allen Byrne2022-03-011-1/+0
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* Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463)jhendersonHDF2022-03-012-15/+84
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* Fix for parallel compression examples on Windows (#1459)jhendersonHDF2022-02-282-11/+23
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* Amend RELEASE.txt with note about parallel compression testing assertion ↵jhendersonHDF2022-02-251-0/+9
| | | | failure (#1458)
* Add release note for #1438 (#1457)Allen Byrne2022-02-252-1/+18
| | | | | * Add release note for #1438 * fix typos.
* Fix release check version logic (#1438)Allen Byrne2022-02-242-11/+11
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* Parallel Compression improvements (#1302)jhendersonHDF2022-02-2428-3356/+9308
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* Enable creation of RPM/DEB binaries GH#1394 (#1398)Allen Byrne2022-02-223-1/+17
| | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Oess 168 utils mirror vfd (#1444)Larry Knox2022-02-215-23/+20
| | | | | | | | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Spelling of preceed was corrected to proceed, but should have been corrected to precede. * Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'. * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox and @gnuoyd reviews. * Eliminate clang warnings listed in PR #1310 without adding new ssize_t variables. * Committing clang-format changes * Add H5_ATTR_UNUSED to wait_for_child call. Remove unneeded casts in mirror_log calls. * Keep ssize_t in mirror_server.c line 479. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Hyo-Kyung Lee <hyoklee@hdfgroup.org>
* Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix ↵David Young2022-02-2113-146/+139
| | | | | | | | | | | | | | | | issues (#1423) * Correct some conversion specifications. * Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few instances where PRIdHSIZE was appropriate. Remove a couple of casts and use correct format strings, instead. * Copy values from a possibly unaligned buffer to aligned local variables instead of casting and dereferencing pointers into the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix cache sanity checking code by moving functions to wider scope (#1435)jhendersonHDF2022-02-212-99/+88
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* Fix issue with copying null new references (#1440)Neil Fortner2022-02-185-49/+57
| | | | | | | | * Fix issue with copying null new references. Fix assertion failure when reference copying fails. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement support for big I/O for independent reads (#1446)Neil Fortner2022-02-182-23/+64
| | | | | | | | | | * Implement big I/O support for independent reads. Add test for this. * Committing clang-format changes * Update big I/O code in H5FD__mpio_write() to match that in H5FD__mpio_read(). Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updated reference for Multi Dataset RFC. (#1442)Gerd Heber2022-02-181-1/+1
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* Add SZ filter and adjust compression file names to avoid conflicts (#1434)Allen Byrne2022-02-179-92/+90
| | | | | | | | | * Updated plugins project required adjustments * Updated plugins need to distinguish external libs * Fix missed rename * Use same name for windows as linux - avoid name clash
* Fixed AbstractDs::getVarLenType documentation (#1441)myd73492022-02-161-1/+1
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* Creating FUNDING.yml (#1427)loricooperhdf2022-02-162-0/+4
| | | | | | | | | | | * Creating FUNDING.yml Will add sponsor this project widget to the repo's page. * Correct file name Add sponsor widget; filename typo fixed. * Update MANIFEST
* Revert "Fix metadata cache bug when resizing a pinned/protected entry ↵Larry Knox2022-02-122-21/+4
| | | | | (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
* Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)Allen Byrne2022-02-112-1/+29
| | | | | * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note
* Make a buffer bigger: GCC 8.3.0 warned that a `snprintf` may be (#1403)David Young2022-02-111-1/+1
| | | | | truncated because the recipient buffer was too small, and the warning is one that we promote to an error. Now there is a warning that the buffer is too big (-Wlarger-than=), but we don't promote those to errors, yet.
* Fixed H5Dget_storage_size_f for zero sized datasets (#1430)Scot Breitenfeld2022-02-111-4/+4
| | | | | | | | | | | * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * fixed handling size 0 datasets * fixed handling size 0 datasets * format
* Fix issue with H5_now_usec() with 32 bit systems (#1416)Neil Fortner2022-02-102-6/+39
| | | | | | | | | | | | | | | | | | | | | | | * Implement H5ESget_requests() to retrieve request pointers and corresponding connector IDs from an event set. Add tests for this function. * Add "order" parameter to H5ESget_requests, to allow the user to specify the order in which requests are returned. * Fix bugs with H5ESinsert_request() * Change H5ESget_requests() API to have separate input and output parameters for the allocated array length(s) (in) and the number of events in the event set (out). * Fix issue with H5_now_usec() with 32 bit systems. Also improve event set test. * Committing clang-format changes * Add comments to H5_now_usec() explaining rationale for uint64_t casts. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix metadata cache bug when resizing a pinned/protected entry (#1358)jhendersonHDF2022-02-082-4/+21
| | | | | | | | | | | | | | When resizing a pinned/protected cache entry, the metadata cache code previously would wait until after resizing the entry to attempt to log the newly-dirtied entry. This would cause H5C_resize_entry to mark the entry as dirty and make H5AC_resize_entry think that it doesn't need to add the newly-dirtied entry to the dirty entries skiplist. Thus, a subsequent H5AC__log_moved_entry would think it needs to allocate a new entry for insertion into the dirty entry skip list, since the entry doesn't exist on that list. This causes an assertion failure, as the code to allocate a new entry assumes that the entry is not dirty.
* Implemented suggestion in #1381 for dtransform test (#1415)Allen Byrne2022-02-042-11/+13
| | | | | | | | | | | | | | | * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name
* Fix a few issues noted by LGTM (#1421)jhendersonHDF2022-02-0410-32/+38
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* Don't use a nonliteral format string in test/fheap.c:begin_test(). (#1401)David Young2022-02-031-87/+60
| | | | | | | | | * Avoid using a non-literal formatting string with sprintf in begin_test. Use snprintf. Don't duplicate a string on the heap unnecessarily. * Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format string any more. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update doc with HDF5_ROOT usage. (#1414)Allen Byrne2022-02-023-14/+16
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* Unify handling of collective metadata reads status (#1206)jhendersonHDF2022-01-2911-136/+357
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* Added another missing override keyword on a dtor (#1384)Sean McBride2022-01-291-1/+1
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* Fix some spelling. (#1402)David Young2022-01-281-3/+3
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* Snprintf2 (#1399)Sean McBride2022-01-2841-425/+467
| | | | | | | | | | | | | * Replaced many uses of sprintf with safer snprintf Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable. * Removed unnecessary use of static on small buffers This improves thread safety. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove const from the argv tools/tests main sig. (#1390)Allen Byrne2022-01-2838-78/+82
| | | | | | | | | * Remove const from the argv tools/tests main sig. * also remove const from H5_get_option and parse_command_line. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Replaced several uses of sprintf with safer snprintf (#1383)Sean McBride2022-01-2824-46/+43
| | | | | | | * Replaced several uses of sprintf with safer snprintf * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Used clang-tidy to change all floating point f suffixes to F (#1359)Sean McBride2022-01-286-8/+8
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* Revert 61464d7e (#1396)Larry Knox2022-01-261-10/+22
| | | | | | | | Commit 61464d7e was a fix for a compiler error on OpenBSD where int_fast8_t is in fact larger than 1 byte. However, the changes broke H5detect.c generation of H5Tinit.c on Power8 big-endian, and probably on all big-endian machines. Switching DETECT_BYTE to DETECT_I for 8 byte types doesn't work on our big-endian Power8 machine because switching the last parameter of DETECT_I_BYTE_CORE from "int" to the 8 byte type incorrectly sets dt->shared->u.atomic.order = H5T_ORDER_LE on a big-endian machine. A different fix to accomodate both big-endian and OpenBSD is needed. See commit 61464d7e for OpenBSD info. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update code owners file with more names (#1386)Allen Byrne2022-01-261-15/+15
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* Fix cmake dynamic analysis on windows (#1373)Allen Byrne2022-01-242-5/+21
| | | | | * Fix sanitizer flag form on windows * Add search paths to windows code-coverage
* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-229-71/+180
| | | | | | | * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Open bsd fixes (#1195)Sean McBride2022-01-203-82/+70
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* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-207-18/+659
| | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix documentation for H5D_space_status_t enum values (#1372)jhendersonHDF2022-01-191-3/+3
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* Do not set CMAKE_INSTALL_PREFIX when built externally (#1380)Matt McCormick2022-01-191-1/+1
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* various cleanup java test, test files, comments (#1363)Allen Byrne2022-01-185-12/+17
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* Develop java newrefs fixes for obj ref datasets (#1354)Allen Byrne2022-01-183-249/+207
| | | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update the java slf4j logging jars to latest 1.7.33 (#1369)Allen Byrne2022-01-1821-32/+32
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* Updated README.txt to README.md (#1375)Scot Breitenfeld2022-01-1410-36/+42
| | | | | | | | | | | * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * Converted README.txt to README.md and updated files referring to README.txt to README.md. * removed references to README.txt * updated MANIFEST
* Documentation fixes right in time for the holidays (#1321)Gerd Heber2022-01-1413-164/+759
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Fix H5ACmpio dirty bytes creation debugging (#1357)jhendersonHDF2022-01-121-5/+5
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* cmake custom command fix (#1356)Allen Byrne2022-01-121-32/+36
| | | | | | | | | | | | | * From gitlab.kitware.com/third-party/hdf5 rework custom commands commit/757aa42ebff8c9819c054f5e00559143c60f653d * Correct stamp file generation * Needs to support pregenerated H5Tinit.c file * Adjust custom command for all build systems types * Custom target only depends on OUTPUT of custom command
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