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* Fixes a bug in the FSM section merge code exposed by VFD SWMR (#1505)Dana Robinson2022-03-171-1/+1
| | | | | | | | | | From Vailin: Fix the FSM bug when setting the FSM threshold to a non-default value. Check for smaller or larger section size after merging and shrinking a section, for this case is the section that is smaller than threshold (see H5MF_xfree() in H5MF.c). It is possible for the section to be smaller after merging/shrinking (see H5MF__sect_large_shrink() in H5MFsection.c).
* Misc fixes highlighted by the checkposix script (#1499)Dana Robinson2022-03-176-29/+33
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* Fix JNI bug, fix warnings noticed in MSVC CI, be modern & portable (#1480)David Young2022-03-102-4/+4
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* Minor tweaks from VFD SWMR normalization (#1474)Dana Robinson2022-03-099-138/+139
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* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-012-4/+4
| | | | | | to MANIFEST (#1460)
* 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)jhendersonHDF2022-03-011-6/+67
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* Fix release check version logic (#1438)Allen Byrne2022-02-241-10/+9
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* Parallel Compression improvements (#1302)jhendersonHDF2022-02-2412-1596/+4793
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* Enable creation of RPM/DEB binaries GH#1394 (#1398)Allen Byrne2022-02-221-0/+1
| | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Oess 168 utils mirror vfd (#1444)Larry Knox2022-02-211-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* 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 Fortner2022-02-181-16/+34
| | | | | | | | | | * 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>
* Revert "Fix metadata cache bug when resizing a pinned/protected entry ↵Larry Knox2022-02-121-4/+4
| | | | | (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
* Fix issue with H5_now_usec() with 32 bit systems (#1416)Neil Fortner2022-02-101-3/+12
| | | | | | | | | | | | | | | | | | | | | | | * 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)jhendersonHDF2022-02-081-4/+4
| | | | | | | | | | | | | | 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.
* Fix a few issues noted by LGTM (#1421)jhendersonHDF2022-02-043-18/+19
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* Unify handling of collective metadata reads status (#1206)jhendersonHDF2022-01-298-80/+259
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* Fix some spelling. (#1402)David Young2022-01-281-3/+3
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* Snprintf2 (#1399)Sean McBride2022-01-283-21/+23
| | | | | | | | | | | | | * 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 Byrne2022-01-282-2/+3
| | | | | | | | | * 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 McBride2022-01-2811-25/+22
| | | | | | | * 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 McBride2022-01-281-1/+1
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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>
* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-228-71/+168
| | | | | | | * 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 McBride2022-01-201-22/+10
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* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-205-14/+167
| | | | | | (#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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* various cleanup java test, test files, comments (#1363)Allen Byrne2022-01-181-1/+1
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* Documentation fixes right in time for the holidays (#1321)Gerd Heber2022-01-146-142/+174
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Corrected H5Oget_info parameter description (#1349)Scot Breitenfeld2022-01-111-3/+3
| | | | | * 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
* Use appropriate printf format specifiers for haddr_t and hsize_t types ↵jhendersonHDF2022-01-1111-173/+129
| | | | directly (#1340)
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x ↵Scot Breitenfeld2022-01-111-3/+3
| | | | releases, HDFFV-11289 (#1335)
* Fix compilation issues with Mingw (#1342)Baljak2022-01-081-1/+3
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* OESS-168: Remove clang warnings. (#1308)H. Joe Lee2022-01-071-1/+4
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* OESS-168: Remove clang warnings. (#1305)H. Joe Lee2022-01-071-2/+4
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* OESS-168: Remove clang warnings. (#1304)H. Joe Lee2022-01-071-1/+5
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* Fix usage of several HDfprintf format specifiers after HDfprintf removal (#1324)jhendersonHDF2022-01-0410-147/+231
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* Fix typo. (#1303)H. Joe Lee2022-01-041-1/+1
| | | chksum -> checksum
* Fix typo. (#1301)H. Joe Lee2022-01-041-1/+1
| | | If the are -> If they are
* OESS-168: Remove clang warnings. (#1300)H. Joe Lee2022-01-041-1/+1
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* OESS-168: Remove clang warnings. (#1297)H. Joe Lee2021-12-151-1/+1
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* Call FUNC_ENTER immediately in H5_init_library (#1287)jhendersonHDF2021-12-131-2/+2
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* Fix free list tracking and cleanup cast alignment warnings (#1288)jhendersonHDF2021-12-131-27/+120
| | | | | * Fix free list tracking and cleanup cast alignment warnings * Add free list tracking code to H5FL 'arr' routines
* Fixes for async operations (#1272)jhendersonHDF2021-12-112-6/+68
| | | | | Setup VOL wrapping context for each "request" callback Set H5ES_event_t "next" pointer to NULL when appending to event list
* Remove duplicate memcpy in chunk_file_cb (#1285)jhendersonHDF2021-12-111-1/+0
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* Initialize filter mask and chunk nbytes for 'Single' chunk index (#1261)jhendersonHDF2021-12-091-1/+7
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