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* Committing clang-format changesfeature/h5detectgithub-actions2022-04-202-12/+11
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* Simplify. Removing the integer detection paved the way for this.David Young2022-04-201-91/+24
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* Quiet a GCC warning: don't turn back on compiler diagnostics thatDavid Young2022-04-201-2/+0
| | | | weren't turned off to begin with.
* Move the alignment computation for miscellaneous types fromDavid Young2022-04-204-64/+36
| | | | | H5detect.c to H5Tnative.c and rename H5T__init_native_int() to H5T__init_native_internal() to try to match its more general purpose.
* Extract struct-offset arithmetic into macro TAG_ALIGNMENT for reuse in aDavid Young2022-04-191-2/+4
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* Merge remote-tracking branch 'thg/develop' into feature/h5detectDavid Young2022-04-14295-4728/+6934
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| * Fix these Doxygen warnings #1581 (#1589)Allen Byrne2022-04-133-11/+10
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| * Removes unused definitions from module headers (#1624)Dana Robinson2022-04-1138-115/+76
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| * Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-08221-2213/+2188
| | | | | | | | | | * Removes the STATIC flavor of FUNC_ENTER macros
| * Minor things discovered while preparing 1.12.2 (#1620)Dana Robinson2022-04-081-2/+2
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| * Fix for unexported global variable on Windows (#1568)Dana Robinson2022-04-011-2/+5
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| * spelling fixes (#1561)Scot Breitenfeld2022-03-314-4/+4
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| * Add H5_CHECK_MPI_VERSION macro to check for at least MPI version of ↵jhendersonHDF2022-03-306-18/+27
| | | | | | | | | | | | | | | | | | (version, subversion) (#1556) * Fix MPI version check for MPI_Aint_diff usage * Add H5_CHECK_MPI_VERSION macro Adds new H5_CHECK_MPI_VERSION macro to check for MPI library version/subversion pair of at least the specified pair
| * Add missing H5FL_TRACK debug parameters to free list array routines (#1555)jhendersonHDF2022-03-301-6/+12
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| * Minor comment corrections (#1544)Allen Byrne2022-03-303-15/+13
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| * Removes unused H5HP (private heap) package (#1548)Dana Robinson2022-03-304-984/+0
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| * Removes unused memory pool (H5MP) package (#1547)Dana Robinson2022-03-307-861/+1
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| * Removes cruft from a few header files (#1534)Dana Robinson2022-03-297-38/+0
| | | | | | | | * Unnecessary extern C guards in cache headers * Non-existent H5Xpublic.h includes hidden behind NOT_YET symbols
| * Merge initial version of selection I/O feature into develop (#1367)Neil Fortner2022-03-2630-344/+4528
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| * Removes HD prefix from pthreads calls (#1507)Dana Robinson2022-03-182-89/+38
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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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* | Committing clang-format changesgithub-actions2022-03-101-4/+4
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* | Merge remote-tracking branch 'thg/develop' into feature/h5detectDavid Young2022-03-1041-2046/+5511
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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>
* | NFCI: write some comments.David Young2022-03-101-3/+19
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* | In a comment, put back a sentence that mentions H5Tget_native_type().David Young2022-03-101-0/+2
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* | Briefly explain alignments_t.David Young2022-03-101-0/+8
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* | To find the alignment of types, use a type instead of an object andDavid Young2022-01-281-141/+141
| | | | | | | | | | offsetof() instead of pointer arithmetic. I hope that this is what MSVC wants.
* | Reorder the initializer macro to try to satisfy MSVC. Put the formatDavid Young2022-01-281-12/+16
| | | | | | | | of the macro back the way it was and disable clang-format.
* | Let the compiler check alignment in H5detect since it does notDavid Young2022-01-281-29/+0
| | | | | | | | | | | | purposefully make unaligned accesses any longer. Remove some setjmp(3)-related code.
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