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* Address some warnings from casting away of const (#1684)jhendersonHDF2022-04-2616-121/+97
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* Minor things noticed while bringing VFD SWMR in line with develop (#1691)Dana Robinson2022-04-254-13/+12
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* Warnings fixes (#1680)jhendersonHDF2022-04-2510-28/+33
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* Replace H5detect's build-time detection of C99 integer properties with a (#1400)David Young2022-04-224-718/+398
| | | | | | | * Replace H5detect's build-time detection of C99 integer properties with a table-driven routine, `H5T__init_native_int()`, that is run at library initialization time.
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)David Young2022-04-161-74/+20
| | | | | | | | | | | | | | | | | * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1376)H. Joe Lee2022-04-152-3/+3
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* Retrieve MPI-IO hints used by MPI library after file open (#1636)Wei-keng Liao2022-04-151-0/+49
| | | | | | H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5.
* Fixes a typo in H5.c (#1639)Dana Robinson2022-04-141-1/+1
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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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* 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>
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