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* Address some warnings from casting away of const (#1684)jhendersonHDF2022-04-2616-121/+97
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* Correct concurrency bugs when running tests, along with a bugfix & small ↵Quincey Koziol2022-04-264-34/+202
| | | | | | | | | | warning cleanup (#1683) * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Minor things noticed while bringing VFD SWMR in line with develop (#1691)Dana Robinson2022-04-254-13/+12
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* Fixes stack size warnings in tcoords.c (#1688)Dana Robinson2022-04-251-14/+48
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* Clean stack size warnings in sio_engine (#1687)Dana Robinson2022-04-251-20/+35
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* Warnings fixes (#1680)jhendersonHDF2022-04-2517-152/+169
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* Improve handling of copying of dynamic libraries and clean them up after (#1681)Quincey Koziol2022-04-245-32/+45
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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.
* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)Dana Robinson2022-04-201-1/+1
| | | So the PR action name is not the same as the one in main.yml
* Adds paths-ignore to the Github pull request workflow (#1663)Dana Robinson2022-04-201-1/+8
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* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)Dana Robinson2022-04-201-15/+15
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* added HDFFV-11306 entry (#1662)Scot Breitenfeld2022-04-191-1/+6
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* Develop clang format java (#1653)Allen Byrne2022-04-19162-10098/+13367
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* HDFFV-11306 Fixed (#1657)Scot Breitenfeld2022-04-199-23/+139
| | | | | | | | * HDFFV-11306, * Fixed it so both h5open_f and h5close_f can be called multiple times. * Fixed an issue with open objects remaining after h5close_f was called. * Added additional tests. * comments clean-up
* Removes HDF Group paths, adds shellcheck fixes (#1656)Dana Robinson2022-04-191-95/+41
| | | | | | For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* Mirror vfd test fixes (#1629)Quincey Koziol2022-04-184-14/+28
| | | | | | | | | | | | | | | | | | | * Use the FAPL that was created earlier in the test (and delete an unused variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd. * Check for testing directory before creating, to avoid warning from bash. Clean out .libs directory before re-using it (after a failed test), to remove any files generated by libtool. * Committing clang-format changes * Increment error count on failed file open and skip tests for VFDs that need modified filenames. * Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking configuration parameters and can't be provided for an automated test that is configured with an environment variable. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cleans up some HL library code that inappropriately returns htri_t values ↵Dana Robinson2022-04-185-196/+144
| | | | | | | | | | | | cast to herr_t (#1651) * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t * Committing clang-format changes * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)David Young2022-04-165-153/+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 Lee2022-04-153-4/+5
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* OESS-168: Remove clang warnings. (#1309)H. Joe Lee2022-04-151-1/+2
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review.
* 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.
* free MPI datatypes previously created (#1637)Wei-keng Liao2022-04-151-5/+33
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* not depend on doIO to free an MPI_Comm object (#1642)Wei-keng Liao2022-04-151-7/+7
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* Adds build and license shields to README.md (#1641)Dana Robinson2022-04-151-0/+3
| | | | | | | * First stab at a Github status bar * Adds a .tokeignore file for counting lines of code accurately * Yanks lines of code calculation since it wildly overcounts
* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)Wei-keng Liao2022-04-151-3/+16
| | | | | * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style
* 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 Robinson2022-04-086-7/+7
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* Updates bin/restore.sh to clean up src/H5config.h.in (#1605)Dana Robinson2022-04-071-0/+3
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* Minor C++ changes noticed while normalizing with 1.12 (#1606)Dana Robinson2022-04-078-6/+5
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* Removes bin/README (#1602)Dana Robinson2022-04-071-2/+0
| | | | This README file refers to scripts that were removed when the MANIFEST went away.
* Adds additional files/paths to ignore for github actions (#1585)Dana Robinson2022-04-051-0/+3
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* Adds release timeline to README.md (#1584)Dana Robinson2022-04-053-0/+65
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* Add missing release note for h5repack timing (#1572)Allen Byrne2022-04-051-0/+8
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* Move error-stack text to top of usage display (#1564)Allen Byrne2022-04-0128-68/+122
| | | | | | | | | * Move error-stack text to top of usage display * Add optional tag ti list * format changes * Revert incorrect change
* Fix for unexported global variable on Windows (#1568)Dana Robinson2022-04-011-2/+5
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* spelling fixes (#1561)Scot Breitenfeld2022-03-3121-25/+25
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* Update command format, avoid policy warning (#1550)Allen Byrne2022-03-301-3/+3
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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
* Update MacOS configure, bringing it closer to Linux configure (#1554)Quincey Koziol2022-03-301-27/+40
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* 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 Robinson2022-03-3010-2076/+2
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* Removes unused memory pool (H5MP) package (#1547)Dana Robinson2022-03-3010-1657/+2
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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
* Fix bugs in test/vfd.c (#1538)Neil Fortner2022-03-291-3/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * 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 * Minor optimization to vector I/O request sort routine. Tested parallel / debug on Jelly. * 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. * Added "ctl" callback to the VFD interfance, and the associated H5FDctl() and H5FD_ctl() calls. Modified the MPIO VFD accordingly -- specifically: Added ctl() call with op-code support to expose rank, size, and communicator. Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(), and H5FD_mpi_get_comm() to use the new ctl() callback. In passing removed the const qualifier from the file parameter of these functions, as the file parameter of the ctl callback is not const. Deleted the old H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and H5FD__mpio_communicator() calls from the MPIO VFD. Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the MPIO VFD accordingly. Note that all VFDs now use H5FD_class_t, with no special class for VFDs that that support MPI. Some minor touch ups to the Neil's selection I/O mods in passing. Tested serial and parallel, debug and production on charis and jelly. * 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. * 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. * Committing clang-format changes * 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. * Committing clang-format changes * fixed spelling (#1353) * Implement big I/O support for vector I/O requests in the MPIO file driver. * Committing clang-format changes * Update dummy file driver in h5test.c to match new struct. * Fix another outdated H5FD_class_t struct. * Free arrays in H5FD__mpio_read/write_vector() as soon as they're not needed, to cut down on memory usage during I/O. * Committing clang-format changes * Address comments from code review. Fix const warnings with H5S_SEL_ITER_INIT(). * Committing clang-format changes * Fix warnings in selection I/O code * Refactor H5FD__mpio_read/write_vector() to bring common code for constructing MPI Datatype into a shared function. * Committing clang-format changes * Fix bugs in selection I/O code. * Fix bugs in selection I/O code * Address comments from review. Add "version" field to H5FD_class_t struct and accompanying H5FD_CLASS_VERSION macro. * Committing clang-format changes * Committing clang-format changes * Address comments from selection I/O PR * Committing clang-format changes * Fix spelling * Fix bugs int test/vfd.c Co-authored-by: mainzer <mainzer#hdfgroup.org> Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Use AC_MSG_RESULT/AC_MSG_ERROR/AC_MSG_WARN instead of echo (#1532)Wei-keng Liao2022-03-281-37/+14
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* Merge initial version of selection I/O feature into develop (#1367)Neil Fortner2022-03-2639-437/+10726
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