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* Onion VFD: Sync with develop. (#1732)Dana Robinson2022-05-0678-30045/+29046
| | | | | | | * Sync with develop. h5dump is broken, so I can't test the tools. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added the support to get the revision count for the onion file into the ↵raylu-hdf2022-05-051-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | h5dump. (#1726) * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * 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 * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) 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. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Added the support to get the revision count for the onion file into the h5dump. * Committing clang-format changes * Changed the function from H5FDget_onion_revision_count to H5FDonion_get_revision_count for better name. * Fixed compiler warnings. Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adding a new API function to get the number of revisions for an onion file ↵raylu-hdf2022-05-031-23/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#1692) * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * 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 * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) 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. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Adding a new API function to get the number of revisions for an onion file. This function uses H5FD_ctl(). * Committing clang-format changes * Removed a few unused variables. * Modified the way that the API function H5FDget_onion_revision_count is organized and added Doxygen comments for the three API functions. * Committing clang-format changes * Minor changes: modified some Doxygen comments. Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD: Misc cleanup (#1693)Dana Robinson2022-04-265-548/+539
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * 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 * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) 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. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * 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> * Cleans up some HL library code that inappropriately returns htri_t values 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> * Mirror vfd test fixes (#1629) * 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> * Removes HDF Group paths, adds shellcheck fixes (#1656) 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... * HDFFV-11306 Fixed (#1657) * 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 * Develop clang format java (#1653) * added HDFFV-11306 entry (#1662) * Adds the -q flag to all swmr test programs, quieting noisy output (#1665) * Adds paths-ignore to the Github pull request workflow (#1663) * Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666) So the PR action name is not the same as the one in main.yml * Replace H5detect's build-time detection of C99 integer properties with a (#1400) * 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. * Improve handling of copying of dynamic libraries and clean them up after (#1681) test finishes. * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Minor things noticed while bringing VFD SWMR in line with develop (#1691) * Removed dead code, weird formatting, and other badness * Fixed remaining stack size warnings in onion VFD * Committing clang-format changes Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
* Onion VFD: Sync with develop (#1685)Dana Robinson2022-04-254-29/+42
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * 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 * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) 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. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * 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> * Cleans up some HL library code that inappropriately returns htri_t values 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> * Mirror vfd test fixes (#1629) * 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> * Removes HDF Group paths, adds shellcheck fixes (#1656) 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... * HDFFV-11306 Fixed (#1657) * 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 * Develop clang format java (#1653) * added HDFFV-11306 entry (#1662) * Adds the -q flag to all swmr test programs, quieting noisy output (#1665) * Adds paths-ignore to the Github pull request workflow (#1663) * Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666) So the PR action name is not the same as the one in main.yml * Replace H5detect's build-time detection of C99 integer properties with a (#1400) * 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. * Improve handling of copying of dynamic libraries and clean them up after (#1681) test finishes. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Onion VFD: Cleanup and refactoring in the onion VFD (#1679)Dana Robinson2022-04-241-1082/+897
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Trivial comment change * Misc refactoring in the onion test * Committing clang-format changes * Fix unused parameter warning * Removed printf debugging statements * checkposix fixes * Cleaned up some function headers * Remove useless casts * Fixes most warnings in the onion VFD test code (exception: stack size warnings) * Make TEST_ERROR semicolons consistent * Much tidying in the onion VFD tests * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adding the support of H5FDctl for the Onion VFD and the test case. (#1677)raylu-hdf2022-04-221-0/+216
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* Onion VFD: Misc refactoring in the tests (#1654)Dana Robinson2022-04-181-142/+84
| | | | | | | | | * Trivial comment change * Misc refactoring in the onion test * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Changed the field name 'revision_id' of H5FD_onion_fapl_info_t to ↵raylu-hdf2022-04-161-71/+71
| | | | | | | | | 'revision_num' for better description (#1650) * Changed the field name 'revision_id' of H5FD_onion_fapl_info_t to 'revision_num' for better description. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge branch 'develop' of https://github.com/HDFGroup/hdf5 into ↵Ray Lu2022-04-081-1/+1
|\ | | | | | | raylu_onion_vfd_7
| * Minor things discovered while preparing 1.12.2 (#1620)Dana Robinson2022-04-081-1/+1
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* | Merge remote-tracking branch 'canonical/develop' into feature/onion_vfdDana Robinson2022-04-06148-4959/+7690
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| * spelling fixes (#1561)Scot Breitenfeld2022-03-314-6/+6
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| * Removes unused H5HP (private heap) package (#1548)Dana Robinson2022-03-306-1092/+2
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| * Removes unused memory pool (H5MP) package (#1547)Dana Robinson2022-03-303-796/+1
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| * 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>
| * Merge initial version of selection I/O feature into develop (#1367)Neil Fortner2022-03-263-70/+2110
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| * Fix JNI bug, fix warnings noticed in MSVC CI, be modern & portable (#1480)David Young2022-03-101-4/+3
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| * Plugin test cleanup (#1479)Dana Robinson2022-03-1020-294/+220
| | | | | | | | | | | | | | | | | | | | | | * Autotools plugin test cleanup * Combines filter, VFD, and VOL plugin tests * Adds VFD plugin tests to the Autotools * Implements a uniform shell script naming scheme in test/ * codespell fix * Changes after code review
| * Minor tweaks from VFD SWMR normalization (#1474)Dana Robinson2022-03-092-4/+3
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| * Fix release check version logic (#1438)Allen Byrne2022-02-241-1/+2
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| * Fix issue with H5_now_usec() with 32 bit systems (#1416)Neil Fortner2022-02-101-3/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
| * Implemented suggestion in #1381 for dtransform test (#1415)Allen Byrne2022-02-041-10/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name
| * 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>
| * Snprintf2 (#1399)Sean McBride2022-01-2820-266/+284
| | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Byrne2022-01-2810-11/+11
| | | | | | | | | | | | | | | | | | * 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 McBride2022-01-284-4/+4
| | | | | | | | | | | | | | * 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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| * Open bsd fixes (#1195)Sean McBride2022-01-201-1/+3
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| * Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-201-4/+485
| | | | | | | | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Fix compilation issues with Mingw (#1342)Baljak2022-01-085-30/+30
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| * Changed to correct return datatype for H5Lexists (#1330)Scot Breitenfeld2022-01-041-4/+5
| | | | | | | | | | * changed to correct return datatype for H5Lexists Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Fix directory variable in shell scripts (#1273)Allen Byrne2021-12-107-146/+51
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix testswmr scripts with utils/test variable * Change format of configure var assignment * quote the variable value in configure * Use sh.in expected var pattern * Only ref builddir in script * Create vars for utils/test and test as H5_<path>_BUILDDIR * Use abs_top_builddir in test scripts * Change script var to make it easier to read. * Use @abs_top_builddir@ directly in paths * Correct typos/comment
| * OESS-168: Remove clang warnings. (#1269)H. Joe Lee2021-12-081-6/+10
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| * Convert vds swmr test script to powershell (#1245)Allen Byrne2021-12-083-13/+769
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fixes const warnings in H5ES package (#1211) * Quiets a 'set but not used' warning in h5diff_array.c (#1210) * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Cleanup review issues * Fix variable assignment * Change the wait function to pass in the path * Disable actual test execution until programs fixed * Adjust copyright text * Fix spelling Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
| * OESS-168: Remove clang warnings. (#1263)H. Joe Lee2021-12-081-3/+3
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| * Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-0780-447/+447
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
| * Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs (#1222)Dana Robinson2021-11-241-0/+99
| | | | | | | | | | | | | | | | | | | | | | | | * Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the library due to missing ID range checks in H5Pget_filter_by_id1/2. The library now returns a normal error code when filter IDs are out of range. Fixes HDFFV-11286. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Create 2D arrays on the heap in a different way (#1169)David Young2021-11-231-50/+9
| | | | | | | | | | | | | | | | | | | | | | | | * Create 2D arrays on the heap by malloc'ing `struct { TYPE arr[ROWS][COLS]; }`. This avoids the double-indirection through pointers and the additional memory of H5TEST_ALLOCATE_2D_ARRAY(). This change will safely quiet the cast warning that PR #1129 was intended to fix. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Make sure plugin interface is initialized before property list interface ↵jhendersonHDF2021-11-231-7/+58
| | | | | | | | phase 2 (#1216)
| * Fixes unused parameter warnings in the null VFD (#1179)Dana Robinson2021-11-131-0/+31
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| * Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-084-133/+25
| | | | | | | | | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * OESS-168: Remove clang warnings. (#1136)H. Joe Lee2021-11-051-2/+2
| | | | | | | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @byrnHDF and @derobinson review.
| * OESS-168: Remove clang warnings. (#1137)H. Joe Lee2021-11-051-68/+69
| | | | | | | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @derobins review.
| * OESS-168: Remove clang warnings. (#1146)H. Joe Lee2021-11-021-3/+3
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| * OESS-168: Remove clang warnings. (#1135)H. Joe Lee2021-11-021-1/+1
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| * Split dir create into separate macro (#1141)Allen Byrne2021-10-282-20/+23
| | | | | | | | | | * Split dir create into separate macro * Correct VFD settings
| * Consolidate VFD create list macro (#1132)Allen Byrne2021-10-261-2/+1
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| * Removes the "try free" behavior from the skip lists (#1126)Dana Robinson2021-10-221-208/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Removes the "try free" behavior from the skip lists This was only used in the ID code when iterating and a callback could delete IDs. It is not used anywhere else in the library and is now pointless overhead. Also quiets the const warnings when returning stored elements. They only need to be const with respect to the skip list code, which should never modify them. The library can do whatever it wants with the elements it stored. * Formatted source
| * Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-2010-147/+113
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
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