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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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* Change ENV to CMake var (#1520)Allen Byrne2022-03-241-2/+1
| | | | | | | * Change ENV to CMake var * Fix typo deletion * Fix typo
* Windows and *nix use different forms for warnings (#1515)Allen Byrne2022-03-243-4/+5
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* Mark minusone as a PARAMETER in tH5A_1_8.F90. Resolves #1379. (#1412)Orion Poplawski2022-03-181-3/+3
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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 Robinson2022-03-177-33/+40
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* free an MPI communicator (#1503)Wei-keng Liao2022-03-171-0/+1
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* Removes the MANIFEST file and unused release files (#1497)Dana Robinson2022-03-1511-6458/+102
| | | | | * Removes the MANIFEST file and unused release files * Updated tar command
* Update release note (#1485)Allen Byrne2022-03-111-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Committing clang-format changes * Update main.yml * Update HISTORY-1_13.txt Missing release note added for changed location of CMake configuration files. * Update HISTORY-1_13.txt Fix typo * Update main.yml revert change Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fixes for format string warnings raised by -Wformat=2/-Wformat-security (#1489)Dana Robinson2022-03-117-30/+13
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* Removes remaining register keywords (#1481)Dana Robinson2022-03-1012-93/+91
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* Fix JNI bug, fix warnings noticed in MSVC CI, be modern & portable (#1480)David Young2022-03-104-12/+11
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* Plugin test cleanup (#1479)Dana Robinson2022-03-1022-323/+247
| | | | | | | | | | | * 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 Robinson2022-03-0912-143/+143
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* Remove addition of non-standalone use of H5_ATTR_FORMAT (#1470)Allen Byrne2022-03-071-1/+1
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* Update HISTORY-1_13.txt and clean RELEASE.txt (#1471)Larry Knox2022-03-072-139/+396
| | | | | | | | | | | | | | | | | | | * 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'. * Update version to 1.13.2-1 after 1.13.1 release. Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk. * Update VERS_RELEASE_EXCEPTIONS with new incompatible release version. * Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to HISTORY-1_13.txt. Clean entries from RELEASE.txt. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Disable memory alloc sanity checks by default for Autotools debug builds (#1468)jhendersonHDF2022-03-032-8/+28
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* Create HISTORY-1_13.txt and update release.txt (#1466)Larry Knox2022-03-013-1419/+1775
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* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-0111-20/+24
| | | | | | to MANIFEST (#1460)
* Fix install config and java test name conflict (#1467)Allen Byrne2022-03-012-3/+2
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* fixed buf definition in h5dfill_f (#1465)Scot Breitenfeld2022-03-011-8/+4
| | | | | | | * 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 * fixed buf definition in h5dfill_f
* 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)jhendersonHDF2022-03-012-15/+84
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* Fix for parallel compression examples on Windows (#1459)jhendersonHDF2022-02-282-11/+23
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* Amend RELEASE.txt with note about parallel compression testing assertion ↵jhendersonHDF2022-02-251-0/+9
| | | | failure (#1458)
* Add release note for #1438 (#1457)Allen Byrne2022-02-252-1/+18
| | | | | * Add release note for #1438 * fix typos.
* Fix release check version logic (#1438)Allen Byrne2022-02-242-11/+11
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* Parallel Compression improvements (#1302)jhendersonHDF2022-02-2428-3356/+9308
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* Enable creation of RPM/DEB binaries GH#1394 (#1398)Allen Byrne2022-02-223-1/+17
| | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Oess 168 utils mirror vfd (#1444)Larry Knox2022-02-215-23/+20
| | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix ↵David Young2022-02-2113-146/+139
| | | | | | | | | | | | | | | | issues (#1423) * Correct some conversion specifications. * Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few instances where PRIdHSIZE was appropriate. Remove a couple of casts and use correct format strings, instead. * Copy values from a possibly unaligned buffer to aligned local variables instead of casting and dereferencing pointers into the buffer. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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 Fortner2022-02-182-23/+64
| | | | | | | | | | * 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>
* Updated reference for Multi Dataset RFC. (#1442)Gerd Heber2022-02-181-1/+1
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* Add SZ filter and adjust compression file names to avoid conflicts (#1434)Allen Byrne2022-02-179-92/+90
| | | | | | | | | * Updated plugins project required adjustments * Updated plugins need to distinguish external libs * Fix missed rename * Use same name for windows as linux - avoid name clash
* Fixed AbstractDs::getVarLenType documentation (#1441)myd73492022-02-161-1/+1
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* Creating FUNDING.yml (#1427)loricooperhdf2022-02-162-0/+4
| | | | | | | | | | | * Creating FUNDING.yml Will add sponsor this project widget to the repo's page. * Correct file name Add sponsor widget; filename typo fixed. * Update MANIFEST
* Revert "Fix metadata cache bug when resizing a pinned/protected entry ↵Larry Knox2022-02-122-21/+4
| | | | | (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
* Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)Allen Byrne2022-02-112-1/+29
| | | | | * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note
* Make a buffer bigger: GCC 8.3.0 warned that a `snprintf` may be (#1403)David Young2022-02-111-1/+1
| | | | | truncated because the recipient buffer was too small, and the warning is one that we promote to an error. Now there is a warning that the buffer is too big (-Wlarger-than=), but we don't promote those to errors, yet.
* Fixed H5Dget_storage_size_f for zero sized datasets (#1430)Scot Breitenfeld2022-02-111-4/+4
| | | | | | | | | | | * 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 * fixed handling size 0 datasets * fixed handling size 0 datasets * format
* Fix issue with H5_now_usec() with 32 bit systems (#1416)Neil Fortner2022-02-102-6/+39
| | | | | | | | | | | | | | | | | | | | | | | * 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)jhendersonHDF2022-02-082-4/+21
| | | | | | | | | | | | | | 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.
* Implemented suggestion in #1381 for dtransform test (#1415)Allen Byrne2022-02-042-11/+13
| | | | | | | | | | | | | | | * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name
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