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* Fix H5F_get_access_plist to copy file locking settings (#4030)jhendersonHDF2024-02-221-0/+27
| | | | | | H5F_get_access_plist previously did not copy over the file locking settings from a file into the new File Access Property List that it creates. This would make it difficult to match the file locking settings between an external file and its parent file.
* Replace deprecated Fortran 'include mpif.h' with 'USE mpi' (#4031)Christoph Niethammer2024-02-211-3/+1
| | | | | | With MPI 4.1 the use of the mpif.h include file has been deprecated. Codes should transition to USE mpi or USE mpi_f08. Signed-off-by: Christoph Niethammer <niethammer@hlrs.de>
* Update install texts (#4010)Glenn Song2024-02-142-18/+12
| | | | | | | | * Update INSTALL_CMake.txt as necessary * Update remaining docs that use HDF5_USE_GNU_DIRS * Update options in HDFMacros in HDF5Examples
* Updated information about obtaining the HDF5 source code to use the repos. ↵bmribler2024-02-081-10/+3
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* Remove ADB signature from RELEASE.txt. (#3986)H. Joe Lee2024-02-061-1/+0
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* Add a missing left parenthesis in RELEASE.txt. (#3990)H. Joe Lee2024-02-061-1/+1
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* Add API support for Fortran MPI_F08 module definitions. (#3959)Scot Breitenfeld2024-01-291-0/+5
| | | | | * revert to using c-stub for _F08 MPI APIs * use mpi compiler wrappers for cmake and nvhpc
* Fix doxygen errors (#3962)Allen Byrne2024-01-292-1/+10
| | | | | | | | | | | * Switch warnings as errors to default OFF * Enable mac docs * Add doxygen action uses step * Use html div around snippet * Allow preset name to be an argument to cmake-ctest.yml
* Add RELEASE.txt note for the fix for issue #1256 (#3955)jhendersonHDF2024-01-261-0/+28
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* Fortran API work. (#3941)Scot Breitenfeld2024-01-231-0/+7
| | | | | | | | | | | | * - Added Fortran APIs: H5FGET_INTENT_F, H5SSELECT_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F, H5SSELECT_ITER_CLOSE_F, H5S_mp_H5SSELECT_ITER_RESET_F - Added Fortran Parameters: H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F - Added tests for new APIs - Removed H5F C wrapper stubs - Documentation misc. cleanup.
* Reorg and update options for doc and cmake config (#3934)Allen Byrne2024-01-091-9/+19
| | | | * Reorg and update options for doc and cmake config * Correct subfiling depends
* New Fortran Examples added (#3916)Scot Breitenfeld2024-01-031-0/+6
| | | | | * added subfiling example * Added filtered writes with no selection example
* Added H5Fdelete_f with test (#3912)Scot Breitenfeld2023-12-301-0/+3
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* Add 'warning density' computation to the warnhist script (#3910)Quincey Koziol2023-12-291-0/+1
| | | | | | | | | * Add 'warning density' computation to the warnhist script, along with several cleanups to it. Add "--enable-show-all-warnings" configure (and CMake) option to disable compiler diagnostic suppression (and therefore show all the otherwise suppressed compiler diagnostics), disabled by default. Clean up a buncn of misc. warnings. Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
* Implement optimized support for vector I/O in Subfiling VFD (#3896)jhendersonHDF2023-12-271-0/+10
| | | | | | | | | | | | Vector I/O requests are now processed within a single set of I/O call batches, rather than each I/O vector entry (tuple constructed from the types, addrs, sizes and bufs arrays) being processed individually. This allows I/O to be more efficiently parallelized among the I/O concentrator processes during large I/O requests. * Fixed some calculations and add test cases for issues spotted from review * Removed a variable that was compensating for previous miscalculations
* Add variable option syncing for examples (#3885)Allen Byrne2023-12-142-0/+17
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* Some changes to portal links when they could be found on docs.hdfgroup.org, ↵Lori Cooper2023-12-131-1/+1
| | | | | | | and changed the helpdesk link to help.hdfgroup.org (#3893) * Updated some portal links to go directly to docs.hdfgroup. * Fixed some portal and help desk links
* Correct urls and handling of external git repos (#3890)Allen Byrne2023-12-131-4/+13
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* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)Allen Byrne2023-11-222-0/+9
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* Add CMake long double cross-compile defaults (#3683)Dana Robinson2023-11-151-0/+20
| | | | | | | | | | | | | | | | | | | HDF5 performs a couple of checks at build time to see if long double values can be converted correctly (IBM's Power architecture uses a special format for long doubles). These checks were performed using TRY_RUN, which is a problem when cross-compiling. These checks now use default values appropriate for most non-Power systems when cross-compiling. The cache values can be pre-set if necessary, which will preempt both the TRY_RUN and the default. Affected values: H5_LDOUBLE_TO_LONG_SPECIAL (default no) H5_LONG_TO_LDOUBLE_SPECIAL (default no) H5_LDOUBLE_TO_LLONG_ACCURATE (default yes) H5_LLONG_TO_LDOUBLE_CORRECT (default yes) H5_DISABLE_SOME_LDOUBLE_CONV (default no) Fixes GitHub #3585
* Remove Autotools sed hack (#3848)Dana Robinson2023-11-131-0/+10
| | | | | | | | | | configure.ac contains a sed line that cleans up incorrect library flags which was added to paper over some bugs in earlier versions of the Autotools. These issues are not a problem with the current versions of the Autootols. The sed line causes problems on MacOS, so it has been removed. Fixes #3843
* Disable FP exceptions in H5T init code (#3837)Dana Robinson2023-11-071-6/+16
| | | | | | | The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. Fixes #3831
* Renamed h5fuse.sh to h5fuse (#3834)Scot Breitenfeld2023-11-071-0/+6
| | | * provide an alternative to mapfile for older bash
* Fortran Wrappers H5VLnative_addr_to_token_f and ↵Scot Breitenfeld2023-11-031-0/+4
| | | | | | | | | H5VLnative_token_to_address_f (#3801) * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests
* Set NVHPC maximum optimization level to -O1 for now (#3800)jhendersonHDF2023-11-011-0/+22
| | | | | | | | | | | | | | * Set NVHPC maximum optimization level to -O1 for now Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved. * Disable nvhpc Java testing in CMake and amend known issues * Re-enable testing of Autotools nvhpc
* Don't install h5tools_test_utils test program on system (#3793)jhendersonHDF2023-10-301-0/+10
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* Fixed a file handle leak in the core VFD (#3779)Dana Robinson2023-10-261-0/+7
| | | | | | When opening a file with the core VFD and a file image, if the file already exists, the file check would leak the POSIX file handle. Fixes GitHub issue #635
* Add release note for H5Pset_evict_on_close change for parallel HDF5 (#3765)jhendersonHDF2023-10-241-0/+12
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* Fix some issues with collective metadata reads for chunked datasets (#3716)jhendersonHDF2023-10-241-0/+40
| | | | | | | | | | Add functions/callbacks for explicit control over chunk index open/close Add functions/callbacks to check if chunk index is open or not so that it can be opened if necessary before temporarily disabling collective metadata reads in the library Add functions/callbacks for requesting loading of additional chunk index metadata beyond the chunk index itself
* Fix hangs during collective I/O with independent metadata writes (#3693)jhendersonHDF2023-10-241-0/+19
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* Bump the ros3 VFD cache to 16 MiB (#3759)Dana Robinson2023-10-241-2/+2
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* Add h5pget_actual_selection_io_mode fortran wrapper (#3746)Scot Breitenfeld2023-10-231-1/+2
| | | | | | | * added h5pget_actual_selection_io_mode_f test * added tests for h5pget_actual_selection_io_mode_f * fixed int_f type conversion
* Update Autotools to correctly configure oneAPI (#3751)Dana Robinson2023-10-231-0/+8
| | | | | | | | | | | | | | | | | | | * Update Autotools to correctly configure oneAPI Splits the Intel config files under the Autotools into 'classic' Intel and oneAPI versions, fixing 'unsupported option' messages. Also turns off `-check uninit` (new in 2023) in Fortran, which kills the H5_buildiface program due to false positives. * Enable Fortran in oneAPI CI workflow * Turn on Fortran in CMake, update LD_LIBRARY_PATH * Go back to disabling Fortran w/ Intel For some reason there's a linking problem w/ Fortran error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory
* Add a simple cache to the ros3 VFD (#3753)Dana Robinson2023-10-231-0/+10
| | | | | | | | | Adds a small cache of the first N bytes of a file opened with the read-only S3 (ros3) VFD, where N is 4kiB or the size of the file, whichever is smaller. This avoids a lot of small I/O operations on file open. Addresses GitHub issue #3381
* Add new API function H5Pget_actual_select_io_mode() (#2974)Neil Fortner2023-10-201-0/+6
| | | This function allows the user to determine if the library performed selection I/O, vector I/O, or scalar (legacy) I/O during the last HDF5 operation performed with the provided DXPL. Expanded existing tests to check this functionality.
* Add an option to disable doxygen warn as error (#3708)Allen Byrne2023-10-192-0/+13
| | | | | | | | | | | | Add for both CMake and the Autotools * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON) * --enable-doxygen-errors: enable/disable (Default: enable) The default will fail compile if the doxygen parsing generates warnings. The option can be disabled if certain versions of doxygen have parsing issues. i.e. 1.9.5, 1.9.8. Fixes #3398
* Fix issue with unmatched messages in ph5diff (#3719)jhendersonHDF2023-10-191-0/+13
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* Some corrections and fix for plugins (#3712)Allen Byrne2023-10-191-6/+5
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* Correct use of set() command with options (#3667) (#3703)jhendersonHDF2023-10-181-9/+9
| | | | | | | * Correct use of set() command with options * Force filter off if not found Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Add support for AOCC & Flang w/ the Autotools (#3674)Dana Robinson2023-10-151-0/+14
| | | | | | | | | | | | | * Adds a config/clang-fflags options file to support Flang * Corrects missing "-Wl," from linker options in the libtool wrappers when using Flang, the MPI Fortran compiler wrappers, and building the shared library. This would often result in unrecognized options like -soname. * Enable -nomp w/ Flang to avoid linking to the OpenMPI library. CMake can build the parallel, shared library w/ Fortran using AOCC and Flang, so no changes were needed for that build system. Fixes GitHub issues #3439, #1588, #366, #280
* Fixes test failure for gfortran -O2 and -O3, -fdefault-real-16 (#3662)Scot Breitenfeld2023-10-131-1/+6
| | | | | | | | | * added cmake ieee flag for nagfor * fixes gfortran -O2 and -O3, -fdefault-real-16 * fixed sync * updated release notes
* Address nagfor exceptions stoppage. (#3658)Scot Breitenfeld2023-10-111-0/+6
| | | | | | | * added cmake ieee flag for nagfor * generalized determining the nag compiler * fixing some misc. NAG warnings
* Update parallel compression feature to support multi-dataset I/O (#3591)jhendersonHDF2023-10-101-1/+10
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* Use real URLs and updated names for plugins (#3651)Allen Byrne2023-10-101-48/+58
| | | * synchronize TGZ naming convention/usage
* Fixes GH#1027 compilation error (#3654)Scot Breitenfeld2023-10-101-1/+8
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* Drop MPI-2 support (#3643)Scot Breitenfeld2023-10-081-0/+6
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* Improve consistency in past tense usage (#3638)H. Joe Lee2023-10-061-1/+1
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* Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624)Allen Byrne2023-10-042-19/+28
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* Disable static + thread-safe on Windows w/ CMake (#3622)Dana Robinson2023-10-031-0/+11
| | | | | | | | | The thread-safety feature on Windows requires a hook in DllMain() and thus is only available when HDF5 is built as a shared library. This was previously a warning, but has now been elevated to a fatal error that cannot be overridden with ALLOW_UNSUPPORTED. Fixes GitHub #3613
* Fix several spelling/grammar issues (#3621)jhendersonHDF2023-10-034-5/+5
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