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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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* Removed the use of -commons linking option on Darwin (#3581)Scot Breitenfeld2023-09-251-0/+5
| | | | Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Fix ifx unused variable hdferr warning. (#3568)H. Joe Lee2023-09-221-0/+4
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* Added new Fortran API wrappers (#3511)Scot Breitenfeld2023-09-071-1/+9
| | | | | | | | | | | | | | | | | | | * Added new wrappers for h5get_free_list_sizes_f H5Sselect_intersect_block_f H5Sselect_shape_same_f h5pget_no_selection_io_cause_f h5pget_mpio_no_collective_cause_f H5Lvisit_by_name_f H5Lvisit_f H5Fget_info_f h5dwrite_chunk_f h5dread_chunk_f * added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests * added fortran tests * Update tH5F.F90
* Fix Subfiling VFD IOC assignment bug (#3456)jhendersonHDF2023-09-011-0/+13
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* Remove extraneous "33" in RELEASE.txt (#3425)Neil Fortner2023-08-241-1/+1
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* Skip atomicity tests for OpenMPI major versions < 5 (#3421)jhendersonHDF2023-08-241-0/+9
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* Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416)Neil Fortner2023-08-231-0/+10
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* Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368)Alex2023-08-231-0/+4
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* Re-enable SZIP default to ON in CMake (#3414)Allen Byrne2023-08-232-1/+4
| | | The Autotools were handled in a separate commit
* Enable szip by default in Autotools (#3412)Dana Robinson2023-08-231-0/+6
| | | | | Since libaec is so prevalent and BSD-licensed for both encode and decode, we build the szip filter by default when the szip or aec libraries are found.
* Fix for CVE-2016-4332 (#3406)Dana Robinson2023-08-221-0/+12
| | | | | | | | | | | | | This CVE issue was previously listed as fixed (via HDFFV-9950) back in 2016, but with no confirmation test. Now that test files exist for the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an assert in debug builds. This fix replaces the assert with pointer checks that don't raise errors or asserts. Since the function is in cleanup code, we do our best to close and free things, even when presented with partially- initialized structs. Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
* Fix serial to parallel chunked dataset file space allocation bug (#3394)jhendersonHDF2023-08-221-0/+11
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* Update presets, examples uncompress, szip cache (#3391)Allen Byrne2023-08-181-1/+1
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