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* Merge branch 'develop' into feature/new_datatypesfeature/new_datatypesDana Robinson2024-03-161-2/+33
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| * Fix error when overwriting an indirectly nested vlen with a shorter sequence ↵Neil Fortner2024-03-151-0/+10
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| * Fix Autotools -Werror cleanup (#4144)Dana Robinson2024-03-151-0/+14
| | | | | | | | | | | | | | | | | | | | | | The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc. so configure checks don't trip over warnings generated by configure check programs. The sed line originally only scrubbed -Werror but not -Werror=something, which would cause errors when the '=something' was left behind in CFLAGS. The sed line has been updated to handle -Werror=something lines. Fixes one issue raised in #3872
| * Update URLs in RELEASE.txt (#4132)bmribler2024-03-141-2/+2
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| * Deprecate bin/cmakehdf5 (#4127)Allen Byrne2024-03-131-0/+7
| | | | | | | | | | * Deprecate bin/cmakehdf5 * Add reference text
* | Merge branch 'develop' into feature/new_datatypesJordan Henderson2024-03-121-2/+127
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| * Overhaul CMake LFS support (#4122)Dana Robinson2024-03-121-0/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Externally visible: * The HDF_ENABLE_LARGE_FILE option (advanced) has been removed * We no longer run a test program to determine if LFS works, which will help with cross-compiling * On Linux we now unilaterally set -D_LARGEFILE_SOURCE and -D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since those options do nothing on 64-bit systems, this seems safe and covers all our bases. We don't set -D_LARGEFILE64_SOURCE since we don't use any of the POSIX 64-bit specific API calls like ftello64, as noted above. * We didn't test for LFS support on non-Linux platforms. We've added comments for how LFS should probably be supported on AIX and Solaris, which seem to be alive, though uncommon. PRs would be appreciated if anyone wishes to test this. Internal: * Drops off64_t size checks since this is unused (as in Autotools) * Remove HDF_EXTRA_FLAGS, which is now unused * Remove hack around deprecated LINUX_LFS Fixes #2395
| * Remove H5B debug checks (#4089)Dana Robinson2024-03-091-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The H5B (version 1 B-tree) package would add some computationally expensive integrity checks when H5B_DEBUG was defined. Due to their negative effects on performance, this option was rarely turned on, making the H5B__assert() check function stale, if not dead, code. This change: * Builds H5B__assert() when NDEBUG is not defined (the function relies on assert()) so it gets compiled more often. * Removes some printf debugging statements in the B-tree code * Removes all H5B "extra debug" checks that are leftover from past debugging sessions. Maintainers can add H5B__assert() selectively to perform integrity checks when debugging. * Removes the HDF5_ENABLE_DEBUG_H5B CMake option H5B_DEBUG now has no effect
| * update macOS support statement (#4084)Scot Breitenfeld2024-03-081-0/+6
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| * Fixed asserts due to H5Pset_est_link_info() values (#4081)Dana Robinson2024-03-081-0/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed asserts due to H5Pset_est_link_info() values If large values for est_num_entries and/or est_name_len were passed to H5Pset_est_link_info(), the library would attempt to create an object header NIL message to reserve enough space to hold the links in compact form (i.e., concatenated), which could exceed allowable object header message size limits and trip asserts in the library. This bug only occurred when using the HDF5 1.8 file format or later and required the product of the two values to be ~64k more than the size of any links written to the group, which would cause the library to write out a too-large NIL spacer message to reserve the space for the unwritten links. The library now inspects the phase change values to see if the dataset is likely to be compact and checks the size to ensure any NIL spacer messages won't be larger than the library allows. Fixes GitHub #1632 * Fix copy-paste comments
| * New option for building with static CRT in Windows (#4062)Allen Byrne2024-03-071-0/+9
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| * Add support for the new MSVC preprocessor (#4078)Dana Robinson2024-03-071-0/+15
| | | | | | | | | | | | | | | | | | | | | | | | Microsoft has added a new, standards-conformant preprocessor to MSVC, which can be enabled with /Zc:preprocessor. This preprocessor trips over our HDopen() function-like variadic macro since it uses a hack that only works with the legacy MSVC preprocessor. This fix adds ifdefs to use the correct HDopen() macro depending on the MSVC preprocessor selected. Fixes #2515
| * Added new H5E with tests. (#4049)Scot Breitenfeld2024-03-071-2/+16
| | | | | | | | | | | | | | | | | | | | | | Added Fortran H5E APIs: h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f, h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f, h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature) Addresses Issue #3987
| * Rename incorrectly named option (#4067)Allen Byrne2024-03-051-0/+10
| | | | | | | | | | | | | | * Rename incorrectly named option * Restore the correct uses of USING_MEMCHECKER * Update release note
| * Fix issue where H5Tset_fields does not account for datatype offsets (#4061)jhendersonHDF2024-03-051-0/+10
| | | | | | | | | | H5Tset_fields did not account for any offset in a floating-point datatype, causing it to fail when a datatype's precision is correctly set such that it doesn't include the offset bits.
* | Update configure checks to account for problematic compilersJordan Henderson2024-03-061-12/+27
| | | | | | Clarify a few things in the RELEASE.txt entry
* | Merge branch 'develop' into feature/new_datatypesJordan Henderson2024-03-041-0/+8
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| * Add options to allow tools type selection and naming (#4046)Allen Byrne2024-03-041-0/+8
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* | Add RELEASE.txt note for _Float16 supportJordan Henderson2024-03-021-0/+104
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* Fix memory leak in H5LTopen_file_image when H5LT_FILE_IMAGE_DONT_COPY flag ↵jhendersonHDF2024-02-261-1/+10
| | | | | | | | | is used (#4021) When the H5LT_FILE_IMAGE_DONT_COPY flag is passed to H5LTopen_file_image, the internally-allocated udata structure gets leaked as the core file driver doesn't have a way to determine when or if it needs to call the 'udata_free' callback. This has been fixed by freeing the udata structure when the 'image_free' callback gets made during file close, where the file is holding the last reference to the udata structure.
* 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.
* 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 Byrne2024-01-291-0/+9
| | | | | | | | | | | * 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.
* 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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* 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 Byrne2023-12-141-0/+14
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* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)Allen Byrne2023-11-221-0/+8
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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 Byrne2023-10-191-0/+12
| | | | | | | | | | | | 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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