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* Add a simple cache to the ros3 VFD (#3753)Dana Robinson2023-10-231-22/+51
| | | | | | | | | 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
* Fix buffer overflow in cache debugging code (#3691)jhendersonHDF2023-10-231-20/+84
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* Add native VOL checks to deprecated functions (#3647)mattjala2023-10-232-58/+145
| | | | | | | * Add native VOL checks to deprecated functions * Remove unneeded native VOL checks * Move native checks to top level calls
* Additional update to the library version matrix for H5Pset_libver_bounds() ↵bmribler2023-10-221-145/+87
| | | | | (#3742) This is the follow-up of PR #3702.
* Update the library version matrix for H5Pset_libver_bounds() (#3702)bmribler2023-10-201-20/+288
| | | | | | | * Fixed #3524 Added 1.12, 1.14, and 1.16 to the table for libver bounds in the H5Pset_libver_bounds docs.
* Add new API function H5Pget_actual_select_io_mode() (#2974)Neil Fortner2023-10-207-46/+362
| | | 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.
* Clean up comments. (#3695)H. Joe Lee2023-10-181-41/+35
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* Sync changes that are only in 1.14 branch (#3704)jhendersonHDF2023-10-181-0/+1
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* Fix unused variable warning in H5F_sfile_assert_num (#3700)Dana Robinson2023-10-171-6/+9
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* Initialize API context MPI types to MPI_BYTE (#3688)jhendersonHDF2023-10-171-0/+5
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* Add Doxygen for H5Pset_fapl_sec2() (#3685)Dana Robinson2023-10-161-1/+17
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* Fix invalid memory access in S3 comms (#3681)Dana Robinson2023-10-161-1/+2
| | | | | | | | | In the ros3 VFD, passing an empty string parameter to an internal API call could result in accessing the -1th element of a string. This would cause failures on big-endian systems like s390x. This parameter is now checked before writing to the string. Fixes GitHub #1168
* Suppress MPI_Waitall warnings w/ MPICH (#3680)Dana Robinson2023-10-162-9/+19
| | | | | | | | | MPICH defines MPI_STATUSES_IGNORE (a pointer) to 1, which raises warnings w/ gcc. This is a known issue that the MPICH devs are not going to fix. See here: https://github.com/pmodels/mpich/issues/5687 This fix suppresses those issues w/ gcc
* Remove CANBE_UNUSED() from subfiling VFD (#3678)Dana Robinson2023-10-163-8/+6
| | | | | This macro was an attempt to quiet warnings about release mode unused variables that only appear in asserts. It resolves to a void cast, which doesn't quiet warnings when an assignment has already taken place.
* Fix a strncpy call to use dest size not src (#3677)Dana Robinson2023-10-151-19/+22
| | | | | | | A strncpy call in a path construction call used the size of the src buffer instead of the dest buffer as the limit n. This was switched to use the dest size and properly terminate the string if truncation occurs.
* Remove clang warnings (#3656)H. Joe Lee2023-10-131-2/+2
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* Add more tests for selection I/O. (#3528)vchoi-hdfgroup2023-10-101-1/+1
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* Update parallel compression feature to support multi-dataset I/O (#3591)jhendersonHDF2023-10-1011-802/+1408
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* Drop MPI-2 support (#3643)Scot Breitenfeld2023-10-086-215/+47
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* Disambiguate error output messages. (#3634)H. Joe Lee2023-10-051-4/+4
| | | | | * Disambiguate error output messages. * Address @brtnfld review.
* Fix grammar (#3635)H. Joe Lee2023-10-051-3/+3
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* Remove unused member from H5D_shared_t struct. (#3628)Neil Fortner2023-10-031-7/+6
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* Fix several spelling/grammar issues (#3621)jhendersonHDF2023-10-0326-44/+44
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* Cleanup unused statements (#3553) (#3617)bmribler2023-09-291-5/+3
| | | Removed unnecessary assert statements and noise comments.
* Fix grammar (#3614)H. Joe Lee2023-09-291-1/+1
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* Fixed unused variable in H5CS.c (#3552) (#3612)bmribler2023-09-291-6/+3
| | | * Fixed #3552
* Fix typos (#3609)H. Joe Lee2023-09-271-1/+1
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* Fix typo behaviour and dependes. (#3605)H. Joe Lee2023-09-271-3/+3
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* Clean up Subfiling VFD header doxygen formatting (#3601)jhendersonHDF2023-09-261-16/+26
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* Replaces HDgetenv with getenv (#3599)Scot Breitenfeld2023-09-2621-37/+34
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* Use HDoff_t with lseek consistently (#3600)Dana Robinson2023-09-261-1/+1
| | | | | lseek on Windows uses __int64 for both the offset and return type instead of off_t like most POSIX systems. This changes ensures we use HDoff_t (which is typdef'd correctly on Windows) w/ lseek.
* Fix docs for H5Acreate2 and H5Acreate_by_name (#3598)jhendersonHDF2023-09-262-30/+30
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* Fix typo: arange->arrange in src/H5Cmpio.c. (#3597)H. Joe Lee2023-09-261-1/+1
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* Fix docs for H5Pset_dxpl_mpio_collective_opt() (#3594)jhendersonHDF2023-09-252-15/+21
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* Fixed GH-3554 (#3584)bmribler2023-09-251-1/+1
| | | Removed the extra condition
* Correct comments about H5Z_FILTER_NONE (#3572)jhendersonHDF2023-09-222-2/+2
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* Adds link to h5fuse.sh in testpar for autotools (#3557)Scot Breitenfeld2023-09-224-1/+8
| | | | * Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.
* Fix grammar (#3545)H. Joe Lee2023-09-191-1/+1
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* Strip HD prefix from string/char C API calls (#3540)Dana Robinson2023-09-15120-1036/+915
| | | | | | | | | | | | | | | | | | | | | * Strip HD prefix from string/char C API calls * HD(f)(put|get)(s|c) * HDstr* * HDv*printf * HD(s)(print|scan)f * HDperror But NOT: * HDstrcase* * HDvasprintf * HDstrtok_r * HDstrndup As those are not C99 and have portability work-around implementations. They will be handled later. * Fix th5_system.c screwup
* Remove HD prefix from math functions (#3538)Dana Robinson2023-09-1412-141/+63
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* Identify functions in a subgroup (#3530)Allen Byrne2023-09-121-21/+5
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* Add missing row for the ROS3 VFD in table #3415 (#3517)Allen Byrne2023-09-113-98/+3
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* Added new Fortran API wrappers (#3511)Scot Breitenfeld2023-09-071-2/+3
| | | | | | | | | | | | | | | | | | | * 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
* Convert hbool_t --> bool in src (#3496)Dana Robinson2023-09-05341-7313/+7279
| | | | | | | | | | | * hbool_t --> bool in src * Does not remove TRUE/FALSE * Public header files are unchanged * Public API calls are unchanged * TRUE/FALSE --> true/false in src * Add deprecation notice for hbool_t
* Fix Subfiling VFD IOC assignment bug (#3456)jhendersonHDF2023-09-013-19/+71
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* Convert some H5MM calls to standard C equivalents (#2382)Dana Robinson2023-08-2521-172/+139
| | | | | | | | | * H5MM_calloc and malloc are now mapped to stdlib C calls * H5MM_memcpy now maps directly to memcpy in release builds * H5MM_memcpy is still implemented as a separate function that checks for buffer overlap when H5MM_DEBUG is defined (default w/ debug builds) * Switches many library memcpy calls to use H5MM_memcpy * Fixes a possible zero allocation in H5Olayout.c
* Put H5T_CONV_ab macros in do..while loops (#3432)Dana Robinson2023-08-251-521/+931
| | | | | | | | | | | Ever since a recent round of macro cleanup, bin/trace and clang-format have been bickering over what H5Tconv.c should look like and neither produces readable code. This change puts the top-level H5T_CONV_ab macros in do..while loops, adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros clang-format recognizes. H5Tconv.c is now readable and both bin/trace and clang-format are happy.
* Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with ↵vchoi-hdfgroup2023-08-251-15/+7
| | | | | | segmenetation fault. (#3427) It is because the object in the testfile points back to the root group. When the tool tries to traverse the object, it goes back to the root group and then back again.
* Remove intel oneapi warning (#3426)H. Joe Lee2023-08-251-1/+1
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* Revise file close assertion failure fix (#3418)jhendersonHDF2023-08-255-42/+63
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