summaryrefslogtreecommitdiffstats
path: root/src/H5CXprivate.h
Commit message (Collapse)AuthorAgeFilesLines
* Sync with develop (#3737)jhendersonHDF2023-10-211-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Correct ld in format strings in cmpd_dset.c (#3697) Removes clang warnings * Clean up comments. (#3695) * Add NVidia compiler support and CI (#3686) * Work around Theta system issue failure in links test (#3710) When the Subfiling VFD is enabled, the links test may try to initialize the Subfiling VFD and call MPI_Init_thread. On Theta, this appears to have an issue that will cause the links test to fail. Reworked the test to check for the same conditions in a more roundabout way that doesn't involved initializing the Subfiling VFD * Fix issue with unmatched messages in ph5diff (#3719) * provide an alternative to mapfile for older bash (#3717) * Attempt to quiet some warnings with cray compilers. (#3724) * Fix CMake VOL passthrough tests by copying files to correct directory (#3721) * Develop intel split (#3722) * Split intel compiler flags into sub-folders * Update Intel options for warnings * Mostly CMake, Autotools needs additional work * Fixes and adjustments to t_filters_parallel (#3714) Broadcast number of datasets to create in multi-dataset I/O cases so that interference with random number generation doesn't cause mismatches between ranks Set fill time for datasets to "never" by default and adjust on a per-test basis to avoid writing fill values to chunks when it's unnecessary Reduce number of loops run in some tests when performing multi-dataset I/O Fix an issue in the "fill time never" test where data verification could fill if file space reuse causes application buffers to be filled with chosen fill value when reading from datasets with uninitialized storage Skip multi-chunk I/O test configurations for multi-dataset I/O configurations when the TestExpress level is > 1 since those tests can be more stressful on the file system Disable use of persistent file free space management for now since it occasionally runs into an infinite loop in the library's free space management code * Suppress cast-qual warning in H5TB Fortran wrapper (#3728) This interface is fundamentally broken, const-wise. * Add new API function H5Pget_actual_select_io_mode() (#2974) 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. * Test scripts now execute in-source with creation of tmp dir (#3723) Fixes a few issues created in #3580: * Fixes a problem where committed tools test files were deleted when cleaning after an in-source build * Fixes issues with test file paths in Autotools tools test scripts * Add -h and --help as flags in h5cc & h5fc (#3729) Adds these common help flags in addition to -help * Update the library version matrix for H5Pset_libver_bounds() (#3702) * Fixed #3524 Added 1.12, 1.14, and 1.16 to the table for libver bounds in the H5Pset_libver_bounds docs. * Remove references to LIBVER_V116 --------- Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Neil Fortner <fortnern@gmail.com> Co-authored-by: Glenn Song <43005495+glennsong09@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* 1.14 sync with develop (#3660)jhendersonHDF2023-10-121-17/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework tools.cmake and add C flags (#3110) * Fix gh pages so that the doxygen files are uploaded (#3102) * Add workspace path * add debug * Make one job so workspace files are available * Put doxygen docs under docs folder in gh-pages * Fix a misc warning in test/vol.c (#3112) The compiler complains about using integers instead of size_t for some sizes. * Remove H5detect and H5make_libsettings (#3104) Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file * clang-tidy clang-analyzer-core issues addressed (#3113) src/H5system.c:1293:13: warning: Dereference of null pointer [clang-analyzer-core.NullDereference] src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains uninitialized data (e.g., via the field chain: 'initial.user') [clang-analyzer-core.CallAndMessage] * Add note for issue 3056 (#3117) * Use 1.14 toolchain (#3116) * Remove the checkposix script (#3122) This script was used to ensure that all non-HDF5 calls were prefixed with 'HD'. We are removing this scheme so this script is no longer needed. * Remove unused HD macros (#3120) * Remove unused HD macros The library prefixes most C and POSIX API calls with 'HD'. We are going to start removing these so the code looks like normal C. This PR removes most of the unused HD markup macros. * Replace ntohl/ntohs * Adds an optional version arg to bin/format_source (#3119) * Clean up mirror VFD code in utils dir (#3121) * Remove dead code * Replace mybzero with memset * Replace hbool_t/TRUE/FALSE with bool/true/false * Fix spelling issues flagged by codespell (#3130) * Make autogen.sh output message consistent (#3128) * Add Python for HDF-EOS zoo description (#3129) * Fix function name in comment in ros3 VFD (#3131) * Revert long double checks (#3133) * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9. * Update comments to reflect newer systems * Add java options to build scripts (#3127) * Add java options to build scripts Previously, cmakehdf5 turned on compiling of the java interface by default due to a value set in cacheinit.cmake. Now, consistent with how Fortran and CPP interfaces are handled, the script overwrites this default value to disable the libraries, fixing #2958. I also implemented the --enable-java/--disable java options for cmakehdf5, and -java for buildhdf5. Allen said these scripts should mention that compilers are to be specified in environment variables, but missing compilers causes errors at the CMake level, and CMake's error messages are already pretty informative (See the one in #2958 about JAVA_COMPILER). * Removed .lnt linter files (#3143) These were last usefully modified in 2004 * Fix path to libhdf5.settings in cmakehdf5 (#3140) * Many clang -Wextra-semi-stmt fixes (#2537) * Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END * Remove HD prefix from network calls (#3142) HDsocket(), etc. Only affects the mirror VFD and its test code. * Remove hbool_t/TRUE/FALSE from java (#3145) Replaces with bool/true/false * CMake: (feature) ROS3 and cmake config file. (#3146) - Added a cmake variable to the hdf5-config.cmake file which indicate if the library has been build with or without the read-only S3 functionality. * Define minimal permissions for new GitHub workflows (#3147) * Track s3 i/o when S3COMMS_DEBUG enabled (#3139) * Track s3 i/o when S3COMMS_DEBUG enabled * Fix the snapshots workflow (#3148) * Add upload url as artifact * Change doxygen path and comment log-url upload * zip doxygen files for upload * add workspace var * chore: fix grammar (#3150) * chore: fix grammar * Removes the HD prefix from java C99 calls (#3149) POSIX calls (HDstrndup, etc.) are unchanged * Correct the zip usage (#3153) * Many fixes to various compiler warnings (#3124) * Fixed various -Wmissing-variable-declarations by adding static keyword * In a few cases, renamed the variable suffix from _g to _s. * Fixed some -Wmissing-variable-declarations by using different declaration macros * Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero * Fixed various -Wcomma warnings * Fixed clang -Wstrict-prototypes warnings * Fixed various -Wunused-variable warnings * Updated some casts to fix the only 3 -Wcast-qual warnings * Fixed the only -Wsometimes-uninitialized warning * Create Security Policy (#3152) * Fix #1978 h5vers usage message. (#3162) Update Platforms Tested in RELEASE.txt. * speed-up building HDF5 (#3087) Disables building the tests when building the netCDF, etc. * Remove dead code behind #ifdef OLD_WAY (#3163) * Remove H5F_evict_tagged_metadata() (#3165) The rest of the library just calls H5AC_evict_tagged_metadata() directly. * Add missing space in zip command (#3167) * Fixed check for a VOL's async compatibility (#3164) * cap flag fix in test * added async comp. output * Update Linux workflows (#3173) * Consolidate environment setup * Turn on ros3 VFD in CMake (Linux only) * Add gh-pages doxygen link (#3175) * Fix the doxygen to gh pages and artifact creation (#3176) * Tidy the list of options in main.yml (#3181) * Remove HD/hbool_t from fortran (#3182) * Remove HD/hbool_t from high-level lib (#3183) * Remove HDva_(arg|copy|end|start) (#3184) * Drop HD prefix & hbool_t from H5TS (#3180) * Remove HD from fork/exec*/wait* (#3190) These are not C99 but are hidden behind ifdefs and are highly unlikely to ever have non-POSIX equivalents. * Fix assertion failure when attempting to use IOC VFD directly (#3187) * Rename HDqsort() to qsort() (#3193) * Rename HDqsort() to qsort() * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Rename HDpipe() to pipe() (#3192) Pipe is POSIX but implemented in Microsoft's CRT * Rename HDassert() to assert() (#3191) * Change HDassert to assert * Fix bin/make_err * Rename HD(f)printf() to (f)printf() (#3194) * Add note about HDF5_VOL_CONNECTOR to tools usage (#3159) * Rename HDsystem() to system() (#3197) system() is only used in the iopipe test and the things it calls (which are POSIX-y) are protected by an ifdef. * Remove HD from HDposix_memalign() (#3196) The posix_memalign call is only used in the direct VFD, which can only be built if posix_memalign() is available. * Remove HD from memory allocate/free calls (#3195) * HDcalloc * HDfree * HDmalloc * HDrealloc * chore: fix grammar (#3207) * docs: remove redundancy in Data Transfer section of user guide (#3208) * Remove checks for setsysinfo, which is unused (#3205) * Autotools * CMake * Remove HD from protected POSIX calls (#3203) These calls are non-C99 but protected by ifdefs and have no Windows equivalents: * HDalarm * HDasprintf * HDclock_gettime * HDfcntl * HDgethostname * HDgetrusage * HDsymlink * Rename HDato*() to ato*() (#3201) * Remove some "Programmer" comments (#3209) These are meaningless noise. Removes the "Programmer" lines on comment start lines: /* Programmer: John Smith These complicate my sed script that will rip out the rest of the comments. * Rename HDexit() and related to exit(), etc. (#3202) * HDatexit * HDexit * HD_exit * Remove HD from strto* calls (#3204) * HDstrtod * HDstrtol * HDstrtoll * HDstrtoul * HDstrtoull * HDstrtoumax * Remove HD from C std lib file ops (#3206) * HDfclose * HDferror * HDfeof * HDfflush * HDfopen * HDfread * HDfwrite * Remove programmer/date from comments (#3210) * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work * Remove HD from HDmem* calls (#3211) * Remove HD from HDis* (e.g., isalpha) (#3212) * HDisalnum * HDisalpha * HDiscntrl * HDisdigit * HDisgraph * HDislower * HDisprint * HDispunct * HDisspace * HDisupper * HDisxdigit * Update actions for release option, fix branch for daily build (#3185) * Update actions for release option, fix branch for daily build * Scheduled workflows run on latest commit on the develop * Add snapshots location * docs: improve consistency in verb form (#3076) (#3188) * fix gh action if statements (#3213) * Adjust presets timeout and fix build script VS versions (#3215) * Several ros3vfd logging improvements * Committing clang-format changes * Update COPYING (#3231) Fixed old support URL. * addresses compilation fortran warnings on Frontier (#3236) * Fix doc for H5allocate_memory (#3240) * merge bbrelease to release (#3232) * merge bbrelease to release * Fix pre-req workflow * Replace support.hdfgroup.org URLs for alternative COPYING file (#3228) * Replace support.hdfgroup.org URLs for alternative COPYING file locations in copyright headers with https://www.hdfgroup.org/licenses. Replace support.hdfgroup.org URL for alternative COPYING_LBNL_HDF5 with github URL. Tweak chkcopyright script for change from UICOPYRIGHTSTR to THGCOPYRIGHTSTR. * Replace 1_10 reference with develop branch (#3227) * Switch CI to use release script (#3242) * Subfiling VFD source cleanup (#3241) * Subfiling VFD source cleanup Modularize Subfiling CMake code into separate CMakeLists.txt file Update Mercury util code to latest version and update Copyright Generate mercury_util_config.h header file instead of using pre-generated file Remove unnecessary Mercury functionality Fix minor warning in Subfiling VFD code * Remove Mercury headers from Autotools publicly-distributed header list * install h5fuse.sh in bin dir. (#3244) * Disable h5py until fixed properly without spack (#3243) * ROS3: (feature) Temporary security credentials (#3030) - Implemented support for AWS temporary security credentials. For this kind of credentials also a session/security token should be included in the request by adding the x-amz-security-token header. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Avoid truncating at null byte when copying to std::string (#3083) --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix CMake builds when Subfiling VFD isn't enabled (#3250) * Fix CMake builds when Subfiling VFD isn't enabled * Add Subfiling VFD entry to hdf5-config.cmake.in * Fix some warnings in developer builds (#3247) * Fix some warnings in developer builds * Switch approach to Winline flag * Fixed more warnings about extra semicolons (#3249) * Require semi-colon after H5_CHECK_OVERFLOW calls Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro (#3259) Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning causing Werror Release builds to fail * Update DEFAULT_API_VERSION documentation for CMake (#3255) * Update DEFAULT_API_VERSION documentation for CMake * Fix hint --------- Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * changed the scope of #ifdef DOXYGEN to now include H5D multi-functions (#3254) * Option changed but not all references (#3252) * Option changed but not all references * remove quotes from binary var * Move 1.12.3 release to October (#3263) * Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized warning (#3260) * removed the use of encoded single apostrophe (#3261) * removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read * updated sanitizer paragraph * fixed brief description for H5Fget_info * ROS3: (fix) Replaced HDfprintf (#3266) - Replaced the HDfprintf() functions by fprintf() to be consistent with other parts of the library. * chore: make VRFY output consistent (#3268) * CMake: (fix) Threads dependency (#3267) - If the HDF5 library has been build with either thread-safety or subfiling VFD feature on it will have an additional dependency on a threading library. This dependency has been added to the hdf-config.cmake.in file. * chore: fix grammar - get hang -> get hung (#3272) * Another round of fixing -Wextra-semi-stmt warnings (#3264) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * chore: fix typo - persent -> present (#3273) * Remove py-pip from h5py action (#3265) * Update release schedule (#3317) * Move 1.12.3 to November * Add 1.14.3 in October * Update README.md w/ 1.4.3 info (#3318) * Switch parallel compression to use vector I/O (#3245) Updates parallel compression feature to use vector I/O instead of creating and passing down MPI derived types to VFD * Fix incorrect error check in H5Ofill.c for undefined fill values (#3312) * Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314) * Fix loading plugin fails with missing directory GH issue #3248 (#3315) * Made HGOTO_ERROR a do-while loop (#3308) * Made HGOTO_ERROR a do-while loop * Update files to skip list and ignore_words_list (#3321) * Update files to skip list and ignore_words_list for codespell to not check files generated by autotools. Autotools generate misspellings that can't be fixed in HDF5 code. * Windows runtime items go into the bin folder (#3320) * A couple of documentation items to fix (#3332) * Fix h5repack for variable-length datatyped datasets (#3331) * Fix CVE-2018-11202 (#3330) A malformed file could result in chunk index memory leaks. Under most conditions (i.e., when the --enable-using-memchecker option is NOT used), this would result in a small memory leak and and infinite loop and abort when shutting down the library. The infinite loop would be due to the "free list" package not being able to clear its resources so the library couldn't shut down. When the "using a memory checker" option is used, the free lists are disabled so there is just a memory leak with no abort on library shutdown. The chunk index resources are now correctly cleaned up when reading misparsed files and valgrind confirms no memory leaks. * Fix CVE-2018-13867 (#3336) * Fixes the last of the -Wextra-semi-stmt warnings (#3326) * Fixed extra semi warning by adjusting alternative macro definitions * Find-replace H5E_END_TRY; -> H5E_END_TRY * Made H5Epush_goto a do-while loop, fixed indentation * Made GOTOERROR and ERRMSG do-while loops * Made Hgoto_error and Hgoto_done do-while loops * Made vrfy_cint_type and vrfy_ctype do-while loops * Made TEST_TYPE_CONTIG and others do-while loops * Removed extraneous semi-colons * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix a typo in RELEASE.txt * Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340) * Make h5dump spacing consistent when printing VLEN datatype (#3351) * Fix for the bug exposed from running test/set_extent.c when selection… (#3319) * Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled. This is a fix from Neil. The test/set_extent.c is modified to test for selection I/O enabled. * Add Fortran ES module to deploy list (#3341) * Add Fortran ES module to deploy list * Change fortran mod file export to use a list of names * test(parallel): verify FALSE case (#3356) * Implementation of the mpio driver with selection I/O. (#3222) * This changes the default selection I/O to on for MPIO. * Work around a testphdf5 failure on Cray MPICH machines (#3361) * set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with (#3364) CMake to fix Fortran build failures. * Add RELEASE.txt notes for recent selection I/O work. (#3374) * Fix possible performance regression introduced with in-place type conversion in 1.14.2 (#3376) * Correct script (#3377) * Correct CI settings (#3384) * Correct CI settings * Correct plugin file name * restore CI tarball name prefix to match bin/release (#3385) * Fix assertion failure during file close on error (#3387) * Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388) * Fix valgrind warning about write of uninitialized bytes (#3389) * Fix valgrind warning about write of uninitialized bytes in ScaleOffset filter (#3390) * Update presets, examples uncompress, szip cache (#3391) * Fix serial to parallel chunked dataset file space allocation bug (#3394) * chore: fix typo (#3405) * Fix for CVE-2016-4332 (#3406) 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 ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407) * Enable szip by default in Autotools (#3412) 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. * Re-enable SZIP default to ON in CMake (#3414) The Autotools were handled in a separate commit * Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368) * Add Intel oneAPI actions (#2949) (#2977) * ci: add Intel oneAPI actions (#2949) * ci: fix CMake installation * ci: use absolute paths for libtool installation * ci(oneAPI): update compiler versions and use cron * Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416) * chore: remove gubbins comment (#3420) * Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] (#3353) * Avoid H5Ocopy in h5repack for variable-length string types (#3419) * Skip atomicity tests for OpenMPI major versions < 5 (#3421) * Fix an issue with use of uninitialized memory in trefer_deprec.c test (#3422) * Add parallel examples in doxygen (#3413) * Fix use of uninitialized value in testpar/t_dset.c test (#3423) * Remove extraneous "33" in RELEASE.txt (#3425) * Revise file close assertion failure fix (#3418) * Remove intel oneapi warning (#3426) * Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with 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. * chore: match function call and VRFY() output (#3428) * Fix the Fortran extension used in example links (#3430) * Put H5T_CONV_ab macros in do..while loops (#3432) 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. * Convert some H5MM calls to standard C equivalents (#2382) * 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 * Add 1.14.4 to the release schedule (#3434) * Output stderr file in CMake testing on failure (#3431) * Add Intel oneAPI badges (#3433) * Add a CVE regression test action (#3445) * * Disable SZIP for Intel oneAPI Action (#3449) * Disable SZIP for Intel oneAPI Action * Disable Fortran and parallel * Update VOL CMake for REST VOL (#3450) * Update VOL CMake for REST VOL * Prevent linking static libs to VOLs * Add an h5py badge to README.md (#3477) * Removed all the ranks printing out testing information (#3457) * Fix Subfiling VFD IOC assignment bug (#3456) * Correct java test dimension (#3482) * Support CMake VOL builds with FetchContent from local directory (#3455) * Update VOL CMake for REST VOL * Prevent linking static libs to VOLs * index on fetch_local: 5c5c3f1505 Prevent linking static libs to VOLs * index on (no branch): 9a36d3e7b1 On fetch_local: WIP:add source dir fetch option for vols * Allow building of VOL from local source * Move LOCAL_DIR option to HDF5_VOL_ALLOW_EXTERNAL * Fix the Fortran include dir in install config files (#3454) * Convert hbool_t --> bool in examples (#3492) * Fix some minor formatting for consistency (#3499) * Create scorecard.yml (#3508) Bring in OSSF Scorecard code scanner as a GitHub action * Convert hbool_t --> bool in testpar (#3495) * hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491) * Convert hbool_t --> bool in test (#3494) * Convert hbool_t --> bool in src (#3496) * 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 * Added new Fortran API wrappers (#3511) * 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 * misc. fortran fixes for failing CI dailty tests (#3523) * fixed H5Lvisit* interface * changed integer type for direct write * Consistent initialization of hid_t in the tests (#3521) * Fix windows cpack with debug (#3525) * Add missing row for the ROS3 VFD in table #3415 (#3517) * fixed nvidia compiler issue (#3527) * Identify functions in a subgroup (#3530) * quiet warning on sunspot (gcc 11.2.0) (#3534) * Add API examples doxygen page (#3500) * removed C_INT32_T from Fortran APIs (#3537) * Add NVHPC 23.7 GitHub Actions (#3509) * Add NVHPC 27.3 GitHub Actions * Address @derobins review * Remove HD prefix from math functions (#3538) * Remove HD prefix from HDlog10 calls (#3539) Was missed in a previous commit and causes building subfiling to fail. * fixed arg to C H5Dwrite_chunk (#3541) * Strip HD prefix from string/char C API calls (#3540) * 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 * Convert main.yml CI into callable workflows (#3529) * Fix broken URL. (#3546) * Fix grammar (#3545) * Update oneAPI-C/A badge yml links. (#3564) * Check return values from HDF5 API calls. (#3556) * Adds link to h5fuse.sh in testpar for autotools (#3557) * Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped. * Some minor formatting and text changes (#3563) * Fix typos and grammar in t_pread. (#3565) * Fix typo (givin->given) in test/testframe.c. (#3567) * Fix ifx unused variable hdferr warning. (#3568) * Correct comments about H5Z_FILTER_NONE (#3572) * Update release script. (#3577) * fixed function declaration (#3579) * Fixed GH-3554 (#3584) Removed the extra condition * Remove h5dwalk.1 man page. (#3589) * Removed the use of -commons linking option on Darwin (#3581) Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used * Fix docs for H5Pset_dxpl_mpio_collective_opt() (#3594) * Fix typo: arange->arrange in src/H5Cmpio.c. (#3597) * Fix docs for H5Acreate2 and H5Acreate_by_name (#3598) * Use HDoff_t with lseek consistently (#3600) 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. * Replaces HDgetenv with getenv (#3599) * Develop tools move (#3580) Reorganizes the tools files to support the VOL tests * Clean up Subfiling VFD header doxygen formatting (#3601) * Remove `sh` to run bash script. (#3590) * Correct path name of ddl file to be changed (#3607) * Fix potential uninitialized variable (#3602) Moves a union initialization up a bit so it's performed before code that can jump to the cleanup target, where file descriptors could be checked without being initialized. This could only happen in test code and only in an out-of-memory situation. Fixes Coverity 1542254 * Remove unnecessary assignment in test generator (#3603) Fixes what looks like a copy/paste/modify error in the format convert test file generator, where an array element is assigned one value and them immediately overwritten by another value. Fixes Coverity issue 1542285 * Remove useless define TRUE/FALSE statements. (#3604) * Fix typo behaviour and dependes. (#3605) * Fix typos (#3609) * Fixed unused variable in H5CS.c (#3552) (#3612) * Fixed #3552 * Fix grammar (#3614) * Cleanup unused statements (#3553) (#3617) Removed unnecessary assert statements and noise comments. * Fix Intel oneAPI icc warning (#3619) * Fix several spelling/grammar issues (#3621) * Add HPC CDash to README.md (#3623) * Disable static + thread-safe on Windows w/ CMake (#3622) 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 * Remove unused member from H5D_shared_t struct. (#3628) * Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624) * Fix grammar (#3635) * Disambiguate error output messages. (#3634) * Disambiguate error output messages. * Address @brtnfld review. * Fail CMake on Windows when sub-filing VFD is enabled (#3636) * Improve consistency in past tense usage (#3638) * Split out test logic to separate file (#3639) * Drop MPI-2 support (#3643) * Switch IEEE flags for NAG Fortran (#3644) Default is -ieee=stop, which causes problems when the H5T module performs floating-point type introspection. The new mode is -ieee=full * Remove 1.10.11 info from README.md (#3646) * Fixes GH#1027 compilation error (#3654) * Remove 1.10 badge (#3650) * Use real URLs and updated names for plugins (#3651) * synchronize TGZ naming convention/usage * Update parallel compression feature to support multi-dataset I/O (#3591) * Add more tests for selection I/O. (#3528) * Adjust 1.14 files after merging ---------
* Sync with develop (#2871)Dana Robinson2023-05-021-0/+6
|
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-1/+1
| | | | | * Update format source to clang 13 * More format changes
* Removes cruft from a few header files (#1534)Dana Robinson2022-03-291-5/+0
| | | | * Unnecessary extern C guards in cache headers * Non-existent H5Xpublic.h includes hidden behind NOT_YET symbols
* Simplify function enter macros for performance benefits (#1024)David Young2021-11-081-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Take a stab at using constructors to initialize instead of function-entry macros. This is a work in progress. It's good enough to run `many_dsets`. * Committing clang-format changes * Add the `many_dsets` benchmark and some scripts I used on jelly for setting up the build/test environment and for recording/flame-graphing profiles. * Committing clang-format changes * Change my Makefile and environment script to work both on jelly and on mayll (and probably on Summit). * Disable clang-format "fix." * Replace the `if (!H5_TERM_GLOBAL)` test in each FUNC_ENTER_ macro with `if (true)`. * Fix bad grammar in a comment. * Instead of labeling the H5*__init_package routines constructors, fold each into an initialization routine, H5*_init(), and call each of the H5*_init() routines. Call most of the H5*_init() routines from H5_init_library() in an explicit order that I found out earlier by instrumenting each __init_package routine and running the library tests. Roll H5FD*__init_package routines into H5FD*_init() routines. This change ends just-in-time initialization of package dependencies by package initializers. Don't track in per-package variables (H5_PKG_INIT_VAR) whether each package has been initialized. Instead, track in a single library variable whether the whole library is initialized or not. Drive the initialization of packages by H5_init_library() with a table of initializer routines. Also drive the termination of packages by H5_term_library() with a table. Perform initialization as needed from FUNC_ENTER_API_INIT(err). This basically restores the old behavior of that macro. Delete a bunch of #definitions in H5private.h that have fallen out of use with these changes. * Committing clang-format changes * Undo the bad auto-formatting that appears to have occurred in spite of my disabling it. Bracket some code in /* clang-format off */ /* clang-format on */ to prevent a recurrence. * Remove a diagnostic abort(). * Fix a logic error: print a comma between every package terminator run, and don't print an initial comma. * Complete the changes I started in H5_term_library() that undo the bad auto-formatting. Stop tracking whether package "tops" were initialized in per-package variables H5*_top_package_initialize_s. H5_term_library() takes care of that for them. Remove H5R_top_term_package() and H5R_term_package(), they don't do anything. * Committing clang-format changes * NFCI. Simplify macro text: replace `if (true) {` with `{`. * Fix formatting and suppress clang-format on a longer range. * Quiet some unused label, unused variable complaints that cropped up after I simplified the FUNC_ENTER_ macros for the sake of performance. * Committing clang-format changes * Delete some programs and scripts that don't belong in the pull request. * Use the right function-entry macro. * Use a sensible format and disable auto-formatting. * Stop calling do-nothing initializer H5FS_init(). Delete it. * Document what changes to make if the default VFD changes. * While I am here, change an `await_prior` flag on the terminator table to `true` to match the previous, non-table-driven code that was here. Found the oversight making the following changes: NFCI: insert an empty line and copy over slightly-edited comments from the previous version, where those comments still correctly explained how library termination operated. * NFCI: lower a staircase. * Replace every occurrence of FUNC_ENTER_NOAPI_INIT(...) with H5_PUSH_FUNC since that is all that that macro does any more. Quiet a bunch of new warnings by changing FUNC_ENTER_NOAPI(...) to FUNC_ENTER_NOAPI_NOERR and removing disused `done:` labels. * NFCI: add curly braces around a multiline statement. * Quiet a signed/unsigned comparison warning. * Add some documentation about library initialization and shutdown. * Make sure that the library is initialized, or else that initialization is already underway, before performing any VFD's initialization. * Committing clang-format changes * Committing clang-format changes * Reduce differences from `develop` branch. * Always initialize `tot_init`. * Committing clang-format changes * Fix typo: H5SL_init initializes skip lists, not VOL. * Remove H5_TERM_GLOBAL test in H5T_init. H5T_init was unusual in that it tested H5_TERM_GLOBAL and exited early if it was set. No other module initializers did that, and I cannot find any reason that should be necessary. Tests still pass when I remove it, so away it goes. * Use HD prefix. * Add function header comments. * Drop the intermediate variable, it's only used once. * Extract subroutine `H5FDperform_init(hid_t (*init)(void))` that initializes the library, if necessary, before calling its VFD-initializer argument. Use H5FDperform_init in the definition of the symbols H5FD_<vfd> (e.g., H5FD_SEC2), which may be evaluated before the library is initialized, like so: ``` ``` I implement H5FDperform_init in its own source file, H5FDperform.c, and exclude that file from trace processing because the `bin/trace` cannot deal with the function-pointer type. * Straggler from last: add new source file src/H5FDperform.c. * Committing clang-format changes * Add a missing file to the MANIFEST. * Switch to FUNC_ENTER_API_NOINIT in H5FDperform_init() and hbool_t in H5_term_library(). Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-231-5/+5
| | | | | | | | | | | | | | | | * Fixed many -Wreserved-id-macro warnings by fixing header guard spelling Removed leading underscore(s) from header guard spelling. Used 2 regexes: ` _H5(.*)_H` ` __H5(.*)_H` Applied case-insensitively to only .h files. * Modified scripts that generate header files to not use underscore prefix Interestingly, there was already no leading underscore in the trailing comment at the end of the file * Fixed remaining -Wreserved-id-macro warning not caught by regex
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Add flag to H5CX_pop that allow setting the properties to return to ↵Quincey Koziol2020-12-011-1/+1
| | | | application to be skipped. (#134)
* Clang-format of source filesAllen Byrne2020-09-301-38/+33
|
* Add object header flags to API contextChris Hogan2019-11-141-0/+2
| | | | | Add missing DCPL to API context state Replace a couple LCPL H5P_get calls with H5CX_get_*
* Add character encoding to lcpl contextChris Hogan2019-11-041-1/+3
|
* Use API context to store/retrieve LCPL when creating intermediate groupsChris Hogan2019-10-291-0/+4
|
* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-2/+2
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Merge branch 'develop' of ↵Songyu Lu2019-04-081-0/+4
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * Setting API context for fapl and libver_bounnds in preparation for the ↵Vailin Choi2019-04-041-0/+4
| | | | | | | | H5Sencode changes.
* | HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce ↵Songyu Lu2019-03-221-8/+0
| | | | | | | | the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work.
* | HDFFV-10658: setting and getting properties in API context:Songyu Lu2019-03-131-0/+12
|/ | | | | 1. external file prefix and VDS prefix. 2. the datatype, dataspace, and LCPL of the dataset for VOL connector.
* Add API routines to retrieve, restore, reset, and free library state.Quincey Koziol2019-03-111-0/+18
| | | | | | (Primarily for use in the async VOL connector, which has to schedule API operations for future execution and then restore the state of the library when the operation actually executes)
* Move 'minimize dataset object header flag' into API contextQuincey Koziol2019-03-051-0/+4
|
* HDFFV-10625 -- Implemented a process-0 read and then broadcast for ↵Quincey Koziol2019-01-071-0/+3
| | | | collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
* Corrected comment in src/H5VLint.c, fixed pass-through info size inQuincey Koziol2019-01-061-0/+2
| | | | | | | src/H5VLpassthru.c, switched to stashing VOL connector ID & info in API context (in src/H5CX.c, src/H5CXprivate.h, src/H5F.c, src/H5Fint.c, and src/H5Fefc.c), patched up all sorts of issues in the tests, to make them work with 'check-vfd' (and 'check-vol' again).
* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-0/+2
| | | | modified: test/dsets.c
* Finished move of H5DOread/write_chunk calls to H5D.Dana Robinson2018-04-301-7/+0
|
* Resolve memory leak of last API context, by freeing it in H5CX terminateQuincey Koziol2018-04-181-1/+0
| | | | routine.
* Correct errors with non-"instrumented library" builds (production & parallel,Quincey Koziol2018-04-051-0/+2
| | | | generally speaking).
* Remove redundant 'is_collective' parameter from H5CX_set_loc.Quincey Koziol2018-03-271-1/+1
|
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-1/+5
| | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-0/+142