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* Remove cached datatype conversion path table entries on file close (#3942)jhendersonHDF2024-02-141-0/+3
| | | | | | | | | | | | | | | | | | | | Remove cached datatype conversion path table entries on file close When performing datatype conversions during I/O, the library checks to see whether it can re-use a cached datatype conversion pathway by performing comparisons between the source and destination datatypes of the current operation and the source and destination datatypes associated with each cached datatype conversion pathway. For variable-length and reference datatypes, a comparison is made between the VOL object for the file associated with these datatypes, which may change as a file is closed and reopened. In workflows involving a loop that opens a file, performs I/O on an object with a variable-length or reference datatype and then closes the file, this can lead to constant memory usage growth as the library compares the file VOL objects between the datatypes as different and adds a new cached conversion pathway entry on each iteration during I/O. This is now fixed by clearing out any cached conversion pathway entries for variable-length or reference datatypes associated with a particular file when that file is closed.
* Sync 1.14 branch with develop (#3923)Larry Knox2024-01-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix build error on freebsd (#3883) Fixes: checking for config freebsd12.1... no checking for config freebsd... found compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0 compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0 stdout: .: cannot open ./config/classic-fflags: No such file or directory * Correct CMake command and example packaging (#3888) * Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot to update them monthly (#3892) * feat: hashpin sensitive dependencies on GHAs Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> * feat: enable dependabot for monthly updates on GHA Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> --------- Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> * Some changes to portal links when they could be found on docs.hdfgroup.org, 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 * Add variable option syncing for examples (#3885) * Add period(.) at the end of the sentence for consistency. (#3897) * Remove redundant backslash character from comment. (#3899) * Disable doxygen as errors for netcdf (#3900) * disable building doxygen for netcdf test * Doc versions (#3903) * Added missing \since tags to H5D. * Committing clang-format changes * Fixed H5T version info. * Committing clang-format changes * Added missing version info to H5E. * Committing clang-format changes * Added version info to H5F public APIs. * Committing clang-format changes * Added missing H5Z public API version info. * Added missing version info to H5G public APIs * Added missing version info to H5I public API. * Added missing version info to H5 public APIs * Committing clang-format changes * Added missing version info to H5P public APIs * Added missing version info to H5R public APIs * Fix comment error. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Change Trouble Shooting to Troubleshooting (#3905) * Implement optimized support for vector I/O in Subfiling VFD (#3896) 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 'warning density' computation to the warnhist script (#3910) * 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> * Added H5Fdelete_f with test (#3912) * New Fortran Examples added (#3916) * added subfiling example * Added filtered writes with no selection example * Version and space corrections. * Restore H5_VERSION definition in configure.ac. * renamed defined H5_VERS* to avoid conflicts (#3926)
* 1.14 sync with develop (#3660)jhendersonHDF2023-10-121-15/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 ---------
* Bring the H5detect removal change from develop (#3648)Dana Robinson2023-10-091-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Bring the H5detect removal change from develop - Removed CMake cross-compiling variables * HDF5_USE_PREGEN * HDF5_BATCH_H5DETECT These were used to work around H5detect and H5make_libsettings and are no longer required. - Running H5make_libsettings is no longer required for cross-compiling The functionality of H5make_libsettings is now handled via template files, so H5make_libsettings has been removed. - Running H5detect is no longer required for cross-compiling The functionality of H5detect is now exercised at library startup, so H5detect has been removed. * 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.
* Merge with develop (#2790)Dana Robinson2023-04-221-6/+3
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* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-14/+14
| | | | | * Update format source to clang 13 * More format changes
* Fix some const cast and stack/static object size warnings (#1700)jhendersonHDF2022-05-011-1/+1
| | | | | | | | | * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now
* Replace H5detect's build-time detection of C99 integer properties with a (#1400)David Young2022-04-221-19/+16
| | | | | | | * Replace H5detect's build-time detection of C99 integer properties with a table-driven routine, `H5T__init_native_int()`, that is run at library initialization time.
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-081-6/+0
| | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)Sean McBride2021-03-091-1/+2
| | | | | | | | | | | | | * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-231-3/+3
| | | | | | | | | | | | | | | | * 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.
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-291-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction
* Fix problems with vlens and refs inside compound using H5VLget_file_type() ↵hdf5-1_13_0-rc5Neil Fortner2021-01-221-2/+2
| | | | | | | | | | | | (#274) * Fixed problems with vlens and refs inside compound using H5VLget_file_type() * Fix date in RELEASE.txt * Add assertions * Move some manipulation of H5VL_object_t struct fields into the H5VL package.
* Bring async branch to develop (#166)Quincey Koziol2020-12-141-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add H5Fwait, H5Dwait, and other changes for async vol connector * Revert temporary testing changes * Add H5Fwait to header file * Add H5VLreset_lib_state() routine. * Correct VOL wrap context when retrieving library state for file open & create. * Manage the API context's VOL connector state as part of the library state. * Set the 'VOL connector property valid' flag when restoring the library state. * Don't push new API context on stack when retrieving "current" one. * Check for NULL VOL wrap context before decrementing refcount on it, when freeing the API context state. * Manage recount of underlying connector for VOL wrap context. * Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and release the global lock on the HDF5 library. * Update library with new functions related to library global lock * Add asynchronous token API * Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the threadsafety (H5TS*) routines. * Sync w/develop * Initial event set code framework. * Elaborate on the H5ES routines, starting to add API routines. Update the "close ID" callbacks to allow asynchronous request tokens to be passed in from an asynchronous close API call. Refactor current asynchronous API routines (H5Fopen/H5Fclose and H5Dread/H5Dread) to use event sets instead of directly working with request tokens from the application. Clean up a few other minor warnings & code style issues. * Implement H5EScreate, H5ESget_count, and H5ESclose. It should be possible to write a simple application that creates an event set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and H5Fclose_async, then calls H5ESclose (which waits for all async events to complete). * Add source file for event set test. * Refactor sync & async API routines to call common routine. Move dataset API read / write routines to src/H5D.c, along with all the other API routines. Progress on "fake" async VOL connector, for testing. * Modify async implementation to wrap async requests in a H5VL_object_t struct so the VOL layer can find the connector when accessing the request at a later point. * Free the requests is H5ESclose. Remove comments implying that request wait, notify, and cancel callbacks should free the request. * Fix bug in error handling in H5Fclose. * Fix bugs in async file routines. Rename H5VL_create_object_generic to H5VL_create_object. * Add explicit async version of H5Fcreate. * Add more _async routines * Correct typo for return value from H5Awrite changes * Add H5EStest and H5ESwait routines * Updated with API tracing info * Fix NULL pointer dereference in H5ES__wait * Add H5is_library_terminating() routine, so that VOL connectors can detect when the library is shutting down. * Fix typo * Remove event from event set's linked list * Move block of code so that vol_obj is valid * Avoid setting properties in the DXPL when reseting the library state (and in the test code). * Refactor argument tracing to implement new capability for tracing arguments of non-API routines, with the H5ARG_TRACE macro. This macro is updated automatically with the bin/trace script that runs as part of the autogen.sh process. Major changes were in src/H5trace.c and bin/trace, with the other changes being cleanups to the argument lists, to improve their presentation in the tracing output. Also - added the "managed string" routines, which can dynamically allocate strings, appending printf-formatted output to the string efficiently. * Release memory for managed strings * Fix printf() formats. * More printf() format fixes. * Add H5Eappend_stack routine and regression tests * Clean up a few missed merge conflicts and update the error stacks. * Remove unnecessary fork() operations and ten second sleep(). * Restore commented out attribute out, to better enable tracking down the previous failure * Allow multiple H5ARG_TRACE macros within a routine to be updated * Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert. * Merge "managed" string routines into "ref-counted" strings, and refactor code to use them. * Add missing file. * Add caller's name and arguments to event, for error reporting * Refactor event set setup for "API common" internal routines * Checkin async API routines for H5A* and H5G* modules as listed in ID-283. Fix couple h5dump expected output files due to the changes. * Add some of the error query routines needed for event sets. * Refactor to make async setup / teardown and "common" routines cleaner * (1) Add async APIs to H5L, H5F, and H5D modules (2) Fix errors in previous checkins of async APIs in H5A and H5G modules (3) h5dump expected output changes * Enhance event info, for better error handling * Change name of temporary vol_obj variable, to help reduce coding errors * Fix oversight with vol_obj pointer * Minor code cleanup * Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state * Run source formatter * Change H5TSmutex lock and release to include a lock count * Update error reporting ideas * Minor updates to improve sanity checking for retrieving / restoring library state * Updated with feedback from h5py team members * Refactor internal event set list and event handling, add implementation for H5ESget_err_info * Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines. * Update API tracing for new H5VL_request_status_t typedef * Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure * Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation * Remove 'canceled' event status from Java constants * Be safer about releasing resources when inserting a newly opened/created object or file into an event set * Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate". * Remove H5ES_STATUS_CANCELED from Java wrappers also * (a) Add async APIs for H5O module as listed in jira issue ID-283. (b) Remove verification of name parameter in async related routines for H55A and H5L modules because it is checked in H5VL_setup* routine. (c) Modify h5dump expected output due to the async changes. * Corrections based on PR feedback. * Further changes to make based on PR feedback. * Fix missed merge marker, and reformatted line * Clean up some warnings * Correct level of indirection * Relocate prototype (and doxygen info) for H5Aclose * Change non-static function declarations to be static * Ensure that H5TSpublic.h header gets installed (#129) * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c. * Add H5Iregister_future routine and tests. * Correct return value for H5Lexists_async * Add H5_DLL macro to public H5ES API routines * Update supported -> flags parameter for introspect_query callback * Remove my email address. Update passthrough VOL connector ID. * Fix comment for post_open_api_common * Remove unused non-blocking VOL connector * Minor cleanup in async branch in preparation for merge to develop * Update CMake and the Autotools to use the new pass-through VOL ID * Fix for SWMR daily test failures (#160) The H5I_register_using_existing_id() call did not initialize the future ID callbacks, causing the library to segfault when it tried to resolve those function pointers. * Added selective async APIs (#150) * Added selective async APIs Description: Added the following APIs: H5Ropen_attr_async H5Ropen_object_async H5Ropen_region_async H5Mcreate_async H5Mopen_async H5Mput_async H5Mget_async H5Mclose_async H5Tcommit_async H5Topen_async H5Tcopy_async H5Tclose_async - Updated an expected output file to include a new internal function in the error stack for the failure case. * Updated async APIs per reviews, including removing async version of H5Tcopy. * Removed statements that were added by mistake in the previous commit. * Fix compile issues in H5M and warnings elsewhere * Reformat code * Brings VOL_LIST changes from develop. (#163) Co-authored-by: Houjun Tang <htang4@lbl.gov> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <derobins@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-2/+1
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Clang-format of source filesAllen Byrne2020-09-301-897/+575
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* Move H5T_vlen_reclaim to package scopeQuincey Koziol2020-08-071-0/+1
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-1/+2
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* H5R: fix encoding of references that are part of compound typesJerome Soumagne2020-07-281-1/+1
| | | | Add corresponding test and some debug information
* Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-261-398/+288
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| * H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-11-261-0/+4
| | | | | | | | | | | | Valid for both deprecated and non-deprecated references Update test
| * Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-13/+15
| | | | | | | | | | | | | | | | | | | | | | location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
| * Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-30/+57
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
| * Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-081-16/+23
| | | | | | | | | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
| * Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-1/+1
| | | | | | | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
| * VOL FEATUREDana Robinson2018-10-101-0/+1
| |
| * Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-1/+3
| |
| * Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-1/+1
| | | | | | | | | | | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-0/+3
| |\ | | | | | | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| | * Fix for daily test failuresVailin Choi2018-02-141-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | Move the declarations for the three arrays of versions from H5Opkg.h: (1) H5O_layout_vers_bounds to H5Dpkg.h (2) H5O_dtype_ver_bounds to H5Tpkg.h (3) H5O_sdspace_ver_bounds to H5Spkg.h This is to fix Windows' complaint for unresolved symbols.
| * | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-351/+195
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* | Changes to make timers within the library monotonic.Quincey Koziol2017-09-031-1/+1
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* [svn-r30017] Description:Quincey Koziol2016-06-061-2/+2
| | | | | | | | | Bring warning cleanusp in r29990, 29993, 29997, 29999, 30004 from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production. (h5committest forthcoming)
* [svn-r27768] Description:Quincey Koziol2015-09-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r27428] Bug fix: DAILYTEST-170Albert Cheng2015-07-241-0/+33
| | | | | | | | | | | | | | | | | | | Description: XL compilers in ostrich (PowerPC64 linux) fail in test/dt_arith because of the removal of the LLONG_TO_LDOUBLE_CORRECT (removed in r26625) and LDOUBLE_TO_LLONG_ACCURATE (removed in r26623). Solution: Reverse revisions r26623: bring back LDOUBLE_TO_LLONG_ACCURATE configure macro r26625: bring back LLONG_TO_LDOUBLE_CORRECT configure macro r26627: bring back WANT_DATA_ACCURACY configure macro which is used together with the above two macros. This also brings back the enable-dconv-accuracy configure option. Tested: h5committested. Also tested in ostrich using the XL compilers.
* [svn-r26625] Description:Quincey Koziol2015-03-271-15/+0
| | | | | | | | | | | Bring r26543 from autotools_rework branch to trunk: Remove the LLONG_TO_LDOUBLE_CORRECT macro/define, it's working around bugs in very old SGI/FreeBSD/Windows compilers. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26623] Description:Quincey Koziol2015-03-271-18/+0
| | | | | | | | | | | Bring r26513 from autotools_rework branch to trunk: Remove the LDOUBLE_TO_LLONG_ACCURATE macro/define, it's working around bugs in older SGI, HP/UX, MacOSX and Windows .NET 2003 compilers. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26606] Description:Quincey Koziol2015-03-261-9/+2
| | | | | | | | | | | Bring r26508 from autotools_rework branch to trunk: Remove HW_FP_TO_LLONG_NOT_WORKS macro/define, it was only addressing Windows .NET 2003 compiler issues. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26605] Description:Quincey Koziol2015-03-261-13/+0
| | | | | | | | | | | | | | Bring r26503 & r26528 from autotools_rework branch back to the trunk: Remove old platform configure files: craynv, dec-flags, hpux11.23, ia64-linux-gnu, nec-superux14.1, sv1-cray, x86_64-redstorm-linux-gnu Also remove CONVERT_DENORMAL_FLOAT, since this was only set in the configure files being removed. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26598] Description:Quincey Koziol2015-03-261-2/+1
| | | | | | | | | | | Bring r26501 from the autotools_rework branch to the trunk: Remove ULLONG_TO_LDOUBLE_PRECISION macro/define, as it's targeting bugs in the FreeBSD and Cygwin compilers. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26596] Description:Quincey Koziol2015-03-261-11/+2
| | | | | | | | | | | Bring r26499 from autotools_rework branch to trunk: Remove ULLONG_TO_FP_CAST_WORKS macro/define, as it only applies to older platforms we aren't supporting any longer. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r26595] Description:Quincey Koziol2015-03-251-8/+0
| | | | | | | | | | | Bring r26494 from autotools_rework branch back to trunk: Remove the LDOUBLE_TO_UINT_ACCURATE macro/define, it was addressing problems with older Intel compilers on Linux that are no longer supported. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for several days)
* [svn-r26591] Description:Quincey Koziol2015-03-251-12/+1
| | | | | | | | | | | | Bring r26492 from autotools_rework branch back to trunk: Remove the FP_TO_ULLONG_ACCURATE and FP_TO_ULLONG_RIGHT_MAXIMUM macros/defines, which were added to address problems with older PGI compilers and HP-UX systems and are no longer supported. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (daily tested on branch for >1 week)
* [svn-r26587] Description:Quincey Koziol2015-03-251-25/+3
| | | | | | | | | | | Bring r26489 from autotools_rework branch to trunk: Remove the ULONG_TO_FP_BOTTOM_BIT_ACCURATE macro/define, as it was added for SGI systems and old Solaris systems, which are no longer supported. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested for >1 week)
* [svn-r26584] Description:Quincey Koziol2015-03-251-1/+1
| | | | | | | | | | | Bring r26485 from the autotools_rework branch to the trunk: Remove the ULONG_TO_FLOAT_ACCURATE macro/define, we no longer support the Sandia system where it was necessary. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (daily tested for >1 week)
* [svn-r26560] Description:Quincey Koziol2015-03-241-8/+2
| | | | | | | | | | | Bring r26483 from autotools_rework branch back to trunk: Remove INTEGER_TO_LDOUBLE_ACCURATE macro/define - we no longer support SGI systems. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (daily tested on branch for >1 week)
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