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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-0854-1953/+10097
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Remove ability to loc by ref from H5VL layerJerome Soumagne2019-10-083-113/+2
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* Add support for retrieving object name by tokenJerome Soumagne2019-10-081-0/+12
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* Add H5VL_OBJECT_GET_TYPE to get object typeJerome Soumagne2019-10-083-1/+63
| | | | Add H5VL_OBJECT_LOOKUP to lookup objects
* Add H5VL_MAX_TOKEN_SIZE and H5VL_token_tJerome Soumagne2019-10-081-0/+7
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* Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.Quincey Koziol2019-10-088-81/+135
| | | | Remove "by address" location for VOL operations. (Switching to "by token")
* Fix H5VL_blob_get to return size of blobJerome Soumagne2019-10-0814-104/+490
| | | | | | | | | | | | | | | | | | | | Fix const in blob API Add H5HG_HEAP_ID_SIZE macro to return native blob size Add maximum size for blobs Fix blob API callbacks to pass VOL file object Add public wrappers for blob VOL API Implement passthrough blob callbacks Update H5Tvlen after callback changes Update trace information for H5VL blob routines Fix public header inclusion in native and passthru headers
* Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-0822-468/+1033
| | | | | | | 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.
* Merge pull request #1985 in HDFFV/hdf5 from ↵Dana Robinson2019-10-042-80/+88
|\ | | | | | | | | | | | | ~DEROBINS/hdf5_der:H5Gget_object_behavior_change to develop * commit 'ff3278f1a0d57663d73caa6aaa7f209864e9a9bd': Fixed a bug (HDFFV-10899) where the behavior of the deprecated H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before.
| * Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-042-80/+88
|/ | | | | | | | H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before.
* Merge pull request #1983 in HDFFV/hdf5 from ↵Dana Robinson2019-10-031-3/+4
|\ | | | | | | | | | | | | ~DEROBINS/hdf5_der:small_develop_tweaks to develop * commit '638d31a78a9ea5db438d30e78f8cbaa1146b7f87': Fixed the java assert issue with H5O cache corking calls.
| * Fixed the java assert issue with H5O cache corking calls.Dana Robinson2019-10-031-3/+4
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* Merge pull request #1980 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-033-370/+214
|\ | | | | | | | | | | * commit '4394f0776b3e695b9ab383421824e4533da821a8': More whitespace changes Whitespace cleanup
| * More whitespace changesAllen Byrne2019-10-032-211/+57
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| * Whitespace cleanupAllen Byrne2019-10-031-159/+157
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* Merge pull request #1973 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-029-302/+198
|\ | | | | | | | | | | * commit 'bc6115931877c6f6d63977f2c03c5e2dbffe3e56': HDFFV-10919 merge synching HDFFV-10408,10918 Add note
| * HDFFV-10919 merge synchingAllen Byrne2019-10-028-301/+189
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| * HDFFV-10408,10918 Add noteAllen Byrne2019-10-021-1/+9
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* Merge pull request #1968 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-022-1/+121
|\ | | | | | | | | * commit '643d298823255a684862f4c6eb85ac5afde4b796': HDFFV-10918 add tests for h5repack ext storage
| * HDFFV-10918 add tests for h5repack ext storageAllen Byrne2019-10-012-1/+121
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* Merge pull request #1966 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-011-0/+1
|\ | | | | | | | | * commit '09e6dcbfbb50d359177c9ee72e662287eb04d9c7': Add new toolchain file
| * Add new toolchain fileAllen Byrne2019-10-011-0/+1
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* | Merge pull request #1959 in HDFFV/hdf5 from ↵Vailin Choi2019-10-012-6/+15
|\ \ | |/ |/| | | | | | | | | ~VCHOI/my_third_fork:bugfix/iteration_error_in_test_versionbounds to develop * commit '9ea386b6a660bd29225e96a246439db0c7f73da2': Fixed the iteration error in test_versionbounds() in test/dtypes.c.
| * Fixed the iteration error in test_versionbounds() in test/dtypes.c.Vailin Choi2019-09-302-6/+15
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* | Merge pull request #1963 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-09-303-58/+61
|\ \ | | | | | | | | | | | | * commit 'bbe81a2155bfa42545579761c4f064353d6f68de': fix for statement declare of type
| * | fix for statement declare of typeAllen Byrne2019-09-303-58/+61
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* | Merge pull request #1958 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:develop to developJake Smith2019-09-301-24/+65
|\ \ | | | | | | | | | | | | | | | | | | * commit 'cab37f63144fd24d1ff39359e3d47a2c16198633': Move function-scope macro definition to file-scope. Refactor external file addition loop to static function. fix declaring variable in for statement
| * | Move function-scope macro definition to file-scope.Jacob Smith2019-09-301-5/+6
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| * | Refactor external file addition loop to static function.Jacob Smith2019-09-291-18/+57
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| * | fix declaring variable in for statementJacob Smith2019-09-281-9/+10
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* | Merge pull request #1960 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-09-301-0/+29
|\ \ | |/ |/| | | | | * commit 'f6d4ce609b16601f3f4733266bb413a2bd765bc1': Add clang toolchain
| * Add clang toolchainAllen Byrne2019-09-301-0/+29
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* Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-09-281-1/+1
|\ | | | | | | | | * commit '3fb711e0ff2516cba7a0cb34f2d8ca38241b06a7': Number of arguments requires H5Dopen2.
| * Number of arguments requires H5Dopen2.Larry Knox2019-09-281-1/+1
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* Merge pull request #1956 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to ↵Dana Robinson2019-09-271-0/+2
|\ | | | | | | | | | | | | develop * commit 'a8a55f3c4863b500c4d0e5a2982d3e2b5a05b3cc': Corrected missing parallel #ifdefs.
| * Corrected missing parallel #ifdefs.Dana Robinson2019-09-271-0/+2
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* Merge pull request #1934 in HDFFV/hdf5 from ↵Vailin Choi2019-09-273-36/+343
|\ | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop * commit '7924eee0e5ee0745b784c635042b8633886fb799': (1) Address the feedback from the PR review (2) Add release notes Fix for HDFFV-10585 investigate hyperslab slowness: 1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace to 1-d contiguous memory dataspace. 2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to a separate routine.
| * (1) Address the feedback from the PR reviewVailin Choi2019-09-263-15/+27
| | | | | | | | (2) Add release notes
| * Merge pull request #21 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2019-09-26106-3647/+4619
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugfix/HDFFV-10585-investigate-slowness-of-regular * commit '0ea77179d507bd2c29f3b9b357a0c35d4077b29c': (39 commits) Fix the errors when updating the versions in the new 1.13 develop branch. add missing version to list Add new versioned filename to list Update N_FSINFO_VERSION_BOUNDS to H5F_LIBVER_NBOUND. Remove file script Update versioning to next major version Update develop branch version to 1.13.0 after creation of hdf5_1_12 branch. Merge Binh-Minh's changes for code improvement to chunk_info.c (PR #1942) to develop branch. Update to current external file population. Revert else-if to single line. Fix missing option and incorrect close Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package." Revert "Fix for H5EA debug package when built in release mode." Change print calls to HD-wrapped. Minor formatting tweaks (inc. regressions and in-file style-matching). Refactor h5repackgentest to have more modular internals, for easier addition of new tests. Update manifest and test script for new hdf5 external-storage .h5 files. Remove obsolete symbol small syntax changes Renamed get/set_time() calls in the tools library to avoid name clash when building static parallel HDF5 w/ static linking to OpenMPI. Change unused variable to generic form Whitespace cleanup ...
| * | Fix for HDFFV-10585 investigate hyperslab slowness:Vailin Choi2019-09-192-36/+331
| | | | | | | | | | | | | | | | | | | | | 1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace to 1-d contiguous memory dataspace. 2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to a separate routine.
| * | Merge pull request #20 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2019-09-1936-895/+1146
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugfix/HDFFV-10585-investigate-slowness-of-regular * commit '4d4a88a9f3775d1c6be820208a2699ae38d586b4': (29 commits) Fix for H5EA debug package when built in release mode. Moved NDEBUG guards to H5EA_DEBUG in H5EA package. Added MPICH_SKIP_MPICXX and OMPI_SKIP_CXX to H5public.h to avoid inadvertant linking to the deprecated MPI C++ wrappers. Fixes HDFFV-10893. Added a release note for HDFFV-10892 (fcntl lock bug). Fix segfault after H5VL_loc_params_t fix merge HDFFV-10901 add missing config options HDFFV-10854 add release note for windows Fix get home dir for windows Use variable for test output Allow tests to dump output if not comparing revert as CHECK will first check for exception Clear exception for getting JNI string to clear the exception Correct Windows check revert windows change Windows ssl headers are not in system loacation Add include dirs and default lib for windows Add policy to use <package>_ROOT Add statement for label if code unimplemented Update Windows require for CURL to CMake 3.13 Fix unused var ...
| * \ \ Merge pull request #19 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2019-09-10224-24054/+27016
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugfix/HDFFV-10585-investigate-slowness-of-regular * commit '2456a36f46a15ca44840cb64c7aac213f0ca8bf8': (53 commits) Fixed some exit calls. Reworked the previously refactorred code. Improvement of test code Fix CMake build of test needing compression libs Fixed error code and error messages Tested on Jelly (very minor) Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR to H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment. Add comment to add tests later to verify conflicting values for MPI-specific properties on multiple opens. Updated comments Updated based on reviews and refactored test code Move ext_path field in H5F_t to H5F_shared_t. Remove unused routine H5F_set_coll_md_read(). Move coll_md_read and coll_md_write fields in H5F_t to H5F_shared_t. Fix namespace usage Fix EXISTS test syntax Update settings Add 32-bit cross-compile toolchain Code cleanup and refactor Re-ordered items w.r.t. date. Whitespace and HD prefix changes Fixed typo Added notes about HDFFV-10677 and HDFFV-10661 ...
| * \ \ \ Merge pull request #18 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2019-08-1989-2253/+4665
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugfix/HDFFV-10585-investigate-slowness-of-regular * commit 'dcf084aff42d3abafaa82b356493a2d1585afb85': (25 commits) Changes based on PR feedback. Correct name of folder Mostly whitespace in testpar, addl changes for tmp dir Whitespace cleanup Added public H5Sselect_adjust_u and H5Shyper_adjust_s calls. Some refactoring prior to implementing new H5P MPI functions. * Macro cleanup and obvious warning fixes in parallel code. * Moved H5FD comm and info dup/free wrapper code to a new H5mpi.c file and separated it to deal with each MPI type separately. Fix compiler warnings with diabled ROS3 and HDFS VFDs. Fix misuse of [HD]strncpy and [HD]snprintf. Minor formatting changes. Fix test cleanup issue with java groups example. Changed the directory name left out from the previous commit. Changed the name of the temporary directory from 'tmp' to a special name to avoid possible conflicts. Fix H5F_get_file_id and H5F__get_file_id to take app_ref parameter HDFFV-10879 fix test varname Fix for HDFFV-10813 H5Fset_metadata_read_retry_info() test fails on jelly with PGI/19. Added map API build status to libhdf5.settings. Updated h5trav.c to emit output that doesn't require ddl changes for map support. HDFFV-10879 set default API version Fixed Map API CMake option Renamed H5Mdelete_key to H5Mdelete and H5Mset to H5Mput. Remove old code Correct error test spelling and use Added ifdef for intel compilers, __GNUC__ has to be defined for header files which use it to work with intel compilers. This gives a warning for intel compiler about fallthrough, so added a check not to include fallthrough if using intel compilers. ...
* | \ \ \ \ Merge pull request #1955 in HDFFV/hdf5 from ↵Dana Robinson2019-09-2711-95/+372
|\ \ \ \ \ \ | |_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:missing_vol_markup to develop * commit '4fb64c89fe52a309150ca2d5bb97eb4763e598e9': Converted H5O MD cache cork calls to use the VOL. Marked up H5Fget/set_mpi_atomicity() to use the VOL.
| * | | | | Converted H5O MD cache cork calls to use the VOL.Dana Robinson2019-09-277-62/+259
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| * | | | | Marked up H5Fget/set_mpi_atomicity() to use the VOL.Dana Robinson2019-09-275-33/+113
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* | | | | Merge pull request #1954 in HDFFV/hdf5 from ↵Vailin Choi2019-09-262-2/+2
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/ver_bounds_114 to develop * commit '50ba969a61f8f90212c97aa6e11674fe19fb89f4': Fix the errors when updating the versions in the new 1.13 develop branch.
| * | | | | Fix the errors when updating the versions in the new 1.13 develop branch.Vailin Choi2019-09-262-2/+2
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* | | | | Merge pull request #1953 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-09-262-3/+3
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'e6b029e77e799292eb1ee074b24a224f4613a3b2': add missing version to list
| * | | | | add missing version to listAllen Byrne2019-09-262-3/+3
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