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* Added the two missing files from the previous PR as requested by LesRichard Warren2019-10-152-7/+9
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* Initial 2GB port from develop to the 1_12 branchRichard Warren2019-10-155-187/+297
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* Merge pull request #2004 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_endian_1_12 ↵Larry Knox2019-10-138-158/+226
|\ | | | | | | | | | | | | to hdf5_1_12 * commit '610fe3c2449a918e1dedc475fc7efb09f684cc5a': Fix encode and decode of tokens in H5VLnative
| * Fix encode and decode of tokens in H5VLnativeJerome Soumagne2019-10-118-158/+226
|/ | | | | | | | Fix encode and decode of deprecated object reference addresses Make H5Rdeprec.c use tokens instead of haddr_t Fix H5Oopen_by_addr() to serialize addr to token
* Merge pull request #2001 in HDFFV/hdf5 from ↵Dana Robinson2019-10-1111-160/+448
|\ | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:1_12_alpha_merges to hdf5_1_12 * commit '75f2ed6167b094431fce2b4b700b3cf9da564c51': 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 the java assert issue with H5O cache corking calls. Corrected missing parallel #ifdefs. Converted H5O MD cache cork calls to use the VOL. Marked up H5Fget/set_mpi_atomicity() to use the VOL.
| * Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-112-80/+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.
| * Fixed the java assert issue with H5O cache corking calls.Dana Robinson2019-10-111-3/+4
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| * Corrected missing parallel #ifdefs.Dana Robinson2019-10-111-0/+2
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| * Converted H5O MD cache cork calls to use the VOL.Dana Robinson2019-10-116-57/+252
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| * Marked up H5Fget/set_mpi_atomicity() to use the VOL.Dana Robinson2019-10-114-23/+105
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* | Merge pull request #2002 in HDFFV/hdf5 from ↵Vailin Choi2019-10-112-6/+15
|\ \ | |/ |/| | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_iteration_error_in_test_versionbounds to hdf5_1_12 * commit 'db8a59fbb2907aac63b21ed7c8e88860b2e0fbc8': Merge pull request #1959 from develop to 1.12.
| * Merge pull request #1959 from develop to 1.12.Vailin Choi2019-10-112-6/+15
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* Merge pull request #1999 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to ↵Jordan Henderson2019-10-1011-27/+131
|\ | | | | | | | | | | | | hdf5_1_12 * commit 'f3f67a5645d2bbc9631894e93c72809eda4897e0': Fix various Java issues when deprecated symbols are disabled
| * Fix various Java issues when deprecated symbols are disabledJordan Henderson2019-10-1011-27/+131
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* Merge pull request #1997 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to ↵Jordan Henderson2019-10-102-9/+14
|\ | | | | | | | | | | | | hdf5_1_12 * commit '38d214fd46118cc7ab898bf5e813d3c655106505': Unify code between H5Lcopy and H5Lmove
| * Unify code between H5Lcopy and H5LmoveJordan Henderson2019-10-102-9/+14
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* Merge pull request #1995 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵Larry Knox2019-10-091-10/+17
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '5c61be3de285b3a9a63d623944e13892a8a8cb94': Final improvements. Fix errors in testh5dump.sh tests that grep for reference error messages.
| * Merge branch 'hdf5_1_12' of ↵Larry Knox2019-10-09105-2890/+12332
| |\ | |/ |/| | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12
* | Merge pull request #1990 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:references_1_12 ↵Larry Knox2019-10-09104-2854/+11989
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to hdf5_1_12 * commit '5d2545ee26d4b7013ed363545705f16a67087549': Fix func enter macro in H5T_ref_reclaim() Update RELEASE.txt for reference changes Fix reference type comparison in h5dump Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() Add new H5R API that abstracts object, region and attribute reference types Remove ability to loc by ref from H5VL layer Add support for retrieving object name by token Add H5VL_OBJECT_GET_TYPE to get object type Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info. Fix H5VL_blob_get to return size of blob Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
| * | Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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| * | Update RELEASE.txt for reference changesJerome Soumagne2019-10-081-0/+10
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| * | Fix reference type comparison in h5dumpJerome Soumagne2019-10-081-1/+5
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| * | Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-0831-274/+276
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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 #1962 in HDFFV/hdf5 from ↵Vailin Choi2019-10-093-36/+343
|\ \ \ | |/ / |/| | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_HDFFV-10585-investigate-slowness-of-regular to hdf5_1_12 * commit 'bffa18b684de83359f4ad25e11f4ad0b15f34040': Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop Merge pull request #1934 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop
| * | Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-09-301-1/+1
| | | | | | | | | | | | | | | * commit '3fb711e0ff2516cba7a0cb34f2d8ca38241b06a7': Number of arguments requires H5Dopen2.
| * | Merge pull request #1934 in HDFFV/hdf5 from ↵Vailin Choi2019-09-303-36/+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.
| | * Final improvements.Larry Knox2019-10-091-38/+15
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| | * Fix errors in testh5dump.sh tests that grep for reference error messages.Larry Knox2019-10-091-0/+30
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* | Merge pull request #1981 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-10-033-370/+214
|\ \ | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'b7fcb63746591d222de7cf7fc516d99aa8491fc8': 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 #1970 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-10-0218-501/+515
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'cc6537dc66555a0f37b687ae8eb32a21ab1fd41d': HDFFV-10919 merge synching HDFFV-10408,10918 add note Whitespace and macro semi-colon Whitespace synch HDFFV-10918 add tests for h5repack ext storage
| * | HDFFV-10919 merge synchingAllen Byrne2019-10-024-179/+68
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| * | HDFFV-10408,10918 add noteAllen Byrne2019-10-021-0/+8
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| * | Whitespace and macro semi-colonAllen Byrne2019-10-0210-263/+260
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| * | Whitespace synchAllen Byrne2019-10-021-58/+58
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| * | HDFFV-10918 add tests for h5repack ext storageAllen Byrne2019-10-022-1/+121
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* | Merge pull request #1969 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-10-0221-1726/+1734
|\ \ | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'c86b21b05bc2e4e45f42969dea7bd82e66f75926': More whitespace synching Cleanup whitespace and comments compared to develop
| * | More whitespace synchingAllen Byrne2019-10-0213-1695/+1693
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| * | Cleanup whitespace and comments compared to developAllen Byrne2019-10-028-31/+41
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* | Merge pull request #1967 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-10-011-0/+1
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'f2bb38e23a08bb39160a7b8270eb542e6f18836a': Add new toolchain file
| * | Add new toolchain fileAllen Byrne2019-10-011-0/+1
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