Commit Graph

20587 Commits

Author SHA1 Message Date
Larry Knox
13502badeb Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12 2019-10-21 17:13:00 -05:00
Larry Knox
736ce8b585 Update MANIFEST. 2019-10-21 17:12:19 -05:00
Larry Knox
a813427395 Merge pull request #2012 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to hdf5_1_12
* commit '41ad7d0f35ab944eec4fa45c844d052a021dc99c':
  Fix typos.
  Add HISTORY-1_10_0-1_12_0.txt.
  Update RELEASE.txt and add HISTORY-1_10_0-1_12_0.txt file. Set version to 1.12.0-alpha0 for snapshot release.
2019-10-21 16:53:12 -05:00
Larry Knox
41ad7d0f35 Fix typos. 2019-10-21 16:09:38 -05:00
Larry Knox
873b98d326 Add HISTORY-1_10_0-1_12_0.txt. 2019-10-21 15:56:28 -05:00
Larry Knox
2c9362c530 Update RELEASE.txt and add HISTORY-1_10_0-1_12_0.txt file.
Set version to 1.12.0-alpha0 for snapshot release.
2019-10-21 15:50:44 -05:00
Allen Byrne
027cd1ff5b Fix missing HD and whitespace 2019-10-21 15:02:48 -05:00
Richard Warren
fcb10fc1bf Merge pull request #2005 in HDFFV/hdf5 from HDFFV-10539-2GB-Write-Independent to hdf5_1_12
* commit 'ce05c4a62dcd3a91760363202105171cac8548b9':
  Added the two missing files from the previous PR as requested by Les
  Initial 2GB port from develop to the 1_12 branch
2019-10-15 16:32:35 -05:00
Richard Warren
ce05c4a62d Added the two missing files from the previous PR as requested by Les 2019-10-15 14:47:10 -04:00
Richard Warren
4284401fde Initial 2GB port from develop to the 1_12 branch 2019-10-15 09:31:24 -04:00
Larry Knox
d7f63be1ac Merge pull request #2004 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_endian_1_12 to hdf5_1_12
* commit '610fe3c2449a918e1dedc475fc7efb09f684cc5a':
  Fix encode and decode of tokens in H5VLnative
2019-10-12 23:05:44 -05:00
Jerome Soumagne
610fe3c244 Fix encode and decode of tokens in H5VLnative
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
2019-10-11 17:47:26 -05:00
Jacob Smith
a34ff89763 Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into hdf5_1_12 2019-10-11 16:26:24 -05:00
Jacob Smith
72560d7ccd Add updates from develop, PR 1958. 2019-10-11 16:17:37 -05:00
Dana Robinson
1fa1ec6190 Merge pull request #2001 in HDFFV/hdf5 from ~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.
2019-10-11 15:02:54 -05:00
Vailin Choi
af2e625041 Merge pull request #2002 in HDFFV/hdf5 from ~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.
2019-10-11 14:17:32 -05:00
Vailin Choi
db8a59fbb2 Merge pull request #1959 from develop to 1.12. 2019-10-11 11:53:41 -05:00
Dana Robinson
75f2ed6167 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.
2019-10-10 20:55:52 -07:00
Dana Robinson
e6065c44f7 Fixed the java assert issue with H5O cache corking calls. 2019-10-10 19:47:30 -07:00
Dana Robinson
c3da9fe70e Corrected missing parallel #ifdefs. 2019-10-10 19:47:02 -07:00
Dana Robinson
71f36b343a Converted H5O MD cache cork calls to use the VOL. 2019-10-10 19:46:22 -07:00
Dana Robinson
75bb8add45 Marked up H5Fget/set_mpi_atomicity() to use the VOL. 2019-10-10 19:46:06 -07:00
Jordan Henderson
3819640e3c Merge pull request #1999 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to hdf5_1_12
* commit 'f3f67a5645d2bbc9631894e93c72809eda4897e0':
  Fix various Java issues when deprecated symbols are disabled
2019-10-10 17:14:22 -05:00
Jordan Henderson
f3f67a5645 Fix various Java issues when deprecated symbols are disabled 2019-10-10 16:03:34 -05:00
Jordan Henderson
3a25a65572 Merge pull request #1997 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to hdf5_1_12
* commit '38d214fd46118cc7ab898bf5e813d3c655106505':
  Unify code between H5Lcopy and H5Lmove
2019-10-10 13:37:06 -05:00
Jordan Henderson
38d214fd46 Unify code between H5Lcopy and H5Lmove 2019-10-10 12:51:49 -05:00
Larry Knox
c56804d692 Merge pull request #1995 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to hdf5_1_12
* commit '5c61be3de285b3a9a63d623944e13892a8a8cb94':
  Final improvements.
  Fix errors in testh5dump.sh tests that grep for reference error messages.
2019-10-09 16:23:51 -05:00
Larry Knox
5c61be3de2 Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12 2019-10-09 15:46:35 -05:00
Larry Knox
984c1bacd9 Merge pull request #1990 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:references_1_12 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.
2019-10-09 15:45:26 -05:00
Larry Knox
daf2b836ee Final improvements. 2019-10-09 15:36:46 -05:00
Larry Knox
262df2adce Fix errors in testh5dump.sh tests that grep for reference error messages. 2019-10-09 15:18:52 -05:00
Vailin Choi
19c2eb2800 Merge pull request #1962 in HDFFV/hdf5 from ~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
2019-10-09 15:03:12 -05:00
Jerome Soumagne
5d2545ee26 Fix func enter macro in H5T_ref_reclaim() 2019-10-09 11:21:18 -05:00
Jerome Soumagne
1a10f7b672 Update RELEASE.txt for reference changes 2019-10-08 15:19:42 -05:00
Jerome Soumagne
b18e4b0f1a Fix reference type comparison in h5dump 2019-10-08 15:19:35 -05:00
Jerome Soumagne
383e7f7871 Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() 2019-10-08 15:19:28 -05:00
Jerome Soumagne
dabdcf9559 Add new H5R API that abstracts object, region and attribute reference types
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
2019-10-08 15:19:21 -05:00
Jerome Soumagne
e9570c198b Remove ability to loc by ref from H5VL layer 2019-10-08 15:19:13 -05:00
Jerome Soumagne
fcc1f0b7c7 Add support for retrieving object name by token 2019-10-08 15:19:06 -05:00
Jerome Soumagne
fd4f6253ce Add H5VL_OBJECT_GET_TYPE to get object type
Add H5VL_OBJECT_LOOKUP to lookup objects
2019-10-08 15:18:57 -05:00
Jerome Soumagne
f4bc0af55c Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t 2019-10-08 15:18:50 -05:00
Quincey Koziol
b571cf6c38 Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.
Remove "by address" location for VOL operations. (Switching to "by token")
2019-10-08 15:18:42 -05:00
Jerome Soumagne
1b766420f1 Fix H5VL_blob_get to return size of blob
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
2019-10-08 15:18:34 -05:00
Quincey Koziol
ff490b4a69 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.

Move encode/decode of sequence lengths into VL datatype callbacks, from native
VOL blob routines.
2019-10-08 15:18:27 -05:00
Allen Byrne
e487737b4f Merge pull request #1981 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to hdf5_1_12
* commit 'b7fcb63746591d222de7cf7fc516d99aa8491fc8':
  More whitespace changes
  Whitespace cleanup
2019-10-03 13:04:23 -05:00
Allen Byrne
b7fcb63746 More whitespace changes 2019-10-03 12:16:01 -05:00
Allen Byrne
7cb7b53175 Whitespace cleanup 2019-10-03 11:42:48 -05:00
Allen Byrne
53a9c011d5 Merge pull request #1970 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to 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
2019-10-02 15:38:53 -05:00
Allen Byrne
cc6537dc66 HDFFV-10919 merge synching 2019-10-02 14:49:57 -05:00
Allen Byrne
73a2f14c49 HDFFV-10408,10918 add note 2019-10-02 13:09:22 -05:00