Commit Graph

6681 Commits

Author SHA1 Message Date
Neil Fortner
ba39bc0891 Merge pull request #2103 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_2 to hdf5_1_12
* commit 'aefd0cbc60eeed3319776f76f0cde889072cc31b':
  Implement support for using H5Dvlen_get_buf_size with non-native VOL connectors.
2019-12-06 17:56:38 -06:00
Neil Fortner
afb6ae776b Add H5VL_MAP_OPTIONAL operation id (unused currently). 2019-12-06 16:45:32 -06:00
Neil Fortner
aefd0cbc60 Implement support for using H5Dvlen_get_buf_size with
non-native VOL connectors.
2019-12-06 16:43:36 -06:00
Neil Fortner
46a3961d08 Add support for scalar dataspaces to H5Sproject_intersection. Add
checking for ank validity.
2019-12-06 16:41:09 -06:00
Neil Fortner
62e6349eab Merge pull request #2101 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_5 to hdf5_1_12
* commit '47f6c293a78aaa92c80b327795b1f1a242ea30a5':
  Fix issues with using H5Pget_fill_value() with file datatypes retrieved from H5VLget_file_type().
2019-12-06 16:39:53 -06:00
Neil Fortner
347f5795bf Merge pull request #2096 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112 to hdf5_1_12
* commit '681d227e9ee7876922fb05e609db18425cb1630d':
  Fix issue where H5R__reopen_file did not make the file "post open" callback.
2019-12-06 16:39:38 -06:00
Neil Fortner
c4b34cb649 Merge pull request #2100 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_4 to hdf5_1_12
* commit '209a86de37497b160ff49b9956f58558194eee25':
  Fix missing free in H5T__ref_mem_read()
  Fix bugs in H5VL file comparison code.  Add short circuit success to H5VL_cmp_connector_cls().
  Implement file comparison VOL callback.  Other changes to allow references to work with non-native connectors.  There is a bug somewhere.
2019-12-06 16:39:21 -06:00
Neil Fortner
9d0ca45ebd Merge pull request #2099 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_3 to hdf5_1_12
* commit '2b14a8fd7e9221e258f3a2ed6dd0f79a30d5221f':
  Add support for point selections to H5S_select_project_intersection.
2019-12-06 16:39:04 -06:00
Neil Fortner
47f6c293a7 Fix issues with using H5Pget_fill_value() with file datatypes retrieved
from H5VLget_file_type().
2019-12-06 16:34:58 -06:00
Neil Fortner
209a86de37 Fix missing free in H5T__ref_mem_read() 2019-12-06 16:32:11 -06:00
Neil Fortner
a5091c0013 Fix bugs in H5VL file comparison code. Add short circuit success to
H5VL_cmp_connector_cls().
2019-12-06 16:32:11 -06:00
Neil Fortner
07c337dc57 Implement file comparison VOL callback. Other changes to allow
references to work with non-native connectors.  There is a bug
somewhere.
2019-12-06 16:32:11 -06:00
Neil Fortner
2b14a8fd7e Add support for point selections to H5S_select_project_intersection. 2019-12-06 16:25:22 -06:00
Neil Fortner
c40934d968 Move checking for zero offset in selection adjust calls to the selection callbacks. This makes the
procedure for checking it consistent across selection types and between
_s and _u, ensures it is always is performed even when called within the H5S package, and removes the redundant check that would occur when callins H5S_select_adjust_s() from outside the H5S package.
2019-12-06 16:12:47 -06:00
Neil Fortner
975eea7940 Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() with
H5Sselect_adjust.  Implement "adjust_s" callback for all selection
types.  Add range checking to H5Sselect_adjust().
2019-12-06 16:12:47 -06:00
Richard Warren
9f9336a5bd Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12 2019-12-06 16:50:47 -05:00
Richard Warren
0c06cfc6ef Merged HDFFV-10929_2GB_testing to hdf5_1_12 2019-12-06 16:42:36 -05:00
Neil Fortner
681d227e9e Fix issue where H5R__reopen_file did not make the file "post open"
callback.
2019-12-06 14:44:12 -06:00
Neil Fortner
33357092c4 Implement public H5Sselect_project_intersection(). Updated internal
algorithm to (optionally) avoid sharing selection data structures.
Tested internal code (including with valgrind) by setting VDS code to
avoid sharing selection, has since been changed to share selection for
performance, so this code is not yet tested in regression tests.  API
has not been tested.
2019-12-06 14:37:41 -06:00
Neil Fortner
63282c1229 Implement H5VLget_file_type() to return a copy of a datatype with the
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.
2019-12-06 14:16:03 -06:00
Vailin Choi
17b8281ce4 Merge pull request #2080 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/112_hyper_ver to hdf5_1_12
* commit '0f1be317c37ca04db263680e6f1fe4d97b937b39':
  More fixes for the PR: (1) Set the version for reference datatype message to H5O_DTYPE_VERSION_4. (2) The tests for the new reference types should work for V112 and beyond.
  Verify the decoded version for hyperslab selection.
2019-12-06 13:35:55 -06:00
Vailin Choi
0f1be317c3 More fixes for the PR:
(1) Set the version for reference datatype message to H5O_DTYPE_VERSION_4.
(2) The tests for the new reference types should work for V112 and beyond.
2019-12-06 12:17:30 -06:00
Jordan Henderson
a7a70824e4 Add OAPL parameter to H5Rcreate_ APIs 2019-12-06 11:12:42 -06:00
Vailin Choi
f3686baaf0 Verify the decoded version for hyperslab selection. 2019-12-05 16:09:49 -06:00
Chris Hogan
6084fbad00 Add changes from PR 2049 to hdf5_1_12 branch 2019-12-03 16:40:37 -06:00
Chris Hogan
a88b14b003 Check for both default LCPL values 2019-11-27 12:26:40 -06:00
Chris Hogan
3aedc32b1c Use API context to store/retrieve LCPL and DCPL properties
Adding changes from PR 2029 to 1.12 branch.
2019-11-27 09:36:58 -06:00
Allen Byrne
e7af459647 Correct file extension 2019-11-14 16:35:01 -06:00
Richard Warren
ca54c5f06e Fixed the H5_set_bigio_count prototype by adding a missing input argument. 2019-10-23 14:45:55 -04:00
Richard Warren
aac6943696 Rename the set/get bigio_count functions. Also add the renamed prototypes to H5private.h. 2019-10-23 14:09:13 -04:00
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
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
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
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
38d214fd46 Unify code between H5Lcopy and H5Lmove 2019-10-10 12:51:49 -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
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
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