Commit Graph

6681 Commits

Author SHA1 Message Date
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
6ae314a698 Whitespace and macro semi-colon 2019-10-02 12:42:31 -05:00
Allen Byrne
c86b21b05b More whitespace synching 2019-10-02 09:40:43 -05:00
Allen Byrne
b6f9fcaec5 Cleanup whitespace and comments compared to develop 2019-10-02 09:22:11 -05:00
Allen Byrne
e8c8c29342 fix for statement declare variable 2019-09-30 14:56:30 -05:00
Vailin Choi
6ffdd4f2d6 Merge pull request #1934 in HDFFV/hdf5 from ~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.
2019-09-30 13:50:59 -05:00
Larry Knox
e7dbf81191 Set versions in initial hdf5_1_12 revision. 2019-09-25 15:57:22 -05:00
Dana Robinson
6eb506eff7 Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package."
This reverts commit 431123503d.
2019-09-24 05:20:30 -05:00
Dana Robinson
40b2eae5e9 Revert "Fix for H5EA debug package when built in release mode."
This reverts commit 911b1ca67f.
2019-09-24 05:19:44 -05:00
Dana Robinson
911b1ca67f Fix for H5EA debug package when built in release mode. 2019-09-18 13:25:02 -07:00
Dana Robinson
431123503d Moved NDEBUG guards to H5EA_DEBUG in H5EA package. 2019-09-17 16:53:18 -07:00
Dana Robinson
f5a84c9856 Added MPICH_SKIP_MPICXX and OMPI_SKIP_CXX to H5public.h to avoid inadvertant
linking to the deprecated MPI C++ wrappers. Fixes HDFFV-10893.
2019-09-17 10:52:16 -07:00
Jordan Henderson
db1022ef5d Fix segfault after H5VL_loc_params_t fix merge 2019-09-16 15:35:09 -05:00
Allen Byrne
c1c522f6ce Merge pull request #1922 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit 'b477f9bcc7bb83d7c06e1d09f428030f51d71897':
  HDFFV-10901 add missing config options
2019-09-16 11:38:30 -05:00
Jordan Henderson
72e8387bc9 Merge pull request #1887 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit '0de0965c61823186ac61c0d6876d4d77578e5bcc':
  Fix issue in H5Lcreate_hard and H5Olink where entire H5VL_loc_params_t structure was passed via varargs
2019-09-16 11:34:00 -05:00
Allen Byrne
b477f9bcc7 HDFFV-10901 add missing config options 2019-09-13 11:34:00 -05:00
Allen Byrne
50287cb9d2 Fix get home dir for windows 2019-09-12 14:22:43 -05:00
Allen Byrne
0d964c2f88 revert windows change 2019-09-06 11:01:25 -05:00
Allen Byrne
acdeee8c6a Windows ssl headers are not in system loacation 2019-09-06 10:17:40 -05:00
Allen Byrne
dcab85c83b Add back missing java implementation 2019-09-05 14:35:33 -05:00
Binh-Minh Ribler
a8af828bbf Merge pull request #1908 in HDFFV/hdf5 from ~BMRIBLER/hdf5-bmr:develop to develop
- Added new chunk query functions: H5Dget_num_chunks(), H5Dget_chunk_info(), and H5Dget_chunk_info_by_coord()
- Fixed iterator issue in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate()

* commit '96dab622e3bbe75d85b0cef3ca2bd5288cf4ac32':
  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.
  Updated comments
  Updated based on reviews and refactored test code
  Code cleanup and refactor
  Re-ordered items w.r.t. date.
  Fixed typo
  Added notes about HDFFV-10677 and HDFFV-10661
  HDFFV-10677 and HDFFV-10661
2019-09-03 11:08:42 -05:00
Binh-Minh Ribler
96dab622e3 Fixed error code and error messages
Tested on Jelly (very minor)
2019-09-03 11:00:29 -05:00
Binh-Minh Ribler
daecf8f06d Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR to
H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment.
2019-09-03 08:03:28 -05:00
Binh-Minh Ribler
b679d11bcc Updated based on reviews and refactored test code 2019-09-01 01:13:08 -05:00
Vailin Choi
eef0cf2694 Move ext_path field in H5F_t to H5F_shared_t.
Remove unused routine H5F_set_coll_md_read().
2019-08-31 01:24:38 -05:00
Vailin Choi
fe3c4567f5 Move coll_md_read and coll_md_write fields in H5F_t to H5F_shared_t. 2019-08-30 23:06:04 -05:00
Allen Byrne
0b6f5e88cd Fix EXISTS test syntax 2019-08-29 14:43:35 -05:00
Binh-Minh Ribler
a633e33334 Code cleanup and refactor 2019-08-29 00:53:40 -05:00
Binh-Minh Ribler
7857a59bf0 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5-bmr into develop 2019-08-28 10:14:10 -05:00
Binh-Minh Ribler
e06bf9d263 HDFFV-10677 and HDFFV-10661
Description:
    - Added functions to query chunk information:
        H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
            Gets the number of written chunks that intersect with the given
            dataspace.  However, in this version, the intersection is not
            yet completed.  Thus, the number of all written chunks will be
            returned.
        H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size)
            Given a chunk's logical coordinates, returns the chunk's filter,
            address, and size.
        H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size)
            Given a chunk's index, returns the chunk's logical coordinates, filter,
            address, and size.  The chunk belongs to a set of chunks that have
            nonempty intersection with the specified dataspace.  However, in
            this version, the intersection is not yet completed, and the index
            is of all the written chunks.
        These functions comply with VOL.

    - Fixed some oversights found in the library for the tests in chunk_info.c
      to work correctly.  The returned value from a callback function was not
      checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate().
      This oversight caused a callback function to continue iterating even though
      it's supposed to stop.
Platforms tested:
    Linux/64 (jelly)
    Linux/64 (platypus)
    Darwin (osx1011test)
2019-08-28 10:08:12 -05:00
Dana Robinson
937616872c Minor tweaks to new H5P MPI code based on code review feedback. 2019-08-27 14:00:49 -07:00
Dana Robinson
477bd6cd77 Merge branch 'develop_minor_pr' into H5Pset_fapl_mpi 2019-08-27 13:28:55 -07:00
Dana Robinson
d42de626b6 Fixed a bug where we incorrectly pass a lock struct to fcntl
for file locking instead of a pointer.
2019-08-27 07:03:51 -07:00
Dana Robinson
68cd4eea0e Merge branch 'develop' into H5Pset_fapl_mpi 2019-08-27 02:42:18 -07:00
Quincey Koziol
6e8c48182f Merge pull request #1897 in HDFFV/hdf5 from ~KOZIOL/hdf5:refactor_file to develop
* commit '3090ac81506094ee510ae89c31749b5c1632aa34':
  Add a 'closing' flag on the shared file struct, and switch several of the "internal" data structures to use it.
2019-08-26 17:25:17 -05:00
Quincey Koziol
3090ac8150 Add a 'closing' flag on the shared file struct, and switch several of the
"internal" data structures to use it.
2019-08-26 14:38:58 -05:00
Dana Robinson
3bcbce5538 Added H5Pset/get_mpi_params calls and unified them with the MPI-I/O
VFD info in H5FDmpio.c.
2019-08-26 10:26:31 -07:00
Vailin Choi
021919206d Fixed the assertion failure for HDFFV-10873. 2019-08-23 15:06:19 -05:00
Quincey Koziol
f42c7cc0d8 Fix major error codes 2019-08-22 17:06:00 -05:00
Quincey Koziol
c36d2eeae7 Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to match
naming convention for shared structs in rest of library data structures.
2019-08-22 13:28:20 -05:00
Quincey Koziol
5d6f27b32b Merge branch 'develop' into shared_file_ptr 2019-08-21 15:36:17 -05:00
Quincey Koziol
0b85fa6004 Small tidy up. 2019-08-21 15:34:43 -05:00
Jordan Henderson
0de0965c61 Fix issue in H5Lcreate_hard and H5Olink where entire H5VL_loc_params_t structure was passed via varargs 2019-08-21 11:56:50 -05:00
Quincey Koziol
d3545afbc5 Progress toward movig H5MF* API to use shared file pointers instead of top
file pointers.
2019-08-20 21:55:16 -05:00
Quincey Koziol
901c42640f Progress on moving the H5MF* interface to using shared file pointers instead of
top file pointers.
2019-08-20 21:32:13 -05:00
Quincey Koziol
53eaeff26a Begin converting the H5MF interface to use shared file pointers instead
of top file pointers.
2019-08-20 21:07:13 -05:00
Quincey Koziol
2ef7eb51b9 Progress toward moving the dataset routines to using the 'shared' file pointer
instead of the 'top' file pointer.
2019-08-20 20:38:10 -05:00
Quincey Koziol
67d7d28c03 Begin converting dataset code to use shared file pointer instead of top file
pointer.
2019-08-20 18:21:53 -05:00
Quincey Koziol
25f982abbd Finish converting H5PB_* routines to use shared file pointer, instead of top
file pointer.
2019-08-20 17:26:10 -05:00