Commit Graph

1585 Commits

Author SHA1 Message Date
Allen Byrne
30c7264c2c CMake and script changes for clang-format 2020-09-04 16:36:52 -05:00
Allen Byrne
6a344232f6 Add testfiles 2020-08-15 18:10:57 -05:00
Allen Byrne
57c4aeb0cc TRILABS-277 Use JIRA number as #ifdef 2020-08-15 17:25:22 -05:00
Allen Byrne
500d87fd1f HDFFV-9984 Add options to merge/prune external links during repack 2020-08-14 12:16:58 -05:00
Quincey Koziol
07e4ef9da4 Clean up private / package / static namespace issues (function naming, which
header file, FUNC_ENTER / LEAVE, etc).  Removed remaining personal email
addresses from library source code (still needs cleaned from other directories).
Misc. warning, style, and whitespace cleanup.
2020-08-06 15:56:04 -05:00
Allen Byrne
1f7fa50137 Correct h5diff filenames 2020-07-29 08:24:30 -05:00
Allen Byrne
a498b4ee79 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '9d3ea366d4bf3278e8260f4d5cdcc88cb4b61c56':
  Update MANIFEST. Add new test to Cmake.
  Fix for jira issue HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
2020-07-17 14:39:25 -05:00
vchoi
3023b34272 Update MANIFEST.
Add new test to Cmake.
2020-07-16 16:40:11 -05:00
Allen Byrne
bac0fc6309 Tools refactor
Move error_stack setup to tools library
Add structure for h5dump properties
Eliminate duplicated h5diff functions
Use properties structure in place of argument lists.
2020-07-15 11:20:16 -05:00
Quincey Koziol
71b601d0d3 Clean up warnings 2020-06-27 20:02:51 -05:00
Dana Robinson
1e038bf495 Fix MANIFEST 2020-06-10 11:40:59 -07:00
Larry Knox
60244c54fc Update MANIFEST for removal of older warnings files. 2020-05-20 09:12:43 -05:00
Allen Byrne
b147797449 Correct path 2020-05-07 08:50:12 -05:00
Allen Byrne
521c3f8ff6 Add github actions 2020-05-06 08:10:37 -05:00
Allen Byrne
f9a3ae5081 TRILAB-244 separate CXX warnings and errors from C 2020-04-23 14:32:29 -05:00
Allen Byrne
e68848f397 TRILAB-192 - cleanup edits and match CMake CXX to autotools 2020-04-13 08:16:57 -05:00
Jacob Smith
075e74e9b2 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a 2020-04-07 10:29:00 -05:00
Jacob Smith
d97c00013d Tidying of Mirror VFD.
* Rename server-stop utility to mirror_server_stop.
* Remove external dependency on bzero().
* Modify test/use_common to use only the public API.
* Rename internal bitswap macro to follow convention.
2020-04-07 10:20:44 -05:00
Allen Byrne
0d701b9ff8 Move intel warnings to subfolder, update autotools files 2020-04-06 09:35:43 -05:00
Allen Byrne
2c2627e7f6 Flag construction must be after compiler detection 2020-04-05 13:38:04 -05:00
Allen Byrne
57f5d00a43 TRILAB-192 add c++ and fortran warnings build systems one file 2020-04-05 10:50:08 -05:00
Allen Byrne
0da53027d9 TRILAB-192 add comparable clang flags 2020-03-27 17:10:53 -05:00
David Young
43e5a89697 Update the MANIFEST for the autoconf/cmake shared warnings files. 2020-03-24 10:24:51 -05:00
Jacob Smith
b65405439d Add Splitter VFD to library.
* "Simultaneous and equivalent" Read-Write and Write-Only channels for
  file I/O.
* Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for
  now, preventing issues with multi-file drivers.

Add Mirror VFD to library.

* Write-only operations over a network.
* Uses TCP/IP sockets.
* Server and auxiliary server-shutdown programs provided in a new directory,
  `utils/mirror_vfd`.
* Automated testing via loopback ("remote" of localhost).
2020-03-13 17:13:17 -05:00
Allen Byrne
1885c3e7d7 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'd24afb233383aa6c945fad430eb1b66edc4d6c63':
  Add missing MANIFEST entry, ./doc/code-conventions.md .
2020-02-24 13:00:25 -06:00
Allen Byrne
f7212df030 HDFFV-11036 add file compare test process 2020-02-24 12:45:22 -06:00
David Young
921278c604 Add missing MANIFEST entry, ./doc/code-conventions.md . 2020-02-20 13:34:33 -06:00
David Young
00608a8756 Merge pull request #2341 in HDFFV/hdf5 from ~DYOUNG/werror:thread_id to develop
* commit 'cefacee21b5ad569e2394b32793648e1b80f3d6b':
  src/H5Eint.c: #include H5TSprivate.h for H5TS_thread_id() definitions.
  Change thread IDs to uint64_t from unsigned long, per Quincey's suggestion.
  Add thread_id.c to the MANIFEST and the CMakeLists.txt per Allen's request.
  Replace pthread_self_ulong() with H5TS_thread_id().  The POSIX Threads implementation ought to be portable to any system that has POSIX Threads.  On Windows, I use the same API call as before.
2020-02-05 13:34:00 -06:00
Allen Byrne
00d68851fc HDFFV-10996 - add java vol tests 2020-02-03 13:45:14 -06:00
David Young
65600cbd72 Add thread_id.c to the MANIFEST and the CMakeLists.txt per Allen's
request.
2020-02-03 12:59:52 -06:00
Allen Byrne
3e9980d20d Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '66a94df13b3801547523f1ea90bc84fe2ee6824b':
  Removed UIUC from copyright, added helpful comment.
  Updated MANIFEST
  Added a config file for ARM (Tested on a Raspberry Pi 3B+ w/ gcc 6).
  Tidying from code review.
  Fixed stack and frame size warnings. Not complete, but fixes most of the easier cases.
2020-01-19 07:45:15 -06:00
Allen Byrne
cf84882b3c Create common build system files for warnings 2020-01-17 13:14:06 -06:00
Dana Robinson
b51ae5f35e Updated MANIFEST 2020-01-17 05:00:23 -08:00
Dana Robinson
a92c735c9b Squashed commit of the token_refactoring branch: 2020-01-16 13:29:34 -08:00
Jerome Soumagne
a7648879d7 Add test for reference shutdown issue 2020-01-15 17:23:33 -06:00
Allen Byrne
f679b7495d Merge pull request #2173 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '576e713924b1802a64ae2f6655d2389d70fadfd1':
  Add new h5diff files
  Fix compile statement order
  HDFFV-10976,-10980 Init obj_type before calling H5Rget_obj_type3
  Add unknown define for h5dump ref objects
  Standalone doesn't use h5test implementation.
  HDFFV-10980 - h5diff uses new ref APIs
2019-12-21 07:49:22 -06:00
Allen Byrne
576e713924 Add new h5diff files 2019-12-21 07:48:23 -06:00
Quincey Koziol
58cf795321 Refactor all the 'H5VL_*_optional' callbacks to move the type of operation out
of the va_list, so it's at least possible for another connector to know what
the operation is and decide whether to implement it or not.

Added a new VOL sub-class called "introspect" where callbacks that report
information about the connector or container can be placed.  Added an
'opt_query' callback to this sub-class, for a connector to report back
to the library whether a particular optional callback operation is supported.
Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t
of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or
the terminal connector, H5VL_GET_CONN_LVL_TERM).

Moved the "post open" operation from a file 'specific' operation to a file
'optional' operation, now that it's possible to detect (with the 'opt_query'
introspection callback) whether a VOL connector implements an optional
operation, without just returning an error.

Added new internal VOL helper routines: H5VL_object_is_native, to determine
if an object is in (or is a) native file, and H5VL_file_is_same, to determine
if two objects are in (or are) the same terminal VOL connector's container.
(And moved the special handling for FILE_IS_EQUAL operation out of internal VOL
callback routine into H5VL_file_is_same)

Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better
with other 'get' operations in API.

Fixed several issues with pass-through connectors, which are now passing the
'make check-passthrough-vol' tests again.

A bunch of warning and style cleanups as well.
2019-12-19 22:41:37 -06:00
Allen Byrne
628c63f125 HDFFV-10980 - h5diff uses new ref APIs 2019-12-19 16:29:43 -06:00
Allen Byrne
74524c5a35 TRILABS-135 Add clang analyzers 2019-12-11 16:49:34 -06:00
Allen Byrne
96cb94a95c Add missing filenames 2019-12-09 14:14:39 -06:00
Allen Byrne
349656ecba Add new test reference 2019-12-08 13:58:35 -06:00
David Young
f1b39ad80e Apparently, + has no special meaning, and neither does \+, in so-called
"obsolete" / POSIX "basic" regular expressions.  Also, not every version of
`sed` out there supports the `-E` option.  So delete the -E flag and use
the regex `[^/][^/]*` instead of `[^/]+`.

Add config/netbsd to the MANIFEST.
2019-11-12 10:43:26 -06:00
Jerome Soumagne
ae490016b9 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 14:30:24 -05:00
Quincey Koziol
eaa65c862b 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 14:30:23 -05:00
Allen Byrne
09e6dcbfbb Add new toolchain file 2019-10-01 10:09:16 -05:00
Jacob Smith
35a9e9c50f Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage 2019-09-23 17:23:02 -05:00
Jacob Smith
aa797af31b 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.
2019-09-23 16:21:37 -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
Allen Byrne
fa540a3af8 Add 32-bit cross-compile toolchain 2019-08-29 10:36:12 -05:00