Commit Graph

5634 Commits

Author SHA1 Message Date
Jordan Henderson
1ce6691a72 Fix bug where incorrect amount of data was being read from the file 2017-08-10 14:12:01 -05:00
Jordan Henderson
50c4bc8835 Add test file to build process 2017-08-03 10:09:47 -05:00
Jordan Henderson
bd79a782b4 Suggested changes from code review 2017-07-07 13:31:43 -05:00
Jordan Henderson
104047e13b Amend header comment error
Suggested fix for allocating too small of a buffer for the chunk data
2017-07-06 14:21:26 -05:00
Jordan Henderson
610e76c75c Clean up remaining warnings 2017-07-06 08:02:29 -05:00
Jordan Henderson
0531d92d74 Add prototype for H5D__cmp_filtered_collective_io_info_entry_owner 2017-07-05 14:36:54 -05:00
Jordan Henderson
0f78b954f2 Add comment for memory copy possibly not being necessary anymore for
Multi-Chunk I/O
2017-07-05 10:38:37 -05:00
Jordan Henderson
a2cdec5ab3 Remove use of H5E_CANTDISTRIBUTE error 2017-07-05 08:48:24 -05:00
Jordan Henderson
3ce78d0d8d Add comment for full overwrite special case 2017-07-05 08:40:09 -05:00
Jordan Henderson
4e121c3913 Add remaining documentation/comments 2017-07-05 08:34:45 -05:00
Jordan Henderson
34fac7abb0 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits)
  Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting
  More minor whitespace cleanup
  Fixed a minor comment typo in H5R.c
  * Reverted removal of H5I_REFERENCE to avoid breaking binary   compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19()   in tmisc.c.
  Added missing free() call to test_misc19().
  Purged the unused H5I_REFERENCE from the library.
  Added a test for VFD IDs to testhdf5.
  Revert "Partial removal of NDEBUG ifdefs from the library."
  Partial removal of NDEBUG ifdefs from the library.
  Removed compiler flag cleanup since Solaris chokes on it.
  Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file.
  Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true.
  Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely).
  Added awk processing to remove extraneous whitespace from H5_ flags in configure.
  Fixed a comment in configure.ac
  HDFFV-10219 another mode change
  HDFFV-10219 change subset to use BINARY mode for h5dump
  HDFFV-10219 default input binary to NATIVE
  Set default of var to NATIVE
  HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed
  ...
2017-07-05 08:05:02 -05:00
Dana Robinson
9a749a64f0 More minor whitespace cleanup 2017-07-03 13:01:58 -07:00
Dana Robinson
dfceb84d47 Fixed a minor comment typo in H5R.c 2017-07-03 13:00:11 -07:00
Dana Robinson
76b9a0e7ef * Reverted removal of H5I_REFERENCE to avoid breaking binary
compatibility.
* Added a quick H5I_REFERENCE smoke check to test_misc19()
  in tmisc.c.
2017-07-03 12:54:14 -07:00
Dana Robinson
0d6930d3c2 Purged the unused H5I_REFERENCE from the library. 2017-06-30 20:53:56 -07:00
Dana Robinson
b6944aeb2a Added a test for VFD IDs to testhdf5.
This required adding some code to generate a fake VFD class
to pass to H5FDregister().

Also, a bunch of whitespace and comment tidying.
2017-06-30 18:35:09 -07:00
Vailin Choi
804a88fafd Fix for HDFFV-10160
Modifications to fix the assertion/abort failure when the application does not close the file.
2017-06-29 01:11:44 -05:00
Vailin Choi
980d5b4266 Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiers
Changes made so that raw data for dataset objects are copied from cached info when possible instead of flushing objects to file and read them back in again.
2017-06-10 19:40:19 -05:00
Dana Robinson
005bf26ff8 Revert "Merge pull request #567 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to develop"
This reverts commit 4242753848, reversing
changes made to b0e79fe6dd.
2017-06-09 18:09:08 -04:00
Dana Robinson
d391d8a690 * Made STATIC free lists EXTERN for H5O_layout_t.
* Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
2017-06-07 18:10:48 -04:00
Dana Robinson
390b5a9feb Updated H5O_layout_t dynamic work to use the H5FL interface. 2017-06-07 13:38:27 -04:00
Dana Robinson
1ccb1b3c1f Made some H5O_layout_t stack allocations dynamic (quiets warnings). 2017-06-06 14:07:09 -04:00
Dana Robinson
1e9354bcf5 Merge branch 'develop' into windows_open 2017-05-31 15:07:49 -07:00
Dana Robinson
343b53d64f Merge branch 'develop' into compat_feature_flag 2017-05-26 17:29:52 -04:00
Dana Robinson
cf80aac401 Merge pull request #538 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:may_dev_warnings to develop
* commit '57f0a296c0b727e3d86cea312ba46efc98d76227':
  Minor warning fix.
  More minor warning fixes.
  Minor warning fixes in the tools.
  Minor type fixes to h5watch.
  A few more warnings fixed.
  Fixed additional minor warnings.
  Fixed many minor warnings.
2017-05-26 10:43:56 -05:00
Frank Willmore
53c5b41ec2 Merge pull request #534 in HDFFV/hdf5 from ~FRANK.WILLMORE/hdf5:fix-set-mpi-err-handler to develop
* commit '1ee90786196c10c2c616a9fb4b8b1f92ebefa1f2':
  updated MPI error handling call for MPICH2 standard
  cleanup
  enabled MPI error handling
  added test file
2017-05-25 13:30:54 -05:00
Dana Robinson
1b74c5ca95 More minor warning fixes. 2017-05-25 10:11:26 -04:00
Dana Robinson
946fd98b8d Fixed many minor warnings. 2017-05-25 06:45:53 -04:00
Dana Robinson
8807f918b9 Added missing casts for the return value of H5I_object_verify(). 2017-05-24 16:13:12 -04:00
Dana Robinson
479f326a26 * Added new public H5FDdriver_query() API call.
* Changed return type of H5FD_driver_query() to herr_t.
* Updated swmr.c to use H5FDdriver_query() instead of the private call.
* Added some flags tests to vfd.c.
2017-05-24 09:41:26 -04:00
Dana Robinson
e5a57c97aa * Made H5FD_driver_query() a private function instead of static.
* Moved H5FD_driver_query() to H5FDint.c.
* Minor typo fixes in H5I.c.
* Updated swmr.c to check the VFD feature flags and skip the
  retries test when the VFD is not compatible with H5P_DEFAULT.
2017-05-24 07:44:18 -04:00
Frank Willmore
1ee9078619 updated MPI error handling call for MPICH2 standard 2017-05-23 19:01:52 -07:00
Frank Willmore
8f25e21e10 enabled MPI error handling 2017-05-23 10:14:35 -07:00
Dana Robinson
14c286d51a Fixed HDFFV-10214:
* Updated comments in the library to accurately reflect the semantics
  of the H5FD_FEAT_POSIX_COMPAT_HANDLE flag.
* Removed the check for the POSIX compatible handle feature flag
  when determining if a VFD supports SWMR.
Partial work for HDFFV-10197:
* Added a new H5FD_FEAT_DEFAULT_VFD_COMPATIBLE feature flag that is
  set when a VFD creates output that is compatible with the default
  VFD. Will be used in the testing but might also be generally useful
  to users.
2017-05-19 14:58:34 -07:00
Vailin Choi
54dff33177 Incorporate additional code changes for the H5DOread_chunk patch from GE Heathcare (HDFFV-9934)
This is the similar set of changes that was checked in to 1.8 branch:
Incorporate the code changes that were missing from the original patch:
(1) Additional tests in hl/test/test_dset_opt.c
(2) Fix in src/H5Dchunk.c for direct access when an entry is in chunk cache but not dirty
Tested on platypus, ostrich, kituo, mayll, osx1010test, moohan, quail, emu.
2017-05-15 10:25:15 -05:00
Dana Robinson
f95ef72a5e Merged HDFFV-10187 direct chunk overwrite bugfix to develop from 1.10 branch. 2017-05-11 23:31:57 -04:00
Allen Byrne
445c805a4c HDFFV-10186 Add endianess to bitfield and fix tests 2017-05-10 10:59:13 -05:00
Vailin Choi
8482314d7d Fix for HDFFV-10051
Fix missing declaration for H5D__layout_compact_dirty_test().
Tested on mayll and osx1010test.
2017-05-09 17:30:20 -05:00
Vailin Choi
e062a77e0e Merge pull request #494 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit 'd436db6c6efdfe7e9dbe06a642715116ef0eb5e3':
  Fix for the two issues reported in HDFFV-10051 Modifications made based on the review comments from pull request #494 Tested on moohan, mayll, kituo, platypus, ostrich, osx1010test, quail, emu.
  Fix for the two issues reported in HDFFV-10051: (1) Repeated open/close of a compact dataset fails due to the increment of ndims in the dataset structure for every open. --This is done only for chunked dataset via H5D__chunk_set_sizes(). (2) layout "dirty" flag for a compact dataset is not reset properly after flushing the data at dataset close. --Reset the "dirty" flag before flushing the message to the object header via H5O_msg_write(). Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
2017-05-09 13:18:26 -05:00
Allen Byrne
5263bc9029 HDFFV-10186 Whitespace changes
Mostly replacing tabs with spaces
Removed empty mod sections
2017-05-09 10:41:00 -05:00
Vailin Choi
d436db6c6e Fix for the two issues reported in HDFFV-10051
Modifications made based on the review comments from pull request #494
Tested on moohan, mayll, kituo, platypus, ostrich, osx1010test, quail, emu.
2017-05-08 22:14:20 -05:00
Vailin Choi
6a4f1187cc Fix for the two issues reported in HDFFV-10051:
(1) Repeated open/close of a compact dataset fails due to the
increment of ndims in the dataset structure for every open.
--This is done only for chunked dataset via H5D__chunk_set_sizes().
(2) layout "dirty" flag for a compact dataset is not reset
properly after flushing the data at dataset close.
--Reset the "dirty" flag before flushing the message to the object header
via H5O_msg_write().
Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
2017-05-06 23:40:44 -05:00
Jordan Henderson
92759cc3b9 Revise shared chunks redistribution algorithm 2017-05-01 10:51:32 -05:00
Jordan Henderson
d367d397e3 Separate shared chunks redistribution code out to its own function 2017-05-01 10:01:53 -05:00
Dana Robinson
734aebc395 Rework of the POSIX file open permissions and macros to clean up
HDopen() calls.

Also fixed a minor const warning in the core VFD.
2017-04-28 18:13:22 -04:00
Dana Robinson
d3b664b6a7 Changed the Windows POSIX open() file permissions to be correct
according to MSDN. Partial fix for HDFFV-9630.
2017-04-28 08:11:29 -07:00
Dana Robinson
80d57c242a Set the HDF5_GENERATE_HEADERS CMake option to default to ON and removed
the option from the CMake cache init files.

Fixes HDFFV-10184
2017-04-27 15:18:18 -04:00
Allen Byrne
a302f508a5 Change position of declaration to top of block 2017-04-27 08:52:34 -05:00
Vailin Choi
bacb45b38a Modifications based on pull request review.
Made couple changes based on the review comments.
2017-04-26 14:00:34 -05:00
Vailin Choi
cb8e82a53d Incorporate patch from GE Healthcare (HDFFV-9934)
This is the same patch that had already been integrated to 1.8 branch (pull request #387).
Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
2017-04-25 18:08:53 -05:00