5587 Commits

Author SHA1 Message Date
Vailin Choi
38b4e97692 Fix for daily test failure
Fix for the compilation error from the PGI compiler.
2017-08-24 11:42:35 -05:00
Vailin Choi
1ef8577a4a Modifications based on comments from pull request review
(1) Remove unnecessary asserts
(2) Add code to insert bad offset values to the test file in gen_bad_offset.c
2017-08-23 16:23:09 -05:00
Vailin Choi
b07eb6efd0 Fix for HDFFV-10216 segfault in H5G_node_cmp3 with corrupt h5 file
Fix H5HL_offset_into() to return error when offset exceeds heap data block size.
Also fix other places that call this routine to detect error return.
2017-08-22 01:36:20 -05:00
Dana Robinson
81340c609b Moved H5PL diagnostic pragmas to comply with old gcc requirements that they
be outside of functions.
2017-08-02 08:32:31 -07:00
Dana Robinson
9bcf8b2f25 Minor tweaks in response to code review. 2017-08-01 04:59:36 -07:00
Dana Robinson
fd0d8738e0 Merge branch 'develop' into h5pl_commit 2017-08-01 04:12:03 -07:00
Vailin Choi
ba17f16e4c Skip test in test/fheap.c when:
a) multi/split drivers and
b) persisting free-space or using paged aggregation strategy
because the library will fail file creation (temporary) for the above conditions.
2017-07-17 23:31:21 -05:00
Vailin Choi
66efce85e7 Changes made based on RFC review comments
Test the changes in a branch via daily testing.
2017-07-17 23:28:31 -05:00
Dana Robinson
d4234d0a98 Major rework of H5PL package code before bringing VOL changes
over.

Brings coding standards in line with the rest of the library,
enforces better software engineering principles, and makes
everything more maintainable.
2017-07-14 09:18:33 -07:00
Richard Warren
516f0e3661 Merge pull request #596 in HDFFV/hdf5 from GreaterThan-2GB-MPIO to develop
* commit '6a5aa46e936340ed540359290374fa909f9213a6':
  Added a brief outline for Large MPI-IO transfers into RELEASE.txt
  Fix up the ExpressMode check for skipping slow running tests.
  Include code fixes and additional modifications pointed out by code reviewers
  Commited changes to the development branch here to allow a pull request to be published
  Commit changes needed for pull request
2017-07-13 12:44:47 -05:00
Richard Warren
0c4c562cc5 Include code fixes and additional modifications pointed out by code reviewers 2017-07-10 16:17:26 -04:00
Vailin Choi
8935c921f7 Fix for HDFFV-10217 infinite loop in H5VM_power2up().
The function H5VM_power2up() returns the next power of 2 for n.
When n exceeds 2^63, it overflows and becomes 0 causing the infinite looping.
The fix ensures that the function checks for n >= 2^63 and returns 0.
2017-07-10 03:22:48 -05:00
Richard Warren
64d33e5e6e Commited changes to the development branch here to allow a pull request to be published 2017-07-05 16:19:57 -04:00
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 4242753848c44ab3b5d226e66225eac2f64db314, reversing
changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
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
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