Commit Graph

6003 Commits

Author SHA1 Message Date
Neil Fortner
d007267f1b Modify VDS to open source files using the SEC2 driver when the VDS file
is openend in parallel.  Disable file locking on these source files.
Add independent read test to t_psubfile (from Richard).  Various
cleanup, etc.
2018-08-02 16:34:15 -05:00
Richard Warren
37ff3a38cc Use a basic VDS example from the documentation with parallel extensions 2018-07-17 18:12:53 -04:00
Richard Warren
8e4cb935fc Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into parallel_vds_develop 2018-07-17 07:56:19 -04:00
Binh-Minh Ribler
fe916ada37 Removed white space 2018-07-16 22:10:50 -05:00
Binh-Minh Ribler
073e0b1f03 Fixed HDFFV-10476, HDFFV-10478, HDFFV-10480
Description:
    Fixed potential out of bound read and NULL pointer dereferences.
Platforms tested:
    Linux/64 (jelly)
    Linux/32 (jam)
    Darwin (osx1010test)
2018-07-16 20:28:27 -05:00
Binh-Minh Ribler
55666ace55 Merge pull request #1134 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop to develop
Fixed HDFFV-10481 and HDFFV-10477

* commit '83ca39ba9a2d6852dd7754b533f7839e9d2a0107':
  Combined macro lines as Dana commented Platforms tested:     Linux/64 (jelly) (very minor)
  Fixed division-by-zero issues Description:     Fixed HDFFV-10481 and HDFFV-10477, division by 0.     Fixed another occurrence beside what were reported.     Also, changed a local variable to avoid an unnecessary cast. Platforms tested:     Linux/64 (jelly)     Linux/32 (jam)     Darwin (osx1010test)
2018-07-16 14:52:43 -05:00
Binh-Minh Ribler
83ca39ba9a Combined macro lines as Dana commented
Platforms tested:
    Linux/64 (jelly) (very minor)
2018-07-16 14:48:11 -05:00
Jerome Soumagne
d5e7134df9 Fix evaluation of __has_attribute(no_sanitize_address) on older GCC versions 2018-07-16 13:33:23 -05:00
Jerome Soumagne
643593dfda Merge pull request #1112 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5_fork:gcc_sanitize to develop
* commit '5afeefe1bae62fa5faf06c0c6f240e10863a2693':
  Fix H5detect to use no_sanitize_address attribute and support GCC sanitizers
2018-07-16 10:39:13 -05:00
Jordan Henderson
f649be9fdc Merge pull request #1127 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit 'a8d6f100cdddbfc42d0c4abfeb4ceb8788b1b087':
  Add note about single chunk caching and serial library
  Add check for actually using the MPI file driver when caching one chunk
  Fix error message mentioning wrong MPI function used
  Fix for HDFFV-10509
  Revise H5D__mpio_array_gatherv() to not allocate memory needlessly
  Add test to continually grow and shrink chunks
  Changes to test with checksum filter as well as deflate filter
  Eliminate warning about signed to unsigned conversion
  Remove unused local variable
  Fix bug in parallel reads of compressed data
  Add data verification to parallel filtered compound write tests
  Add seven of fourteen parallel filtered data partial read tests
2018-07-16 09:37:54 -05:00
Richard Warren
963954e756 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into parallel_vds_develop 2018-07-16 07:47:29 -04:00
Binh-Minh Ribler
fa5d96dc5e Fixed division-by-zero issues
Description:
    Fixed HDFFV-10481 and HDFFV-10477, division by 0.
    Fixed another occurrence beside what were reported.
    Also, changed a local variable to avoid an unnecessary cast.
Platforms tested:
    Linux/64 (jelly)
    Linux/32 (jam)
    Darwin (osx1010test)
2018-07-15 23:31:09 -05:00
Binh-Minh Ribler
fafa49ef7f Merge pull request #1133 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop to develop
Fixed HDFFV-10404

* commit 'ec31438afdaf575368938e930eb3af0865a342b3':
  Fixed HDFFV-10404 Description:     Applied the typo fixes from user's report.     The previous pull request couldn't be merged because it was too old,     and it was too complicated for me to resolve conflicts. Platform tested:     Linux/64 (jelly) - very minor
2018-07-14 08:10:49 -05:00
Richard Warren
1657e0324d Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into parallel_vds_develop 2018-07-13 20:31:31 -04:00
Binh-Minh Ribler
ec31438afd Fixed HDFFV-10404
Description:
    Applied the typo fixes from user's report.
    The previous pull request couldn't be merged because it was too old,
    and it was too complicated for me to resolve conflicts.
Platform tested:
    Linux/64 (jelly) - very minor
2018-07-13 13:40:22 -05:00
Jordan Henderson
a8d6f100cd Add note about single chunk caching and serial library 2018-07-13 10:20:16 -05:00
Vailin Choi
ef30425b1c Merge pull request #1129 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit '08de02c838c05993fea5febb9c320a679e7f841a':
  Changes based on feedback from pull request.
  Fix test_misc33() in test/tmisc.c Open the test file read-only so that it can be accessed for testing.
  Modifications made based on feedback from pull request.
  Fix for HDFFV-10333: 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
  Fix daily test failure.
2018-07-13 10:02:24 -05:00
Jordan Henderson
0dc6c3c8b5 Add check for actually using the MPI file driver when caching one chunk
Better explain rationale behind chunk caching issue fix
2018-07-13 09:26:41 -05:00
Jordan Henderson
30d3bc2c91 Fix error message mentioning wrong MPI function used 2018-07-13 08:09:48 -05:00
Vailin Choi
92bf81a0fb Changes based on feedback from pull request. 2018-07-12 18:25:49 -05:00
Vailin Choi
cf38292064 Fix for HDFFV-10333:
1) Check for valid object header version for a refcount messge
2) Check for invalid fill value size
3) Check for invalid dimension size in a layout message
4) Add --enable-error-stack option to h5stat
5) Add error checks to h5stat.c
6) Add tests to h5stat and h5dump
2018-07-10 22:00:14 -05:00
Richard Warren
6ad9585342 Fix some commentary around the H5FD_mpio_cmp function and remove test_printf and test_all from testpar/t_pvds.c to remove issues with testing printf style parallel VDS. 2018-07-05 16:30:08 -04:00
Jordan Henderson
ef10aa6211 Fix for HDFFV-10509 2018-07-03 21:09:19 -05:00
Jordan Henderson
6190641722 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'b6fcbf4bb0f693fd6a0517f0ff3f74d52b329d1e': (400 commits)
  Fix ptr arith
  Correct function call
  Remove writeVL option
  Region reference in compounds need class check
  Correct cast formatting
  Correct var name
  Need to cast from void ptr
  Update Java util lib, Refactor H5D write VL to match read
  Fix attribute Read
  Correct "," handling
  Revert "Merge pull request #1116 in HDFFV/hdf5 from ~HDFTEST/hdf5_hft:hdf5_1_10 to develop"
  Snapshot version 1.10 release 3 (snap3)
  Remove debug statements
  Split/fix utility for vl types
  fix whitespace
  HDFVIEW compound vlen needed vlen_t size
  Update documents
  Update document
  Update document
  HDFFV-10433 Update file with fix for issues
  ...
2018-07-03 09:57:13 -05:00
Richard Warren
5ce8d5da40 Addresses the PR issues raised by Neil. 2018-07-02 08:52:30 -04:00
hdftest
b193bc11c9 Revert "Merge pull request #1116 in HDFFV/hdf5 from ~HDFTEST/hdf5_hft:hdf5_1_10 to develop"
This reverts commit e9f476dad4, reversing
changes made to 2ff00b1b93.
2018-06-24 18:04:23 -05:00
hdftest
25f80cbbec Snapshot version 1.10 release 3 (snap3) 2018-06-24 17:35:05 -05:00
hdftest
67d6f8d405 Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)
* commit '87829e06189cd9b29583b5ca8065b52b1f4cd523': (30 commits)
  HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
  HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
  HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
  Cleaned up H5Fmount/unmount code.
  Normalization with vol_integration branch.
  Add fortran MPI to test and example
  Add mpi include folders for fortran C objects
  Normalization with the vol_integration branch.
  Fixed MANIFEST
  Fix usage of compression lib in shared tests
  Fix jni function call version
  Fix the error found after earlier checkin.
  H5O_info fixes for java and examples
  Added a RELASE.txt entry for HDFFV-10505.
  Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags.
  (1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463.
  Normalize with vol_integration.
  Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c.
  Restored some unused #defines to the deprecated section of H5Dpublic.h.
  Changes made based on feedback from pull request #1039.
  ...
2018-06-16 17:47:39 -05:00
Jerome Soumagne
5afeefe1ba Fix H5detect to use no_sanitize_address attribute and support GCC sanitizers 2018-06-15 16:49:54 -05:00
Scot Breitenfeld
87829e0618 Merge pull request #1111 in HDFFV/hdf5 from hdf5_1_10.sync to hdf5_1_10
* commit '57f64b92d19fed2879ee9bafe1d29bfac865d54c': (30 commits)
  HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
  HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
  HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
  Cleaned up H5Fmount/unmount code.
  Normalization with vol_integration branch.
  Add fortran MPI to test and example
  Add mpi include folders for fortran C objects
  Normalization with the vol_integration branch.
  Fixed MANIFEST
  Fix usage of compression lib in shared tests
  Fix jni function call version
  Fix the error found after earlier checkin.
  H5O_info fixes for java and examples
  Added a RELASE.txt entry for HDFFV-10505.
  Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags.
  (1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463.
  Normalize with vol_integration.
  Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c.
  Restored some unused #defines to the deprecated section of H5Dpublic.h.
  Changes made based on feedback from pull request #1039.
  ...
2018-06-15 13:53:36 -05:00
Richard Warren
38ebfd7f4d Made code updates to reflect John Mainzer's comments. Also made a change unrelated to parallel vds, i.e. changed one instance of MPI_Type_extent to MPI_Type_get_extent to remove deprecated errors reported by OpenMPI 3.1 2018-06-14 20:24:11 -04:00
Richard Warren
8d7d1f1ab6 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into parallel_vds_develop 2018-06-14 19:28:48 -04:00
M. Scot Breitenfeld
57f64b92d1 Merge branch 'develop' into hdf5_1_10.sync 2018-06-14 09:17:06 -05:00
Richard Warren
9b23d85f51 Add some merge changes to bring the PR changes up to date. Includes removal of H5D__virtual_insert_gh_obj in favor of a merged version of H5D__virtual_store_layout 2018-06-11 19:53:41 -04:00
Dana Robinson
18fbdebb97 Cleaned up H5Fmount/unmount code. 2018-06-06 23:08:29 -07:00
Dana Robinson
91089de53f Normalization with vol_integration branch. 2018-06-06 21:34:11 -07:00
Jordan Henderson
8da8a1dcb5 Revise H5D__mpio_array_gatherv() to not allocate memory needlessly 2018-06-06 13:29:03 -05:00
Dana Robinson
1a5e7d821b Normalization with the vol_integration branch. 2018-06-05 22:20:22 -07:00
M. Scot Breitenfeld
f484649347 Merge branch 'develop' into hdf5_1_10.sync 2018-06-04 14:41:12 -05:00
hdftest
afe28b7607 Snapshot version 1.10 release 3 (snap2) 2018-06-03 21:53:30 -05:00
Dana Robinson
dec2f588ac Merge pull request #1043 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:h5do_direct_chunk_hl_to_src to develop
* commit '1da9c5545c013ebc540ba3044810889d4acfa5be':
  Restored some unused #defines to the deprecated section of H5Dpublic.h.
  Added deprecated symbol wrappers for the H5DOwrite/read_chunk wrappers.
  Updated commenting in the H5DO compat test.
  Stripped out most of the duplicated functionality in the H5DO compat test.
  * Added H5DO compatibility functions. * Changed the offset copy to use an array on the stack. * Yanked some unused #defines.
  * Fixed the error tests * Moved common functionality into helper functions
  Normalize with trunk prior to update merge
  Fixed a warning.
  Finished move of H5DOread/write_chunk calls to H5D.
  First stage of moving H5DOread/write_chunk() to src/ and making them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to   direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform   and renamed to direct_write_perf. * Updated autotools and CMake files.
2018-05-31 18:14:24 -05:00
Vailin Choi
796dc16e34 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'e8ece625f223032db0d26cfffafc045e4ccdf37d':
  Normalize with vol_integration.
2018-05-31 11:50:24 -05:00
Richard Warren
2a24cb0d0f Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into parallel_vds_develop 2018-05-31 10:02:46 -04:00
Richard Warren
de129217a4 Rebase parallel VDS work to develop branch for testing and review 2018-05-30 16:21:46 -04:00
Vailin Choi
584a810764 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'd184e6db94163dcc8761182744a6c524a4850887':
  Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c.
  Correct script names
  Fix typo
  Minor H5FS tweaks.
  Put back CTRL-L chars
  Update support link
  Update text
  Valgrind fixed by checking for prefix_len of 0
2018-05-30 14:48:19 -05:00
Dana Robinson
384a1ec709 Normalize with vol_integration. 2018-05-29 14:06:01 -07:00
hdftest
f8690c40b9 Updated version to 1.10.3-snap2 2018-05-29 15:16:31 -05:00
M. Scot Breitenfeld
cc611c696f Merge branch 'develop' into hdf5_1_10.sync 2018-05-25 08:39:47 -05:00
Dana Robinson
448cc37a90 Removed unused H5MF functions and updated FUNC_ENTER macros and
naming in H5MFsection.c.
2018-05-24 14:05:47 -07:00
Dana Robinson
a2bafdc7a1 Minor H5FS tweaks. 2018-05-23 23:40:23 -07:00