Commit Graph

19033 Commits

Author SHA1 Message Date
Dana Robinson
07b76068a4 Merge branch 'develop' into vfd_init_cleanup 2018-12-31 17:19:39 -08:00
Allen Byrne
c3cad8e5f3 HDFFV-10664 minimized dataset headers for java interface 2018-12-31 16:34:07 -06:00
Jacob Smith
8324be7fad fix wrong function name that is missed by correctional macro 2018-12-31 15:18:13 -06:00
Allen Byrne
fa6077332b Merge pull request #1416 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '0e6cf18b06d71dc8da9307dddce5e1833f197e19':
  Fix runtest case for data to stdout in tool
2018-12-31 14:07:57 -06:00
Allen Byrne
0e6cf18b06 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'b30a1fe44aa804a67f2291005bf8135ac5c2dc99':
  Updated the parallel install docs.
  Eliminated the need for a separate script variable.
  Added a helpful message to the flush script.
  Added a shell script so we can run the parallel flush test on OpenMPI.
2018-12-31 14:06:43 -06:00
Dana Robinson
b30a1fe44a Merge pull request #1400 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:openmpi_tweaks to develop
* commit 'd6c2a96ac2f103d90b96d5b39814810e6a31ef99':
  Updated the parallel install docs.
  Eliminated the need for a separate script variable.
  Added a helpful message to the flush script.
  Added a shell script so we can run the parallel flush test on OpenMPI.
2018-12-31 13:33:31 -06:00
Allen Byrne
028d47d707 Fix runtest case for data to stdout in tool 2018-12-31 12:38:09 -06:00
Dana Robinson
fba448b145 Merge pull request #1413 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:yay_plugins to develop
* commit '3ca19cca5395d79be69209f8d7d0a2b06834a648':
  Flipped swapped testing strings.
  Added test_vol_plugin.sh to the list of scripts to clean
  Fixed a CMake build issue (CMake still doesn't run the VOL plugin tests)
  Added more sub-tests to the VOL plugin test.
  Added a simple test for registration of VOL connector plugins. Autotools only for right now, but this will be fleshed out in future work.
2018-12-31 10:28:25 -06:00
Larry Knox
72124031ec Add libhdf5_hl_fortran symlinks for libhdf5hl_fortran files.
Set ctest*.lsf.in.cmake scripts for sierra.
Correct src/CMakelists.txt syntax error.
2018-12-31 09:20:27 -06:00
Dana Robinson
d6c2a96ac2 Updated the parallel install docs. 2018-12-31 05:07:30 -08:00
Dana Robinson
4faca62679 Eliminated the need for a separate script variable. 2018-12-31 05:04:30 -08:00
Larry Knox
715272eeb7 Correct syntax error in CMakeLists.txt. 2018-12-31 06:23:13 -06:00
Dana Robinson
a3faa92653 Merge branch 'develop' into openmpi_tweaks 2018-12-30 22:24:42 -08:00
Vailin Choi
e035c7abdd Changes based on feedback from pull request. 2018-12-31 00:11:45 -06:00
jake.smith
905c3ca3d7 Merge pull request #1372 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:dset_ohdr_minimize to develop
Dataset object header minimization
Jira TRILAB-45

* commit 'f54fb420d08ea0a7e7b026150c0ab559803e0acd': (34 commits)
  Specify variable type. Remove unnecessary whitespace.
  OHDR tests now accept h5_fileaccess() fapls. Formatting, informative comments, and minor renaming.
  Fix some CMake listings
  Add error checking to the minimized dset header size calculation. Update printf->HDprintf statements.
  Remove `#if 0` block of deprecated code.
  Fix mistake with H5E_BEGIN_TRY {...} H5E_END_TRY block containing ERROR-raising macros. Formatting tweaks.
  Add "compact" storage test to relative header size comparisons.
  Formatting adjustments.
  Formatting adjustments
  Move H5Fset_dset_no_attrs_hint VOL operations to native. Move minimzied object header tests from separate file to test/ohdr.c Some formatting changes.
  Re-format test/ohdr_mindset.c Fix a few transcription errors in other test files.
  formatting adjustments
  Reformat to be more consistent with existing code. Fix a few typos.
  add missing paramter - macro seemingly unused, but absence results in compiler complaint
  fix reference; move declaration in file
  Remove unused debugging print in '#if 0' block
  Fix typo. Fix CHECK of wrong ID (dset[2|3]_id).
  change test file name and apply 'h5_fixname' to it
  Sidestep and hide&flag minor issues causing test failures.
  Incorporate minimized dset ohdr tests into extant suite.
  ...
2018-12-29 14:31:31 -06:00
Larry Knox
126d1e6176 Add .lsf batch scripts and insert the build directory into the scripts
during configuration.
2018-12-28 16:50:48 -06:00
Vailin Choi
f808c108ed Fix for HDFFV-10659: The library abort with "infinite loop closing library"
after deleting attributes in densed storage.
The fix: When deleting attribute nodes from the name index v2 B-tree,
if an attribute is found in the intermediate B-tree nodes, which may be
merged/redistributed in the process, we need to free the dynamically
allocated spaces for the intermediate decoded attribute.
2018-12-28 16:49:11 -06:00
Dana Robinson
3ca19cca53 Flipped swapped testing strings. 2018-12-28 12:56:49 -08:00
Dana Robinson
dac76c579b Merge branch 'develop' into yay_plugins 2018-12-28 12:55:15 -08:00
Jacob Smith
f54fb420d0 Merge branch 'develop' into dset_ohdr_minimize 2018-12-28 12:45:10 -06:00
Jacob Smith
30493ce9b9 Specify variable type.
Remove unnecessary whitespace.
2018-12-28 10:17:09 -06:00
Dana Robinson
ba095e6a53 Merge pull request #1406 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:md_cache_logging_squash to develop
* commit '1ff756a1047d58f71c70deb48c797cb860904292':
  Updated the log function names.
  Squash merge of MDC logging changes.
2018-12-28 07:22:32 -06:00
Dana Robinson
1ff756a104 Updated the log function names. 2018-12-28 05:15:58 -08:00
Dana Robinson
552fec96e9 Merge branch 'develop' into md_cache_logging_squash 2018-12-27 22:22:24 -08:00
Dana Robinson
75dd3c9cab Merge branch 'develop' into yay_plugins 2018-12-27 22:20:09 -08:00
Dana Robinson
3a05e7109a Added test_vol_plugin.sh to the list of scripts to clean 2018-12-27 21:42:51 -08:00
Jordan Henderson
fe30b71086 Merge pull request #1386 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit 'b4fe787bb9fe4bfc4709a124df59dd987c9a09d2':
  Add test for H5Arename NULL/empty attribute name fix
  align H5Arename behavior with H5Arename_by_name
2018-12-27 23:05:20 -06:00
Dana Robinson
fafee5b8ae Fixed a CMake build issue (CMake still doesn't run the VOL plugin
tests)
2018-12-27 19:56:21 -08:00
Dana Robinson
544ab1c78a Added more sub-tests to the VOL plugin test. 2018-12-27 19:42:02 -08:00
Dana Robinson
621014be28 Added a simple test for registration of VOL connector plugins.
Autotools only for right now, but this will be fleshed out in future
work.
2018-12-27 15:50:04 -08:00
Dana Robinson
5b57c69ed4 Merge pull request #1412 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:yay_plugins to develop
* commit '9cc406633c29d4167031dc85b950858f90163cbc':
  Fixed plugin loading so it actually checks the plugin type.
2018-12-27 16:10:57 -06:00
Dana Robinson
9cc406633c Fixed plugin loading so it actually checks the plugin type. 2018-12-27 14:00:32 -08:00
Jacob Smith
29497cc4e1 Merge branch 'develop' into dset_ohdr_minimize 2018-12-27 12:33:32 -06:00
Dana Robinson
1cc890e333 Merge pull request #1410 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to develop
* commit '9152547b766919eefb7163e17f0c03052a2d73f2':
  H5VLregister_by_value() should not set _BY_NAME when searching for plugins.
2018-12-27 11:10:05 -06:00
Dana Robinson
9152547b76 H5VLregister_by_value() should not set _BY_NAME when searching for
plugins.
2018-12-27 08:56:43 -08:00
Jacob Smith
b2afa88fa0 OHDR tests now accept h5_fileaccess() fapls.
Formatting, informative comments, and minor renaming.
2018-12-26 14:35:22 -06:00
Binh-Minh Ribler
9c6744778e Fixed documentation - typo only 2018-12-23 00:51:17 -06:00
Binh-Minh Ribler
c3f51c52d0 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop 2018-12-23 00:18:42 -06:00
Binh-Minh Ribler
251ba120b5 Fixed CVE division-by-zero issues
Description:
    Fixed HDFFV-10577 and similar issues found in H5Dchunk.c.  All
    the occurrences are in:
        H5D__create_chunk_map_single
        H5D__create_chunk_file_map_hyper
        H5D__chunk_allocate
        H5D__chunk_update_old_edge_chunks
        H5D__chunk_prune_by_extent
        H5D__chunk_copy_cb
        H5D__chunk_collective_fill
Platforms tested:
    Linux/64 (jelly)
    Linux/64 (platypus)
    Darwin (osx1010test)
2018-12-23 00:18:13 -06:00
Jacob Smith
cfdbb220d8 Fix some CMake listings 2018-12-21 16:18:05 -06:00
Jacob Smith
db9cc49a6b Add error checking to the minimized dset header size calculation.
Update printf->HDprintf statements.
2018-12-21 15:47:49 -06:00
Allen Byrne
7d28a4295e Merge pull request #1407 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '991996b25122ff010b9af1bbb6cc05be491ce038':
  Remove unused CMake files
  Update option text
  Add reference file to list
  HDFFV-10656 remove moved source
  HDFFV-10656 Add CHECK_VOL support to CMake
2018-12-21 14:41:29 -06:00
Allen Byrne
991996b251 Remove unused CMake files 2018-12-21 12:22:32 -06:00
Allen Byrne
909fa39bc7 Update option text 2018-12-21 11:41:02 -06:00
Allen Byrne
99d1f614f1 Add reference file to list 2018-12-21 10:39:15 -06:00
Dana Robinson
18e6ec82d0 Squash merge of MDC logging changes. 2018-12-20 20:41:42 -08:00
Dana Robinson
d6adb6526d Merge pull request #1399 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:vol_tweaks to develop
* commit '75a03ea0c36f24a6a3982b75a8c52325879bb569':
  Moved private native VOL connector functions to H5VLnative_private.h.
  Moved the remainder of the code into separate files.
  Split the native VOL connector code into multiple files and moved the attribute code over.
2018-12-20 19:48:36 -06:00
Quincey Koziol
830fac2fea Merge pull request #1402 in HDFFV/hdf5 from stackable_vol_fix_13 to develop
* commit '9e8cacaa5531f418f5d9d447c1251eb705da785a':
  Remove core VFD-specific property list call and regenerate encoded property lists.
2018-12-20 15:45:11 -06:00
Allen Byrne
3c8b00dbd8 HDFFV-10656 remove moved source 2018-12-20 15:35:37 -06:00
Allen Byrne
7e8923957f HDFFV-10656 Add CHECK_VOL support to CMake 2018-12-20 15:11:27 -06:00