Commit Graph

16574 Commits

Author SHA1 Message Date
Jordan Henderson
906c181918 Merge pull request #422 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '606529f5e0cffcea26af66106f094fbe350c5bac':
  Due to HDFVIEW-19 add read VL as string function
2017-04-13 10:15:16 -05:00
Vailin Choi
7ff4c5fd7a Merge pull request #421 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit '3d1b227a67b557da247f6b683f58617b6d75bfdb':
  Skip tests for page buffering in test/fheap.c for parallel build Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel. Activate full testing when this feature is re-enabled in the future for parallel build.
2017-04-13 10:06:19 -05:00
Allen Byrne
53132d8864 Due to HDFVIEW-19 add read VL as string function 2017-04-13 10:02:15 -05:00
Vailin Choi
3d1b227a67 Skip tests for page buffering in test/fheap.c for parallel build
Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel.
Activate full testing when this feature is re-enabled in the future for parallel build.
2017-04-13 02:47:23 -05:00
Allen Byrne
606529f5e0 Due to HDFVIEW-19 add read VL as string function 2017-04-12 17:21:43 -05:00
Scot Breitenfeld
f574d627d8 Merge pull request #410 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:develop to develop
* commit '265950a83a68ea55b5bc8dcbefa2d09b4f8110be':
  updated with README changes
  Combined the README_DEVEL and README, and removed out-dated README material
2017-04-12 11:03:42 -05:00
Vailin Choi
f6920ad11c Merge pull request #416 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:hdf5_1_10 to hdf5_1_10
* commit 'f75379d780dc6d2a262d0b613e588a8c0629c848':
  Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.
2017-04-12 03:23:57 -05:00
Vailin Choi
f75379d780 Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771)
1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0
2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.
2017-04-11 23:48:51 -05:00
Vailin Choi
6efca6717c Merge pull request #409 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit '7eda1e3c6a57f79b59fc35518816db4e3a2b382d':
  Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.
2017-04-11 19:19:51 -05:00
Vailin Choi
7eda1e3c6a Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '2821b8bd768138db6b5f917a5b7325f878f8f7d0':
  Fix URL name
  DAILYTEST-250 change test props to reduce timeout
2017-04-11 18:09:03 -05:00
Allen Byrne
4a37934b5d Merge pull request #413 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
* commit 'e76d9217f49a300501cff55ded22e4c8107d2582':
  Fix URL name
  DAILYTEST-250 change test props to reduce timeout
2017-04-11 16:57:27 -05:00
Allen Byrne
2821b8bd76 Merge pull request #412 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '8a9e4b94c3938f4c42ad9399737afc6478ded160':
  Fix URL name
  DAILYTEST-250 change test props to reduce timeout
2017-04-11 16:57:14 -05:00
Allen Byrne
e76d9217f4 Fix URL name 2017-04-11 15:12:27 -05:00
Allen Byrne
6efdeb7630 DAILYTEST-250 change test props to reduce timeout 2017-04-11 15:12:03 -05:00
Allen Byrne
8a9e4b94c3 Fix URL name 2017-04-11 15:10:02 -05:00
M. Scot Breitenfeld
265950a83a updated with README changes 2017-04-11 13:16:16 -05:00
Allen Byrne
a79ab2d39e DAILYTEST-250 change test props to reduce timeout 2017-04-11 12:57:19 -05:00
M. Scot Breitenfeld
e3d8dacaad Combined the README_DEVEL and README, and removed out-dated README material 2017-04-11 12:18:49 -05:00
Vailin Choi
9742792f8c Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771)
1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0
2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.
2017-04-11 11:59:27 -05:00
Larry Knox
725b443f1f Merge pull request #408 in HDFFV/hdf5 from develop to hdf5_1_10
* commit 'ccb4e9ed9a5e0af27db9f1504a628e35d7f4cf92': (27 commits)
  Removed commeted out code from H5C_dump_coll_write_list()
  Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055).
  HDFFV-10143 add missing javadoc param
  Add missing test status
  Fix CMake regex commands
  Modify test/fheap.c to run with various file space strategies and/or page buffering Modify test/fheap.c to run with different combinations of file space strategies and page buffering only when ExpressMode is 0 (HDF5TestExpress is 0). Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo.
  Updated the H5L.c error message after additional thought. Fix for HDFFV-10141.
  Updated an error message in H5L.c to be more helpful. Fixes HDFFV-10141.
  Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
  Fix typo deletion
  HDFFV-10143 Update new feature section.
  HDFFV-10143 clean up format and function return
  HDFFV-10143 Add plugin APIs to Java interface
  Update with checks for index bounds
  Update tools issues
  HDFFV-10143 fix use before set
  HDFFV-10143 surround will fail with try block
  HDFFV-10143 typo cleanup
  HDFFV-10143 typo removed
  Fix code error and use H5PL_MAX_PATH_NUM in test
  ...
2017-04-11 09:24:47 -05:00
John Mainzer
ccb4e9ed9a Merge pull request #405 in HDFFV/hdf5 from ~MAINZER/hdf5_jrm:develop to develop
* commit 'eb75dc1bb02e13902d73a36caafe763eea585d02':
  Removed commeted out code from H5C_dump_coll_write_list()
  Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055).
2017-04-07 13:20:11 -05:00
mainzer
eb75dc1bb0 Removed commeted out code from H5C_dump_coll_write_list() 2017-04-07 13:17:08 -05:00
Allen Byrne
3140697e40 Merge pull request #403 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
* commit '38b1b534c986696dcf146352e7314c2919affbf5':
  HDFFV-10143 add missing javadoc param
  Add missing test status
2017-04-07 08:07:56 -05:00
Vailin Choi
bbf8689353 Merge pull request #396 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit 'b3ff39585c3f8e6e9096fc84f02dd049f0d3ae36':
  Modify test/fheap.c to run with various file space strategies and/or page buffering Modify test/fheap.c to run with different combinations of file space strategies and page buffering only when ExpressMode is 0 (HDF5TestExpress is 0). Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo.
2017-04-06 22:15:44 -05:00
Vailin Choi
b3ff39585c Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '4a05d27c6fcef81612e005b6f6429ab362247492':
  HDFFV-10143 add missing javadoc param
  Add missing test status
  Fix CMake regex commands
2017-04-06 21:32:23 -05:00
mainzer
a859e70992 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~mainzer/hdf5_jrm into develop
Update to permit push to develop_jrm fork
2017-04-06 18:14:47 -05:00
mainzer
94c34773ce Checkin of fix for CGNS bug
(https://jira.hdfgroup.org/browse/HDFFV-10055).

    Briefly, in H5C_collective_write() in H5Cmpio.c,
the metadata cache attempts to perform a collective
write of metadata cache entries.

    This worked fine as long as all processes had at
least one entry to write.

    However, when the process has no entries, the
function tries to participate in the collective write
by calling MPI_File_set_view(),
MPI_File_write_all() and then MPI_File_set_view()
again, to match the calls in H5FD_mpio_write().

   After pull request 183, the CGNS test benchmark_hdf5
started failing.  On investigation, I determined that
the failure occurred in the first call to MPI_File_set_view()
in the "no data to write" path through H5C_collective_write().
Note that pull request 183 did not create the problem,
it only exposed it.  The bug can be observed after pull
request 182 if one executes the CGNS progam
src/ptests/benchmark_hdf5 with 90 processes.

    The problem appears to have been that the calls to
MPI_File_set_view() in H5C_collective_write() and
H5FD_mpio_write() were using different values for the
info parameter.  I patched the problem by adding a
MPI specific VFD call allowing me to get the MPI_Info
used in H5FD_mpio_write() for use in
MPI_File_set_view() calls in H5C_collective_write().

    Tested serial & parallel, debug & production on
Jelly.
2017-04-06 18:11:21 -05:00
Allen Byrne
4a05d27c6f Merge pull request #402 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '4b11c4fd518026667944b50b4cd4cb41bec7e25a':
  HDFFV-10143 add missing javadoc param
  Add missing test status
2017-04-06 15:51:49 -05:00
Allen Byrne
38b1b534c9 HDFFV-10143 add missing javadoc param 2017-04-06 15:01:30 -05:00
Allen Byrne
4b11c4fd51 HDFFV-10143 add missing javadoc param 2017-04-06 15:00:48 -05:00
Allen Byrne
388051ba2d Add missing test status 2017-04-06 14:33:09 -05:00
Allen Byrne
177a8ba30e Add missing test status 2017-04-06 14:29:47 -05:00
Larry Knox
fdcde1834d Merge pull request #398 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
* commit '75d6ac058e71b3f46333e7f6c7566e4214ccd091':
  Fix CMake regex commands
2017-04-06 12:01:21 -05:00
Larry Knox
a84864e732 Merge pull request #397 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit 'f1ad2feb0b253302895a0bc9835ade8f2f2484e8':
  Fix CMake regex commands
2017-04-06 12:00:58 -05:00
Allen Byrne
75d6ac058e Fix CMake regex commands 2017-04-06 11:30:56 -05:00
Allen Byrne
5806dd2711 Merge pull request #378 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
* commit 'a4038aed6e895b9d1e686073c135f8aaacc9adab': (21 commits)
  Fix typo deletion
  HDFFV-10143 Update new feature section.
  HDFFV-10143 clean up format and function return
  HDFFV-10143 Add plugin APIs to Java interface
  Update with checks for index bounds
  HDFFV-10143 fix use before set
  HDFFV-10143 surround will fail with try block
  HDFFV-10143 typo cleanup
  HDFFV-10143 typo removed
  Fix code error and use H5PL_MAX_PATH_NUM in test
  HDFFV-10143 Cleanup due to comments
  HDFFV-10143 remove debugging output
  HDFFV-10143 change h5PLget to use buffer like H5Iget_name
  HDFFV-10143 change put to replace and add const
  HDFFV-10143 Use Windows A version of ExpandEnvironmentStrings
  Remove redundant code
  HDFFV-10143 Fix initial issues from review
  HDFFV-10143 add APIs to manipulate plugin path table
  Remove duplicated paths, add new paths
  HDFFV-10143 add APIs to manipulate plugin path table
  ...
2017-04-06 11:28:33 -05:00
Allen Byrne
f1ad2feb0b Fix CMake regex commands 2017-04-06 11:22:29 -05:00
Vailin Choi
ad2963de60 Modify test/fheap.c to run with various file space strategies and/or page buffering
Modify test/fheap.c to run with different combinations of file space strategies and page buffering
only when ExpressMode is 0 (HDF5TestExpress is 0).
Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo.
2017-04-05 15:43:00 -05:00
Allen Byrne
60167ae875 Merge pull request #395 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '1e0ecb4481e226239c1fd51bd214bd7e7490805d':
  Fix typo deletion
  HDFFV-10143 Update new feature section.
  HDFFV-10143 clean up format and function return
  HDFFV-10143 Add plugin APIs to Java interface
  Update with checks for index bounds
  Update tools issues
  HDFFV-10143 fix use before set
  HDFFV-10143 surround will fail with try block
  HDFFV-10143 typo cleanup
  HDFFV-10143 typo removed
  Fix code error and use H5PL_MAX_PATH_NUM in test
  HDFFV-10143 Cleanup due to comments
  HDFFV-10143 remove debugging output
  HDFFV-10143 change h5PLget to use buffer like H5Iget_name
  HDFFV-10143 change put to replace and add const
  Remove redundant code
  HDFFV-10143 Use Windows A version of ExpandEnvironmentStrings
  HDFFV-10143 Fix initial issues from review
  Remove duplicated paths, add new paths
  HDFFV-10143 add APIs to manipulate plugin path table
2017-04-05 13:28:37 -05:00
Allen Byrne
1e0ecb4481 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'b56fb149c9a3c9dca11b406b7a2488f0c93ee187':
  Updated the H5L.c error message after additional thought. Fix for HDFFV-10141.
  Updated an error message in H5L.c to be more helpful. Fixes HDFFV-10141.
2017-04-05 13:24:07 -05:00
Dana Robinson
b56fb149c9 Merge pull request #394 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to develop
* commit '9876155d3fdb073dd3769f18665c86d04cda4806':
  Updated the H5L.c error message after additional thought. Fix for HDFFV-10141.
  Updated an error message in H5L.c to be more helpful. Fixes HDFFV-10141.
2017-04-05 10:07:24 -05:00
Allen Byrne
857f515325 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '60bb3fd1108e2006a79b008d031a0f68a1e6b393':
  Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
2017-04-05 09:41:32 -05:00
Dana Robinson
9876155d3f Updated the H5L.c error message after additional thought.
Fix for HDFFV-10141.
2017-04-05 02:26:36 -04:00
Dana Robinson
2e295975b9 Updated an error message in H5L.c to be more helpful.
Fixes HDFFV-10141.
2017-04-05 02:26:20 -04:00
Dana Robinson
60bb3fd110 Merge pull request #393 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to develop
* commit 'f060e05999849c1eb3ef653c08977e4b154749d8':
  Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
2017-04-04 21:52:27 -05:00
Dana Robinson
f060e05999 Re-enabled fixed array index testing in the test_random_rank4_vl() test
in test/set_extent. This was fixed some time ago, but the test was
never re-enabled for that index type.
2017-04-04 20:20:12 -04:00
Allen Byrne
a4038aed6e Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)
* commit 'd6ea49f5cbcaa852cd0caf34278ec61108667bc3':
  Switch to using flag in signal handler, to trigger dropping out of main loop and shutdown cleanly, instead of calling leave() from the signal handler.
  Fix HDFFV-8089 Description:     Some code within an "ifdef H5D_CHUNK_DEBUG" block was using outdated     data structure but not caught because the case of H5D_CHUNK_DEBUG being     defined was never tested.  It was commented out.     I defined H5D_CHUNK_DEBUG, tested, and commented out again. Platforms tested:     Linux/32 2.6 (jam)     Linux/64 (platypus)     Darwin (osx1010test)
2017-04-04 12:15:32 -05:00
Allen Byrne
48687ab50f Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'd522632b9e1f1d88db2117e89f3caba0dc4cf38b':
  Switch to using flag in signal handler, to trigger dropping out of main loop and shutdown cleanly, instead of calling leave() from the signal handler.
2017-04-04 12:15:27 -05:00
Allen Byrne
db9eeb9f6a Fix typo deletion 2017-04-04 10:16:30 -05:00
Allen Byrne
c2941faa66 Fix typo deletion 2017-04-04 10:15:56 -05:00