Commit Graph

16502 Commits

Author SHA1 Message Date
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
Allen Byrne
f17ce1b06e HDFFV-10143 Update new feature section. 2017-04-04 10:09:13 -05:00
Allen Byrne
9b17c2e124 HDFFV-10143 Update new feature section. 2017-04-04 10:07:41 -05:00
Allen Byrne
ed98dc0419 HDFFV-10143 clean up format and function return 2017-04-04 09:54:23 -05:00
Allen Byrne
cbdc1250ce HDFFV-10143 clean up format and function return 2017-04-04 09:53:42 -05:00
Larry Knox
d6ea49f5cb Merge pull request #390 in HDFFV/hdf5 from develop to hdf5_1_10
* 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.
  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)
2017-04-03 18:48:51 -05:00
Quincey Koziol
d522632b9e Merge pull request #389 in HDFFV/hdf5 from fix_h5watch_signal to develop
* commit '1e4b2588b671a2172827bb422aee9ba96c0320b6':
  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.
2017-04-03 14:26:36 -05:00
Allen Byrne
f9199536d0 HDFFV-10143 Add plugin APIs to Java interface 2017-04-03 14:12:54 -05:00
Allen Byrne
4bd667bfde HDFFV-10143 Add plugin APIs to Java interface 2017-04-03 14:06:47 -05:00
Quincey Koziol
1e4b2588b6 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.
2017-04-03 11:56:52 -07:00
Allen Byrne
399060c17a Update with checks for index bounds 2017-04-03 12:35:38 -05:00
Allen Byrne
1f88a34fa7 Update with checks for index bounds 2017-04-03 12:34:17 -05:00
Allen Byrne
d86d708aea Update tools issues 2017-04-03 11:33:01 -05:00
Allen Byrne
dd2749d1be Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)
* commit '6387f7099d22c66dab415c57f9fd547eb86e4ad5':
  Small corrections to DOPYING file.
  Add new file COPYING_LBNL_HDF5.
  Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch.  Entries"
  Add LBNL license file and modify COPYING file accordingly.
  Omnibus checkin for several relatively minor modifications:
2017-04-03 09:23:33 -05:00
Allen Byrne
87e8da6600 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '2412158ed8326a3f3d62fbd947e470667d0b5951':
  Add new file COPYING_LBNL_HDF5.
  Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch.  Entries"
  Add LBNL license file and modify COPYING file accordingly.
  Omnibus checkin for several relatively minor modifications:
  Clear hdf5 1.10 entries from RELEASE.txt in the develop branch.  Entries in this branch version of RELEASE.txt should be intended for the future 1.12.0 release.
  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)
2017-04-03 09:23:27 -05:00
Binh-Minh Ribler
2412158ed8 Merge pull request #374 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp3:develop to develop
Fix HDFFV-8089

* commit '52f8c2ed494ea1b89374981ecc6901abe8fd5fed':
  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)
2017-04-03 08:37:30 -05:00
Larry Knox
6387f7099d Merge pull request #385 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10
* commit '194f604ad04ec976a1d761090aa892f9f28514c3':
  Small corrections to DOPYING file.
  Add new file COPYING_LBNL_HDF5.
  Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch.  Entries"
  Add LBNL license file and modify COPYING file accordingly.
  Omnibus checkin for several relatively minor modifications:
2017-03-31 14:07:38 -05:00
lrknox
194f604ad0 Small corrections to DOPYING file. 2017-03-31 12:17:50 -05:00
lrknox
f4b64cd845 Merge branch 'develop' into hdf5_1_10 2017-03-31 11:59:20 -05:00
Allen Byrne
c99679337a HDFFV-10143 fix use before set 2017-03-30 17:41:35 -05:00
Allen Byrne
0892bf320c HDFFV-10143 fix use before set 2017-03-30 17:40:44 -05:00
Allen Byrne
f1e64c512a HDFFV-10143 surround will fail with try block 2017-03-30 17:13:28 -05:00
Allen Byrne
037e7a4a72 HDFFV-10143 typo cleanup 2017-03-30 17:13:21 -05:00