Commit Graph

19241 Commits

Author SHA1 Message Date
Allen Byrne
3f727a272c Merge pull request #1454 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit 'b88df58cc952563c35107daa1b8ced24b0cc03b5':
  Add missing define created in configure.ac
  Correct regex option
2019-01-08 14:59:29 -06:00
Allen Byrne
b88df58cc9 Add missing define created in configure.ac 2019-01-08 14:31:46 -06:00
Songyu Lu
b02de315b9 NNSA Tri-LabsTRILAB-98: Another two test cases out. 2019-01-08 14:31:41 -06:00
Allen Byrne
25f272b4cb Correct regex option 2019-01-08 13:25:11 -06:00
Songyu Lu
2efc28cf63 NNSA Tri-Labs TRILAB-98: Taking out a few more test cases. 2019-01-08 12:45:01 -06:00
Jordan Henderson
206da2919d Merge pull request #1452 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit '805b64685371982e9c7fd693497865197990cbd6':
  Fix for parallel filters tests with new read-proc0-broadcast feature
2019-01-08 11:32:42 -06:00
Scot Breitenfeld
9b6fe52bcf Merge pull request #1409 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10443 to develop
* commit 'b4d4d371a03158c39f120b1bde6c4bd51f1b2eb6':
  HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs.
  Added chunked dataset, H5S_ALL test
  typo
  typo
  updated defined constants
  Documented HDFFV-10652
  HDFFV-10652 Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
  Removed reason for breaking read-proc0-and-bcast
  switched to using CX instead of a global var.
  HDFFV-10652 Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
2019-01-08 11:29:48 -06:00
Scot Breitenfeld
b4d4d371a0 HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs. 2019-01-08 11:24:00 -06:00
Neil Fortner
7e50055920 Merge pull request #1453 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to develop
* commit '0dd2c29f284b1ec2a3c070d39805f657f44b216d':
  Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since space for it was removed.
2019-01-08 10:45:46 -06:00
Neil Fortner
0dd2c29f28 Merge branch 'develop' of ssh://bitbucket.hdfgroup.org:7999/~nfortne2/hdf5_naf into develop 2019-01-08 10:37:28 -06:00
Neil Fortner
214abbfd59 Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since
space for it was removed.
2019-01-08 10:36:34 -06:00
Dana Robinson
c8c0cf9fa2 Merge pull request #1451 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:fortran_squash to develop
* commit '905766fa3e51a470c02328a63d92182d4a8481bf':
  Fortran wrappers for dataset obj header minimization API calls.
2019-01-08 10:14:26 -06:00
M. Scot Breitenfeld
1421059cfb Merge remote-tracking branch 'upstream/develop' into develop 2019-01-08 09:55:29 -06:00
Jordan Henderson
805b646853 Fix for parallel filters tests with new read-proc0-broadcast feature 2019-01-08 09:45:35 -06:00
Dana Robinson
905766fa3e Fortran wrappers for dataset obj header minimization API calls. 2019-01-08 07:34:58 -08:00
Larry Knox
74a41f92a4 Merge pull request #1443 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'e27df5a5fe365480b0809ce523b0e9cd1096a43d':
  Add variables to set up module switch between configure and build for cross compiling on CrayXC40.
  Remove install-exec-hook from hl/fortran/Makefile.am. Add check for existing links in hl/fortran/src/Makefile.am.
  Configure build directory in batch scripts.
  Add libhdf5_hl_fortran symlinks for libhdf5hl_fortran files. Set ctest*.lsf.in.cmake scripts for sierra. Correct src/CMakelists.txt syntax error.
  Correct syntax error in CMakeLists.txt.
  Add .lsf batch scripts and insert the build directory into the scripts during configuration.
2019-01-07 21:01:06 -06:00
Larry Knox
e27df5a5fe Add variables to set up module switch between configure and build for
cross compiling on CrayXC40.
2019-01-07 20:57:18 -06:00
Binh-Minh Ribler
90d13bef33 Fixed typo
Platforms tested:
    Darwin (osx1010test)
2019-01-07 20:46:55 -06:00
Binh-Minh Ribler
78d0564c2a Refixed HDFFV-10578
Description:
    Applied Neil's fix for this issue after removing previous
    attempt.  The resources are now released in init_objs() when
    failure occurs there.
    Neil will fix HDFFV-10676 separately.
Platforms tested:
    Linux/64 (jelly)
    Linux/64 (platypus)
    Darwin (osx1010test)
2019-01-07 20:36:34 -06:00
Songyu Lu
75c105a2a4 NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on sierra.llnl.gov: According to the group decision, simply provide a macro to disable some failing test cases on sierra (IBM power9 cpu). All failing cases involve long double data type. 2019-01-07 20:28:37 -06:00
Neil Fortner
9c12b625fd Merge pull request #1448 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to develop
Avoid potential invalid read when decoding unknown object header message.

* commit '685288beabc4f4383d69ec07be05c067fab78544':
  Delay checking if decoded message's "shareable" flag is appropriate for the message type until we've verified we understand the message type. Reduce size of H5O_msg_class_g to *not* include space for H5O_BOGUS_INVALID.  Make bogus messages shareable.  Add new bogus message test with shareable messages to cover the formerly problematic code.  Re-run gen_bogus.c to add this test case and also to fix the bogus_invalid messages that were no longer H5O_BOGUS_INVLAID due to a new message class being added in a previous commit.  Added comment to remind developers to run gen_bogus.c when adding a new message class.
2019-01-07 19:30:26 -06:00
Scot Breitenfeld
d9b1ec3ce8 Merge pull request #1439 in HDFFV/hdf5 from rank0_bcast to develop
* commit 'ab5fe769ab711f736238abc89ef215a6ecff5f7e':
  HDFFV-10625 -- Implemented a process-0 read and then broadcast for collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
  indent change
  changed logic statement in if
  Added chunking test, fixed issue with CX set
  Correct another git merge failure.
  Correct misplaced line from git merge.
  Updated and refined version of Scot's "rank 0 bcast" changes.
2019-01-07 17:08:33 -06:00
M. Scot Breitenfeld
ab5fe769ab Merge branch 'rank0_bcast' of ssh://bitbucket.hdfgroup.org:7999/hdffv/hdf5 into rank0_bcast 2019-01-07 16:57:39 -06:00
Quincey Koziol
fed17ed383 HDFFV-10625 -- Implemented a process-0 read and then broadcast for collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator. 2019-01-07 16:55:59 -06:00
M. Scot Breitenfeld
c9ae4fd62e indent change 2019-01-07 16:09:22 -06:00
M. Scot Breitenfeld
030cde7a20 changed logic statement in if 2019-01-07 16:09:22 -06:00
M. Scot Breitenfeld
98ed401a6c Added chunking test, fixed issue with CX set 2019-01-07 16:09:22 -06:00
Quincey Koziol
b7f660f432 Correct another git merge failure. 2019-01-07 16:09:22 -06:00
Quincey Koziol
a6fe79251b Correct misplaced line from git merge. 2019-01-07 16:09:22 -06:00
Quincey Koziol
8001a4c1c4 Updated and refined version of Scot's "rank 0 bcast" changes. 2019-01-07 16:09:22 -06:00
Neil Fortner
685288beab Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '5dfe00629588a54dbfb6f2d09dfbd88177e37cc2':
  HDFFV-10674 handle time as natural number
2019-01-07 15:54:02 -06:00
Allen Byrne
5dfe006295 Merge pull request #1444 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '591205127a167b914ef5557f30aa58b2dff96a85':
  HDFFV-10674 handle time as natural number
2019-01-07 15:43:00 -06:00
Neil Fortner
b043126e5e Delay checking if decoded message's "shareable" flag is appropriate for
the message type until we've verified we understand the message type.
Reduce size of H5O_msg_class_g to *not* include space for
H5O_BOGUS_INVALID.  Make bogus messages shareable.  Add new bogus
message test with shareable messages to cover the formerly problematic
code.  Re-run gen_bogus.c to add this test case and also to fix the
bogus_invalid messages that were no longer H5O_BOGUS_INVLAID due to a
new message class being added in a previous commit.  Added comment to
remind developers to run gen_bogus.c when adding a new message class.
2019-01-07 15:40:44 -06:00
Vailin Choi
e52e68c82f Merge pull request #1445 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit '982852c603c03a06ca24f219127f49616c7d42cb':
  Fix for daily test failure: too many arguments to function 'H5Gopen1'
2019-01-07 14:15:05 -06:00
Jordan Henderson
0bc3d1567b Merge pull request #1434 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit 'fe6bed2ad722578d0b701e29d22f591923d2fe9f':
  Fix TESTING_2 macro to align output with TESTING macro
2019-01-07 14:11:07 -06:00
Binh-Minh Ribler
6c7462b1a9 Removed previous change in H5O__chunk_deserialize(). 2019-01-07 14:09:30 -06:00
Jordan Henderson
fe6bed2ad7 Fix TESTING_2 macro to align output with TESTING macro
Add more indentation to TESTING_2 macro
2019-01-07 14:08:34 -06:00
Binh-Minh Ribler
c092f9167c Removed the previous change in H5O__chunk_deserialize() 2019-01-07 14:07:25 -06:00
Binh-Minh Ribler
5b721a060e Removed previous change in table_list_add(). 2019-01-07 14:03:22 -06:00
Binh-Minh Ribler
463515f7db Removed the previous change in table_list_add() 2019-01-07 14:00:56 -06:00
Vailin Choi
982852c603 Fix for daily test failure: too many arguments to function 'H5Gopen1' 2019-01-07 11:49:53 -06:00
Allen Byrne
591205127a HDFFV-10674 handle time as natural number 2019-01-07 10:39:09 -06:00
M. Scot Breitenfeld
b4828e7feb Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into develop 2019-01-07 09:49:52 -06:00
Larry Knox
61d3403d12 Remove install-exec-hook from hl/fortran/Makefile.am.
Add check for existing links in hl/fortran/src/Makefile.am.
2019-01-06 21:59:35 -06:00
Binh-Minh Ribler
820d8e34c5 Updated per review
Description:
    HDFFV-10676 - CVE-2018-13873
        Changed the new assert to if statement, per Dana's comment.
Platforms tested:
    Linux/64 (jelly)
2019-01-06 21:42:16 -06:00
Larry Knox
619b0abfd6 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '7bf6d847ae36940f1b1147820356795c7764dbeb':
  Remove incorrect comment.
  Updated error stacks for h5dump testing.
  Corrected comment in src/H5VLint.c, fixed pass-through info size in src/H5VLpassthru.c, switched to stashing VOL connector ID & info in API context (in src/H5CX.c, src/H5CXprivate.h, src/H5F.c, src/H5Fint.c, and src/H5Fefc.c), patched up all sorts of issues in the tests, to make them work with 'check-vfd' (and 'check-vol' again).
  Clean up style issues, make function callbacks static, correct debug statements, etc.  No functionality changes at all.
2019-01-06 17:31:51 -06:00
Quincey Koziol
7bf6d847ae Merge pull request #1440 in HDFFV/hdf5 from stackable_vol_fix_14 to develop
* commit 'f0656a57dc3baf02709e1ad5e496cf63cf820877':
  Remove incorrect comment.
  Updated error stacks for h5dump testing.
  Corrected comment in src/H5VLint.c, fixed pass-through info size in src/H5VLpassthru.c, switched to stashing VOL connector ID & info in API context (in src/H5CX.c, src/H5CXprivate.h, src/H5F.c, src/H5Fint.c, and src/H5Fefc.c), patched up all sorts of issues in the tests, to make them work with 'check-vfd' (and 'check-vol' again).
2019-01-06 16:28:06 -06:00
Quincey Koziol
ca1c9cff1a Merge pull request #1438 in HDFFV/hdf5 from mpio_vfd_neaten to develop
* commit '8a5d2c130a93a665933cda8db8554d006b7ca093':
  Clean up style issues, make function callbacks static, correct debug statements, etc.  No functionality changes at all.
2019-01-06 01:55:26 -06:00
Quincey Koziol
f0656a57dc Remove incorrect comment. 2019-01-06 01:49:02 -06:00
Binh-Minh Ribler
aa62951a5f Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop 2019-01-06 01:45:15 -06:00