Commit Graph

19172 Commits

Author SHA1 Message Date
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
Binh-Minh Ribler
e1b59919bb HDFFV-10578 and HDFFV-10676
Description:
    HDFFV-10578 - CVE-2018-17234
        The file has some issue, however, there was a bug in h5dump that caused
        memory leaks after the problem in the file was encountered. The bug
        was that an if statement was missing in the function table_list_add()
        resulting in the memory not being freed at a later time.
        After the fix had been applied, there were no more leaks after h5dump
        detected the issue in the file and reported the error.

        In H5O__chunk_deserialize, replaced an assert with an if statement
        and reporting error, per Neil's recommendation

    HDFFV-10676 - CVE-2018-13873
        Also in H5O__chunk_deserialize, added an assertion to detect
        out of bound ids
2019-01-06 01:44:40 -06:00
Quincey Koziol
8ecd9cc1a1 Updated error stacks for h5dump testing. 2019-01-05 23:41:43 -06:00
Quincey Koziol
92300f954f 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).
2019-01-05 23:06:45 -06:00
Quincey Koziol
8a5d2c130a Clean up style issues, make function callbacks static, correct debug statements,
etc.  No functionality changes at all.
2019-01-05 17:13:40 -06:00
Larry Knox
3be0fbd817 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop 2019-01-05 07:50:15 -06:00
Larry Knox
25fe692c5c Configure build directory in batch scripts. 2019-01-05 07:49:19 -06:00
Larry Knox
cceb9f06b8 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '0e34f0feaaeb6d2286f87f695f25fae45c070a42': (26 commits)
  HDFFV-10664 update reference file
  HDFFV-10664 update reference files
  HDFFV-10664 add missing function and check for restriction
  Remove "bad" statements at end of TEST_ERROR.     Formerly arguments to FAIL_PUTS_ERROR
  Add RELEASE.txt entry for HDFFV-10596.
  Add semicolon at end of TEST_ERROR() invocation for consistency.
  Uninstall should remove the libhdf5_hl_fortran links.
  Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files.
  Change FAIL_PUTS_ERROR to TEST_ERROR.
  Cleaned up the parallel flush test and set t_pflush1 to always fail. Also set CMake to handle this.
  Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2.
  Removed a comment.
  Fix comment
  Align H5Lcreate_ud behavior with documentation for NULL udata pointer
  Update toolchain comment
  Use c99 standard cmake variable
  Add PGI toolchain
  Correction based on code review.
  HDFFV-10664 add check for state before set call
  HDFFV-10546 refactor variable name
  ...
2019-01-05 07:41:12 -06:00
Larry Knox
0e34f0feaa Merge pull request #1433 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '564565b15ed38d78cb7b29b8c9d9b322d224ab42':
  HDFFV-10664 update reference file
  HDFFV-10664 update reference files
  HDFFV-10664 add missing function and check for restriction
2019-01-04 14:31:51 -06:00
Jordan Henderson
b0feaecdb9 Merge pull request #1425 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit '659dd9bccf69f32bfdd01dc49410116ec5c1b0bb':
  Align H5Lcreate_ud behavior with documentation for NULL udata pointer
2019-01-04 14:06:10 -06:00
Allen Byrne
564565b15e HDFFV-10664 update reference file 2019-01-04 13:29:22 -06:00
Allen Byrne
e07fb46bdc HDFFV-10664 update reference files 2019-01-04 13:29:01 -06:00
Larry Knox
8887c357ee Merge pull request #1429 in HDFFV/hdf5 from HDFFV-10596-fortran-library-names-differ to develop
* commit 'f4c9ec5d41aa53829617274d3286f1e9a45ae57e':
  Add RELEASE.txt entry for HDFFV-10596.
  Uninstall should remove the libhdf5_hl_fortran links.
  Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files.
2019-01-04 13:04:41 -06:00
Larry Knox
f4c9ec5d41 Merge remote-tracking branch 'origin/develop' into HDFFV-10596-fortran-library-names-differ 2019-01-04 13:02:27 -06:00
Allen Byrne
28d5d987b5 HDFFV-10664 add missing function and check for restriction 2019-01-04 12:52:37 -06:00
jake.smith
46bf1647d4 Merge pull request #1430 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:dset_ohdr_minimize to develop
* commit 'f7115c31363e80e850c0a228e63a5a035c48b74a':
  Remove "bad" statements at end of TEST_ERROR.     Formerly arguments to FAIL_PUTS_ERROR
  Add semicolon at end of TEST_ERROR() invocation for consistency.
2019-01-04 11:46:54 -06:00
Jacob Smith
f7115c3136 Remove "bad" statements at end of TEST_ERROR.
Formerly arguments to FAIL_PUTS_ERROR
2019-01-04 11:28:39 -06:00
Dana Robinson
f012602d3a Merge pull request #1428 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:openmpi_tweaks to develop
* commit 'd59aa1d75cb6d0ae4f5964d017e275aa53394eb6':
  Cleaned up the parallel flush test and set t_pflush1 to always fail. Also set CMake to handle this.
2019-01-04 10:35:22 -06:00
Larry Knox
482d95c8f9 Add RELEASE.txt entry for HDFFV-10596. 2019-01-04 09:34:18 -06:00
Jacob Smith
a0c6e622e4 Add semicolon at end of TEST_ERROR() invocation for consistency. 2019-01-04 09:07:55 -06:00