Commit Graph

19161 Commits

Author SHA1 Message Date
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
Larry Knox
cc0421291e Uninstall should remove the libhdf5_hl_fortran links. 2019-01-04 08:50:10 -06:00
Larry Knox
30abf02de2 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.

Add missing ';' to test/dsets.c line 13075.
2019-01-04 07:26:15 -06:00
jake.smith
9ac12ce299 Merge pull request #1427 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:dset_ohdr_minimize to develop
* commit '763db8178e673fdcae4a370fe2e6d345f905d5f1':
  Change FAIL_PUTS_ERROR to TEST_ERROR.
  Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2.
2019-01-03 23:16:12 -06:00
Jacob Smith
763db8178e Change FAIL_PUTS_ERROR to TEST_ERROR. 2019-01-03 23:02:20 -06:00
Dana Robinson
d59aa1d75c Cleaned up the parallel flush test and set t_pflush1 to always fail.
Also set CMake to handle this.
2019-01-03 20:45:58 -08:00
Allen Byrne
2a28b92e2b Merge pull request #1426 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit 'f4516d40feb7ea696e228253bc64a94f55296cbb':
  Fix comment
  Update toolchain comment
  Use c99 standard cmake variable
  Add PGI toolchain
2019-01-03 14:47:10 -06:00
Jacob Smith
3b53747b3a Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2. 2019-01-03 14:44:57 -06:00
Binh-Minh Ribler
5daddcc2d4 Merge pull request #1408 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_fixbug:develop to develop
Merged to catch daily test.

* commit '40c55f24ecbdd322fba527d768689fbdbd268374':
  Removed a comment.
  Fixed documentation - typo only
  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)
2019-01-03 09:50:01 -06:00
M. Scot Breitenfeld
390a3f6728 Added chunked dataset, H5S_ALL test 2019-01-03 09:47:14 -06:00
Binh-Minh Ribler
40c55f24ec Removed a comment. 2019-01-03 09:47:01 -06:00
Allen Byrne
f4516d40fe Fix comment 2019-01-03 09:36:00 -06:00