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| * | | | Updated per reviewBinh-Minh Ribler2019-01-071-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: HDFFV-10676 - CVE-2018-13873 Changed the new assert to if statement, per Dana's comment. Platforms tested: Linux/64 (jelly)
| * | | | Merge branch 'develop' of ↵Binh-Minh Ribler2019-01-06111-4977/+9119
| |\ \ \ \ | | | | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
| * | | | | HDFFV-10578 and HDFFV-10676Binh-Minh Ribler2019-01-062-4/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* | | | | | Merge pull request #1450 in HDFFV/hdf5 from ↵Ray Lu2019-01-085-9/+128
|\ \ \ \ \ \ | |_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:TRILAB-98-dt_arith-and-cpp_testhdf5-tests to develop * commit 'b02de315b93ac29d2483a91d526b110a25073505': NNSA Tri-LabsTRILAB-98: Another two test cases out. NNSA Tri-Labs TRILAB-98: Taking out a few more test cases. 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.
| * | | | | NNSA Tri-LabsTRILAB-98: Another two test cases out.Songyu Lu2019-01-081-1/+18
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| * | | | | NNSA Tri-Labs TRILAB-98: Taking out a few more test cases.Songyu Lu2019-01-082-13/+25
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| * | | | | NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on ↵Songyu Lu2019-01-085-2/+92
| | | | | | | | | | | | | | | | | | | | | | | | 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.
* | | | | | Merge pull request #1456 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:develop to developScot Breitenfeld2019-01-081-1/+22
|\ \ \ \ \ \ | |_|_|_|/ / |/| | | | / | | |_|_|/ | |/| | | * commit 'fb5d83e146679f4d0ca16cf54b410f04a262451e': Updated Fortran Bug and new features
| * | | | Updated Fortran Bug and new featuresM. Scot Breitenfeld2019-01-081-1/+22
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* | | | Merge pull request #1454 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-01-082-37/+40
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'b88df58cc952563c35107daa1b8ced24b0cc03b5': Add missing define created in configure.ac Correct regex option
| * | | | Add missing define created in configure.acAllen Byrne2019-01-081-0/+3
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| * | | | Correct regex optionAllen Byrne2019-01-081-37/+37
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* | | | Merge pull request #1452 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to developJordan Henderson2019-01-081-4/+8
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | * commit '805b64685371982e9c7fd693497865197990cbd6': Fix for parallel filters tests with new read-proc0-broadcast feature
| * | | | Fix for parallel filters tests with new read-proc0-broadcast featureJordan Henderson2019-01-081-4/+8
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* | | | | Merge pull request #1409 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10443 to developScot Breitenfeld2019-01-0812-70/+605
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | | | | HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs.Scot Breitenfeld2019-01-0814-78/+600
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| * | | | | Merge remote-tracking branch 'upstream/develop' into developM. Scot Breitenfeld2019-01-0835-335/+627
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| * | | | | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵M. Scot Breitenfeld2019-01-07208-10362/+16177
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| * | | | | Added chunked dataset, H5S_ALL testM. Scot Breitenfeld2019-01-031-3/+111
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| * | | | | Merge branch 'develop' of ↵M. Scot Breitenfeld2019-01-021-1/+7
| |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~brtnfld/hdf5_msb into develop
| | * | | | | typoM. Scot Breitenfeld2019-01-021-1/+1
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| | * | | | | Merge branch 'develop' of ↵M. Scot Breitenfeld2019-01-021-1/+7
| | |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~brtnfld/hdf5_msb into develop
| | | * | | | | Documented HDFFV-10652M. Scot Breitenfeld2019-01-021-1/+7
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| * | | | | | | typoM. Scot Breitenfeld2019-01-021-1/+1
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| * | | | | | updated defined constantsM. Scot Breitenfeld2019-01-021-6/+10
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| * | | | | Merge branch 'develop' of ↵M. Scot Breitenfeld2019-01-022-0/+67
| |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~brtnfld/hdf5_msb into develop
| | * | | | | Removed reason for breaking read-proc0-and-bcastM. Scot Breitenfeld2019-01-023-9/+2
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| | * | | | | switched to using CX instead of a global var.M. Scot Breitenfeld2018-12-315-6/+65
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| | * | | | | Merge branch 'develop' of ↵M. Scot Breitenfeld2018-12-132-0/+67
| | |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~brtnfld/hdf5_msb into develop
| | * | | | | | HDFFV-10652M. Scot Breitenfeld2018-12-127-118/+388
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
| * | | | | | | HDFFV-10652M. Scot Breitenfeld2019-01-029-119/+441
| |/ / / / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
* | | | | | | Merge pull request #1453 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to ↵Neil Fortner2019-01-081-6/+1
|\ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit '0dd2c29f284b1ec2a3c070d39805f657f44b216d': Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since space for it was removed.
| * \ \ \ \ \ \ Merge branch 'develop' of ↵Neil Fortner2019-01-0832-229/+1220
| |\ \ \ \ \ \ \ | |/ / / / / / / |/| | | | | | | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~nfortne2/hdf5_naf into develop
* | | | | | | | Merge pull request #1451 in HDFFV/hdf5 from ↵Dana Robinson2019-01-086-3/+240
|\ \ \ \ \ \ \ \ | |_|_|_|_|/ / / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:fortran_squash to develop * commit '905766fa3e51a470c02328a63d92182d4a8481bf': Fortran wrappers for dataset obj header minimization API calls.
| * | | | | | | Fortran wrappers for dataset obj header minimization API calls.Dana Robinson2019-01-086-3/+240
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* | | | | | | | Merge pull request #1443 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-01-0811-65/+74
|\ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | | | | | | | Add variables to set up module switch between configure and build forLarry Knox2019-01-081-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | cross compiling on CrayXC40.
| * | | | | | | | Remove install-exec-hook from hl/fortran/Makefile.am.Larry Knox2019-01-072-14/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add check for existing links in hl/fortran/src/Makefile.am.
| * | | | | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-0627-790/+1030
| |\ \ \ \ \ \ \ \ | | | |_|_|_|/ / / | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | | | | | | | Merge branch 'develop' of ↵Larry Knox2019-01-0540-433/+1099
| |\ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| | * \ \ \ \ \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-0540-433/+1099
| | |\ \ \ \ \ \ \ \ | | | | |_|_|_|_|_|/ | | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 ...
| * | | | | | | | | Configure build directory in batch scripts.Larry Knox2019-01-058-65/+10
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| * | | | | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-0255-2079/+4331
| |\ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'af21ce90d9465e805807f17da21f93e64e03492a': (46 commits) Changed to Unix line endings and chmod -x. Fix runtest case for data to stdout in tool Updated the parallel install docs. Eliminated the need for a separate script variable. Flipped swapped testing strings. Specify variable type. Remove unnecessary whitespace. Added test_vol_plugin.sh to the list of scripts to clean Fixed a CMake build issue (CMake still doesn't run the VOL plugin tests) Added more sub-tests to the VOL plugin test. Added a simple test for registration of VOL connector plugins. Autotools only for right now, but this will be fleshed out in future work. OHDR tests now accept h5_fileaccess() fapls. Formatting, informative comments, and minor renaming. Fix some CMake listings Add error checking to the minimized dset header size calculation. Update printf->HDprintf statements. Remove `#if 0` block of deprecated code. Fix mistake with H5E_BEGIN_TRY {...} H5E_END_TRY block containing ERROR-raising macros. Formatting tweaks. Added a helpful message to the flush script. Added a shell script so we can run the parallel flush test on OpenMPI. Add "compact" storage test to relative header size comparisons. Formatting adjustments. Formatting adjustments ...
| * | | | | | | | | Add libhdf5_hl_fortran symlinks for libhdf5hl_fortran files.Larry Knox2018-12-314-12/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Set ctest*.lsf.in.cmake scripts for sierra. Correct src/CMakelists.txt syntax error.
| * | | | | | | | | Correct syntax error in CMakeLists.txt.Larry Knox2018-12-311-3/+3
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| * | | | | | | | | Add .lsf batch scripts and insert the build directory into the scriptsLarry Knox2018-12-284-0/+51
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | during configuration.
* | | | | | | | | | Merge pull request #1448 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to ↵Neil Fortner2019-01-088-19/+52
|\ \ \ \ \ \ \ \ \ \ | |_|_|_|_|/ / / / / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * | | | | | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Neil Fortner2019-01-071-37/+37
| |\ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '5dfe00629588a54dbfb6f2d09dfbd88177e37cc2': HDFFV-10674 handle time as natural number
* | \ \ \ \ \ \ \ \ \ Merge pull request #1439 in HDFFV/hdf5 from rank0_bcast to developScot Breitenfeld2019-01-0714-124/+869
|\ \ \ \ \ \ \ \ \ \ \ | |_|/ / / / / / / / / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | | | | | | | | | Merge branch 'rank0_bcast' of ssh://bitbucket.hdfgroup.org:7999/hdffv/hdf5 ↵M. Scot Breitenfeld2019-01-070-0/+0
| |\ \ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | into rank0_bcast