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* Delta reduction against hyperslab_updates branch.Quincey Koziol2019-01-116-139/+122
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* Add API routines to wrap and retrieve objectsQuincey Koziol2019-01-112-0/+72
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* Merge pull request #1455 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to developJordan Henderson2019-01-091-0/+2
|\ | | | | | | | | * commit '2d7eb9a4c3a841f7612b88f6b559792cb6143930': Align behavior of H5Aget_name_by_idx with H5Aget_name when a NULL buffer is supplied
| * Align behavior of H5Aget_name_by_idx with H5Aget_name when a NULL buffer is ↵Jordan Henderson2019-01-081-0/+2
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* | Merge pull request #1441 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-092-2/+3
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr_fixbug:develop to develop * commit '90d13bef33f9e2e80b23996a0c39f16f7c34ecf8': Fixed typo Platforms tested: Darwin (osx1010test) 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) Removed previous change in H5O__chunk_deserialize(). Removed the previous change in H5O__chunk_deserialize() Removed previous change in table_list_add(). Removed the previous change in table_list_add() 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) 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.
| * Refixed HDFFV-10578Binh-Minh Ribler2019-01-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | 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)
| * Removed previous change in H5O__chunk_deserialize().Binh-Minh Ribler2019-01-071-1/+0
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| * Removed the previous change in H5O__chunk_deserialize()Binh-Minh Ribler2019-01-071-2/+0
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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 Ribler2019-01-0647-2374/+4265
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
| * | HDFFV-10578 and HDFFV-10676Binh-Minh Ribler2019-01-061-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 #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 branch 'develop' of ↵Neil Fortner2019-01-0812-50/+359
|\ \ \ \ | | | | | | | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~nfortne2/hdf5_naf into develop
| * \ \ \ Merge pull request #1451 in HDFFV/hdf5 from ↵Dana Robinson2019-01-081-1/+1
| |\ \ \ \ | | |/ / / | |/| | | | | | | | | | | | | | | | | | | | | | | ~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 Robinson2019-01-081-1/+1
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| * | | | Merge pull request #1443 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-01-081-0/+15
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| | * \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-068-506/+457
| | |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2019-01-053-5/+60
| | |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| | | * \ \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-053-5/+60
| | | |\ \ \ \ \ | | | | | |_|_|/ | | | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2019-01-051-2/+2
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| | * | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-0224-156/+779
| | |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2018-12-311-10/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Knox2018-12-281-0/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | during configuration.
| * | | | | | | Merge pull request #1448 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to ↵Neil Fortner2019-01-085-19/+34
| |\ \ \ \ \ \ \ | | |_|_|_|_|/ / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * | | | | | | HDFFV-10625 -- Implemented a process-0 read and then broadcast for ↵Quincey Koziol2019-01-0710-49/+343
| | |_|_|_|/ / | |/| | | | | | | | | | | | | | | | | | | collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
* | | | | | | Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, sinceNeil Fortner2019-01-081-6/+1
| |/ / / / / |/| | | | | | | | | | | | | | | | | space for it was removed.
* | | | | | Delay checking if decoded message's "shareable" flag is appropriate forNeil Fortner2019-01-075-19/+34
|/ / / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | | | | Merge pull request #1440 in HDFFV/hdf5 from stackable_vol_fix_14 to developQuincey Koziol2019-01-067-31/+138
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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).
| * | | | | Corrected comment in src/H5VLint.c, fixed pass-through info size inQuincey Koziol2019-01-067-31/+138
| | |_|/ / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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,Quincey Koziol2019-01-051-475/+319
|/ / / / | | | | | | | | | | | | etc. No functionality changes at all.
* | | | Merge pull request #1425 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to developJordan Henderson2019-01-041-0/+2
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | * commit '659dd9bccf69f32bfdd01dc49410116ec5c1b0bb': Align H5Lcreate_ud behavior with documentation for NULL udata pointer
| * | | | Align H5Lcreate_ud behavior with documentation for NULL udata pointerJordan Henderson2019-01-031-0/+2
| | | | | | | | | | | | | | | | | | | | Add test for H5Lcreate_ud fix
* | | | | Merge pull request #1408 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-031-3/+25
|\ \ \ \ \ | |/ / / / |/| | | / | | |_|/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | ~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)
| * | | Removed a comment.Binh-Minh Ribler2019-01-031-1/+0
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| * | | Merge branch 'develop' of ↵Binh-Minh Ribler2018-12-23104-9626/+16111
| |\ \ \ | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
| * | | | Fixed CVE division-by-zero issuesBinh-Minh Ribler2018-12-231-3/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* | | | | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Vailin Choi2019-01-0224-156/+779
|\ \ \ \ \ | | |_|_|/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | develop Resolve conflicts: Conflicts: test/Makefile.am
| * | | | Merge branch 'develop' into vfd_init_cleanupDana Robinson2019-01-0168-6064/+8083
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| | * \ \ \ Merge pull request #1413 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:yay_plugins ↵Dana Robinson2018-12-312-8/+5
| | |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '3ca19cca5395d79be69209f8d7d0a2b06834a648': Flipped swapped testing strings. 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.
| | | * \ \ \ Merge branch 'develop' into yay_pluginsDana Robinson2018-12-2820-2211/+3427
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| | | * | | | Merge branch 'develop' into yay_pluginsDana Robinson2018-12-281-2/+8
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| | | * | | | | Added more sub-tests to the VOL plugin test.Dana Robinson2018-12-282-8/+5
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| | * | | | | | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-2823-2215/+3450
| | |\ \ \ \ \ \ | | | | |_|/ / / | | | |/| | | |
| | * | | | | | Specify variable type.Jacob Smith2018-12-282-2/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Remove unnecessary whitespace.
| | * | | | | | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-2724-3511/+3686
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| | * | | | | | | OHDR tests now accept h5_fileaccess() fapls.Jacob Smith2018-12-261-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Formatting, informative comments, and minor renaming.
| | * | | | | | | Add error checking to the minimized dset header size calculation.Jacob Smith2018-12-211-15/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Update printf->HDprintf statements.
| | * | | | | | | Remove `#if 0` block of deprecated code.Jacob Smith2018-12-201-4/+0
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