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* Merge branch 'develop' into parallel_vds_developM. Scot Breitenfeld2019-02-0853-817/+1318
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| * Add ID type (of eventual hid_t) to the VOL "wrap" callback.Quincey Koziol2019-02-075-16/+20
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| * Modification based on feedback from pull request.Vailin Choi2019-02-063-2/+7
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| * Modification based on feedback from pull request.Vailin Choi2019-02-051-1/+1
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| * There is performance issue when closing an object. The slow down is due to ↵Vailin Choi2019-02-055-2/+46
| | | | | | | | | | | | | | | | | | | | the search of the "tag_list" to find out the "corked" status of an object. The fix: (1) Add a counter "num_objs_corked" in the cache structure to track the number of "corked" objects. (2) Skip the search of "tag_list" if the counter is zero i.e. no "corked" objects.
| * Merge pull request #1515 in HDFFV/hdf5 from ↵Dana Robinson2019-02-014-19/+77
| |\ | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:pread_vfd_squash to develop * commit '055208b71c573be3d4b1047b840d4d8b255bc25e': Minor tweak to CMake preadwrite entry. Updated sec2, log, and core VFDs to use pread/pwrite when available (can be controlled via a configure/CMake option)
| | * Updated sec2, log, and core VFDs to use pread/pwrite whenDana Robinson2019-01-314-19/+77
| | | | | | | | | | | | available (can be controlled via a configure/CMake option)
| * | Merge pull request #1516 in HDFFV/hdf5 from ↵Dana Robinson2019-02-016-21/+15
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:valgrind_fixes to develop * commit '5f1f231310bcb3278f11a51e1ea47782f6ee3235': Updated H5Dio.c comment. Fixed a valgrind issue with the unprotect log message. The logging call was placed after the point where the cache entry was freed. The fix was to just use the entry's address directly in the log call instead of the entry itself. Fixed a bug revealed by the dtransform test. A datatype transform buffer needed to be calloc'd.
| | * | Updated H5Dio.c comment.Dana Robinson2019-02-011-5/+2
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| | * | Fixed a valgrind issue with the unprotect log message. The loggingDana Robinson2019-01-315-15/+12
| | | | | | | | | | | | | | | | | | | | | | | | call was placed after the point where the cache entry was freed. The fix was to just use the entry's address directly in the log call instead of the entry itself.
| | * | Fixed a bug revealed by the dtransform test. A datatype transformDana Robinson2019-01-311-1/+1
| | |/ | | | | | | | | | buffer needed to be calloc'd.
| * | Add more specific batch scripts.Larry Knox2019-01-311-0/+6
| |/ | | | | | | | | | | Add script raybsub to handle submitting .lsf files on ray with bsub < script.lsf syntax that we couldn't handle with CMake. Add hpc-cmake-tgz option for bin/release.
| * Added test for HDFFV-10588Binh-Minh Ribler2019-01-241-1/+1
| | | | | | | | | | | | | | Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
| * Fixed HDFFV-10684Binh-Minh Ribler2019-01-202-21/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: The test for HDFFV-10588 has revealed a bug in H5Ewalk. H5Ewalk did not stop midway even when the call back function returns H5_ITER_STOP. This is because a condition is missing from the for loops in H5E__walk causing the callback functions unable to stop until all the errors in the stack are iterated. Quincey advised on the final fix. In this fix, "status" is switched to "ret_value" and HGOTO_ERROR to HERROR, and the for loops won't continue when "ret_value" is not 0. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
| * Merge branch 'develop' of ↵Binh-Minh Ribler2019-01-1532-722/+1053
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
| | * 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
| | | | | | | | | | | | | | | | supplied
| | * | 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.
| | * | 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.
| * | | | | Fixed HDFFV-10586 and HDFFV-10588Binh-Minh Ribler2019-01-151-1/+6
| | |_|_|/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters Added a check for zero value HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper This is actually an Invalid read issue. It was found that the attribute name length in an attribute message was corrupted, which caused the buffer pointer to be advanced too far and later caused an invalid read. Added a check to detect attribute name and its length mismatch. The fix is not perfect, but it'll reduce the chance of this issue when a name length is corrupted or the attribute name is corrupted. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
| * | | | 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
| | * | | 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)
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