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* Merge pull request #1543 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to ↵Allen Byrne2019-02-141-0/+6
|\ | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit 'f4f8be19125002764715f6cd25372477c729f809': Script changes from develop Added TRILABS-111 note Add HDFFV-10628 known problem TRILAB-111 Update MPI CMake
| * Script changes from developAllen Byrne2019-02-141-1/+1
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| * TRILAB-111 Update MPI CMakeAllen Byrne2019-02-131-0/+6
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* | Re-write of Java JNI error handlingJordan Henderson2019-02-141-2/+2
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* Merge pull request #1536 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_10 to ↵Jordan Henderson2019-02-126-64/+29
|\ | | | | | | | | | | | | | | hdf5_1_10 * commit '2e44998a70924b77f186f6cb60924035fd24441d': Add RELEASE.txt note for collective metadata read fixes Fix some collective metadata read issues
| * Fix some collective metadata read issuesJordan Henderson2019-02-126-64/+29
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* | I'm bringing the fixes for the following Jira issues from the develop branch ↵Songyu Lu2019-02-126-18/+31
|/ | | | | | | | | to 1.10 branch: HDFFV-10571: Divided by Zero vulnerability. HDFFV-10601: Issues with chunk cache hash value calcuation. HDFFV-10607: Patches for warnings in the core libraries. HDFFV-10635: HDF5 library segmentation fault with H5Sselect_element.
* Merge pull request #1522 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2019-02-065-2/+51
| | | | | | | | | | | | | develop * commit '7f5741825db0737db5ac46c43009681508a73002': Add release notes information. Modification based on feedback from pull request. Modification based on feedback from pull request. There is performance issue when closing an object. The slow down is due to 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. Conflicts: release_docs/RELEASE.txt
* Merge of changes from develop for 1.10.5.Dana Robinson2019-02-0410-40/+92
| | | | Added RELEASE.txt entries for new features.
* Merge branch 'hdf5_1_10' of ↵Binh-Minh Ribler2019-01-316-516/+437
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_1_10_bmr into hdf5_1_10
| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)Allen Byrne2019-01-282-2/+3
| |\ | | | | | | | | | | | | * commit '611ecb5db4051cbf762cc24944ee75ea5284c5d2': Fixed HDFFV-10578
| | * Merge pull request #1480 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-282-2/+3
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_1_10_bmr:hdf5_1_10 to hdf5_1_10 * commit '2880ef43eb03526e7d75551720547b85e66a3086': Fixed HDFFV-10578
| * | | Remove Not_yet_versioned filesAllen Byrne2019-01-281-5/+0
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| * | CMake fix, makefile fix, direct_chunk valgrind fixAllen Byrne2019-01-251-1/+1
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| * | HDFFV-10686 revert H5Oget_info1 to H5Oget_info(H5Ovisit)Allen Byrne2019-01-244-510/+436
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* | | Fixed HDFFV-10586, HDFFV-10588, and HDFFV-10684Binh-Minh Ribler2019-01-313-23/+25
| |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: HDFFV-10586 CVE-2018-17434 Divide by zero in h5repack_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 does not cover all cases, but it'll reduce the chance of this issue when a name length is corrupted or the attribute name is corrupted. HDFFV-10684 H5Ewalk does not stop until all errors in the stack are visited 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 (osx1011test)
* | Merge branch 'hdf5_1_10' of ↵Binh-Minh Ribler2019-01-151-1/+1
|\ \ | |/ | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_1_10_bmr into hdf5_1_10
| * Fix for debug assert in H5FDmpio.cDana Robinson2019-01-141-1/+1
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* | Fixed HDFFV-10578Binh-Minh Ribler2019-01-152-2/+3
|/ | | | | | | | | | | Description: - HDFFV-10578 - CVE-2018-17234 Memory leak in H5O__chunk_deserialize() Actually, the leak was in h5tools_util. Applied Neil's fix. - Changed an assert to if/HGOTO_ERROR to fail gracefully. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* Fix for parallel filters tests with new read-proc0-broadcast featureJordan Henderson2019-01-111-4/+8
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* misc. merge clean-upM. Scot Breitenfeld2019-01-113-47/+40
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* merged:M. Scot Breitenfeld2019-01-1010-74/+374
| | | | | HDFFV-10652 HDFFV-10443
* Merge pull request #1457 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to ↵Allen Byrne2019-01-091-0/+15
|\ | | | | | | | | | | | | | | | | hdf5_1_10 * commit '46f63b0faafe574ca2a32380ea85cac8206b1028': Fix deprecated H5Pget_version Fix java regex Merge CMake changes from develop
| * Merge CMake changes from developAllen Byrne2019-01-081-0/+15
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* | Merge pull request #1459 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:hdf5_1_10 to ↵Dana Robinson2019-01-091-1/+1
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit '688074781ac7be2b7e799e8804378ba1f1563db1': Fortran wrappers for dataset obj header minimization API calls.
| * | Fortran wrappers for dataset obj header minimization API calls.Dana Robinson2019-01-091-1/+1
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* | Delay checking if decoded message's "shareable" flag is appropriate forNeil Fortner2019-01-095-19/+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. Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since space for it was removed.
* | Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, sinceNeil Fortner2019-01-091-6/+1
|/ | | | space for it was removed.
* Fix for HDFFV-10659: The library aborts with "infinite loop closing library"Vailin Choi2019-01-061-2/+33
| | | | | | | | after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
* Merge branch 'hdf5_1_10' of ↵Binh-Minh Ribler2019-01-0461-4313/+4512
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_1_10_bmr into hdf5_1_10
| * Merge branch 'hdf5_1_10' of ↵Jacob Smith2019-01-046-22/+28
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into dset_ohdr_minimize_110
| | * Merge pull request #1380 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-026-22/+28
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_1_10_bmr:hdf5_1_10 to hdf5_1_10 This is merged now so it can be tested. * commit '74a3710a996fca5ed7fcb4dd8919a7a8521de1de': Revised per review. Description: Changed H5EA_iterate and H5FA_iterate as suggested. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test) Addressed HDFFV-10661 Description: - Fixed a bug triggered by tests in chunk_info.c. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Vailin confirmed. - Addressed review comments and made various improvements on the tests. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
| * | | Change FAIL_PUTS_ERROR to TEST_ERROR.Jacob Smith2019-01-041-8/+0
| | | | | | | | | | | | | | | | Remove VOL-related merge cruft.
| * | | Remove unnecessary sJacob Smith2019-01-022-6/+0
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| * | | Merge branch 'hdf5_1_10' of ↵Jacob Smith2018-12-3154-4260/+3793
| |\ \ \ | | |/ / | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into dset_ohdr_minimize_105
| | * | Merge of logging framework updates.Dana Robinson2018-12-3119-2209/+3425
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| | * | Updated the H5I debug function so it's more robust and alwaysDana Robinson2018-12-312-35/+35
| | | | | | | | | | | | | | | | available.
| | * | Removed 'VOL' from some H5PL comments.Dana Robinson2018-12-312-5/+4
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| | * | Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-12-3131-2008/+312
| | | | | | | | | | | | | | | | orginally intended to support the full SWMR feature (from develop).
| | * | Replaced all MPI-1 calls with MPI-2 equivalents (from develop).Dana Robinson2018-12-312-3/+17
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| * | | Incoporate minimized dataset headers code and tests.Jacob Smith2018-12-3112-44/+670
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| * | HDFFV-10660,-10594 merge from developAllen Byrne2018-12-131-9/+63
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* | | Fixed CVE division-by-zero issuesBinh-Minh Ribler2019-01-041-4/+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 Also updated RELEASE.txt for the chunk query functions and removed some blank lines in chunk_info.c. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* | Revised per review.Binh-Minh Ribler2018-12-262-12/+22
| | | | | | | | | | | | | | | | | | Description: Changed H5EA_iterate and H5FA_iterate as suggested. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* | Addressed HDFFV-10661Binh-Minh Ribler2018-12-156-22/+18
|/ | | | | | | | | | | | | Description: - Fixed a bug triggered by tests in chunk_info.c. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Vailin confirmed. - Addressed review comments and made various improvements on the tests. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* Merge pull request #1359 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:hdf5_1_10 to ↵Dana Robinson2018-12-0715-330/+91
|\ | | | | | | | | | | | | hdf5_1_10 * commit '21e73fd58d64fdba5e06e73e59be30d2a4c3fd59': Moved fixes for incorrectly installed header files to 1.10.
| * Moved fixes for incorrectly installed header files to 1.10.Dana Robinson2018-12-0615-330/+91
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* | Fixed typos.Binh-Minh Ribler2018-12-072-14/+10
|/ | | | | Platforms tested: Linux/64 (jelly)
* Fix for HDFFV-10629Jordan Henderson2018-12-051-0/+2
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* Renamed h5repart's -family_to_sec2 to -family_to_single.Dana Robinson2018-11-234-24/+25
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