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* Script changes from developAllen Byrne2019-02-142-0/+3
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* TRILAB-111 Update MPI CMakeAllen Byrne2019-02-132-62/+135
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* Changing functions H5Dcreate and H5Dopen to H5Dcreate2 and H5Dopen2 for ↵Songyu Lu2019-02-131-4/+4
| | | | backward compatibility.
* I'm bringing the fixes for the following Jira issues from the develop branch ↵Songyu Lu2019-02-121-0/+102
| | | | | | | | | 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.
* Refactor TIMEOUT valuesAllen Byrne2019-02-062-16/+16
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* Renamed data fileBinh-Minh Ribler2019-02-013-2/+2
| | | | | | | | | Description: Renamed data file with long name to a shorter name. Revised an entry in RELEASE.txt Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
* Merge branch 'hdf5_1_10' of ↵Binh-Minh Ribler2019-01-314-153/+216
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_1_10_bmr into hdf5_1_10
| * Fixed a bug identified by valgrind in the cork test.Dana Robinson2019-01-291-9/+9
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| * HDFFV-10686 Remove version 1 reference namesAllen Byrne2019-01-281-44/+44
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| * CMake fix, makefile fix, direct_chunk valgrind fixAllen Byrne2019-01-251-91/+91
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| * Merge pull request #1450 in HDFFV/hdf5 from ↵Ray Lu2019-01-181-9/+72
| | | | | | | | | | | | | | | | | | ~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.
* | Fixed HDFFV-10586, HDFFV-10588, and HDFFV-10684Binh-Minh Ribler2019-01-313-0/+102
|/ | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* Work around compiler fussiness on platypus.Quincey Koziol2019-01-141-13/+39
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* Delay checking if decoded message's "shareable" flag is appropriate forNeil Fortner2019-01-093-0/+18
| | | | | | | | | | | | | | 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.
* Merge pull request #1449 in HDFFV/hdf5 from ↵Larry Knox2019-01-082-14/+14
|\ | | | | | | | | | | | | ~JAKE.SMITH/hdf5:dset_ohdr_minimize_110 to hdf5_1_10 * commit '00f835f6403728c3caf298636522e526996010a2': Fix fapl passed into h5_fixname() calls in minimized tests. Fix creation of duplicate, unclosed FAPL. Fix wrong statement-string after TEST_ERROR macro (refactoring mistake).
| * Fix fapl passed into h5_fixname() calls in minimized tests.Jacob Smith2019-01-072-14/+14
| | | | | | | | | | Fix creation of duplicate, unclosed FAPL. Fix wrong statement-string after TEST_ERROR macro (refactoring mistake).
* | Merge pull request #1442 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:hdf5_1_10 to ↵Vailin Choi2019-01-076-16/+267
|\ \ | |/ |/| | | | | | | | | | | | | | | hdf5_1_10 * commit '1a50622733c14d89b3fd8c6bab684af9205a3b96': Fix for daily test failure: too many arguments to function 'H5Gopen1'. Fix the git merge leftover in RELEASE.txt. Fix the git merge leftovers in RELEASE.txt. Fix for HDFFV-10659: The library aborts with "infinite loop closing library" 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.
| * Fix for daily test failure: too many arguments to function 'H5Gopen1'.vchoi2019-01-071-1/+1
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| * Fix for HDFFV-10659: The library aborts with "infinite loop closing library"Vailin Choi2019-01-066-16/+267
| | | | | | | | | | | | | | | | 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.
* | Merged the rest of the parallel flush test code.Dana Robinson2019-01-071-1/+1
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* Merge branch 'hdf5_1_10' of ↵Binh-Minh Ribler2019-01-0410-1431/+2536
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_1_10_bmr into hdf5_1_10
| * Remove "bad" statements from end of TEST_ERROR.Jacob Smith2019-01-041-18/+18
| | | | | | | | Formerly arguments to FAIL_PUTS_ERROR.
| * Add semicolon at end of TEST_ERROR() invocation for consistency.Jacob Smith2019-01-041-1/+1
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| * Merge branch 'hdf5_1_10' of ↵Jacob Smith2019-01-041-175/+1356
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into dset_ohdr_minimize_110
| | * Merge pull request #1380 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-021-175/+1356
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~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 Smith2019-01-041-17/+17
| | | | | | | | | | | | | | | | Remove VOL-related merge cruft.
| * | | Change H5Dcreate() to H5Dcreate2().Jacob Smith2019-01-032-20/+20
| | | | | | | | | | | | | | | | Fix return value (int -> void).
| * | | Change H5Acreate to H5Acreate2Jacob Smith2019-01-021-1/+1
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| * | | Incoporate minimized dataset headers code and tests.Jacob Smith2018-12-3110-1430/+2531
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| * | HDFFV-10632 separate stderr and stdout in testsAllen Byrne2018-12-131-0/+4
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* | | Fixed CVE division-by-zero issuesBinh-Minh Ribler2019-01-041-4/+4
| |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* | Addressed HDFFV-10661Binh-Minh Ribler2018-12-151-175/+1356
|/ | | | | | | | | | | | | 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)
* Fixed typos.Binh-Minh Ribler2018-12-071-14/+3
| | | | | Platforms tested: Linux/64 (jelly)
* Merge pull request #1314 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2018-11-134-160/+209
| | | | | | | | | develop * commit '51076d40617aa6f0236809c2c919cc6921b3bbc1': Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)Allen Byrne2018-11-082-347/+13
|\ | | | | | | | | | | | | * commit 'ec72efcd4ddb17145323bf93c5cc28fc59695c55': Improved comments Removed an old comment line. Moved tests to another file
| * Improved commentsBinh-Minh Ribler2018-11-081-2/+6
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| * Removed an old comment line.Binh-Minh Ribler2018-11-081-1/+0
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| * Moved tests to another fileBinh-Minh Ribler2018-11-071-344/+7
| | | | | | | | | | | | | | | | Description: Moved the test function test_get_chunk_info from dsets.c to chunk_info.c because chunk_info.c was created for the purpose of testing chunk information. Platforms tested: Linux/64 (jelly)
* | TRILABS: Merge CMake changes from developAllen Byrne2018-11-072-24/+28
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* Updated new API functionsBinh-Minh Ribler2018-11-063-35/+414
| | | | | | | | | | | Description: - Addressed additional review comments - Moved the test function test_get_chunk_info from dsets.c to chunk_info.c because chunk_info.c was created for the purpose of testing chunk information. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* Updated new API functionsBinh-Minh Ribler2018-11-051-17/+77
| | | | | | | | | | | | | | Description: - Per Vailin's review, revised H5Dget_chunk_info_by_coord to handle non-existing chunk and H5Dget_num_chunks and H5Dget_chunk_info to handle dataset with no data. - Addressed other review comments - Note that additional tests will be added as we need to send users these functions asap for feedback. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* New API functionsBinh-Minh Ribler2018-10-291-1/+280
| | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Added functions to query chunk information: H5Dget_num_chunks(dset_id, fspace_id, *nchunks) Gets the number of written chunks that intersect with the given dataspace. However, in this version, the intersection is not yet completed. Thus, the number of all written chunks will be returned. H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) Given a chunk's coordinates, returns the chunk's filter, address, and size. H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) Given a chunk's index, returns the chunk's coordinates, filter, address, and size. The chunk belongs to a set of chunks that have nonempty intersection with the specified dataspace. However, in this version, the intersection is not yet completed, and the index is of all the written chunks. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* HDFFV-10594, 10332, 10531Allen Byrne2018-09-262-13/+55
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* Update system commands with HD prefix and whitespaceAllen Byrne2018-08-288-1899/+1387
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* Add swmr tests, fix java scriptAllen Byrne2018-07-273-28/+492
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* Fix for HDFFV-9277: update the ainfo message after removing an attribute.Vailin Choi2018-07-261-0/+94
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* Apply Cygwin pathches from Marco Atzeri.Larry Knox2018-07-261-0/+2
| | | | Commit Joe Lee's typo corrections for src/H5MF.c.
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-269-41/+41
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Fix test_misc33() in test/tmisc.cVailin Choi2018-07-261-1/+1
| | | | Open the test file read-only so that it can be accessed for testing.
* fixed typo.Hyo-Kyung Lee2018-07-261-1/+1
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