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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Neil Fortner2019-03-157-49/+786
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| * Merge pull request #1601 in HDFFV/hdf5 from ↵Jerome Soumagne2019-03-131-3/+3
| |\ | | | | | | | | | | | | | | | | | | ~JSOUMAGNE/hdf5:topic_thread_private to develop * commit 'dc69df49e6a8896606c9e4bd0987613a02f7a25a': CMake: fix pthread linking to only be private
| | * CMake: fix pthread linking to only be privateJerome Soumagne2019-03-131-3/+3
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| * | Add API routines to retrieve, restore, reset, and free library state.Quincey Koziol2019-03-116-46/+783
| |/ | | | | | | | | | | (Primarily for use in the async VOL connector, which has to schedule API operations for future execution and then restore the state of the library when the operation actually executes)
* | Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-069-9/+130
|/ | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* Fix typo.Quincey Koziol2019-03-051-1/+1
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* Move 'minimize dataset object header flag' into API contextQuincey Koziol2019-03-053-6/+107
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* HDFFV-10705: Fixed memory leak in scale offset filter.Songyu Lu2019-02-281-0/+5
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* Revise "management" VOL callbacks into 'info' and object 'wrap / retrieval'Quincey Koziol2019-02-237-130/+156
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* Merge pull request #1569 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:topic_threadsafe ↵Jerome Soumagne2019-02-221-0/+5
|\ | | | | | | | | | | | | to develop * commit 'bcf5c400c06bf06820b25c37eceaa97245f15f1f': Fix CMake H5_HAVE_THREADSAFE to set value in H5pubconf.h
| * Fix CMake H5_HAVE_THREADSAFE to set value in H5pubconf.hJerome Soumagne2019-02-211-0/+5
| | | | | | | | | | | | Add REQUIRED to find_package(Threads) Link against thread library if static and not WIN32 platform
* | Merge branch 'develop' into c_stdlib_posix_call_cleanupDana Robinson2019-02-1943-4648/+3646
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| * Merge pull request #1548 in HDFFV/hdf5 from merge_hyperslab_updates_04 to ↵Quincey Koziol2019-02-1510-2797/+1654
| |\ | | | | | | | | | | | | | | | | | | develop * commit '320eaf91b9adb36bb0fed9264d460e4a808200b7': More changes to align with incoming selection improvements.
| | * More changes to align with incoming selection improvements.Quincey Koziol2019-02-1410-2797/+1654
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| * | Use STREQUALAllen Byrne2019-02-141-1/+1
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| * | CMake if statement correctionAllen Byrne2019-02-141-1/+1
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| * Merge pull request #1540 in HDFFV/hdf5 from merge_hyperslab_changes_01 to ↵Quincey Koziol2019-02-1416-1609/+1616
| |\ | | | | | | | | | | | | | | | | | | develop * commit 'fb5d1a37c11bca613175a48262a2147e99c9dede': Align develop with incoming hyperslab_updates branch changes.
| | * Align develop with incoming hyperslab_updates branch changes.Quincey Koziol2019-02-1316-1609/+1616
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| * | TRILAB-111 fixes for parallel testingAllen Byrne2019-02-131-1/+1
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| * Merge in latest from developJordan Henderson2019-02-1221-60/+171
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| | * Re-write of Java JNI error handlingJordan Henderson2019-02-111-2/+2
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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.
| * | Fix some collective metadata read issuesJordan Henderson2019-02-126-64/+29
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| * 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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| * | 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)
* | | C and POSIX call cleanupDana Robinson2019-01-1129-88/+90
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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
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