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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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* Merge branch 'develop' of ↵Vailin Choi2019-02-051-0/+1
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~vchoi/my_hdf5_fork into develop
| * Merge pull request #1520 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:cmake_tweaks ↵Dana Robinson2019-02-041-0/+1
| |\ | | | | | | | | | | | | | | | | | | to develop * commit '91c7ff81dcac1af7a7b609698aa69f0c213a6184': Added a line for the CMake pread/write option to INSTALL_CMake.txt.
| | * Added a line for the CMake pread/write option to INSTALL_CMake.txt.Dana Robinson2019-02-041-0/+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 #1518 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-02-046-11/+15
|\ | | | | | | | | | | * commit '6c2a4b728f3c8eadb18d4e10d41bdbd7d1c8f3e8': Add LOCAL_BATCH_SCRIPT_ARG variable for submitting account information and other batch command variations with ctest command. Add batchscript options that work when running ctest directly.
| * Add LOCAL_BATCH_SCRIPT_ARG variable for submitting account informationLarry Knox2019-02-043-6/+6
| | | | | | | | and other batch command variations with ctest command.
| * Merge branch 'develop' of ↵Larry Knox2019-02-0414-44/+154
| |\ | |/ |/| | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
* | Merge pull request #1517 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-02-0310-25/+53
|\ \ | | | | | | | | | | | | | | | | | | | | | * commit 'c348d453b583ec9092152e6aef1f7fa9854cf5d9': Correct H5DIFF to PH5DIFF in *ctestS.sl.in.cmake list of parallel tests reserved for *ctestP.sl.cmake. Revise options to run batch tests and alternative options for cross compile in HPC/*-HDF5options.cmake. Change examples file to zip for CMake zip file. Update bin/release for filename changes and HPC-CMake tar file corrections. Add new files to MANIFEST. Update permissions for raybsub to 755.
* \ \ Merge pull request #1515 in HDFFV/hdf5 from ↵Dana Robinson2019-02-018-23/+139
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~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)
| * | | Minor tweak to CMake preadwrite entry.Dana Robinson2019-02-011-1/+1
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| * | | Updated sec2, log, and core VFDs to use pread/pwrite whenDana Robinson2019-01-318-23/+139
| | | | | | | | | | | | | | | | 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 batchscript options that work when running ctest directly.Larry Knox2019-02-043-5/+9
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| | * Correct H5DIFF to PH5DIFF in *ctestS.sl.in.cmake list of parallel testsLarry Knox2019-02-027-18/+32
| | | | | | | | | | | | | | | | | | reserved for *ctestP.sl.cmake. Revise options to run batch tests and alternative options for cross compile in HPC/*-HDF5options.cmake.
| | * Change examples file to zip for CMake zip file.Larry Knox2019-02-011-1/+1
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| | * Update bin/release for filename changes and HPC-CMake tar fileLarry Knox2019-02-011-7/+11
| | | | | | | | | | | | corrections.
| | * Add new files to MANIFEST.Larry Knox2019-02-012-0/+10
| |/ |/| | | | | Update permissions for raybsub to 755.
* | Merge pull request #1508 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-01-3118-10/+553
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'bae744199b69eb7c3f5eda2441cca30cb8c6175f': Add more specific batch scripts. 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. Account info can be submitted as an argument to run the batch scripts. Special versions for sandia are not needed. Add HDF5options.cmake files for serial and parallel tests on HPC machines (where tests are to be run as batch jobs. Add README_HPC file with instructions for setting up configuration to use batch scripts for running tests on HPC machines and some pointers for cross compiling. Remove knl configuration from ctestS.sl.in.cmake. Add sandia batch files with account info. Add batch files with batch parameters specific to cori and ray. Release.txt entry for skipping long double dt_arith tests on ppc64.
| * | Add more specific batch scripts.Larry Knox2019-01-318-7/+157
| | | | | | | | | | | | | | | | | | 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.
| * | Account info can be submitted as an argument to run the batch scripts.Larry Knox2019-01-282-33/+0
| | | | | | | | | | | | Special versions for sandia are not needed.
| * | Merge branch 'develop' of ↵Larry Knox2019-01-281-1/+1
| |\ \ | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| | * \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-281-1/+1
| | |\ \ | | | |/ | | | | | | | | | | | | * commit '9149d5a5352de4e0b9a2e57c91525a6cad767760': Revert build name setting
| * | | Add HDF5options.cmake files for serial and parallel tests on HPCLarry Knox2019-01-283-0/+313
| |/ / | | | | | | | | | | | | | | | | | | machines (where tests are to be run as batch jobs. Add README_HPC file with instructions for setting up configuration to use batch scripts for running tests on HPC machines and some pointers for cross compiling.
| * | Remove knl configuration from ctestS.sl.in.cmake.Larry Knox2019-01-273-1/+33
| | | | | | | | | | | | Add sandia batch files with account info.
| * | Merge branch 'develop' of ↵Larry Knox2019-01-2614-50/+159
| |\ \ | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| * | | Add batch files with batch parameters specific to cori and ray.Larry Knox2019-01-269-5/+86
| | | | | | | | | | | | | | | | Release.txt entry for skipping long double dt_arith tests on ppc64.
* | | | Merge pull request #1513 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to ↵Neil Fortner2019-01-301-0/+6
|\ \ \ \ | |_|_|/ |/| | | | | | | | | | | | | | | | | | | develop * commit '261c22e0459f63fd81c8942992ffe3668969f0cd': Add RELEASE.txt note for unknown message fix (pull request 1448)
| * | | Merge branch 'develop' of ↵Neil Fortner2019-01-3042-527/+567
| |\ \ \ | |/ / / |/| | | | | | | ssh://bitbucket.hdfgroup.org:7999/~nfortne2/hdf5_naf into develop
* | | | Merge pull request #1504 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-01-281-1/+1
|\ \ \ \ | |_|_|/ |/| | | | | | | | | | | * commit 'f26ee27b1fd85d192b37d9e45fb6d20f1b7e23db': Revert build name setting
| * | | Revert build name settingAllen Byrne2019-01-271-1/+1
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* | | Merge pull request #1503 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-261-0/+1
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr_fixbug:develop to develop Added test file for CMake * commit '55d1931dc6af168adc3804586a0da22287b29187': Added test file for CMake
| * \ \ Merge branch 'develop' of ↵Binh-Minh Ribler2019-01-267-26/+28
| |\ \ \ | |/ / / |/| | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
* | | | Merge pull request #1499 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-01-262-2/+3
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'ad906dc708fc803e8c5f17963fafa63591d3cc8d': Invalid position of declaration fixed. Fix CMake on Windows
| * | | | Invalid position of declaration fixed.Allen Byrne2019-01-251-1/+2
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| * | | | Fix CMake on WindowsAllen Byrne2019-01-251-1/+1
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* | | | | Merge pull request #1500 in HDFFV/hdf5 from ↵Dana Robinson2019-01-251-9/+9
|\ \ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:valgrind_fixes to develop * commit '3fac85c00d6253f7b2c96ca46c7b9718d0203029': Fixed a bug identified by valgrind in the cork test.
| * | | | Fixed a bug identified by valgrind in the cork test.Dana Robinson2019-01-251-9/+9
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* | | | Merge pull request #1498 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-252-0/+1
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr_fixbug:develop to develop * commit '0247f7b78d056b04fa08f74a2d4c4eea37f48d22': Added data file for test and updated MANIFEST
* \ \ \ \ Merge pull request #1496 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-01-255-15/+16
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '73fcbbee97c6385fb2b5009e5858ae1d6c28b3c3': CMake fix Java html fix and cmake update Update CMake
| * \ \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-01-255-24/+129
| |\ \ \ \ \ | |/ / / / / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '2fe69e7639198b174da393e47a029d0ac35b31c8': Added test for HDFFV-10588 Fixed HDFFV-10684 Fixed HDFFV-10586 and HDFFV-10588 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)
| * | | | | CMake fixAllen Byrne2019-01-241-1/+1
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| * | | | | Java html fix and cmake updateAllen Byrne2019-01-243-11/+8
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| * | | | | Update CMakeAllen Byrne2019-01-233-5/+9
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| | | * | Added test file for CMakeBinh-Minh Ribler2019-01-261-0/+1
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| | * | Merge branch 'develop' of ↵Binh-Minh Ribler2019-01-2512-83/+110
| | |\ \ | |_|/ / |/| | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
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