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* Merge pull request #1654 in HDFFV/hdf5 from ↵Vailin Choi2019-04-181-0/+30
|\ | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10579-h5arename-function-fails-when to develop * commit '53a5c3be903ce7c24d02a6bd3a8d9b07a3f82404': Change the checking to H5I_INVALID_HID in test_attr_dense_rename(). Fix for HDFFV-10579 H5Arename fails when creation order of attributes is tracked. The attribute needs to be removed from the creation order index v2 B-tree before re-inserting the renamed attribute via H5A__dense_insert().
| * Fix for HDFFV-10579 H5Arename fails when creation order of attributes is ↵Vailin Choi2019-04-121-0/+30
| | | | | | | | | | | | | | tracked. The attribute needs to be removed from the creation order index v2 B-tree before re-inserting the renamed attribute via H5A__dense_insert().
* | Merge pull request #1600 in HDFFV/hdf5 from ↵Ray Lu2019-04-188-39/+220
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:HDFFV-10658-performance-drop-from-1-8 to develop * commit 'b5ef82a1786605ae86502bc82086047720b7d4ca': (21 commits) Moving the handling of null prefix into H5_combine_path. Changing the prefix of external file and VDS from empty string to null for performance improvement. Improving the condition checking of empty string. Replacing string operation strdup with assignment for empty string. Adding back links_env.out which I accidentally removed in my previous commit. Taking out two unnecessary diff output files. Taking out unnecessary diff files for output. Adding some comments. Some coding style changes. Adding the standard output files for the external_env.c and vds_env.c tests. Small correction for my previous commit. Forgot to add external_common.c and external_common.h. Updated CMake for the splitting of external.c and vds.c. Minor fix: removal of unnecessary enum values. Minor fixes: updating the test vds_env.c according to the set up of vds.c. Left out this file in previous commit. HDFFV-10658 - setting and getting properties in API context: 1. switched to use the existing H5F_prefix_open_t for enum type; 2. put the common private function used by external.c and external_env.c into external_common.c This commit basically has the following changes: 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get. HDFFV-10658: I left out this file in my previous commit. HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work. ...
| * | Moving the handling of null prefix into H5_combine_path.Songyu Lu2019-04-172-17/+7
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| * | Changing the prefix of external file and VDS from empty string to null for ↵Songyu Lu2019-04-172-25/+30
| | | | | | | | | | | | performance improvement.
| * | Improving the condition checking of empty string.Songyu Lu2019-04-171-8/+8
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| * | Replacing string operation strdup with assignment for empty string.Songyu Lu2019-04-171-11/+18
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| * | Merge branch 'develop' of ↵Songyu Lu2019-04-154-0/+51
| |\ \ | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * | | Adding some comments.Songyu Lu2019-04-111-6/+6
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| * | | Minor fix: removal of unnecessary enum values.Songyu Lu2019-04-101-3/+1
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| * | | Minor fixes: updating the test vds_env.c according to the set up of vds.c.Songyu Lu2019-04-101-1/+1
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| * | | Merge branch 'develop' of ↵Songyu Lu2019-04-0917-273/+1216
| |\ \ \ | | | |/ | | |/| | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * | | HDFFV-10658 - setting and getting properties in API context:Songyu Lu2019-04-093-16/+14
| | | | | | | | | | | | | | | | | | | | 1. switched to use the existing H5F_prefix_open_t for enum type; 2. put the common private function used by external.c and external_env.c into external_common.c
| * | | Merge branch 'develop' of ↵Songyu Lu2019-04-0819-122/+334
| |\ \ \ | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * \ \ \ Merge branch 'develop' of ↵Songyu Lu2019-04-04131-827/+1710
| |\ \ \ \ | | | | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * | | | | This commit basically has the following changes:Songyu Lu2019-04-042-8/+54
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get.
| * | | | | HDFFV-10658: I left out this file in my previous commit.Songyu Lu2019-03-221-5/+6
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| * | | | | HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce ↵Songyu Lu2019-03-225-253/+42
| | | | | | | | | | | | | | | | | | | | | | | | the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work.
| * | | | | HDFFV-10658: setting and getting properties in API context:Songyu Lu2019-03-136-42/+391
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1. external file prefix and VDS prefix. 2. the datatype, dataspace, and LCPL of the dataset for VOL connector.
* | | | | | Correct set extent operation on VDS to iterate over # of used sub-datasetsQuincey Koziol2019-04-161-1/+1
| |_|_|_|/ |/| | | | | | | | | | | | | | instead of # of allocated sub-datasets.
* | | | | Add trace macro.Quincey Koziol2019-04-121-0/+1
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* | | | | Add H5Fget_fileno() API routine.Quincey Koziol2019-04-124-0/+50
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* | | | Modifications based on PR feedback:Vailin Choi2019-04-081-0/+1
| | | | | | | | | | | | | | | | | | | | (1) Add H5Sdeprec.c to src/CMakeLists.txt (2) Add test for H5Sencode1.
* | | | Modification for num_elem based on PR feedback.Vailin Choi2019-04-081-1/+1
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* | | | HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.Vailin Choi2019-04-0616-273/+1215
| |_|/ |/| | | | | | | | This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* | | Merge pull request #1644 in HDFFV/hdf5 from ↵Vailin Choi2019-04-061-0/+1
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10271-version-2-hyperslab-encoding to develop * commit '7fe665ebff3e86aaf1eef92199f757a5c0d1fe80': Fix for HDFFV-10271 hyperslab encoding incorrect length.
| * | | Fix for HDFFV-10271 hyperslab encoding incorrect length.Vailin Choi2019-04-051-0/+1
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* | | | Merge pull request #1642 in HDFFV/hdf5 from ↵Vailin Choi2019-04-066-117/+194
|\ \ \ \ | |/ / / |/| | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/separate_selection_specific to develop * commit '4142d8b7d4ac48cffcc2b92af4a54352b329865b': Move dataspace selection-specific coding to the callbacks as preparation for the H5Sencode changes.
| * | | Move dataspace selection-specific coding to the callbacks as preparation for ↵Vailin Choi2019-04-056-117/+194
| | |/ | |/| | | | | | | the H5Sencode changes.
* | | Merge pull request #1639 in HDFFV/hdf5 from ↵Vailin Choi2019-04-0511-4/+17
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/add_v112_version_bounds to develop * commit '0073f198978dea0116bd74816b3119dfeb09144b': Set V112 as the latest format and extend the arrays of version bounds.
| * | | Set V112 as the latest format and extend the arrays of version bounds.Vailin Choi2019-04-0411-4/+17
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* | | Setting API context for fapl and libver_bounnds in preparation for the ↵Vailin Choi2019-04-042-0/+123
|/ / | | | | | | H5Sencode changes.
* | Merge remote-tracking branch 'origin/develop' into env_vol_loadQuincey Koziol2019-04-03124-541/+870
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| * | Snapshot version 1.11 release 4.hdftest2019-04-011-2/+2
| | | | | | | | | | | | Update version to 1.11.5.
| * | Merge branch 'develop' of ↵Binh-Minh Ribler2019-03-20162-5284/+5424
| |\ \ | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
| | * | Commented out memcpy overlap check while we investigateDana Robinson2019-03-191-0/+5
| | | | | | | | | | | | | | | | parallel filters issues.
| | * | Yanked check for memcpy n > 0Dana Robinson2019-03-171-1/+0
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| | * | - Added H5MMprivate.h #includes where neededDana Robinson2019-03-1644-10/+48
| | | | | | | | | | | | | | | | | | | | - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
| | * | Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-16115-513/+546
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| | * | Merge pull request #1602 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:wopen_squash ↵Dana Robinson2019-03-152-6/+134
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '0c20c65e2f3abf390ad87c9167daca4cdff2de39': Added the HDopen work-around on windows to pio_engine.c Adds _wopen support on Windows so that files with UTF-8 names can be opened.
| | | * | Adds _wopen support on Windows so that files with UTF-8 namesDana Robinson2019-03-152-6/+134
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | can be opened. Fixes: HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691
| | * | | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Neil Fortner2019-03-157-49/+786
| | |\ \ \ | | | |/ / | | | | | | | | | | develop
| | | * | 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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| | * | | 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.
| * | | Fixed HDFFV-10210 and HDFFV-10587Binh-Minh Ribler2019-03-202-0/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Added parameter validation (HDFFV-10210) - Added detection of division by zero (HDFFV-10587 - CVE-2018-17438) - Fixed typos in various tests Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* | | | Merge remote-tracking branch 'origin/develop' into env_vol_loadQuincey Koziol2019-03-126-46/+783
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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)
* | | Specify the default VOL connector to use with an environment variable.Quincey Koziol2019-03-1013-286/+840
|/ / | | | | | | | | | | | | | | This implicitly adds support for changing the VOL connector for command-line tools or any application linked with the library. Also, add 'make check-vol' support for all directories, clearing up necessary issues in testing scripts, etc.
* | Fix typo.Quincey Koziol2019-03-051-1/+1
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