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* fix reference; move declaration in fileJacob Smith2018-12-131-2/+2
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* Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-131-0/+2
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| * align H5Aget_info behavior with H5Gget_info when null attribute pointer is ↵Jordan Henderson2018-12-121-0/+2
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* | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-121-2/+17
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2018-12-101-2/+2
| |\ | | | | | | | | | | | | * commit '6f52793adcd5a14aa63731e3c33c9737b5a04d16': Minor tweak to address JIRA HDFFV-10611 (which was already fixed).
| * | Add stamp files for generated filesAllen Byrne2018-12-071-2/+17
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* | | Merge branch 'dset_ohdr_minimize' of ↵Jacob Smith2018-12-121-5/+0
|\ \ \ | | | | | | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into dset_ohdr_minimize Incorporate a few housekeeping changes and one fix.
| * | | Remove unused debugging print in '#if 0' blockJacob Smith2018-12-121-5/+0
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* | | | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-12232-11595/+27969
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| * | Minor tweak to address JIRA HDFFV-10611 (which was already fixed).Dana Robinson2018-12-081-2/+2
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| * Merge pull request #1348 in HDFFV/hdf5 from ↵Ray Lu2018-12-071-1/+8
| |\ | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:bugfix/HDFFV-10635-hdf5-library-segmentation-fault to develop * commit '3e8599591504c95d8a97100b9546174f6132dc97': HDFFV-10635: Some minor changes to the test case and the comments in the library. HDFFV-10635: add a test case. HDFFV-10635: Allowing to write the same variable-length element more than once.
| | * HDFFV-10635: Some minor changes to the test case and the comments in the ↵Songyu Lu2018-12-061-2/+3
| | | | | | | | | | | | library.
| | * HDFFV-10635: Allowing to write the same variable-length element more than once.Songyu Lu2018-11-301-1/+7
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| * | Fix build errors VOL changes, when using --disable-deprecated-symbols.Quincey Koziol2018-12-062-4/+20
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| * | Correct Windows build.Quincey Koziol2018-12-051-1/+1
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| * | Refactor allocating & releasing pass through wrapper objects.Quincey Koziol2018-12-031-558/+184
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| * | Fix typoQuincey Koziol2018-11-301-1/+1
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| * | Add a couple of missing prototypes for static routines, along with updatingQuincey Koziol2018-11-301-0/+6
| | | | | | | | | | | | a comment from VOL plugin -> connector.
| * | Switch H5VL_class_value_t from unsigned to int, and add "invalid" ID value.Quincey Koziol2018-11-291-1/+2
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| * | Switch H5VL_class_value_t from enum to unsigned integerQuincey Koziol2018-11-293-43/+26
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| * | Add support for "make check-vol", along with a few minor cleanups, etc.Quincey Koziol2018-11-291-1/+1
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| * | Refactor infrastructure for setting FAPL information from environmentQuincey Koziol2018-11-2812-89/+19
| | | | | | | | | | | | | | | | | | variables during testing, including connecting native, pass-through, and dynamically loaded VOL connectors. Also bring native and pass-through VOL connectors into alignment, removing the "H5VLnative_private.h" header.
| * | Add pass-through VOL connectorQuincey Koziol2018-11-285-4/+3114
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| * | Update API tracing info for VOL functions and regenerate trace macros for VOLQuincey Koziol2018-11-283-19/+73
| | | | | | | | | | | | API calls.
| * | Added 'notify' callback for async requests; switched VOL class and infoQuincey Koziol2018-11-289-82/+256
| | | | | | | | | | | | | | | | | | comparison to return comparison value as parameter, so they can return error values; "cancelled" -> "canceled"; switched order of 'wrap_object' and 'free_wrap_ctx' management callbacks.
| * | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-285-7/+21
| |\ \ | | | | | | | | | | | | stackable_vol
| | * \ Merge pull request #1344 in HDFFV/hdf5 from ↵Ray Lu2018-11-273-4/+4
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:bugfix/HDFFV-10607-patches-for-warnings-in-the-core to develop * commit '14de476c8cb1b797ad43bea3c71dfb32bcd2131c': HDFFV-10607 Fixing two compiler warnings in the library.
| | | * | HDFFV-10607 Fixing two compiler warnings in the library.Songyu Lu2018-11-273-4/+4
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| | * | Yanked all MPI-1 callsDana Robinson2018-11-272-17/+9
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| | * | Updated H5S to use the MPI-2 function MPI_Type_get_exten()Dana Robinson2018-11-271-2/+24
| | |/ | | | | | | | | | | | | | | | where available. OpenMPI 4.0 removed the deprecated MPI-1 MPI_type_extent() call by default, so this avoids needing a special OpenMPI build.
| * | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-221-19/+26
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| | * Move wait_H5init.cmake up to config/cmake.Larry Knox2018-11-201-1/+1
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| | * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Larry Knox2018-11-206-37/+45
| | |\ | | | | | | | | | | | | develop
| | * | Changes to CMake code to pause cmake/ctest, waiting for batch jobs toLarry Knox2018-11-201-16/+18
| | | | | | | | | | | | | | | | run and finish.
| | * | Add script and changes to wait for H5Tinit.cLarry Knox2018-11-141-10/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Add more sample batch scripts, specifically for sbatch, not for knl cross compile. Don't run parallel tests when no parallel test script is configured in HDF5options.cmake.
| * | | Switch loc_params to VOL callbacks to pass struct by pointer instead of byQuincey Koziol2018-11-2221-437/+436
| | | | | | | | | | | | | | | | value.
| * | | Add info_to_str and str_to_info "management" callbacks for serializing andQuincey Koziol2018-11-2111-53/+293
| | | | | | | | | | | | | | | | deserializing a connector's info object.
| * | | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-202-1/+10
| |\ \ \ | | | |/ | | |/| | | | | stackable_vol
| | * | Merge pull request #1335 in HDFFV/hdf5 from ↵Ray Lu2018-11-192-1/+10
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:bugfix/HDFFV-10571-cve-2018-17237-divided-by-zero to develop * commit 'c923cdad6e515c842f3795a5b6d754ad94021e09': HDFFV-10571: Minor format changes. HDFFV-10571: Minor change - reformatting the error check. HDFFV-10571: Minor change - adding the error check right after decoding of chunk dimension for safeguard. HDFFV-10571: Minor change - revised the comment to be clearer. HDFFV-10571 Divided by Zero vulnerability. Minor fix: I added an error check to make sure the chunk size is not zero.
| | | * | HDFFV-10571: Minor format changes.Songyu Lu2018-11-152-2/+1
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| | | * | HDFFV-10571: Minor change - reformatting the error check.Songyu Lu2018-11-151-1/+2
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| | | * | HDFFV-10571: Minor change - adding the error check right after decoding of ↵Songyu Lu2018-11-152-5/+10
| | | | | | | | | | | | | | | | | | | | chunk dimension for safeguard.
| | | * | HDFFV-10571: Minor change - revised the comment to be clearer.Songyu Lu2018-11-141-1/+1
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| | | * | HDFFV-10571 Divided by Zero vulnerability. Minor fix: I added an error ↵Songyu Lu2018-11-141-0/+4
| | | |/ | | | | | | | | | | | | check to make sure the chunk size is not zero.
| * | | Revert some of the changes to support the original property list value ofQuincey Koziol2018-11-182-4/+2
| | | | | | | | | | | | | | | | metadata read attempts.
| * | | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-185-36/+35
| |\ \ \ | | |/ / | | | | | | | | stackable_vol
| | * | Merge pull request #1316 in HDFFV/hdf5 from ↵Ray Lu2018-11-151-12/+10
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:bugfix/HDFFV-10601-issues-with-chunk-cache-hash to develop * commit 'cd13d24e5140578a880aebe4e2d8b899179d0870': HDFFV-10601: I added error checking to the HDF5 functions. HDFFV10601: Adding performance test to verify the improvement. HDFFV-10601: I changed to a better way to calculate the number of chunks in a dataset. HDFFV-10601 Issues with chunk cache hash value calcuation:
| | | * | HDFFV-10601: I changed to a better way to calculate the number of chunks in ↵Songyu Lu2018-11-081-5/+3
| | | | | | | | | | | | | | | | | | | | a dataset.
| | | * | Merge branch 'develop' of ↵Songyu Lu2018-11-082-2/+6
| | | |\ \ | | | | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into bugfix/HDFFV-10601-issues-with-chunk-cache-hash
| | | * | | HDFFV-10601 Issues with chunk cache hash value calcuation:Songyu Lu2018-11-021-12/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1. H5D__chunk_hash_val: When the number of chunks in the fastest changing dimension is larger than the number of slots in the hash table, H5D__chunk_hash_val abandons the normal hash value calculation algorithm and simply uses the scaled dimension. This will cause chunks a selection that cuts across chunks in dimensions other than the fastest changing to all have the same hash value, and they will therefore always evict each other from the cache, having an obvious major performance impact. Eliminated the check for the number of slots in this function and always use the full algorithm. 2. H5D__chunk_init: When the scaled dimensions (number of chunks in each dimension) are calculated in H5D__chunk_init, a simple divide ("/") operator is used with the dataset size in elements and the chunk size in elements. While this is fine when the dataset size is an exact multiple of the chunk size, in other cases, since "/" rounds down, it results in a scaled dimension one less than it should (it ignores the partial edge chunk). This has trickle down effects on hash value calculation that can cause excess hash value collisions and therefore performance issues. Changed the calculation to (((dataset_size - 1) / chunk_size) + 1). Tested the build with Autotool and CMake.
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