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* HDFFV-10632 - split stderr and stdout in cmakeAllen Byrne2018-12-0388-248/+520
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* Merge pull request #1345 in HDFFV/hdf5 from ↵Dana Robinson2018-11-271-2/+2
|\ | | | | | | | | | | | | ~DEROBINS/hdf5_der:openmpi_tweaks to develop * commit '6fccabed2e8b522747ee8056a196273917af78c7': Missed some function renames in error text.
| * Missed some function renames in error text.Dana Robinson2018-11-271-2/+2
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* | 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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* | | Merge pull request #1343 in HDFFV/hdf5 from ↵Dana Robinson2018-11-273-13/+27
|\ \ \ | | |/ | |/| | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:openmpi_tweaks to develop * commit '8cf3bfb14bd2a80f13d269a9e84cd99f86f19254': Yanked all MPI-1 calls Updated H5S to use the MPI-2 function MPI_Type_get_exten() where available. OpenMPI 4.0 removed the deprecated MPI-1 MPI_type_extent() call by default, so this avoids needing a special OpenMPI build.
| * | Yanked all MPI-1 callsDana Robinson2018-11-273-27/+19
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| * | Merge branch 'develop' into openmpi_tweaksDana Robinson2018-11-270-0/+0
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* | | Merge pull request #1341 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to ↵Dana Robinson2018-11-271-11/+1
|\ \ \ | |_|/ |/| | | | | | | | | | | | | | develop * commit 'd517bdf9d36f423e7abad34e109b6ce694fd03c8': Pulled the RELEASE.txt note concerning HDFFV-10633 since that change was pushed to hdf5_1_10 in case we release the Windows VFD in 1.10.5.
| | * 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.
| * Pulled the RELEASE.txt note concerning HDFFV-10633 since thatDana Robinson2018-11-241-11/+1
|/ | | | | change was pushed to hdf5_1_10 in case we release the Windows VFD in 1.10.5.
* Merge pull request #1334 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2018-11-219-59/+170
|\ | | | | | | | | | | | | | | * commit '7bf6e98bd921c4ef1899144ab8a1f0d66a141141': Move wait_H5init.cmake up to config/cmake. Changes to CMake code to pause cmake/ctest, waiting for batch jobs to run and finish. Really don't run parallel tests without option specifying script. Add script and changes to wait for H5Tinit.c 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.
| * Move wait_H5init.cmake up to config/cmake.Larry Knox2018-11-203-2/+2
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Larry Knox2018-11-2023-386/+980
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* | Merge pull request #1338 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developLarry Knox2018-11-202-34/+39
|\ \ | | | | | | | | | | | | | | | | | | | | | * commit '3dc4055aaf2c0917569cba38d47df051cc0eeb79': Fix typo Standardize script add max count to options file Check PARALLEL_LEVEL maximum
| * | Fix typoAllen Byrne2018-11-191-1/+1
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| * | Standardize scriptAllen Byrne2018-11-191-11/+7
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| * | add max count to options fileAllen Byrne2018-11-191-22/+26
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| * | Check PARALLEL_LEVEL maximumAllen Byrne2018-11-191-1/+6
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* | | 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.
* | | Merge pull request #1337 in HDFFV/hdf5 from ↵Ray Lu2018-11-182-77/+26
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:bugfix/HDFFV-10601-issues-with-chunk-cache-hash2 to develop * commit '4f5a52e595194562644517b7600f3b96d4008c17': HDFFV-10601: Adding the new hdf5/tools/test/perform/chunk_cache.c to MANIFEST. HDFFV-10601: Some compiler doesn't support clock_gettime(). So I changed to use gettimeofday (HDgettimeofday in the HDF5 library).
| * | | HDFFV-10601: Adding the new hdf5/tools/test/perform/chunk_cache.c to MANIFEST.Songyu Lu2018-11-161-0/+1
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| * | | HDFFV-10601: Some compiler doesn't support clock_gettime(). So I changed to ↵Songyu Lu2018-11-161-77/+25
|/ / / | | | | | | | | | use gettimeofday (HDgettimeofday in the HDF5 library).
* | | Merge pull request #1316 in HDFFV/hdf5 from ↵Ray Lu2018-11-154-14/+479
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~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 added error checking to the HDF5 functions.Songyu Lu2018-11-141-65/+161
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| * | | HDFFV10601: Adding performance test to verify the improvement.Songyu Lu2018-11-133-2/+373
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| * | | 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 Lu2018-11-0837-675/+678
| |\ \ \ | | | | | | | | | | | | | | | 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.
* | | | | Merge pull request #1325 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10511 to developScot Breitenfeld2018-11-156-44/+178
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '9bbaca66ca1f987ede2f5c7e9c5938523a47262f': fixed sp. HDFFV-10511 -- Make fortran specific subroutines names PRIVATE
| * | | | | fixed sp.M. Scot Breitenfeld2018-11-091-1/+1
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| * | | | | HDFFV-10511 -- Make fortran specific subroutines names PRIVATEM. Scot Breitenfeld2018-11-096-44/+178
| | |/ / / | |/| | | | | | | | | | | | | Made non-public APIs private.
* | | | | Merge pull request #1336 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:sec2_to_posix ↵Dana Robinson2018-11-149-54/+86
|\ \ \ \ \ | |_|_|/ / |/| | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '3edd97731e90b7fc3a378e2c6e9c043a23327d93': Renamed h5repart's -family_to_sec2 to -family_to_single.
| * | | | Renamed h5repart's -family_to_sec2 to -family_to_single.Dana Robinson2018-11-149-54/+86
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| | | * Changes to CMake code to pause cmake/ctest, waiting for batch jobs toLarry Knox2018-11-203-27/+27
| | | | | | | | | | | | | | | | run and finish.
| | | * Merge branch 'develop' of ↵Larry Knox2018-11-141-10/+24
| | | |\ | |_|_|/ |/| | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
* | | | Merge pull request #1332 in HDFFV/hdf5 from ↵Dana Robinson2018-11-131-10/+24
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:java_test_error_stack to develop * commit '110c1b671ea7f2f5e8154d66f6ca6fcfb00b2bb2': The Java tests will no longer fail when the zlib is not present.
| * | | | The Java tests will no longer fail when the zlib is not present.Dana Robinson2018-11-131-10/+24
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| | | | * Really don't run parallel tests without option specifying script.Larry Knox2018-11-141-16/+15
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| | | | * Add script and changes to wait for H5Tinit.cLarry Knox2018-11-149-304/+416
| |_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | 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.
* | | | Merge pull request #1331 in HDFFV/hdf5 from ↵Dana Robinson2018-11-123-98/+107
|\ \ \ \ | |/ / / | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:java_test_error_stack to develop * commit 'ef29549f0d66612fcdeefc763785c6826c67ad8b': Updated the Java tests so that they don't fail when the error stack changes.
| * | | Updated the Java tests so that they don't fail when theDana Robinson2018-11-123-98/+107
| | | | | | | | | | | | | | | | error stack changes.
* | | | Merge pull request #1327 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2018-11-122-7/+13
|\ \ \ \ | |/ / / |/| | | | | | | | | | | | | | | | | | | * commit '7e204759f861f4f482db2032127a4dc406fcd1d6': Fix generate file commands Fix target depends Fix target files for commands
| * | | Fix generate file commandsAllen Byrne2018-11-121-10/+9
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| * | | Fix target dependsAllen Byrne2018-11-121-2/+9
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