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* HDFFV-10635: Allowing to write the same variable-length element more than once.Songyu Lu2018-11-301-1/+7
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* 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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| * | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2018-11-121-12/+0
| |\ \ \ | |/ / / |/| | | | | | | | | | | * commit '6a2e97bead3c4d366f28b6a1e4e338fc07014954': HDFFV-10537: Remove installation of Fortran test mod files
* | | | Merge pull request #1329 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10537 to developScot Breitenfeld2018-11-091-12/+0
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | * commit 'cd73b837db95493de0641b2c63537b42b8b57a84': HDFFV-10537: Remove installation of Fortran test mod files
| * | | | HDFFV-10537: Remove installation of Fortran test mod filesM. Scot Breitenfeld2018-11-091-12/+0
| | |/ / | |/| | | | | | | | | | Removed from autools install, cmake does not have this issue.
| | * | Fix target files for commandsAllen Byrne2018-11-091-2/+2
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* | | Merge pull request #1324 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2018-11-091-35/+12
|\ \ \ | |/ / |/| | | | | | | | * commit '1d2f7ca4901d126d677a32ecb4e2bc60b3b41182': TRILAB-36 only copy shared generated
| * | TRILAB-36 only copy shared generatedAllen Byrne2018-11-091-35/+12
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* | Merge pull request #1298 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2018-11-0716-545/+529
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '4616c1e863ab756d22af696672ba9bc2fe0eea25': Add custom target to force wait on generated file TRILAB-81 fix typo TRILAB-82 fixed errors found in review Update windows test machine info TRILAB-81 Output error if filename length is greater then 255 TRILAB-81 check for func success before using value TRILAB-81 Coverity fix Move options to root CMakeLists.txt TRILAB-34 fix required through testing TRILAB-34 add batch option (also patch2 from 10633) TRILAB-81 coverity fixes
| * \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2018-11-0612-117/+133
| |\ \ | |/ / |/| | | | | | | | | | | | | | | | | * commit '1652a60fcbe9894d7c34a778fb24dce1979fb9a9': HDFFV-10605 Only test plugins if SHARED enabled Correct platforms Correct extlib depends Commit version changes for additional files for 1.11.3 snapshot release.
* | | Merge pull request #1319 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developAllen Byrne2018-11-063-11/+11
|\ \ \ | | | | | | | | | | | | | | | | * commit '81cb24ac1db0f4936b19067cdb7fa4e14e0d00db': Commit version changes for additional files for 1.11.3 snapshot release.
| * | | Commit version changes for additional files for 1.11.3 snapshot release.Larry Knox2018-11-063-11/+11
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