Commit Graph

18675 Commits

Author SHA1 Message Date
Allen Byrne
4bc283a0f2 Standardize script 2018-11-19 11:03:42 -06:00
Allen Byrne
d9fbacff90 add max count to options file 2018-11-19 11:02:20 -06:00
Allen Byrne
a26aedce04 Check PARALLEL_LEVEL maximum 2018-11-19 10:03:18 -06:00
Ray Lu
e9125d6a99 Merge pull request #1337 in HDFFV/hdf5 from ~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).
2018-11-17 19:03:30 -06:00
Songyu Lu
4f5a52e595 HDFFV-10601: Adding the new hdf5/tools/test/perform/chunk_cache.c to MANIFEST. 2018-11-16 16:25:50 -06:00
Songyu Lu
d25afb294c HDFFV-10601: Some compiler doesn't support clock_gettime(). So I changed to use gettimeofday (HDgettimeofday in the HDF5 library). 2018-11-16 12:06:30 -06:00
Ray Lu
e07d097da1 Merge pull request #1316 in HDFFV/hdf5 from ~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:
2018-11-15 09:43:46 -06:00
Scot Breitenfeld
73f881a838 Merge pull request #1325 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10511 to develop
* commit '9bbaca66ca1f987ede2f5c7e9c5938523a47262f':
  fixed sp.
  HDFFV-10511 -- Make fortran specific subroutines names PRIVATE
2018-11-15 09:27:16 -06:00
Songyu Lu
cd13d24e51 HDFFV-10601: I added error checking to the HDF5 functions. 2018-11-14 17:30:23 -06:00
Dana Robinson
e890eb89d2 Merge pull request #1336 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:sec2_to_posix to develop
* commit '3edd97731e90b7fc3a378e2c6e9c043a23327d93':
  Renamed h5repart's -family_to_sec2 to -family_to_single.
2018-11-14 16:21:08 -06:00
Dana Robinson
3edd97731e Renamed h5repart's -family_to_sec2 to -family_to_single. 2018-11-14 13:37:31 -08:00
Dana Robinson
ca1788e082 Merge pull request #1332 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:java_test_error_stack to develop
* commit '110c1b671ea7f2f5e8154d66f6ca6fcfb00b2bb2':
  The Java tests will no longer fail when the zlib is not present.
2018-11-13 16:38:43 -06:00
Songyu Lu
2fe10c647c HDFFV10601: Adding performance test to verify the improvement. 2018-11-13 11:37:29 -06:00
Dana Robinson
110c1b671e The Java tests will no longer fail when the zlib is not present. 2018-11-13 07:45:56 -08:00
Dana Robinson
f515574dcf Merge pull request #1331 in HDFFV/hdf5 from ~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.
2018-11-12 16:05:16 -06:00
Dana Robinson
ef29549f0d Updated the Java tests so that they don't fail when the
error stack changes.
2018-11-12 13:31:10 -08:00
Allen Byrne
c2ceeb02b6 Merge pull request #1327 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '7e204759f861f4f482db2032127a4dc406fcd1d6':
  Fix generate file commands
  Fix target depends
  Fix target files for commands
2018-11-12 13:45:05 -06:00
Allen Byrne
7e204759f8 Fix generate file commands 2018-11-12 12:26:11 -06:00
Allen Byrne
ba609275d8 Fix target depends 2018-11-12 11:52:46 -06:00
Allen Byrne
fde902cb45 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '6a2e97bead3c4d366f28b6a1e4e338fc07014954':
  HDFFV-10537: Remove installation of Fortran test mod files
2018-11-12 08:55:11 -06:00
Scot Breitenfeld
6a2e97bead Merge pull request #1329 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10537 to develop
* commit 'cd73b837db95493de0641b2c63537b42b8b57a84':
  HDFFV-10537: Remove installation of Fortran test mod files
2018-11-09 16:51:24 -06:00
M. Scot Breitenfeld
cd73b837db HDFFV-10537: Remove installation of Fortran test mod files
Removed from autools install, cmake does not have this issue.
2018-11-09 16:00:34 -06:00
Allen Byrne
6b959b1e21 Fix target files for commands 2018-11-09 14:38:11 -06:00
Allen Byrne
6e74d2f2ed Merge pull request #1324 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '1d2f7ca4901d126d677a32ecb4e2bc60b3b41182':
  TRILAB-36 only copy shared generated
2018-11-09 14:05:59 -06:00
M. Scot Breitenfeld
9bbaca66ca fixed sp. 2018-11-09 11:29:24 -06:00
M. Scot Breitenfeld
4fbd6bb8a5 HDFFV-10511 -- Make fortran specific subroutines names PRIVATE
Made non-public APIs private.
2018-11-09 11:24:42 -06:00
Allen Byrne
1d2f7ca490 TRILAB-36 only copy shared generated 2018-11-09 11:20:48 -06:00
Songyu Lu
3a13bb72e8 HDFFV-10601: I changed to a better way to calculate the number of chunks in a dataset. 2018-11-08 15:41:49 -06:00
Songyu Lu
709704528c Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into bugfix/HDFFV-10601-issues-with-chunk-cache-hash 2018-11-08 10:16:47 -06:00
Allen Byrne
40338b9e40 Merge pull request #1298 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* 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
2018-11-07 10:02:49 -06:00
Allen Byrne
4616c1e863 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* 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.
2018-11-06 16:01:35 -06:00
Allen Byrne
1652a60fcb Merge pull request #1319 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '81cb24ac1db0f4936b19067cdb7fa4e14e0d00db':
  Commit version changes for additional files for 1.11.3 snapshot release.
2018-11-06 16:01:16 -06:00
Allen Byrne
0f4f4cf5dd Merge pull request #1320 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:develop to develop
* commit '79903575e64e1e8f46ce27e6212d5d5939a8a900':
  HDFFV-10605 Only test plugins if SHARED enabled
  Correct platforms
  Correct extlib depends
2018-11-06 15:47:10 -06:00
Allen Byrne
79903575e6 HDFFV-10605 Only test plugins if SHARED enabled 2018-11-06 15:45:58 -06:00
Allen Byrne
c77d044dd0 Correct platforms 2018-11-06 15:30:15 -06:00
Allen Byrne
b9b89705c3 Correct extlib depends 2018-11-06 15:10:55 -06:00
Allen Byrne
7f5d91fa8f Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '9f299a6eeb91b8bc59196ccbb7067285b23e6085':
  TRILAB-36 add custom target on generated files
  Fix typo in whitespace area
2018-11-06 15:08:36 -06:00
Allen Byrne
9f299a6eeb Merge pull request #1318 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:develop to develop
* commit '1bd3a2885865f4745209233ea84045a22e6dce9c':
  TRILAB-36 add custom target on generated files
  Fix typo in whitespace area
2018-11-06 15:07:37 -06:00
Larry Knox
81cb24ac1d Commit version changes for additional files for 1.11.3 snapshot release. 2018-11-06 10:56:36 -06:00
Allen Byrne
1bd3a28858 TRILAB-36 add custom target on generated files 2018-11-06 09:35:11 -06:00
Allen Byrne
a6a46fb27f Add custom target to force wait on generated file 2018-11-06 09:32:34 -06:00
Allen Byrne
e753904d0b Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'e6545faa5699aae4d5dca23ed40e3080fa9dc72d':
  Update HDF5-Examples version to be included in CMake-* tar/zip files.
  Snapshot version 1.11 release 3.
2018-11-05 16:57:51 -06:00
Allen Byrne
05419b19fc Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'e6545faa5699aae4d5dca23ed40e3080fa9dc72d':
  Update HDF5-Examples version to be included in CMake-* tar/zip files.
  Snapshot version 1.11 release 3.
2018-11-05 16:57:39 -06:00
Larry Knox
e6545faa56 Merge pull request #1317 in HDFFV/hdf5 from ~HDFTEST/hdf5_hft:develop to develop
* commit 'be0d6b206aaa04f7d9cb406a71aeeb458ba67975':
  Update HDF5-Examples version to be included in CMake-* tar/zip files.
  Snapshot version 1.11 release 3.
2018-11-05 15:49:11 -06:00
hdftest
be0d6b206a Update HDF5-Examples version to be included in CMake-* tar/zip files. 2018-11-05 12:40:04 -06:00
hdftest
db48399bd8 Snapshot version 1.11 release 3. 2018-11-05 12:21:13 -06:00
Allen Byrne
550674d28a Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '20ad15a1a8e9008103fe7d30401408eaa2aff6e5':
  Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
  Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
  Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
2018-11-05 09:09:26 -06:00
Allen Byrne
9e0eb2fdca Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit '20ad15a1a8e9008103fe7d30401408eaa2aff6e5':
  Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
  Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
  Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
2018-11-05 09:09:09 -06:00
Songyu Lu
6fa26d7e49 HDFFV-10601 Issues with chunk cache hash value calcuation:
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.
2018-11-02 14:53:35 -05:00
Vailin Choi
20ad15a1a8 Merge pull request #1314 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit '51076d40617aa6f0236809c2c919cc6921b3bbc1':
  Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
  Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
  Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
2018-11-01 16:12:07 -05:00