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Author SHA1 Message Date
Grzegorz Kowal
b60ebe52ae WORKSPACE: Only notify that the workspace is too small for OpenMP. 
We cannot resize the workspace with OpenMP. It should be allocated
large enough from the beginning. If OpenMP is used, just notify about
the workspace too small and return an error.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 16:20:57 -03:00
Grzegorz Kowal
9ebb9a5e9d CMAKE: Rename OMP to OPENMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 13:05:16 -03:00
Grzegorz Kowal
2151d483ec EVOLUTION: Make some variable threadprivate in update_increment(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-07 20:53:57 -03:00
Grzegorz Kowal
ddb9c83608 MESH: Build data block list after each mesh update. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-07 20:51:22 -03:00
Grzegorz Kowal
e20cd5de6c BLOCKS: Add subroutine to prepare the vector of data blocks. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-07 20:49:03 -03:00
Grzegorz Kowal
c6fc8d5194 OPENMP: Declare some local variables as threadprivate. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-07 19:55:30 -03:00
Grzegorz Kowal
ea0b9b83dc WORKSPACE: Make workspace thread safe. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-07 10:46:18 -03:00
Grzegorz Kowal
2c336a4d74 CMAKE, MAKE: Add support for OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-07 10:37:56 -03:00
Grzegorz Kowal
e1fa68b54f EVOLUTION: Fix alignment. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 19:56:26 -03:00
Grzegorz Kowal
67835ffdff SOURCES: Remove empty if statement. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 19:55:53 -03:00
Grzegorz Kowal
c5d65de44c IO: XDMF works only with deflate or uncompressed HDF5 files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 11:55:30 -03:00
Grzegorz Kowal
fcce326245 IO: Fix generation of XDMF files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 11:54:19 -03:00
Grzegorz Kowal
8d27d95a76 BOUNDARIES: Stop compiler complaining if MPI is off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:58:57 -03:00
Grzegorz Kowal
7112a12e1c AMUN: Stop compiler complaining if MPI is off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:55:46 -03:00
Grzegorz Kowal
afe0d3fe83 MPITOOLS: Stop compiler complaining if MPI is off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:54:17 -03:00
Grzegorz Kowal
4a9a8d71a6 MESH: Remove cruft code with directive DEBUG. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:51:53 -03:00
Grzegorz Kowal
0c7e7eca15 STATISTICS: Stop compiler complaining if MPI is off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:48:07 -03:00
Grzegorz Kowal
6cb82114b8 AMUN, SYSTEM: Stop compiler complaining if SIGNALS is off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:43:07 -03:00
Grzegorz Kowal
34d551e9a6 IO: Stop compiler complaining if HDF5 is off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:35:56 -03:00
Grzegorz Kowal
b382734476 MESH: Remove unnecessary 'if' condition. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:32:48 -03:00
Grzegorz Kowal
09cbb1b812 COMPRESSION: Declare explicit kind in lz4_iserror() and zstd_iserror(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:25:21 -03:00
Grzegorz Kowal
c21839e4f1 HASH: Initialize hash in digest(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-03 10:17:08 -03:00
Grzegorz Kowal
5792fe60a0 IO: Store data type and dimensions for XML-binary format. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-02 10:43:03 -03:00
Grzegorz Kowal
ce1f6cee4a IO: Tune chunking for compressions in store_dataset_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-02 09:15:35 -03:00
Grzegorz Kowal
43ad4a7af3 IO: Add SZIP compression to HDF5 snapshots. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 21:52:41 -03:00
Grzegorz Kowal
1664a37e10 Update README.md 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 21:36:29 -03:00
Grzegorz Kowal
c85831a386 IO: Rewrite HDF5 compression code and add ZFP compression. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 19:00:24 -03:00
Grzegorz Kowal
80b9c6d6a2 IO: Compress only variable datasets in HDF5 regular snapshots. 
Do not compress HDF5 restart snapshots at all.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 18:59:21 -03:00
Grzegorz Kowal
a364281184 IO: Fix restore_metablocks_h5() for 3D. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 18:17:29 -03:00
Grzegorz Kowal
b85dfafef1 IO: Rewrite file division in read_restart_snapshot_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 09:19:06 -03:00
Grzegorz Kowal
e50c65e7dd IO: Rewrite file division in read_restart_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 08:55:39 -03:00
Grzegorz Kowal
cc48f69803 IO: Fix the restart from the XML files with less processes. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 22:53:53 -03:00
Grzegorz Kowal
657a608ce0 PYTHON: Add support for XXH3 hash. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 19:02:32 -03:00
Grzegorz Kowal
0ac1fec2d7 IO: Rewrite read_restart_snapshot_xml() a bit. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 18:22:21 -03:00
Grzegorz Kowal
863b7c5a85 IO: Rewrite write_binary_xml() so it accepts a pointer instead of array. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 17:45:33 -03:00
Grzegorz Kowal
cb2d7b09cf HASH, IO: Pass pointers to the hash functions instead of arrays. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 14:23:22 -03:00
Grzegorz Kowal
398b3e331d HASH: Rewrite internal xxh64() to accept pointer instead of array. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 12:59:43 -03:00
Grzegorz Kowal
b5183dfa0e IO: Store hashes as integers in read_restart_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 12:20:14 -03:00
Grzegorz Kowal
a53601ff92 HASH, IO: Rewrite module HASH. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 12:04:30 -03:00
Grzegorz Kowal
1fd1ee7602 IO: Add compression suffix to files individually. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-29 12:23:26 -03:00
Grzegorz Kowal
b10b49c8c3 COMPRESSION: Add compression_suffix to store the file extension. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-29 12:08:42 -03:00
Grzegorz Kowal
de81332cf8 COMPRESSION: Reset clen in case the compression is unsupported. 
This will indicate that no compression should be used.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-29 08:27:21 -03:00
Grzegorz Kowal
88cdf23078 COMPRESSION, IO: Remove double buffer for compression. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 23:27:03 -03:00
Grzegorz Kowal
9ddf7c7b44 IO: Use compression_bound() to determine the buffer size. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 22:38:30 -03:00
Grzegorz Kowal
e4ffa62714 COMPRESSION: Add function to determine the compression buffer size. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 22:32:51 -03:00
Grzegorz Kowal
e6fc8e5d24 COMPRESSION: Pass the input length to compress(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 22:19:50 -03:00
Grzegorz Kowal
20282539f9 COMPRESSION: Use ENUM to enumerate compression formats. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 09:59:20 -03:00
Grzegorz Kowal
82dfcf3c29 USER_PROBLEM: Remove unused stuff. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 17:15:02 -03:00
Grzegorz Kowal
3081ac0d5f BOUNDARIES: Fix wrong conditions in block_boundary_specific(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 17:07:31 -03:00
Grzegorz Kowal
8fb3abacbf PROBLEM, SYSTEM: Move USER_PROBLEM initialization to SYSTEM. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 16:48:54 -03:00