gkowal/amun-code
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
2,780 Commits 5 Branches 0 Tags
Commit Graph

2780 Commits

This Branch
This Branch
All Branches
Author SHA1 Message Date
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
Grzegorz Kowal
fd40fffc64 BOUNDARIES: Add interface to custom boundaries. 
Also return the call status from block_boundary_specific().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 16:42:53 -03:00
Grzegorz Kowal
4ceb008987 SHAPES: Do not pull update_user_shapes() from module USER_PROBLEM. 
The pointer to update_shapes can be associated in
initialize_user_problem().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 13:47:05 -03:00
Grzegorz Kowal
25ad944f44 SOURCES: Add procedure interface for extra source terms. 
A user defined source terms can be pointer to the procedure pointer
'update_extra_sources'.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 13:37:25 -03:00