gkowal/amun-code
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
2,655 Commits 5 Branches 0 Tags
Commit Graph

808 Commits

Author SHA1 Message Date
Grzegorz Kowal
bb72ee3a5b MESH: Parallelize check_block_refinement() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-10 10:22:09 -03:00
Grzegorz Kowal
e936ade934 BOUNDARIES: Parallelize update_ghost_cells() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-10 10:03:42 -03:00
Grzegorz Kowal
c54539a379 EVOLUTION: Parallelize initialize_time_step() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-10 09:44:02 -03:00
Grzegorz Kowal
535b5274c9 MESH: Remove unused variables. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 22:08:31 -03:00
Grzegorz Kowal
21cbecef26 EVOLUTION: Remove unused variables. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 22:07:36 -03:00
Grzegorz Kowal
46696e4790 EVOLUTION: Rename local variables c to something else. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 22:00:09 -03:00
Grzegorz Kowal
93068909d9 EVOLUTION: Add 4th order 5-step SSPRK(5,4) method. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 21:45:14 -03:00
Grzegorz Kowal
416c35ed9a EVOLUTION: Parallelize evolve_ssprk410() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 16:23:53 -03:00
Grzegorz Kowal
aa8f9b6fe9 EVOLUTION: Parallelize evolve_ssprk35() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 16:03:22 -03:00
Grzegorz Kowal
df5791f0b5 EVOLUTION: Parallelize evolve_ssprk34() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 13:36:03 -03:00
Grzegorz Kowal
b4622f3c48 EVOLUTION: Parallelize evolve_ssprk3() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 12:58:55 -03:00
Grzegorz Kowal
7b13e8fdf1 EVOLUTION: Parallelize evolve_ssprk2() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 12:38:40 -03:00
Grzegorz Kowal
a5202090a4 EVOLUTION: Parallelize evolve_euler() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-09 12:23:53 -03:00
Grzegorz Kowal
a61c4fa52a EVOLUTION: Parallelize evolve_ssprk21m() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 22:12:22 -03:00
Grzegorz Kowal
fce5e43b2a EVOLUTION: Parallelize new_time_step() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 21:54:40 -03:00
Grzegorz Kowal
c680b7772a EVOLUTION: Parallelize evolve_ssprk32m() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 21:40:59 -03:00
Grzegorz Kowal
ee89bc42e6 EVOLUTION: Parallelize evolve_ssp324() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 18:27:43 -03:00
Grzegorz Kowal
537f8693bc EVOLUTION: Parallelize update_errors_max() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 17:36:46 -03:00
Grzegorz Kowal
806d74d4cf EVOLUTION: Parallelize update_errors_l2() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 17:18:55 -03:00
Grzegorz Kowal
beca028b2f EVOLUTION: Parallelize evolve_3sstarplus() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 16:58:12 -03:00
Grzegorz Kowal
8568dbb709 EVOLUTION: Parallelize update_variables() using OpenMP. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-08 16:40:10 -03:00
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
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
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