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132 Commits

Author SHA1 Message Date
Grzegorz Kowal
894d5d0680 IO: Add subroutine restore_datablocks_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:58:53 -03:00
Grzegorz Kowal
0d65f08499 IO: Rewrite subroutine store_datablocks_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:58:02 -03:00
Grzegorz Kowal
7dd68c6ea7 IO: Rewrite subroutine store_coordinates_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:55:59 -03:00
Grzegorz Kowal
6287c18ded IO: Rewrite subroutine store_variables_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:54:57 -03:00
Grzegorz Kowal
ad6e1592c4 IO: Add interface for restore_attribute_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:53:22 -03:00
Grzegorz Kowal
9cf04971eb IO: Add subroutine restore_attribute_string_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:51:57 -03:00
Grzegorz Kowal
583ec00232 IO: Add subroutine restore_attribute_number_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:50:45 -03:00
Grzegorz Kowal
6bb123b407 IO: Rewrite store_attribute_string_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:49:05 -03:00
Grzegorz Kowal
02538128fc IO: Rewrite store_attribute_number_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:47:50 -03:00
Grzegorz Kowal
2e1b974aed IO: Add subroutine read_dataset_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:46:02 -03:00
Grzegorz Kowal
726cd16fcb IO: Rewrite store_dataset_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 09:44:23 -03:00
Grzegorz Kowal
e2f2df6cd6 IO: Remove all HDF5 write_array subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 20:34:48 -03:00
Grzegorz Kowal
f1bcb4322a IO: Remove unused variable in write_restart_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 20:29:33 -03:00
Grzegorz Kowal
68e6e95b7b IO: Rewrite write_metablocks_h5() and rename it. 
The new name is store_metablocks_h5().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 19:38:45 -03:00
Grzegorz Kowal
9e87eb0740 IO: Rewrite write_restart_snapshot_h5(). 
Also rename it to store_restart_snapshot_h5().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 17:27:22 -03:00
Grzegorz Kowal
ab20167cb5 IO: Remove old HDF5 write_attribute subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 17:19:05 -03:00
Grzegorz Kowal
9a6d53c2fc IO: Rewrite write_datablocks_h5() and rename to store_datablocks_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 17:13:02 -03:00
Grzegorz Kowal
4fe5b5bfc3 IO: Pass data, not pointer to store_dataset_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 17:04:41 -03:00
Grzegorz Kowal
10644dc093 IO: Rewrite store_attributes_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 12:12:53 -03:00
Grzegorz Kowal
f85fb4004a IO: Add interface for store_attribute_h5. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 12:12:07 -03:00
Grzegorz Kowal
fba584904e IO: Handle string and number HDF5 attributes separately. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-21 12:00:49 -03:00
Grzegorz Kowal
c93031cdcf IO: Handle properly strings and scalars in store_attribute_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 20:30:25 -03:00
Grzegorz Kowal
20c8946912 IO: Add store_attribute_h5(). 
This is a generic subroutine to store any attribute at any location.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 12:22:14 -03:00
Grzegorz Kowal
3b96c3c63d IO: Rewrite store_attributes_h5(). 
It was renamed from write_attributes_h5().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 11:26:17 -03:00
Grzegorz Kowal
17d6e4a73f IO: Rename write_snapshot_h5() to store_snapshot_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 10:12:24 -03:00
Grzegorz Kowal
30f9a6c520 IO: Use store_dataset_h5() in store_coordinates_h5(). 
The subroutine write_coordinates_h5() was renamed to store_coordinates_h5().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 10:03:35 -03:00
Grzegorz Kowal
192ddc4d7e IO: Use store_dataset_h5() in store_variables_h5(). 
The subroutine write_variables_h5() was renamed to store_variables_h5().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 09:43:16 -03:00
Grzegorz Kowal
90052f4c62 IO: Add subroutine to store a generic dataset in a HDF5 file. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 09:31:20 -03:00
Grzegorz Kowal
de424f2d5d IO: Rewrite write_coordinates_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 00:47:09 -03:00
Grzegorz Kowal
c727702e79 IO: Polish a bit write_variables_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 00:14:15 -03:00
Grzegorz Kowal
cc6cca3cef IO: Remove option to store with or without ghost zones. 
Snapshots are always stored with the ghost zones.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 00:12:10 -03:00
Grzegorz Kowal
69d5ac374b IO: Rewrite write_variables_h5(). 
Store whole blocks with ghost zones.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-20 00:10:19 -03:00
Grzegorz Kowal
0cde0a8d0d IO: Remove selection of the HDF5 snapshot type. 
Only snapshots storing primitive variables are supported.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-19 23:49:12 -03:00
Grzegorz Kowal
ff74b6828a IO: Remove write_conservative_variables_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-19 23:46:03 -03:00
Grzegorz Kowal
3987c45cfe IO: Rewrite write_snapshot_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-19 23:44:04 -03:00
Grzegorz Kowal
ff4f600922 IO: Slightly rewrite the public subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-19 21:26:56 -03:00
Grzegorz Kowal
3962bb2550 IO: Use print_message() in Amun-XML subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-19 20:07:28 -03:00
Grzegorz Kowal
bd5fde97f6 HASH, IO: Properly handle the digest type. 
Allow to select the digest type by the user. For the restart files we
always use the XXH64 hash.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-19 10:07:46 -03:00
Grzegorz Kowal
8eca13d556 IO: Do not set hash type if libxxhash is not used. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-18 23:20:50 -03:00
Grzegorz Kowal
a10d7d5499 CMAKE, HASH, IO: Detect and use the system libxxhash. 
If it is available, allow to choose between XXH64 (default) and XXH3
hash algorithms provided by the library XXHASH.

If it is not available, the internal slower implementation is used.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-18 23:15:51 -03:00
Grzegorz Kowal
f659000e8c PROFILE: Remove all custom profiling. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-16 15:22:15 -03:00
Grzegorz Kowal
ea010e0ff3 IO: Pass the problem's name as argument to snapshots. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-16 12:31:10 -03:00
Grzegorz Kowal
8297482639 IO: Store 'cmax' so we can properly resume jobs. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-10-23 11:23:58 -03:00
Grzegorz Kowal
27041d0feb DRIVER, EVOLUTION, IO: Rewrite handling precise snapshots. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-10-19 14:03:57 -03:00
Grzegorz Kowal
55b0d24b77 EVOLUTION: Rework slightly the way new time step is calculated. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-10-19 13:28:25 -03:00
Grzegorz Kowal
6dbda8bf14 IO: Use the same array to store each variable in write_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-20 17:56:51 -03:00
Grzegorz Kowal
6532c998fb IO: Implement restoring from version 2.0 of AmunXML restart snapshots. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-15 12:57:34 -03:00
Grzegorz Kowal
3b44444211 IO: Implement storing the version 2.0 of AmunXML restart snapshots. 
This version avoids allocation of big arrays to store the array fields
of data blocks. Fields with primitive and conservative variables are
stores separately for each block.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-15 12:06:48 -03:00
Grzegorz Kowal
9b5e809ca9 IO: Make sure only available block's %uu fields are re/stored. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 14:31:15 -03:00
Grzegorz Kowal
3d45fcca34 BLOCKS: Use %uu instead of %u0, %u1, and %u2. 
Block field %uu addopts its size according to the used integration
methods. Use it for all operation insteado of fields %u0, %u1, and %u2.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 14:05:00 -03:00