36996e6f76
IO: Add compressed field to the XML file attribute.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 16:22:37 -03:00
1d154ab492
IO: Support compression in write_binary_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 16:03:46 -03:00
08b7e81f6a
COMPRESSION, IO: Initialize compression in initialize_io().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 15:34:20 -03:00
d3e7ab7c5d
IO: Fix job restart after with new XML structure for binary files.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 11:51:23 -03:00
42951cd48c
IO: Use new XML structure for binary files in write_restart_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 10:55:06 -03:00
7867d9d062
IO: Use new XML structure for binary files in write_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 10:32:17 -03:00
220c6028b1
IO: Add subroutine to write binary file attribute.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 10:23:36 -03:00
97887b2ad6
IO: Return the number of bytes written to file from write_binary_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 10:09:59 -03:00
35f3e3f2eb
IO: Add binary file extension before write_binary_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-10 10:04:05 -03:00
c7daa08545
IO: Slightly reorganize write_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-08 23:19:09 -03:00
d368e7f863
IO: Slightly reorganize write_restart_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-08 23:15:56 -03:00
c51ce6cd5a
IO: Use write_binary_xml() in write_restart_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-08 22:58:11 -03:00
e623a3a001
IO: Use write_binary_xml() in write_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-08 22:45:18 -03:00
34d5f75315
IO: Create a subroutine to store binary data and return its digest.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-08 22:36:01 -03:00
ebccb96d0f
FORCING, IO: Make conversion to complex numbers double precision.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-08-06 10:30:43 -03:00
85496f7a78
IO: Remove unused procedures and variables.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-07-31 12:52:33 -03:00
7fe1711454
BLOCKS: Remove unused subroutines, variables, and arguments.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-07-31 10:48:14 -03:00
e1087c6fb7
IO: Intel Fortran need directory=, not file= in INQUIRE.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-07-30 17:12:20 -03:00
cf95264a88
IO: Intel compiler does not accept sizeof() as argument.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-07-30 12:41:31 -03:00
ebc24c3f03
IO: Avoid using the same names for variables and modules.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-07-30 12:02:13 -03:00
d41ec74665
IO: Use generic xxh64() to calculate all hashes.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-13 17:31:59 -03:00
97e572ec94
IO: Make sure bounds have the same domensions while stored and read.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-13 06:49:53 -03:00
ca3580e2ec
IO: Fix wrong warning while reading from an XML+binary restart snapshot.
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If the forcing is off, the number of forcing modes is zero, but it is
not the same as a wrong number of forcing modes stored in the restart
file.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-13 06:47:38 -03:00
7c1d028805
IO: Store hashes in write_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-11 18:42:05 -03:00
c2294cbe5e
IO: Store hashes with leading zeros in write_restart_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-11 18:29:18 -03:00
5a9ea1dc92
IO: Verify hashes while reading XML+binary restart snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-11 18:19:33 -03:00
52d899aa72
IO: Store hashes of binary files in XML+binary restar snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-11 15:19:25 -03:00
5c554a2b2d
IO: Do not store driving coefficients if nmodes == 0.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-01 21:06:34 -03:00
add0759308
IO: Handle properly seeds and driving coeffs in HDF5 restart files.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-01 20:58:27 -03:00
13858e6456
IO: Implement XML+binary format of the regular snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-05-01 11:40:37 -03:00
4550af59d4
IO: Fix mismatch in the XML restart snapshot.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-04-30 14:31:01 -03:00
59bc5482ea
IO: Fix calling read_snapshot_parameter_h5().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-04-30 07:57:34 -03:00
07e74abfa9
IO: Implement XML+binary format of the restart snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-04-29 17:38:41 -03:00
408f42151d
IO, DRIVER: Store x/y/zblocks separately.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-04-28 14:40:04 -03:00
24d33316ae
RANDOM: Change Marsaglia's xorshift to Vigna's xoshiro256+ generator.
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Completely rewrite the random generator module. The new method is
true 64-bit floating point generator in contrast to 32-bit Marsaglia's
methods. Add recommended seeds' initialization and jump for parallel
computations. Make function names more meaningful and add new functions
in IO module to store the seeds properly.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-04-25 18:37:58 -03:00
ad0303d3ba
Update copyright.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-03-02 13:18:53 -03:00
76d7cf8826
IO, DRIVER, PYTHON: Fix domain block dimensions with job restart.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-21 15:58:38 -03:00
d205696410
BLOCKS: Add status argument to append/remove_datablock().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-11 12:42:25 -02:00
9e9c903cc1
BLOCKS: Add status argument to append/remove_metablock().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-11 12:34:20 -02:00
601adc8037
IO, DRIVER: Allow for restart with different number of ghost zones.
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Now we can restart from restart snapshots with different number of ghost
zones. Also, remove the old restart snapshot format support from
read_datablocks_h5().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-11 11:02:36 -02:00
6d421e6efb
IO: Update the initialization/finalization status flag.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-11 10:01:35 -02:00
ec9a5ee2bd
IO: Use nb, ne instead of ib, ie, jb, je, kb, ke.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-05 13:02:27 -02:00
af62878ba9
IO: Use bcells instead of im, jm, km.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-05 11:02:35 -02:00
af2c7213f3
COORDINATES: Use ncells instead of in, jn, and kn.
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Also rename ng to nghosts.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-04 14:43:10 -02:00
43b3581a9e
COORDINATES: Replace ir, jr, kr with domain_base_dims(:).
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-02-03 22:31:05 -02:00
67a842f24c
IO: Use helper subroutines in print_io().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-30 22:48:30 -02:00
e7d5d00da8
DRIVER, IO: Move precise_snapshot variable to IO module.
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Also improve a bit print_io().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-30 12:06:26 -02:00
7a2d694629
DRIVER, IO: Initialize I/O after reading parameters.
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Use it to handle parameters from restart snapshots. Also separate
printing I/O parameters from I/O module initialization.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 15:07:50 -02:00
2a6062cbd5
DRIVER, COORDINATES, IO: Pass more fixed parameters to initialize_coordinates().
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Parameters such block dimensions, the base level dimensions, or the
domain extrema cannot be modified when the job is restarted, so read
them from the restart snapshots.
Also add new subroutine to IO read integer vector attribute from the
HDF5 snapshots.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:38:16 -02:00
4aa92643ab
DRIVER, PROBLEMS, IO: Initiate problems earlier.
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Also store the problem name in the restart snapshot.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 09:59:09 -02:00
