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MITgcm/N-BLING with Compressed Staggered Grids #640

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merged 67 commits into from
Mar 12, 2024
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d67b475
Initial commit of the adaptive close_state_caching
Jun 6, 2022
874cf22
Comment out the close_state_cach = .false. in get_close_state_cached
Jun 6, 2022
0428283
Add do_output for the print statements
Jun 10, 2022
774b9cc
New I/O scheme with offline processing of large input state
Jul 8, 2022
5a8b812
Merge branch 'main' into netcdf-reduce
hkershaw-brown Aug 16, 2022
7d5867f
moved dart_nc_reduce one directory up to compile
hkershaw-brown Aug 16, 2022
d376f80
grid size is harded coded - change to small case
hkershaw-brown Aug 17, 2022
869d89d
using dart netcdf utilites and types modules
hkershaw-brown Aug 17, 2022
fbbb201
mirror of dart_nc_reduce. untested.
hkershaw-brown Aug 18, 2022
b14007d
ZC is double - check dart_nc_reduce
hkershaw-brown Aug 19, 2022
d9e2979
zc double dart_nc_expand
hkershaw-brown Aug 22, 2022
d197e63
netcdf and model_mod_check for comparision with main
hkershaw-brown Aug 22, 2022
e9273c8
Merge branch 'main' into netcdf-reduce
hkershaw-brown Aug 22, 2022
a409ff4
function for defining variables mit2dart
hkershaw-brown Aug 25, 2022
3d0c053
function for dart to mit. untested.
hkershaw-brown Aug 25, 2022
e007252
bug-fix: returns need to be inside if statement
hkershaw-brown Aug 26, 2022
fba76b4
bitwise mit_to_dart non-compressed with main, log and nolog
hkershaw-brown Aug 26, 2022
951235c
bitwise with main dart_to_mit, no compression
hkershaw-brown Aug 26, 2022
60c742c
size of compressed variables
hkershaw-brown Aug 26, 2022
8b556ba
partway through compressed write, I think separate writes for 2d vs
hkershaw-brown Aug 29, 2022
b239419
write compressed. untested. missing coord
hkershaw-brown Aug 29, 2022
1a7bf39
note on delX,Y - does delX,Y vary?
hkershaw-brown Aug 30, 2022
d4c3905
record indices for X,Y,Z
hkershaw-brown Aug 31, 2022
39568db
compressing out vals=0.0
hkershaw-brown Aug 31, 2022
329cd42
replace hardcoded 0.0_r8 with binary_fill variable
hkershaw-brown Aug 31, 2022
6fbbdf0
somthing funky with ETA
hkershaw-brown Sep 1, 2022
a7d60db
bug-fix: 2D ETA variable is th k=1 slice
hkershaw-brown Sep 1, 2022
0c2c781
revert assim_tools_mod to main
hkershaw-brown Sep 2, 2022
80e22dc
move initializing to fill outside read_compressed
hkershaw-brown Sep 2, 2022
0a30429
Merge branch 'main' into netcdf-reduce
hkershaw-brown Sep 16, 2022
3d1746f
bug fix: was not setting binary fill correctly for 2d
hkershaw-brown Sep 16, 2022
5709e68
Merge branch 'main' into netcdf-reduce
hkershaw-brown Sep 19, 2022
9951fd8
removed dart_nc_reduce/expand as these functions are now part of mit_…
hkershaw-brown Sep 19, 2022
720f763
revert mpas input.nml to main
hkershaw-brown Sep 19, 2022
b2b218d
remove whitespace only differences
hkershaw-brown Sep 19, 2022
1e7e186
get_state_meta data and get_val
hkershaw-brown Sep 19, 2022
25769ca
compressed lon,lat is r4. compressed depth r8
hkershaw-brown Sep 19, 2022
3e92f58
note on perturbing compressed vs non-compressed state
hkershaw-brown Sep 19, 2022
43e74ca
bug-fix: masked initialized to false for compresed and not compressed
hkershaw-brown Sep 23, 2022
e641695
style: switch tabs for spaces
hkershaw-brown Sep 23, 2022
32df048
2d and staggered variables are incorrect
hkershaw-brown Sep 23, 2022
12fa6c0
Merge branch 'main' into netcdf-reduce
hkershaw-brown Sep 23, 2022
8dcb481
fix: depth dimension first in compression so 2d index search is correct
hkershaw-brown Sep 30, 2022
03564a4
program to expand compressed netcdf to full X,Y,Z
hkershaw-brown Oct 3, 2022
63c19b5
recl2d and recl3d set in static_init_trans
hkershaw-brown Oct 7, 2022
d54cbfb
doc: compressed netcdf files
fnrliu Oct 7, 2022
e926fe0
Merge branch 'main' into netcdf-reduce
hkershaw-brown Oct 11, 2022
cd107d1
Option to output CHL for dart_to_mit
hkershaw-brown Oct 11, 2022
2c0b275
Merge branch 'main' into netcdf-reduce
hkershaw-brown Oct 21, 2022
5fe6781
Merge branch 'main' into netcdf-reduce
hkershaw-brown Nov 3, 2022
630b5a1
Merge branch 'main' into netcdf-reduce
hkershaw-brown Nov 9, 2022
d048a05
one place to set recl3d recl2d
hkershaw-brown Feb 9, 2023
134570b
Merge branch 'main' into netcdf-reduce
hkershaw-brown Feb 9, 2023
f0da199
Merge branch 'main' into netcdf-reduce
hkershaw-brown May 8, 2023
de015c6
Merge branch 'main' into netcdf-reduce
hkershaw-brown May 10, 2023
a2c0d26
Merge branch 'main' into netcdf-reduce
hkershaw-brown Jun 22, 2023
41b35e3
Merge branch 'main' into netcdf-reduce
hkershaw-brown Jun 27, 2023
92142d8
Merge branch 'main' into netcdf-reduce
hkershaw-brown Nov 7, 2023
e0dd62b
Merge branch 'main' into netcdf-reduce
hkershaw-brown Nov 9, 2023
58f3c97
Compression that supports staggered grids
mgharamti Jan 26, 2024
e9001e2
Changes after cycling DA testing
mgharamti Feb 20, 2024
0febdfe
Merge branch 'main' into MITgcm_comp
hkershaw-brown Feb 29, 2024
ecfdb88
remove expand netcdf program
hkershaw-brown Mar 11, 2024
ce1fcb6
Merge branch 'main' into MITgcm_comp
hkershaw-brown Mar 11, 2024
058cdac
Merge branch 'main' into MITgcm_comp
hkershaw-brown Mar 12, 2024
1fe14ea
revert netcdf utilties to main, since expand_netcdf.f90 no longer par…
hkershaw-brown Mar 12, 2024
1044da3
bump conf.py and CHANGELOG for release
hkershaw-brown Mar 12, 2024
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style: switch tabs for spaces
note the get_compressed_dart_vector index needs checking for 2d variables.
Is the ZC(kloc)=1?
hkershaw-brown committed Sep 23, 2022

Verified

This commit was signed with the committer’s verified signature.
mike182uk Michael Barrett
commit e64169565d82c503e39b03ed71b730c73ca88848
36 changes: 18 additions & 18 deletions models/MITgcm_ocean/model_mod.f90
Original file line number Diff line number Diff line change
@@ -1009,24 +1009,24 @@ function get_compressed_dart_vector_index(iloc, jloc, kloc, dom_id, var_id)
! Find the index in the compressed state
! HK you could read in {X,Y,Z}comp_ind if you did not want to do this search
do i=1, comp3d
lon_found = .false.
lat_found = .false.
depth_found = .false.
! If we find the value
if ( XC_sq(i) == lon ) then
lon_found = .true.
endif
if ( YC_sq(i) == lat ) then
lat_found = .true.
endif
if ( ZC_sq(i) == depth ) then
depth_found = .true.
endif
if (lon_found .and. lat_found .and. depth_found )then
get_compressed_dart_vector_index = offset + i - 1
exit
endif
lon_found = .false.
lat_found = .false.
depth_found = .false.

if ( XC_sq(i) == lon ) then
lon_found = .true.
endif
if ( YC_sq(i) == lat ) then
lat_found = .true.
endif
if ( ZC_sq(i) == depth ) then
depth_found = .true.
endif
if (lon_found .and. lat_found .and. depth_found )then
get_compressed_dart_vector_index = offset + i - 1
exit
endif
enddo

end function get_compressed_dart_vector_index