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Merge branch 'develop' into feature/rreichle/surfturb_numerical_derivatives
2 parents 6aebb70 + 8185f71 commit f330d24

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‎.circleci/config.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ workflows:
4545
- docker-hub-creds
4646
matrix:
4747
parameters:
48-
compiler: [gfortran, ifort]
48+
compiler: [ifort]
4949
requires:
5050
- build-GEOSgcm-on-<< matrix.compiler >>
5151
repo: GEOSgcm

‎.github/workflows/spack-ci.yml‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -56,9 +56,11 @@ jobs:
5656
mepo develop GEOSgcm_GridComp GEOSgcm_App GMAO_Shared GEOS_Util
5757
mepo status
5858
59+
- name: Debug PR branch
60+
run: echo "PR is coming from ${{ github.event.pull_request.head.ref }}"
61+
5962
- name: Update other branches
60-
if:
61-
"!contains('refs/heads/main,refs/heads/develop', github.ref)"
63+
if: ${{ github.event.pull_request.head.ref != 'main' && github.event.pull_request.head.ref != 'develop' }}
6264
run: |
6365
mepo checkout-if-exists ${GITHUB_HEAD_REF}
6466
mepo status

‎.github/workflows/workflow.yml‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ jobs:
2121
if: "!contains(github.event.pull_request.labels.*.name, '0 diff trivial')"
2222
runs-on: ubuntu-24.04
2323
container:
24-
image: gmao/ubuntu24-geos-env:v7.32.0-intelmpi_2021.13-ifort_2021.13
24+
image: gmao/ubuntu24-geos-env:v7.33.0-intelmpi_2021.13-ifort_2021.13
2525
# Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
2626
# It seems like we might not need secrets on GitHub Actions which is good for forked
2727
# pull requests
@@ -66,9 +66,11 @@ jobs:
6666
mepo develop GEOSgcm_GridComp GEOSgcm_App GMAO_Shared GEOS_Util
6767
mepo status
6868
69+
- name: Debug PR branch
70+
run: echo "PR is coming from ${{ github.event.pull_request.head.ref }}"
71+
6972
- name: Update other branches
70-
if:
71-
"!contains('refs/heads/main,refs/heads/develop', github.ref)"
73+
if: ${{ github.event.pull_request.head.ref != 'main' && github.event.pull_request.head.ref != 'develop' }}
7274
run: |
7375
mepo checkout-if-exists ${GITHUB_HEAD_REF}
7476
mepo status

‎GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSsurface_GridComp/Utils/Raster/makebcs/CMakeLists.txt‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -55,6 +55,7 @@ file(GLOB MAKE_BCS_PYTHON CONFIGURE_DEPENDS "./make_bcs*.py")
5555
list(FILTER MAKE_BCS_PYTHON EXCLUDE REGEX "make_bcs_shared.py")
5656
install(PROGRAMS ${MAKE_BCS_PYTHON} DESTINATION bin)
5757
install(PROGRAMS TileFile_ASCII_to_nc4.py DESTINATION bin)
58+
install(PROGRAMS ExtractBCsFromOrig.py DESTINATION bin)
5859

5960
set(file ./make_bcs_shared.py)
6061
configure_file(${file} ${file} @ONLY)

‎GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSsurface_GridComp/Utils/Raster/makebcs/ExtractBCsFromOrig.py‎

Lines changed: 163 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,163 @@
1+
#!/usr/bin/env python3
2+
3+
from netCDF4 import Dataset
4+
from scipy.io import FortranFile
5+
import numpy as np
6+
import sys
7+
import os
8+
import glob
9+
10+
def get_i_j_pf(til_file):
11+
"""
12+
This is just for cubed-sphere text tile.
13+
"""
14+
ii = []
15+
jj = []
16+
pfaf = []
17+
with open(til_file, 'r') as f:
18+
for line in f:
19+
data = line.split()
20+
if data[0] == '100' :
21+
ii.append(int(data[4]))
22+
jj.append(int(data[5]))
23+
pfaf.append(int(data[8]))
24+
return ii, jj, pfaf
25+
26+
def create_reduced_nc4(input_file, output_file, indices):
27+
"""
28+
Create a new nc4 file with with indices of for the input file.
29+
30+
Parameters:
31+
input_file (str): Path to the input nc4 file
32+
output_file (str): Path to the output nc4 file
33+
indices(int array):
34+
"""
35+
36+
# Open the input file in read mode
37+
try:
38+
src = Dataset(input_file, 'r')
39+
print(f"Successfully opened input file: {input_file}")
40+
except Exception as e:
41+
print(f"Error opening input file: {e}")
42+
return
43+
44+
# Create the output file in write mode
45+
try:
46+
dst = Dataset(output_file, 'w', format='NETCDF4')
47+
print(f"Creating output file: {output_file}")
48+
except Exception as e:
49+
print(f"Error creating output file: {e}")
50+
src.close()
51+
return
52+
53+
# Copy global attributes
54+
dst.setncatts(src.__dict__)
55+
56+
# Copy dimensions with reduced size for unlimited/time dimensions
57+
for name, dimension in src.dimensions.items():
58+
if name == 'tile':
59+
dst.createDimension(name, len(indices))
60+
else:
61+
dst.createDimension(name, len(dimension))
62+
# Copy variables with reduced data
63+
for name, variable in src.variables.items():
64+
# Create variable with same attributes but possibly reduced dimensions
65+
dims = variable.dimensions
66+
new_dims = []
67+
for dim in dims:
68+
new_dims.append(dim)
69+
# Create the variable in the output file
70+
dst_var = dst.createVariable(
71+
name,
72+
variable.datatype,
73+
new_dims,
74+
)
75+
76+
# Copy variable attributes
77+
dst[name].setncatts(variable.__dict__)
78+
79+
# Get the data and reduce it
80+
if len(dims) == 2 :
81+
dst_var[:,:] = variable[:,indices]
82+
if len(dims) == 1 :
83+
dst_var[:] = variable[indices]
84+
85+
86+
# Close both files
87+
src.close()
88+
dst.close()
89+
print(f"Successfully created reduced file: {output_file}")
90+
91+
def create_reduced_bin(input_file, output_file, indices):
92+
"""
93+
Create a new ibinary file with with indices of for the input file.
94+
95+
Parameters:
96+
input_file (str): Path to the input binary file
97+
output_file (str): Path to the output binaryfile
98+
indices(int array):
99+
"""
100+
nland = len(indices)
101+
fout = FortranFile(output_file, 'w')
102+
with FortranFile(input_file, 'r') as f:
103+
while True :
104+
try:
105+
a = f.read_reals(dtype=np.float32)
106+
b = f.read_reals(dtype=np.float32)
107+
a[12] = np.float32(nland)
108+
fout.write_record(a)
109+
b = b[indices]
110+
fout.write_record(b)
111+
except :
112+
break
113+
fout.close()
114+
print(f"Successfully created reduced file: {output_file}")
115+
116+
# Example usage
117+
if __name__ == "__main__":
118+
# Replace these with your actual file paths
119+
# input_nc4 = "/discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles/v13/land/CF1440x6C/clsm/catchcn_params.nc4"
120+
# output_nc4 = "output_file_reduced.nc"
121+
bcs_dir = sys.argv[1]
122+
bcs_ver = sys.argv[2]
123+
air_res = sys.argv[3]
124+
ocn_res = sys.argv[4]
125+
agname = air_res + '_' + air_res
126+
orig_tile = bcs_dir + '/' + bcs_ver + '/geometry/' + agname + '/' + agname +'-Pfafstetter.til'
127+
if not os.path.exists(orig_tile) :
128+
print( "The original tile file must exist " + orig_tile)
129+
exit()
130+
131+
mom_tile = 'til/' + air_res + '_' + ocn_res + '-Pfafstetter.til'
132+
if not os.path.exists(mom_tile) :
133+
print( "The MOM tile file must exist " + mom_tile)
134+
exit()
135+
136+
ii1, jj1, pf1 = get_i_j_pf(orig_tile)
137+
ii2, jj2, pf2 = get_i_j_pf(mom_tile)
138+
i1 = 0
139+
indices =[]
140+
for i2 in range(len(ii2)):
141+
match = ii1[i1] == ii2[i2] and jj1[i1] == jj2[i2] and pf1[i1] == pf2[i2]
142+
while not match :
143+
i1 = i1 +1
144+
match = ii1[i1] == ii2[i2] and jj1[i1] == jj2[i2] and pf1[i1] == pf2[i2]
145+
indices.append(i1)
146+
i1 = i1 + 1
147+
148+
catch_params_file = bcs_dir + '/' + bcs_ver + '/land/' + air_res + '/clsm/catch_params.nc4'
149+
catchcn_params_file = bcs_dir + '/' + bcs_ver + '/land/' + air_res + '/clsm/catchcn_params.nc4'
150+
mom_catch_params_file = 'clsm/catch_params.nc4'
151+
mom_catchcn_params_file = 'clsm/catchcn_params.nc4'
152+
153+
create_reduced_nc4(catch_params_file, mom_catch_params_file, indices)
154+
create_reduced_nc4(catchcn_params_file, mom_catchcn_params_file, indices)
155+
156+
files = glob.glob(bcs_dir + '/' + bcs_ver + '/land/' + air_res + '/*.da*')
157+
for file in files:
158+
fname = os.path.basename(file)
159+
if 'vegdyn' in fname:
160+
create_reduced_nc4( file,'clsm/vegdyn.data', indices)
161+
else:
162+
shortname = 'clsm/' + fname.split('_')[0] + '.dat'
163+
create_reduced_bin(file, shortname, indices)

‎GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSsurface_GridComp/Utils/Raster/makebcs/TileFile_ASCII_to_nc4.F90‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
program TileFile_ASCII_to_nc4
99
use, intrinsic :: iso_fortran_env, only: REAL64
1010
use MAPL
11-
use LogRectRasterizeMod, only: WriteTilingNC4, MAPL_UNDEF_R8
11+
use LogRectRasterizeMod, only: MAPL_UNDEF_R8
1212
use EASE_conv, only: ease_extent
1313

1414
implicit none
@@ -29,7 +29,7 @@ program TileFile_ASCII_to_nc4
2929
real :: cell_area
3030

3131
integer :: n_tile, n_grid, n_lon1, n_lat1, n_cat, tmp_in1, tmp_in2
32-
integer :: n_lon2, n_lat2, nx, ny, num, ll, maxcat
32+
integer :: n_lon2, n_lat2, nx, ny, num, ll, maxcat
3333
logical :: file_exists
3434

3535
! ----------------------------------------------------------------------
@@ -47,7 +47,7 @@ program TileFile_ASCII_to_nc4
4747

4848
open (newunit=unit, file=trim(tile_file), form='formatted', action='read')
4949

50-
read (unit,*) tmpline ! header line 1: N_tile [maxcat] nx ny (see below)
50+
read (unit,"(A)") tmpline ! header line 1: N_tile [maxcat] nx ny (see below)
5151
read (unit,*) N_grid ! header line 2: N_grid [=1 for EASE, =2 otherwise]
5252
read (unit,*) gName1 ! header line 3: name of atm grid
5353
read (unit,*) n_lon1 ! header line 4: N_lon of atm grid
@@ -76,11 +76,11 @@ program TileFile_ASCII_to_nc4
7676
! in some legacy bcs, dummy ocean grid info is included in header (despite N_grid=1);
7777
! read next line and decide if it is dummy header or info for first tile
7878

79-
read (unit,*) tmpline
79+
read (unit,"(A)") tmpline
8080
if (index(tmpline,'OCEAN')/=0) then
8181
read (unit,*)
8282
read (unit,*)
83-
read (unit,*) tmpline
83+
read (unit,"(A)") tmpline
8484
endif
8585

8686
else
@@ -90,7 +90,7 @@ program TileFile_ASCII_to_nc4
9090
read (unit,*) gName2
9191
read (unit,*) n_lon2
9292
read (unit,*) n_lat2
93-
read (unit,*) tmpline ! read info for first tile (to accommodate legacy EASE grid issues above)
93+
read (unit,"(A)") tmpline ! read info for first tile (to accommodate legacy EASE grid issues above)
9494

9595
endif
9696

@@ -181,9 +181,9 @@ program TileFile_ASCII_to_nc4
181181
! write nc4 file
182182

183183
if (N_grid == 1) then
184-
call WriteTilingNC4(filenameNc4, [gName1 ], [n_lon1 ], [n_lat1 ], nx, ny, iTable, rTable, N_PfafCat=maxcat)
184+
call MAPL_WriteTilingNC4(filenameNc4, [gName1 ], [n_lon1 ], [n_lat1 ], nx, ny, iTable, rTable, N_PfafCat=maxcat)
185185
else
186-
call WriteTilingNC4(filenameNc4, [gName1, gName2], [n_lon1, n_lon2], [n_lat1, n_lat2], nx, ny, iTable, rTable, N_PfafCat=maxcat)
186+
call MAPL_WriteTilingNC4(filenameNc4, [gName1, gName2], [n_lon1, n_lon2], [n_lat1, n_lat2], nx, ny, iTable, rTable, N_PfafCat=maxcat)
187187
endif
188188

189189
contains

‎GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSsurface_GridComp/Utils/Raster/makebcs/make_bcs_cube.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -41,9 +41,12 @@
4141
bin/CombineRasters.x -f 0 -t {NT} {OCEAN_VERSION}{DATENAME}{IMO}x{POLENAME}{JMO} Pfafstetter >/dev/null
4242
bin/CombineRasters.x -t {NT} CF{NC}x6C{SGNAME} {OCEAN_VERSION}{DATENAME}{IMO}x{POLENAME}{JMO}-Pfafstetter
4343
bin/mk_runofftbl.x -g CF{NC}x6C{SGNAME}_{OCEAN_VERSION}{DATENAME}{IMO}x{POLENAME}{JMO}-Pfafstetter -v {lbcsv}
44-
setenv OMP_NUM_THREADS {NCPUS}
45-
if ({SKIPLAND} != True) bin/mkCatchParam.x -x {NX} -y {NY} -g CF{NC}x6C{SGNAME}_{OCEAN_VERSION}{DATENAME}{IMO}x{POLENAME}{JMO}-Pfafstetter -v {lbcsv}
46-
setenv OMP_NUM_THREADS 1
44+
45+
if ({SKIPLAND} != True) then
46+
bin/mkCatchParam.x -x {NX} -y {NY} -g CF{NC}x6C{SGNAME}_{OCEAN_VERSION}{DATENAME}{IMO}x{POLENAME}{JMO}-Pfafstetter -v {lbcsv} -p no
47+
bin/ExtractBCsFromOrig.py {BCS_DIR} {lbcsv} CF{NC}x6C{SGNAME} {OCEAN_VERSION}{DATENAME}{IMO}x{POLENAME}{JMO}
48+
endif
49+
4750
chmod 755 bin/create_README.csh
4851
bin/create_README.csh
4952
endif
@@ -144,6 +147,7 @@ def make_bcs_cube(config):
144147
SCRATCH_DIR = scratch_dir, \
145148
bin_dir = bin_dir, \
146149
MAKE_BCS_INPUT_DIR = config['inputdir'], \
150+
BCS_DIR = config['bcs_dir'], \
147151
DATENAME = DATENAME, \
148152
POLENAME = POLENAME, \
149153
OCEAN_VERSION = OCEAN_VERSION, \

‎GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSsurface_GridComp/Utils/Raster/makebcs/make_bcs_questionary.py‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -43,6 +43,8 @@ def get_configs_from_answers(answers):
4343
else:
4444
make_bcs_input_dir = '/nobackup/gmao_SIteam/ModelData/make_bcs_inputs/'
4545

46+
bcs_dir ='/discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles/'
47+
4648
user = get_user()
4749
expdir = answers["out_path"]
4850
now = datetime.now()
@@ -148,6 +150,7 @@ def get_configs_from_answers(answers):
148150
config ['expdir'] = expdir
149151
config ['outdir'] = outdir
150152
config ['inputdir'] = make_bcs_input_dir
153+
config ['bcs_dir'] = bcs_dir
151154
config ['NCPUS'] = 16
152155

153156
for x in answers.get('Stretched_CS',[]):

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