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Merged
sanAkel merged 8 commits into from
Jan 13, 2026
Merged

Ncoda ufs cycle #97

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746ba78
Address issue #93
Dec 11, 2025
51f432c
issue 93, rename 3DVAR job
zgarraffo Dec 18, 2025
24ce444
Address issue #93 extra changes to script for 3Dvar
zgarraffo Dec 29, 2025
810fc9e
issue 93, don't link hycom grid and depth files
zgarraffo Jan 3, 2026
b75dc8b
changes ncodaz_inc2mom6nc_glb_lyr.f, style only, no changes in results
zgarraffo Jan 12, 2026
ada29da
mom6 incremental update input
zgarraffo Jan 12, 2026
5f76b87
issue 98 update exrtofs_glo_ncoda_inc.sh for mom
zgarraffo Jan 12, 2026
dedf37f
issue 98 update authorship
zgarraffo Jan 12, 2026
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0 jobs/JRTOFS_GLO_NCODA_HYCOM_VAR → jobs/JRTOFS_GLO_NCODA_3DVAR
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16 changes: 5 additions & 11 deletions parm/rtofs_glo.hycom.oanl.in
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,9 @@
bias_lmt = 3., 8.,
bias_mld = .true.,
bias_opt = 'tsuv',
bias_wt = 1.,
clm_wt = 0.5, 0.5, 1.0, 0.0
cluster(2) = 2.,
cluster(3) = 2.,
cluster(5) = 2.,
cluster(6) = 2.,
conflict(1) = .false.,
bias_wt = 0.5,
clm_wt = 0.5, 0.5, 1.2, 0.1,
cluster = 1.5, 1.5, 1.5, 1.5, 1.5, 1.5,
corr_mdl(2) = 1,
debug(1) = .true.,
debug(2) = .true.,
Expand All @@ -28,17 +24,14 @@
fcst(3) = .true.,
fcst(4) = .true.,
fcst(6) = .true.,
fcst_tau = 192,
fgat = 1, 1, 1, 1, 1, 24,
fgat_rec = 8, 16, 17, 13, 14, 1,
global = .true.,
hafs = .false.,
himem = .true.,
ice_asm = .true.,
ice_rec = 8, 15, 16, 1,
lndz = 1.99,
lvl_nmo = 2000.,
mask_opt = '3D',
mld_rec = 425,
mld_src = 'modl',
mx_asm_lvl = 2500., 2500., 2500., 2500., 2500.,
n_pass = 2,
Expand All @@ -48,6 +41,7 @@
over(3) = 1.,
over(5) = 1.,
over(6) = 1.,
priors = 'instant',
prf_corr = 0.8,
prf_hrs = 120,
prf_slct(1) = 3.,
Expand Down
57 changes: 57 additions & 0 deletions parm/rtofs_glo_ncoda_inc2mom6nc_lyr.input
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Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
MOM.res.nc
MOM.res_1.nc
MOM.res_3.nc
MOM.res_4.nc
&TShincname
&UVincname
&IDM 'idm ' = longitudinal array size
&JDM 'jdm ' = latitudinal array size
&KDM 'kk ' = number of layers restart
&KDM 'kncoda' = number of NCODA levels equal to kk for layer increments
0.50 'zl ' = nominal depth of layer 1 from MOM archive
1.90 'zl ' = nominal depth of layer 2
4.42 'zl ' = nominal depth of layer 3
8.38 'zl ' = nominal depth of layer 4
13.185 'zl ' = nominal depth of layer 5
18.555 'zl ' = nominal depth of layer 6
24.895 'zl ' = nominal depth of layer 7
32.33 'zl ' = nominal depth of layer 8
40.33 'zl ' = nominal depth of layer 9
48.33 'zl ' = nominal depth of layer 10
56.33 'zl ' = nominal depth of layer 11
64.33 'zl ' = nominal depth of layer 12
72.33 'zl ' = nominal depth of layer 13
80.33 'zl ' = nominal depth of layer 14
88.33 'zl ' = nominal depth of layer 15
96.33 'zl ' = nominal depth of layer 16
104.33 'zl ' = nominal depth of layer 17
112.33 'zl ' = nominal depth of layer 18
120.33 'zl ' = nominal depth of layer 19
128.33 'zl ' = nominal depth of layer 20
136.33 'zl ' = nominal depth of layer 21
144.33 'zl ' = nominal depth of layer 22
152.33 'zl ' = nominal depth of layer 23
161.33 'zl ' = nominal depth of layer 24
174.53 'zl ' = nominal depth of layer 25
200.69 'zl ' = nominal depth of layer 26
239.84 'zl ' = nominal depth of layer 27
286.04 'zl ' = nominal depth of layer 28
340.56 'zl ' = nominal depth of layer 29
404.89 'zl ' = nominal depth of layer 30
480.8 'zl ' = nominal depth of layer 31
570.375 'zl ' = nominal depth of layer 32
676.075 'zl ' = nominal depth of layer 33
800.8 'zl ' = nominal depth of layer 34
947.975 'zl ' = nominal depth of layer 35
1121.645 'zl ' = nominal depth of layer 36
1326.57 'zl ' = nominal depth of layer 37
1568.38 'zl ' = nominal depth of layer 38
1899.27 'zl ' = nominal depth of layer 39
2399.27 'zl ' = nominal depth of layer 40
5449.635 'zl ' = nominal depth of layer 41
&seatmpinc
&salintinc
&uvelinc
&vvelinc
NONE
&lyrthkname
38 changes: 17 additions & 21 deletions scripts/exrtofs_glo_ncoda_hycom_var.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -57,16 +57,18 @@ fi
ln -sf $COMIN/ncoda/ocnqc $DATA

# 1.b link in topo files
ln -f -s ${FIXrtofs}/${RUN}_${modID}.${inputgrid}.regional.grid.a ${DATA}/regional.grid.a
ln -f -s ${FIXrtofs}/${RUN}_${modID}.${inputgrid}.regional.grid.b ${DATA}/regional.grid.b
ln -f -s ${FIXrtofs}/${RUN}_${modID}.${inputgrid}.regional.depth.a ${DATA}/regional.depth.a
ln -f -s ${FIXrtofs}/${RUN}_${modID}.${inputgrid}.regional.depth.b ${DATA}/regional.depth.b
ln -f -s ${FIXrtofs}/${RUN}_${modID}.${inputgrid}.iso.sigma.a iso.sigma.a
ln -f -s ${FIXrtofs}/${RUN}_${modID}.${inputgrid}.iso.sigma.b iso.sigma.b

# 1.c check if hycom restart file available
if [[ ! -s $COMINm1/${RUN}_${modID}.t00z.n00.restart.a ||
! -s $COMINm1/${RUN}_${modID}.t00z.n00.restart.b ]]
ln -f -s ${FIXrtofs}/regional.mom6.nc ${DATA}/regional.mom6.nc
ln -f -s ${FIXrtofs}/depth_GLBb0.08_09m11ob2_mom6.nc depth_GLBb0.08_09m11ob2_mom6.nc

# 1.c check if restart files are available
if [[ ! -s $COMINm1/RESTART/${PDY}.000000.MOM.res.nc ||
! -s $COMINm1/RESTART/${PDY}.000000.MOM.res_1.nc ||
! -s $COMINm1/RESTART/${PDY}.000000.MOM.res_2.nc ||
! -s $COMINm1/RESTART/${PDY}.000000.MOM.res_3.nc ||
! -s $COMINm1/RESTART/${PDY}.000000.MOM.res_4.nc ||
! -s $COMINm1/RESTART/${PDY}.000000.MOM.res_5.nc ||
! -s $COMINm1/RESTART/${PDY}.000000.MOM.res_16.nc ]]

then
$USHrtofs/${RUN}_abort.sh "FATAL ERROR: $job No restart file found" \
"in $COMINm1" 15
Expand Down Expand Up @@ -98,10 +100,9 @@ cat << eof2 > ogridnl
kkm = 41,
kko = 41,
m = 4500,
n = 3298,
n = 3297,
nnest = 1,
nproj = -1,
rlat = 70.2,
&end
eof2

Expand All @@ -121,45 +122,40 @@ mkdir -p $log_dir

echo timecheck RTOFS_GLO_HYCOM start setup at $(date)
#NCODA setup
$EXECrtofs/rtofs_ncoda_setup 3D hycom ogridnl $ddtg > pout1
$EXECrtofs/rtofs_ncoda_setup 3D mom ogridnl $ddtg > pout1
err=$?; export err ; err_chk
echo " error from rtofs_ncoda_setup=",$err

#NCODA prep
echo timecheck RTOFS_GLO_HYCOM start prep at $(date)
mpiexec -n 72 --cpu-bind core $EXECrtofs/rtofs_ncoda_prep 3D hycom ogridnl $ddtg > pout2
mpiexec -n 72 --cpu-bind core $EXECrtofs/rtofs_ncoda_prep 3D mom ogridnl $ddtg > pout2
err=$?; export err ; err_chk
echo " error from rtofs_ncoda_prep=",$err

#NCODA var
echo timecheck RTOFS_GLO_HYCOM start ncoda3d at $(date)
mpiexec -n $NPROCS --cpu-bind core $EXECrtofs/rtofs_ncoda 3D hycom ogridnl $ddtg > pout3
mpiexec -n $NPROCS --cpu-bind core $EXECrtofs/rtofs_ncoda 3D mom ogridnl $ddtg > pout3
err=$?; export err ; err_chk
echo " error from rtofs_ncoda=",$err

#NCODA post
echo timecheck RTOFS_GLO_HYCOM start post at $(date)
. prep_step
mpiexec -n $NPROCS --cpu-bind core $EXECrtofs/rtofs_ncoda_post 3D hycom ogridnl $ddtg relax > pout4
mpiexec -n $NPROCS --cpu-bind core $EXECrtofs/rtofs_ncoda_post 3D mom ogridnl $ddtg relax > pout4
err=$?; export err ; err_chk
echo " error from rtofs_ncoda_post=",$err

# rename local files
[[ -f fort.32 ]] && mv fort.32 $log_dir/hycom_var.$ddtg.rej
[[ -f fort.33 ]] && mv fort.33 $log_dir/hycom_var.$ddtg.prf
[[ -f fort.34 ]] && mv fort.34 $log_dir/hycom_var.$ddtg.gpt
[[ -f fort.36 ]] && mv fort.36 $log_dir/hycom_var.$ddtg.mvo
[[ -f fort.37 ]] && mv fort.37 $log_dir/hycom_var.$ddtg.drc
[[ -f fort.38 ]] && mv fort.38 $log_dir/hycom_var.$ddtg.lyp
[[ -f fort.39 ]] && mv fort.39 $log_dir/hycom_var.$ddtg.fix
[[ -f fort.40 ]] && mv fort.40 $log_dir/hycom_var.$ddtg.sus
[[ -f fort.41 ]] && mv fort.41 $log_dir/hycom_var.$ddtg.dup
[[ -f fort.42 ]] && mv fort.42 $log_dir/hycom_var.$ddtg.ssh
[[ -f fort.52 ]] && mv fort.52 $log_dir/hycom_var.$ddtg.sal
[[ -f fort.67 ]] && mv fort.67 $log_dir/hycom_var.$ddtg.obs
[[ -f fort.68 ]] && mv fort.68 $log_dir/hycom_var.$ddtg.grd
[[ -f fort.69 ]] && mv fort.69 $log_dir/hycom_var.$ddtg.via
[[ -f fort.88 ]] && mv fort.88 $log_dir/hycom_var.$ddtg.dbg

# create data coverage graphics
DoGraphics=NO
Expand Down
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