Merge remote-tracking branch 'origin/develop' into feature/ss_180

* origin/develop: Turn on OMA diagnostics after JEDI minimization (NOAA-EMC#1274) Adding AHI and SEVIRI satwnd thinning, enrolling AHI-H9, SEVIRI-M9, SEVIRI-M10 (NOAA-EMC#1263) add ctest to create yaml for lgetkf observer ctest (NOAA-EMC#1272) add soca fix yaml file for 1deg (NOAA-EMC#1270) Fix to marine post and archiving (NOAA-EMC#1266) Add JPSSRR sea-ice product to ioda converter (NOAA-EMC#1259) enable atmospheric lgetkf ctests to run in combined and split modes (NOAA-EMC#1262)
DavidHuber-NOAA · Sep 9, 2024 · 10edded · 10edded
2 parents 55c8f74 + b853fe9
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diff --git a/parm/aero/variational/3dvar_fgat_gfs_aero.yaml.j2 b/parm/aero/variational/3dvar_fgat_gfs_aero.yaml.j2
@@ -96,6 +96,8 @@ variational:
 final:
   diagnostics:
     departures: anlmob
+  prints:
+    frequency: PT3H
   increment:
     geometry:
       fms initialization:

diff --git a/parm/aero/variational/3dvar_gfs_aero.yaml.j2 b/parm/aero/variational/3dvar_gfs_aero.yaml.j2
@@ -87,6 +87,8 @@ variational:
 final:
   diagnostics:
     departures: anlmob
+  prints:
+    frequency: PT3H
   increment:
     geometry:
       fms initialization:

diff --git a/parm/atm/jcb-base.yaml.j2 b/parm/atm/jcb-base.yaml.j2
@@ -23,6 +23,7 @@ window_length: "{{ ATM_WINDOW_LENGTH }}"
 bound_to_include: begin
 minimizer: DRPCG
 final_diagnostics_departures: anlmob
+final_prints_frequency: PT3H
 number_of_outer_loops: 2
 analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 

diff --git a/parm/ioda/bufr2ioda/bufr2ioda_satwnd_amv_ahi.json b/parm/ioda/bufr2ioda/bufr2ioda_satwnd_amv_ahi.json
@@ -6,10 +6,11 @@
   "dump_directory"   : "{{ DMPDIR }}",
   "ioda_directory"   : "{{ COM_OBS }}",
   "subsets"          : [ "NC005044", "NC005045", "NC005046" ],
-  "data_description" : "NC005044 JMA SATWIND, AHI HIM8 IR(LW)/VIS/WV-CT/WV-CS;  NC005045 JMA SATWIND, HIMAWARI-8 IR(LW)/VIS/WV-CT/WV-CS; NC005046 JMA SATWIND, HIMAWARI-8 IR(LW)/VIS/WV-CT/WV-CS", 
+  "data_description" : "NC005044 JMA SATWIND, AHI HIMAWARI IR(LW)/VIS/WV-CT/WV-CS;  NC005045 JMA SATWIND, AHI HIMAWARI IR(LW)/VIS/WV-CT/WV-CS; NC005046 JMA SATWIND, AHI HIMAWARI IR(LW)/VIS/WV-CT/WV-CS", 
   "data_provider"    : "JMA",
   "sensor_info"      : { "sensor_name": "AHI",  "sensor_full_name": "Advanced Himawari Imager",  "sensor_id": 999 },
   "satellite_info"   : [
                           { "satellite_name": "H8", "satellite_full_name": "Himawari-8", "satellite_id": 173, "launch time": "YYYYMMDD" },
-                      ]
+                          { "satellite_name": "H9", "satellite_full_name": "Himawari-9", "satellite_id": 174, "launch time": "YYYYMMDD" },
+                       ]
 }
diff --git a/parm/ioda/bufr2ioda/bufr2ioda_satwnd_amv_seviri.json b/parm/ioda/bufr2ioda/bufr2ioda_satwnd_amv_seviri.json
@@ -11,6 +11,8 @@
   "sensor_info"      : { "sensor_name": "SEVIRI",  "sensor_full_name": "Spinning Enhanced Visible and InfraRed Imager",  "sensor_id": 999 },
   "satellite_info"   : [
                           { "satellite_name": "M8", "satellite_full_name": "METEOSAT-8", "satellite_id": 55, "launch time": "YYYYMMDD" },
+                          { "satellite_name": "M9", "satellite_full_name": "METEOSAT-9", "satellite_id": 56, "launch time": "YYYYMMDD" },
+                          { "satellite_name": "M10", "satellite_full_name": "METEOSAT-10", "satellite_id": 57, "launch time": "YYYYMMDD" },
                           { "satellite_name": "M11", "satellite_full_name": "METEOSAT-11", "satellite_id": 70, "launch time": "YYYYMMDD" },
                        ]
 }
diff --git a/parm/jcb-gdas b/parm/jcb-gdas
diff --git a/parm/snow/jcb-base.yaml.j2 b/parm/snow/jcb-base.yaml.j2
@@ -40,7 +40,7 @@ snow_increment_time_fv3: "{{ bkg_time_fv3 }}"
 analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 minimizer: DRPCG
 final_diagnostics_departures: anlmob
-
+final_prints_frequency: PT3H
 cost_type: 3D-Var
 number_of_outer_loops: 2
 

diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
@@ -22,6 +22,7 @@ window_length: '{{ATM_WINDOW_LENGTH}}'
 bound_to_include: begin
 minimizer: RPCG
 final_diagnostics_departures: oman
+final_prints_frequency: PT3H
 number_of_outer_loops: 1
 analysis_variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
 

diff --git a/parm/soca/soca_fix_stage_100.yaml.j2 b/parm/soca/soca_fix_stage_100.yaml.j2
@@ -0,0 +1,25 @@
+# TODO(AFE): make resolution dependent
+mkdir:
+- "{{ DATA }}/INPUT"
+######################################
+# fix files to copy
+######################################
+copy:
+- ["{{ SOCA_INPUT_FIX_DIR }}/rossrad.nc", "{{ DATA }}/rossrad.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/field_table", "{{ DATA }}/field_table"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/diag_table", "{{ DATA }}/diag_table"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/MOM_input", "{{ DATA }}/MOM_input"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/grid_spec.nc", "{{ DATA }}/INPUT/grid_spec.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/hycom1_75_800m.nc", "{{ DATA }}/INPUT/hycom1_75_800m.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/layer_coord.nc", "{{ DATA }}/INPUT/layer_coord.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_hgrid.nc", "{{ DATA }}/INPUT/ocean_hgrid.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_mosaic.nc", "{{ DATA }}/INPUT/ocean_mosaic.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/topog.nc", "{{ DATA }}/INPUT/topog.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/vgrid_75_2m.nc", "{{ DATA }}/INPUT/vgrid_75_2m.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/KH_background_2d.nc", "{{ DATA }}/INPUT/KH_background_2d.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/tidal_amplitude.nc", "{{ DATA }}/INPUT/tidal_amplitude.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/interpolate_zgrid_40L.nc", "{{ DATA }}/INPUT/interpolate_zgrid_40L.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/interpolate_zgrid_46L.nc", "{{ DATA }}/INPUT/interpolate_zgrid_46L.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/topo_edits_011818.nc", "{{ DATA }}/INPUT/topo_edits_011818.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/MOM_channels_SPEAR", "{{ DATA }}/INPUT/MOM_channels_SPEAR"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/seawifs_1998-2006_smoothed_2X.nc", "{{ DATA }}/INPUT/seawifs_1998-2006_smoothed_2X.nc"]
diff --git a/parm/soca/variational/3dvarfgat.yaml b/parm/soca/variational/3dvarfgat.yaml
@@ -51,6 +51,8 @@ output:
 final:
   diagnostics:
     departures: oman
+  prints:
+    frequency: PT3H
   increment:
     output:
       state component:

diff --git a/test/atm/global-workflow/3dvar.ref b/test/atm/global-workflow/3dvar.ref
@@ -88,3 +88,7 @@ sensorScanAngle_order_2:  Min= -5.1097259522434877,  Max= 2.8632600312042698,  N
 ---------------------------------------------------------------
 
 
+CostJb   : Nonlinear Jb = 0.0000033199535370
+CostJo   : Nonlinear Jo(AMSUA N19) = 39476.8510817764617968, nobs = 73667, Jo/n = 0.5358824315063252, err = 6.2697697603632934
+CostJo   : Nonlinear Jo(sondes) = 10639.2476170353256748, nobs = 4255, Jo/n = 2.5004107208073623, err = 10.9811231401273197
+CostFunction: Nonlinear J = 50116.0987021317414474
diff --git a/test/atm/global-workflow/CMakeLists.txt b/test/atm/global-workflow/CMakeLists.txt
@@ -36,6 +36,11 @@ add_test(NAME test_gdasapp_atm_jjob_ens_letkf
           ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
 	  WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
 
+add_test(NAME test_gdasapp_atm_jjob_ens_init_split
+  COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/jjob_ens_init_split.sh
+          ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
+  WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
+
 add_test(NAME test_gdasapp_atm_jjob_ens_obs
   COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/jjob_ens_obs.sh
           ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}

diff --git a/test/atm/global-workflow/config.yaml b/test/atm/global-workflow/config.yaml
@@ -17,7 +17,8 @@ atmanl:
   LAYOUT_Y_ATMANL: 1
 
 atmensanl:
-  JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf.yaml.j2"
+  JCB_ALGO_YAML_LETKF: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf.yaml.j2"
+  JCB_ALGO_YAML_OBS: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_observer.yaml.j2"
   LAYOUT_X_ATMENSANL: 1
   LAYOUT_Y_ATMENSANL: 1
 

diff --git a/test/atm/global-workflow/jjob_ens_init.sh b/test/atm/global-workflow/jjob_ens_init.sh
@@ -110,6 +110,10 @@ for imem in $(seq 1 $NMEM_ENS); do
     done
 done
 
+# Set lobsdiag_forenkf=.false. to run letkf as single observer and solver job
+# NOTE:  atmensanlinit creates input yaml for atmensanlletkf job
+cp $EXPDIR/config.base_lobsdiag_forenkf_false $EXPDIR/config.base
+
 # Execute j-job
 if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmensanlinit-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE

diff --git a/test/atm/global-workflow/jjob_ens_init_split.sh b/test/atm/global-workflow/jjob_ens_init_split.sh
@@ -0,0 +1,122 @@
+#! /usr/bin/env bash
+
+set -x
+bindir=$1
+srcdir=$2
+
+# Set g-w HOMEgfs
+topdir=$(cd "$(dirname "$(readlink -f -n "${bindir}" )" )/../../.." && pwd -P)
+export HOMEgfs=$topdir
+
+# Set variables for ctest
+export PSLOT=gdas_test
+export EXPDIR=$bindir/test/atm/global-workflow/testrun/experiments/$PSLOT
+export PDY=20210323
+export cyc=18
+export CDATE=${PDY}${cyc}
+export ROTDIR=$bindir/test/atm/global-workflow/testrun/ROTDIRS/$PSLOT
+export RUN=enkfgdas
+export CDUMP=enkfgdas
+export DATAROOT=$bindir/test/atm/global-workflow/testrun/RUNDIRS/$PSLOT
+export COMIN_GES=${bindir}/test/atm/bkg
+export pid=${pid:-$$}
+export jobid=$pid
+export COMROOT=$DATAROOT
+export NMEM_ENS=3
+export ACCOUNT=da-cpu
+export COM_TOP=$ROTDIR
+
+# Set GFS COM paths
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/parm/config/gfs/config.com"
+
+# Set python path for workflow utilities and tasks
+wxflowPATH="${HOMEgfs}/ush/python"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
+export PYTHONPATH
+
+# Detemine machine from config.base
+machine=$(echo `grep 'machine=' $EXPDIR/config.base | cut -d"=" -f2` | tr -d '"')
+
+# Set NETCDF and UTILROOT variables (used in config.base)
+if [[ $machine = 'HERA' ]]; then
+    NETCDF=$( which ncdump )
+    export NETCDF
+    export UTILROOT="/scratch2/NCEPDEV/ensemble/save/Walter.Kolczynski/hpc-stack/intel-18.0.5.274/prod_util/1.2.2"
+elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    ncdump=$( which ncdump )
+    NETCDF=$( echo "${ncdump}" | cut -d " " -f 3 )
+    export NETCDF
+    export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
+fi
+
+# Set date variables for previous cycle
+GDATE=`date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - 6 hours"`
+gPDY=$(echo $GDATE | cut -c1-8)
+gcyc=$(echo $GDATE | cut -c9-10)
+GDUMP="gdas"
+
+# Set file prefixes
+gprefix=$GDUMP.t${gcyc}z
+oprefix=$GDUMP.t${cyc}z
+
+# Generate COM variables from templates
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+    COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
+
+# Link observations
+dpath=gdas.$PDY/$cyc/obs
+mkdir -p $COM_OBS
+flist="amsua_n19.$CDATE sondes.$CDATE"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.${file}.nc4 $COM_OBS/${oprefix}.${file}.nc
+done
+
+# Link radiance bias correction files
+dpath=gdas.$gPDY/$gcyc/analysis/atmos
+mkdir -p $COM_ATMOS_ANALYSIS_PREV
+flist="amsua_n19.satbias amsua_n19.satbias_cov"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.${file}.nc4 $COM_ATMOS_ANALYSIS_PREV/$gprefix.${file}.nc
+done
+flist="amsua_n19.tlapse.txt"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.$file $COM_ATMOS_ANALYSIS_PREV/$gprefix.$file
+done
+
+# Link member atmospheric background on tiles and atmf006
+dpath=enkfgdas.$gPDY/$gcyc
+for imem in $(seq 1 $NMEM_ENS); do
+    memchar="mem"$(printf %03i $imem)
+
+    MEMDIR=${memchar} RUN=${RUN} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -x \
+	COM_ATMOS_HISTORY_PREV_ENS:COM_ATMOS_HISTORY_TMPL \
+	COM_ATMOS_RESTART_PREV_ENS:COM_ATMOS_RESTART_TMPL
+    COM_ATMOS_RESTART_PREV_DIRNAME_ENS=$(dirname $COM_ATMOS_RESTART_PREV_ENS)
+
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model/atmos/history
+    target=$COM_ATMOS_HISTORY_PREV_ENS
+    mkdir -p $target
+    rm -rf $target/enkfgdas.t${gcyc}z.atmf006.nc
+    ln -fs $source/enkfgdas.t${gcyc}z.atmf006.nc $target/
+
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model/atmos/history
+    target=$COM_ATMOS_HISTORY_PREV_ENS
+    flist=("cubed_sphere_grid_atmf006.nc" "cubed_sphere_grid_sfcf006.nc")
+    for file in "${flist[@]}"; do
+	rm -rf $target/enkf${gprefix}.${file}
+        ln -fs $source/enkf${gprefix}.${file} $target/
+    done
+done
+
+# Set lobsdiag_forenkf=.true. to run letkf as separate observer and solver jobs
+# NOTE:  atmensanlinit creates input yaml for atmensanlobs and atmensanlsol jobs
+cp $EXPDIR/config.base_lobsdiag_forenkf_true $EXPDIR/config.base
+
+# Execute j-job
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmensanlinit-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
+else
+    ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
+fi
diff --git a/test/atm/global-workflow/jjob_ens_letkf.sh b/test/atm/global-workflow/jjob_ens_letkf.sh
@@ -48,6 +48,9 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
 fi
 
+# Set lobsdiag_forenkf=.false. to run letkf as combined observer and solver job
+cp $EXPDIR/config.base_lobsdiag_forenkf_false $EXPDIR/config.base
+
 # Execute j-job
 if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait --output=atmensanlletkf-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF

diff --git a/test/atm/global-workflow/jjob_ens_obs.sh b/test/atm/global-workflow/jjob_ens_obs.sh
@@ -48,6 +48,9 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
 fi
 
+# Set lobsdiag_forenkf=.true. to run letkf as stand-alone observer job
+cp $EXPDIR/config.base_lobsdiag_forenkf_true $EXPDIR/config.base
+
 # Execute j-job
 if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=debug --time=00:30:00 --export=ALL --wait --output=atmensanlobs-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_OBS

diff --git a/test/atm/global-workflow/jjob_ens_sol.sh b/test/atm/global-workflow/jjob_ens_sol.sh
@@ -48,6 +48,9 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
 fi
 
+# Set lobsdiag_forenkf=.true. to run letkf as stand-alone solver job
+cp $EXPDIR/config.base_lobsdiag_forenkf_true $EXPDIR/config.base
+
 # Execute j-job
 if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
     sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=debug --time=00:30:00 --export=ALL --wait --output=atmensanlsol-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_SOL

diff --git a/test/atm/global-workflow/setup_workflow_exp.sh b/test/atm/global-workflow/setup_workflow_exp.sh
@@ -51,4 +51,9 @@ echo " "
 echo "$expdir/../config.yaml is"
 cat $expdir/../config.yaml
 
+# config.base contains with lobsdiag_forenkf=.true.  Create config.base with lobsdiag_forenkf=.false. for jjob_ens_letkf.sh
+EXPDIR=$expdir/$pslot
+cp $EXPDIR/config.base $EXPDIR/config.base_lobsdiag_forenkf_true
+sed 's/export lobsdiag_forenkf=".true."/export lobsdiag_forenkf=".false."/' $EXPDIR/config.base > $EXPDIR/config.base_lobsdiag_forenkf_false
+
 exit $?