From faa95efb18f0f52acab2cf09b17f78406f9b48b1 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue, 3 Sep 2024 15:36:22 -0400
Subject: [PATCH] add ctest to create yaml for lgetkf observer ctest (#1272)

---
 test/atm/global-workflow/CMakeLists.txt       |   5 +
 test/atm/global-workflow/config.yaml          |   3 +-
 .../global-workflow/jjob_ens_init_split.sh    | 122 ++++++++++++++++++
 3 files changed, 129 insertions(+), 1 deletion(-)
 create mode 100755 test/atm/global-workflow/jjob_ens_init_split.sh

diff --git a/test/atm/global-workflow/CMakeLists.txt b/test/atm/global-workflow/CMakeLists.txt
index e9e4e1f1..925a7367 100644
--- 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
index 9d896736..c0601962 100644
--- 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_split.sh b/test/atm/global-workflow/jjob_ens_init_split.sh
new file mode 100755
index 00000000..4128ac01
--- /dev/null
+++ 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