Change YAML and add jjob CTest for new "atmensanlfv3inc" job in Globa…

…l Workflow (#1104)

This PR is a companion to Global Workflow PR
#[2593](NOAA-EMC/global-workflow#2592), which
adds the "atmensanlfv3inc" job to Global Workflow. That job converts the
JEDI ensemble increments into FV3 readable increments. This JCB-GDAS
companion PR is #[3](NOAA-EMC/jcb-gdas#3), which
updates the input YAMLs for the FV3 increment converter

This PR does two things:
1. It adds a jjob CTest to GDASApp to test this new job.
2. It modifies the LETKF input YAML to write out cubed-sphere history
increments, rather than Gaussian increments, so the FV3 increment
converter can read the resulting increment off the native grid and then
itself write out a Gaussian increment.

---------

Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>

parm/atm/jcb-base.yaml.j2

@@ -11,7 +11,7 @@ app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle
 # ------------------------------------------------------------
 #final_increment_file: final_increment_gaussian
 final_increment_file: final_increment_cubed_sphere
-output_ensemble_increments_file: output_ensemble_increments_gaussian
+output_ensemble_increments_file: output_ensemble_increments_cubed_sphere
 model_file: model_pseudo
 initial_condition_file: background  # Initial conditions for 4D apps is background
 

test/atm/global-workflow/CMakeLists.txt

@@ -34,6 +34,11 @@ add_test(NAME test_gdasapp_atm_jjob_ens_init
 add_test(NAME test_gdasapp_atm_jjob_ens_run
   COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/jjob_ens_run.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_inc
+  COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/jjob_ens_inc.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_final

test/atm/global-workflow/jjob_ens_inc.sh

@@ -0,0 +1,55 @@
+#! /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
+
+# Set python path for workflow utilities and tasks
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow"
+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
+
+# Execute j-job
+if [[ $machine = 'HERA' ]]; then
+    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
+elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
+else
+    ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
+fi

test/atm/global-workflow/jjob_ens_run.sh

@@ -50,9 +50,9 @@ fi
 
 # Execute j-job
 if [[ $machine = 'HERA' ]]; then
-    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_RUN
+    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
 elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_RUN
+    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
 else
-    ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_RUN
+    ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
 fi