Fix some bugs and make other changes so ctest in GDASApp works (#1172)

Fix some bugs and make other changes so ctest in GDASApp works.

`$CDATE` is used instead of `$cyc` for the time being, since `cyc` isn't defined before that point in the scripts.

Fix some lines where multiple arguments were enclosed in quotation marks when they should be separate.

Update `config.ocnanal` to template out some variables and add them to the defaults yaml.

Fixes #1164 
Fixes #1173
Companion PR to [GDASApp/PR234](NOAA-EMC/GDASApp#234)
See also [GDASApp/232](NOAA-EMC/GDASApp#232)

Author: guillaumevernieres

env/ORION.env

@@ -91,7 +91,7 @@ elif [ ${step} = "ocnanalrun" ]; then
 
     export NTHREADS_OCNANAL=${nth_ocnanalrun:-${nth_max}}
     [[ $NTHREADS_OCNANAL -gt ${nth_max} ]] && export NTHREADS_OCNANAL=${nth_max}
-    export APRUN_OCNANAL="${launcher} -n ${npe_aeroanlrun}"
+    export APRUN_OCNANAL="${launcher} -n ${npe_ocnanalrun}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST

@@ -5,7 +5,7 @@ source "${HOMEgfs}/ush/preamble.sh"
 ##############################################
 # make temp directory
 ##############################################
-export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}} # TODO (G): Switch to {cyc} when the downstream code is ready
 mkdir -p "${DATA}"
 cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP

@@ -5,7 +5,7 @@ source "${HOMEgfs}/ush/preamble.sh"
 ##############################################
 # make temp directory
 ##############################################
-export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}} # TODO (G): Switch to {cyc} when the downstream code is ready
 rm -rf "${DATA}"  # Ensure starting with a clean DATA
 mkdir -p "${DATA}"
 cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
@@ -42,7 +42,7 @@ done
 ##########################################
 # Source machine runtime environment
 ##########################################
-. "${HOMEgfs}/env/${machine}.env ocnanalprep"
+. "${HOMEgfs}/env/${machine}.env" ocnanalprep
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN

@@ -6,7 +6,7 @@ source "${HOMEgfs}/ush/preamble.sh"
 ##############################################
 # make temp directory
 ##############################################
-export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}} # TODO (G): Switch to {cyc} when the downstream code is ready
 mkdir -p "${DATA}"
 cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
@@ -42,7 +42,7 @@ done
 ##########################################
 # Source machine runtime environment
 ##########################################
-. "${HOMEgfs}/env/${machine}.env ocnanalrun"
+. "${HOMEgfs}/env/${machine}.env" ocnanalrun
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 

parm/config/config.ocnanal

@@ -9,17 +9,17 @@ export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
 export OBS_YAML=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
 export OBS_LIST=${OBS_YAML_DIR}/obs_list.yaml
 export FV3JEDI_STAGE_YAML=${HOMEgfs}/sorc/gdas.cd/test/soca/testinput/dumy.yaml
-export SOCA_INPUT_FIX_DIR=/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25/soca # TODO: Should be moved somewhere else
+export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
 export SOCA_VARS=tocn,socn,ssh
-export SOCA_NINNER=50
-export CASE_ANL="C48"
+export SOCA_NINNER=@SOCA_NINNER@
+export CASE_ANL=@CASE_ANL@
 export DOMAIN_STACK_SIZE=2000000
 export JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin
 
 # TODO: Move the R2D2 configuration to a common space
 export R2D2_OBS_DB=shared
-export R2D2_OBS_DUMP=s2s_v1
-export R2D2_OBS_SRC=gdas_marine
+export R2D2_OBS_DUMP=@R2D2_OBS_DUMP@
+export R2D2_OBS_SRC=@R2D2_OBS_SRC@
 export R2D2_OBS_WINDOW=24     # TODO: Check if the R2D2 sampling DB window is still needed
-export COMIN_OBS=/scratch2/NCEPDEV/marineda/r2d2
+export COMIN_OBS=@COMIN_OBS@
 echo "END: config.ocnanal"

parm/config/config.ocnanalpost

@@ -6,5 +6,5 @@
 echo "BEGIN: config.ocnanalpost"
 
 # Get task specific resources
-. "${EXPDIR}/config.resources ocnanalpost"
+. "${EXPDIR}/config.resources" ocnanalpost
 echo "END: config.ocnanalpost"

parm/config/config.ocnanalprep

@@ -6,5 +6,5 @@
 echo "BEGIN: config.ocnanalprep"
 
 # Get task specific resources
-. "${EXPDIR}/config.resources ocnanalprep"
+. "${EXPDIR}/config.resources" ocnanalprep
 echo "END: config.ocnanalprep"

parm/config/config.ocnanalrun

@@ -6,6 +6,6 @@
 echo "BEGIN: config.ocnanalrun"
 
 # Get task specific resources
-. "${EXPDIR}/config.resources ocnanalrun"
+. "${EXPDIR}/config.resources" ocnanalrun
 
 echo "END: config.ocnanalrun"

parm/config/yaml/defaults.yaml

@@ -1,3 +1,11 @@
 aeroanl:
   IO_LAYOUT_X: 1
   IO_LAYOUT_Y: 1
+
+ocnanal:
+  SOCA_INPUT_FIX_DIR: '/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25'
+  CASE_ANL: 'C48'
+  COMIN_OBS: '/scratch2/NCEPDEV/marineda/r2d2'
+  SOCA_NINNER: 50
+  R2D2_OBS_SRC: 'gdas_marine'
+  R2D2_OBS_DUMP: 's2s_v1'