Adding steps to workflow scripts that compute the diffusion parameters.

env/AWSPW.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"

env/CONTAINER.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"

env/HERA.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -84,15 +84,25 @@ elif [[ "${step}" = "atmensanlfv3inc" ]]; then
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
     export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc} --cpus-per-task=${NTHREADS_ATMENSANLFV3INC}"    
 
-elif [[ "${step}" = "aeroanlrun" ]]; then
+elif [[ "${step}" = "aeroanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    nth_max=$((npe_node_max / npe_node_aeroanlrun))
+    nth_max=$((npe_node_max / npe_node_aeroanlvar))
 
-    export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
+    export NTHREADS_AEROANL=${nth_aeroanlvar:-${nth_max}}
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
-    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun} --cpus-per-task=${NTHREADS_AEROANL}"
+    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlvar} --cpus-per-task=${NTHREADS_AEROANL}"
+
+elif [[ "${step}" = "aeroanlgenb" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_aeroanlgenb))
+
+    export NTHREADS_AEROGENB=${nth_aeroanlgenb:-${nth_max}}
+    [[ ${NTHREADS_AEROGENB} -gt ${nth_max} ]] && export NTHREADS_AEROGENB=${nth_max}
+    export APRUN_AEROGENB="${launcher} -n ${npe_aeroanlgenb} --cpus-per-task=${NTHREADS_AEROGENB}"
 
 elif [[ "${step}" = "atmanlfv3inc" ]]; then
 

env/HERCULES.env

@@ -89,15 +89,25 @@ case ${step} in
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
     export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc} --cpus-per-task=${NTHREADS_ATMENSANLFV3INC}"
  ;;
- "aeroanlrun")
+ "aeroanlvar")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    nth_max=$((npe_node_max / npe_node_aeroanlrun))
+    nth_max=$((npe_node_max / npe_node_aeroanlvar))
 
-    export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
+    export NTHREADS_AEROANL=${nth_aeroanlvar:-${nth_max}}
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
-    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun} --cpus-per-task=${NTHREADS_AEROANL}"
+    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlvar} --cpus-per-task=${NTHREADS_AEROANL}"
+ ;;
+  "aeroanlgenb")
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_aeroanlgenb))
+
+    export NTHREADS_AEROGENB=${nth_aeroanlgenb:-${nth_max}}
+    [[ ${NTHREADS_AEROGENB} -gt ${nth_max} ]] && export NTHREADS_AEROGENB=${nth_max}
+    export APRUN_AEROGENB="${launcher} -n ${npe_aeroanlgenb} --cpus-per-task=${NTHREADS_AEROGENB}"
  ;;
  "snowanl")
 

env/JET.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -72,15 +72,25 @@ elif [[ "${step}" = "atmensanlfv3inc" ]]; then
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
     export APRUN_ATMENSANLFV3INC="${launcher} ${npe_atmensanlfv3inc}"
 
-elif [[ "${step}" = "aeroanlrun" ]]; then
+elif [[ "${step}" = "aeroanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    nth_max=$((npe_node_max / npe_node_aeroanlrun))
+    nth_max=$((npe_node_max / npe_node_aeroanlvar))
 
-    export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
+    export NTHREADS_AEROANL=${nth_aeroanlvar:-${nth_max}}
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
-    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
+    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlvar}"
+
+elif [[ "${step}" = "aeroanlgenb" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_aeroanlgenb))
+
+    export NTHREADS_AEROGENB=${nth_aeroanlgenb:-${nth_max}}
+    [[ ${NTHREADS_AEROGENB} -gt ${nth_max} ]] && export NTHREADS_AEROGENB=${nth_max}
+    export APRUN_AEROGENB="${launcher} -n ${npe_aeroanlgenb}"
 
 elif [[ "${step}" = "snowanl" ]]; then
 

env/ORION.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -80,15 +80,25 @@ elif [[ "${step}" = "atmensanlfv3inc" ]]; then
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
     export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc} --cpus-per-task=${NTHREADS_ATMENSANLFV3INC}"
 
-elif [[ "${step}" = "aeroanlrun" ]]; then
+elif [[ "${step}" = "aeroanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    nth_max=$((npe_node_max / npe_node_aeroanlrun))
+    nth_max=$((npe_node_max / npe_node_aeroanlvar))
 
-    export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
+    export NTHREADS_AEROANL=${nth_aeroanlvar:-${nth_max}}
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
-    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun} --cpus-per-task=${NTHREADS_AEROANL}"
+    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlvar} --cpus-per-task=${NTHREADS_AEROANL}"
+
+elif [[ "${step}" = "aeroanlgenb" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_aeroanlgenb))
+
+    export NTHREADS_AEROGENB=${nth_aeroanlgenb:-${nth_max}}
+    [[ ${NTHREADS_AEROGENB} -gt ${nth_max} ]] && export NTHREADS_AEROGENB=${nth_max}
+    export APRUN_AEROGENB="${launcher} -n ${npe_aeroanlgenb} --cpus-per-task=${NTHREADS_AEROGENB}"
 
 elif [[ "${step}" = "snowanl" ]]; then
 

env/S4.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -72,15 +72,25 @@ elif [[ "${step}" = "atmensanlfv3inc" ]]; then
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
     export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc}"    
 
-elif [[ "${step}" = "aeroanlrun" ]]; then
+elif [[ "${step}" = "aeroanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    nth_max=$((npe_node_max / npe_node_aeroanlrun))
+    nth_max=$((npe_node_max / npe_node_aeroanlvar))
 
-    export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
+    export NTHREADS_AEROANL=${nth_aeroanlvar:-${nth_max}}
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
-    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
+    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlvar}"
+
+elif [[ "${step}" = "aeroanlgenb" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_aeroanlgenb))
+
+    export NTHREADS_AEROGENB=${nth_aeroanlgenb:-${nth_max}}
+    [[ ${NTHREADS_AEROGENB} -gt ${nth_max} ]] && export NTHREADS_AEROGENB=${nth_max}
+    export APRUN_AEROGENB="${launcher} -n ${npe_aeroanlgenb}"
 
 elif [[ "${step}" = "snowanl" ]]; then
 

env/WCOSS2.env

@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
+    echo "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlvar snowanl"
     echo "anal sfcanl fcst post metp"
     echo "eobs eupd ecen esfc efcs epos"
     echo "postsnd awips gempak"
@@ -66,15 +66,25 @@ elif [[ "${step}" = "atmensanlfv3inc" ]]; then
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
     export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc}"
 
-elif [[ "${step}" = "aeroanlrun" ]]; then
+elif [[ "${step}" = "aeroanlvar" ]]; then
 
     export APRUNCFP="${launcher} -np \$ncmd ${mpmd_opt}"
 
-    nth_max=$((npe_node_max / npe_node_aeroanlrun))
+    nth_max=$((npe_node_max / npe_node_aeroanlvar))
 
-    export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
+    export NTHREADS_AEROANL=${nth_aeroanlvar:-${nth_max}}
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
-    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
+    export APRUN_AEROANL="${launcher} -n ${npe_aeroanlvar}"
+
+elif [[ "${step}" = "aeroanlgenb" ]]; then
+
+    export APRUNCFP="${launcher} -np \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_aeroanlgenb))
+
+    export NTHREADS_AEROGENB=${nth_aeroanlgenb:-${nth_max}}
+    [[ ${NTHREADS_AEROGENB} -gt ${nth_max} ]] && export NTHREADS_AEROGENB=${nth_max}
+    export APRUN_AEROGENB="${launcher} -n ${npe_aeroanlgenb}"
 
 elif [[ "${step}" = "snowanl" ]]; then
 

jobs/JGLOBAL_AERO_ANALYSIS_GENERATE_BMATRIX

@@ -0,0 +1,55 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}aerogenb_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlgenb" -c "base aeroanl aeroanlgenb"
+
+##############################################
+# Set variables used in the script
+##############################################
+# shellcheck disable=SC2153
+GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+gPDY=${GDATE:0:8}
+gcyc=${GDATE:8:2}
+GDUMP="gdas"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS COM_CHEM_ANALYSIS
+
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+    COM_CHEM_ANALYSIS_PREV:COM_CHEM_ANALYSIS_TMPL \
+    COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
+
+mkdir -m 775 -p "${COM_CHEM_ANALYSIS}"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASAEROBMATPY:-${SCRgfs}/exglobal_aero_analysis_generate_bmatrix.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
+exit 0

jobs/JGLOBAL_AERO_ANALYSIS_RUN → jobs/JGLOBAL_AERO_ANALYSIS_VARIATIONAL

@@ -3,7 +3,7 @@
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
 export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
-source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlrun" -c "base aeroanl aeroanlrun"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlvar" -c "base aeroanl aeroanlvar"
 
 ##############################################
 # Set variables used in the script
@@ -16,7 +16,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlrun" -c "base aeroanl aeroanlr
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASAERORUNSH:-${SCRgfs}/exglobal_aero_analysis_run.py}
+EXSCRIPT=${GDASAEROVARSH:-${SCRgfs}/exglobal_aero_analysis_variational.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/rocoto/aeroanlgenb.sh

@@ -0,0 +1,24 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="aeroanlgenb"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_AERO_ANALYSIS_GENERATE_BMATRIX"
+status=$?
+exit "${status}"

jobs/rocoto/aeroanlrun.sh → jobs/rocoto/aeroanlvar.sh

@@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="aeroanlrun"
+export job="aeroanlvar"
 export jobid="${job}.$$"
 
 ###############################################################
@@ -19,6 +19,6 @@ export PYTHONPATH
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}/jobs/JGLOBAL_AERO_ANALYSIS_RUN"
+"${HOMEgfs}/jobs/JGLOBAL_AERO_ANALYSIS_VARIATIONAL"
 status=$?
 exit "${status}"

parm/config/gfs/config.aeroanl

@@ -19,6 +19,8 @@ export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
 export JEDIEXE="${EXECgfs}/gdas.x"
+export BMATEXE="${EXECgfs}/gdasapp_chem_diagb.x"
+export DIFFUSIONEXE="${EXECgfs}/gdas_fv3jedi_error_covariance_toolbox.x"
 
 if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"

parm/config/gfs/config.aeroanlgenb

@@ -0,0 +1,18 @@
+#!/bin/bash -x
+
+########## config.aeroanlgenb ##########
+# Aerosol Variance specific
+
+echo "BEGIN: config.aeroanlgenb"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" aeroanlgenb
+
+export BMATYAML="${PARMgfs}/gdas/aero/berror/aero_diagb.yaml.j2"
+export DIFFUSIONYAML="${PARMgfs}/gdas/aero/berror/aero_diffusionparm.yaml.j2"
+export diff_iter=10
+export horiz_len=2500e3
+export fixed_val=1.0
+
+
+echo "END: config.aeroanlgenb"