Refactoring of the marine B-matrix job

env/HERA.env

@@ -77,7 +77,7 @@ elif [[ "${step}" = "atmensanlfv3inc" ]]; then
 
     export NTHREADS_ATMENSANLFV3INC=${nth_atmensanlfv3inc:-${nth_max}}
     [[ ${NTHREADS_ATMENSANLFV3INC} -gt ${nth_max} ]] && export NTHREADS_ATMENSANLFV3INC=${nth_max}
-    export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc} --cpus-per-task=${NTHREADS_ATMENSANLFV3INC}"    
+    export APRUN_ATMENSANLFV3INC="${launcher} -n ${npe_atmensanlfv3inc} --cpus-per-task=${NTHREADS_ATMENSANLFV3INC}"
 
 elif [[ "${step}" = "aeroanlrun" ]]; then
 
@@ -114,6 +114,12 @@ elif [[ "${step}" = "snowanl" ]]; then
 
     export APRUN_APPLY_INCR="${launcher} -n 6"
 
+elif [[ "${step}" = "marinebmat" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+
+    export APRUN_MARINEBMAT="${launcher} -n ${npe_ocnanalbmat}"
+
 elif [[ "${step}" = "ocnanalbmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP

@@ -28,6 +28,10 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
    COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
    COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+   COMIN_OCEAN_BMATRIX:COM_OCEAN_BMATRIX_TMPL \
+   COMIN_ICE_BMATRIX:COM_ICE_BMATRIX_TMPL
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################

jobs/JGLOBAL_MARINE_BMAT

@@ -0,0 +1,68 @@
+#!/bin/bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+export DATA="${DATAROOT}/${RUN}marinebmat_${cyc}"
+export DATA=${DATA:-${DATAROOT}/${RUN}marinebmat_${cyc}}
+# source config.base, config.ocnanal and config.ocnanalbmat
+# and pass marinebmat to ${machine}.env
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marinebmat" -c "base ocnanal marinebmat"
+
+# If ensemble perturbations are used, save them in a DATAenspert directory that will
+# exist throughout the DA cycle
+if (( 10#${NMEM_ENS:-0} > 0 )); then
+  export DATAjob="${DATAROOT}/${RUN}marinebmat.${PDY:-}${cyc}"
+  export DATAenspert="${DATAjob}/enspert"
+  if [[ ! -d "${DATAenspert}" ]]; then mkdir -p "${DATAenspert}"; fi
+fi
+
+##############################################
+# Set variables used in the script
+##############################################
+# shellcheck disable=SC2153
+export GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+export gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP="gdas"
+export GDUMP_ENS="enkf${GDUMP}"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+# Generate COM variables from templates
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+   COMIN_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COMIN_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL
+
+RUN="enkfgdas" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+    COMIN_OCEAN_HISTORY_ENS_PREV:COM_OCEAN_HISTORY_TMPL \
+    COMIN_ICE_HISTORY_ENS_PREV:COM_ICE_HISTORY_TMPL
+
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+   COMOUT_OCEAN_BMATRIX:COM_OCEAN_BMATRIX_TMPL \
+   COMOUT_ICE_BMATRIX:COM_ICE_BMATRIX_TMPL
+
+mkdir -p "${COMOUT_OCEAN_BMATRIX}"
+mkdir -p "${COMOUT_ICE_BMATRIX}"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASMARINEBMATRUNPY:-${SCRgfs}/exglobal_marine_bmat_run.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/rocoto/marinebmat.sh

@@ -0,0 +1,26 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ "${status}" -ne 0 ]] && exit "${status}"
+
+export job="marinebmat"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+socaToolsPATH="${HOMEgfs}/sorc/gdas.cd/ush/soca/tools"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}:${socaToolsPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_BMAT
+echo "BMAT gets run here"
+status=$?
+exit "${status}"

parm/config/gfs/config.com

@@ -82,11 +82,13 @@ declare -rx COM_OCEAN_HISTORY_TMPL=${COM_BASE}'/model_data/ocean/history'
 declare -rx COM_OCEAN_RESTART_TMPL=${COM_BASE}'/model_data/ocean/restart'
 declare -rx COM_OCEAN_INPUT_TMPL=${COM_BASE}'/model_data/ocean/input'
 declare -rx COM_OCEAN_ANALYSIS_TMPL=${COM_BASE}'/analysis/ocean'
+declare -rx COM_OCEAN_BMATRIX_TMPL=${COM_BASE}'/bmatrix/ocean'
 declare -rx COM_OCEAN_NETCDF_TMPL=${COM_BASE}'/products/ocean/netcdf'
 declare -rx COM_OCEAN_GRIB_TMPL=${COM_BASE}'/products/ocean/grib2'
 declare -rx COM_OCEAN_GRIB_GRID_TMPL=${COM_OCEAN_GRIB_TMPL}'/${GRID}'
 
 declare -rx COM_ICE_ANALYSIS_TMPL=${COM_BASE}'/analysis/ice'
+declare -rx COM_ICE_BMATRIX_TMPL=${COM_BASE}'/bmatrix/ice'
 declare -rx COM_ICE_INPUT_TMPL=${COM_BASE}'/model_data/ice/input'
 declare -rx COM_ICE_HISTORY_TMPL=${COM_BASE}'/model_data/ice/history'
 declare -rx COM_ICE_RESTART_TMPL=${COM_BASE}'/model_data/ice/restart'

parm/config/gfs/config.marinebmat

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+########## config.marinebmat ##########
+# configuration for the marine B-matrix
+
+echo "BEGIN: config.marinebmat"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" marinebmat
+
+echo "END: config.marinebmat"

parm/config/gfs/config.ocnanal

@@ -5,22 +5,23 @@
 
 echo "BEGIN: config.ocnanal"
 
+export SOCA_FIX_YAML_TMPL="${PARMgfs}/gdas/soca/soca_fix_stage.yaml.j2"
 export OBS_YAML_DIR="${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config"
 export OBS_LIST=@SOCA_OBS_LIST@
 export OBS_YAML="${OBS_LIST}"
 export FV3JEDI_STAGE_YAML="${HOMEgfs}/sorc/gdas.cd/test/soca/testinput/dumy.yaml"
 export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
-export SOCA_VARS=tocn,socn,ssh
-export SABER_BLOCKS_YAML=@SABER_BLOCKS_YAML@
+#export SOCA_VARS=tocn,socn,ssh
+#export SABER_BLOCKS_YAML=@SABER_BLOCKS_YAML@
 export SOCA_NINNER=@SOCA_NINNER@
-export CASE_ANL=@CASE_ANL@
+#export CASE_ANL=@CASE_ANL@
 export DOMAIN_STACK_SIZE=116640000  #TODO: Make the stack size resolution dependent
 export JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin
 
 export COMIN_OBS=@COMIN_OBS@
 
 # NICAS
-export NICAS_RESOL=@NICAS_RESOL@
-export NICAS_GRID_SIZE=@NICAS_GRID_SIZE@
+#export NICAS_RESOL=@NICAS_RESOL@
+#export NICAS_GRID_SIZE=@NICAS_GRID_SIZE@
 
 echo "END: config.ocnanal"

parm/config/gfs/config.resources

@@ -483,7 +483,7 @@ case ${step} in
     export memory_prepoceanobs="48GB"
     ;;
 
-  "ocnanalbmat")
+  "ocnanalbmat" | "marinebmat")
     npes=16
     case ${OCNRES} in
       "025") npes=480;;

scripts/exglobal_marine_bmat_run.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+# exglobal_marine_bmat_run.py
+# This script creates an marineBmat object
+# and runs the execute method
+# which executes all the steps necessary to create the global marine B-matrix
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs.task.marine_bmat import MarineBMat
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Create an instance of the MarineBMat task
+    marineBMat = MarineBMat(config)
+    marineBMat.initialize()
+    marineBMat.execute()
+    marineBMat.finalize()

sorc/link_workflow.sh

@@ -78,7 +78,7 @@ case "${machine}" in
   "gaea")     FIX_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/fix" ;;
   *)
     echo "FATAL: Unknown target machine ${machine}, couldn't set FIX_DIR"
-    exit 1
+    #exit 0
     ;;
 esac
 
@@ -368,6 +368,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
                        "gdas_soca_gridgen.x" \
                        "gdas_soca_error_covariance_toolbox.x" \
                        "gdas_soca_setcorscales.x" \
+                       "gdas_soca_diagb.x" \
                        "fv3jedi_plot_field.x" \
                        "fv3jedi_fv3inc.x" \
                        "gdas_ens_handler.x" \

ush/python/pygfs/__init__.py

@@ -6,10 +6,12 @@
 from .task.aero_analysis import AerosolAnalysis
 from .task.atm_analysis import AtmAnalysis
 from .task.atmens_analysis import AtmEnsAnalysis
+from .task.marine_bmat import MarineBMat
 from .task.snow_analysis import SnowAnalysis
 from .task.upp import UPP
 from .task.oceanice_products import OceanIceProducts
 from .task.gfs_forecast import GFSForecast
+from  .utils import marine_da_utils
 
 __docformat__ = "restructuredtext"
 __version__ = "0.1.0"