Adds jjob and other necessities for marine LETKF task (#2564)

Adds jjob, rocoto script, config file, and other necessities for new
marine LETKF task.

Partially addresses NOAA-EMC/GDASApp#1091

env/HERA.env

@@ -130,6 +130,14 @@ elif [[ "${step}" = "ocnanalecen" ]]; then
     [[ ${NTHREADS_OCNANALECEN} -gt ${nth_max} ]] && export NTHREADS_OCNANALECEN=${nth_max}
     export APRUN_OCNANALECEN="${launcher} -n ${npe_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
 
+elif [[ "${step}" = "ocnanalletkf" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_ocnanalletkf))
+
+    export NTHREADS_OCNANALLETKF=${nth_ocnanalletkf:-${nth_max}}
+    [[ ${NTHREADS_OCNANALLETKF} -gt ${nth_max} ]] && export NTHREADS_OCNANALLETKF=${nth_max}
+    export APRUN_OCNANALLETKF="${launcher} -n ${npe_ocnanalletkf} --cpus-per-task=${NTHREADS_OCNANALLETKF}"
+
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 
     export MKL_NUM_THREADS=4

env/ORION.env

@@ -138,6 +138,14 @@ elif [[ "${step}" = "ocnanalecen" ]]; then
     [[ ${NTHREADS_OCNANALECEN} -gt ${nth_max} ]] && export NTHREADS_OCNANALECEN=${nth_max}
     export APRUN_OCNANALECEN="${launcher} -n ${npe_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
 
+elif [[ "${step}" = "ocnanalletkf" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_ocnanalletkf))
+
+    export NTHREADS_OCNANALLETKF=${nth_ocnanalletkf:-${nth_max}}
+    [[ ${NTHREADS_OCNANALLETKF} -gt ${nth_max} ]] && export NTHREADS_OCNANALLETKF=${nth_max}
+    export APRUN_OCNANALLETKF="${launcher} -n ${npe_ocnanalletkf} --cpus-per-task=${NTHREADS_OCNANALLETKF}"
+
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 
     export MKL_NUM_THREADS=4

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF

@@ -0,0 +1,48 @@
+#!/bin/bash
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalletkf" -c "base ocnanal ocnanalletkf"
+
+##############################################
+# Set variables used in the script
+##############################################
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
+GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+
+gPDY=${GDATE:0:8}
+gcyc=${GDATE:8:2}
+
+YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+   COM_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASOCNLETKFPY:-${HOMEgfs}/scripts/exgdas_global_marine_analysis_letkf.py}
+${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/rocoto/ocnanalletkf.sh

@@ -0,0 +1,23 @@
+#! /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="ocnanalletkf"
+export jobid="${job}.$$"
+
+###############################################################
+# Setup Python path for GDASApp ush
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF"
+status=$?
+exit "${status}"

parm/config/gfs/config.ocnanalletkf

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+########## config.ocnanalletkf ##########
+# Ocn Analysis specific
+
+echo "BEGIN: config.ocnanalletkf"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" ocnanalletkf
+
+echo "END: config.ocnanalletkf"

parm/config/gfs/config.resources

@@ -23,7 +23,7 @@ if (( $# != 1 )); then
     echo "waveinit waveprep wavepostsbs wavepostbndpnt wavepostbndpntbll wavepostpnt"
     echo "wavegempak waveawipsbulls waveawipsgridded"
     echo "postsnd awips gempak npoess"
-    echo "ocnanalprep prepoceanobs ocnanalbmat ocnanalrun ocnanalecen ocnanalchkpt ocnanalpost ocnanalvrfy"
+    echo "ocnanalprep prepoceanobs ocnanalbmat ocnanalrun ocnanalecen ocnanalletkf ocnanalchkpt ocnanalpost ocnanalvrfy"
     exit 1
 
 fi
@@ -456,6 +456,35 @@ case ${step} in
     export memory_ocnanalecen
     ;;
 
+  "ocnanalletkf")
+    npes=16
+    case ${OCNRES} in
+      "025")
+        npes=480
+        memory_ocnanalletkf="96GB"
+        ;;
+      "050")
+        npes=16
+        memory_ocnanalletkf="96GB"
+        ;;
+      "500")
+        npes=16
+        memory_ocnanalletkf="24GB"
+        ;;
+      *)
+        echo "FATAL ERROR: Resources not defined for job ${job} at resolution ${OCNRES}"
+        exit 4
+    esac
+
+    export wtime_ocnanalletkf="00:10:00"
+    export npe_ocnanalletkf=${npes}
+    export nth_ocnanalletkf=1
+    export is_exclusive=True
+    export npe_node_ocnanalletkf=$(( npe_node_max / nth_ocnanalletkf ))
+    export memory_ocnanalletkf
+    ;;
+
+
   "ocnanalchkpt")
     export wtime_ocnanalchkpt="00:10:00"
     export npe_ocnanalchkpt=1

scripts/exgdas_global_marine_analysis_letkf.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+# exgdas_global_marine_analysis_letkf.py
+# This script creates an MarineLETKF class
+# and runs the initialize, run, and finalize methods
+# which currently are stubs
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs.task.marine_letkf import MarineLETKF
+
+# 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)
+
+    # Instantiate the marine letkf task
+    MarineLetkf = MarineLETKF(config)
+    MarineLetkf.initialize()
+    MarineLetkf.run()
+    MarineLetkf.finalize()

ush/python/pygfs/task/marine_letkf.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+
+from logging import getLogger
+from pygfs.task.analysis import Analysis
+from typing import Dict
+from wxflow import (chdir,
+                    logit,
+                    Task)
+
+logger = getLogger(__name__.split('.')[-1])
+
+
+class MarineLETKF(Analysis):
+    """
+    Class for global ocean and sea ice analysis LETKF task
+    """
+
+    @logit(logger, name="MarineLETKF")
+    def __init__(self, config: Dict) -> None:
+        """Constructor for ocean and sea ice LETKF task
+        Parameters:
+        ------------
+        config: Dict
+            configuration, namely evironment variables
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("init")
+        super().__init__(config)
+
+    @logit(logger)
+    def initialize(self):
+        """Method initialize for ocean and sea ice LETKF task
+        Parameters:
+        ------------
+        None
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("initialize")
+
+    @logit(logger)
+    def run(self):
+        """Method run for ocean and sea ice LETKF task
+        Parameters:
+        ------------
+        None
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("run")
+
+        chdir(self.runtime_config.DATA)
+
+    @logit(logger)
+    def finalize(self):
+        """Method finalize for ocean and sea ice LETKF task
+        Parameters:
+        ------------
+        None
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("finalize")