Move the variational scripts to this repository

ci/cases/gfsv17/ocnanal.yaml

@@ -16,7 +16,7 @@ base:
   FHMAX_GFS: 240
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
 
-ocnanal:
+marineanl:
   SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca
   SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
   SOCA_NINNER: 100

env/CONTAINER.env

@@ -26,7 +26,7 @@ ulimit -s unlimited
 ulimit -a
 
 
-if [ "${step}" = "ocnanalrun" ]; then
+if [ "${step}" = "marineanlvar" ]; then
     export NTHREADS_OCNANAL=1
-    export APRUN_OCNANAL="${launcher} -n 2"
+    export APRUN_MARINEANLVAR="${launcher} -n 2"
 fi

env/HERA.env

@@ -138,17 +138,15 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
     export APRUN_MARINEBMAT="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
 
-    export APRUN_OCNANAL="${APRUN_default}"
-
-elif [[ "${step}" = "ocnanalchkpt" ]]; then
+elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
-
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLCHKPT="${APRUN_default}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 

env/HERCULES.env

@@ -133,10 +133,10 @@ case ${step} in
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEBMAT="${APRUN_default}"
  ;;
- "ocnanalrun")
+ "marineanlvar")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
  ;;
 "ocnanalecen")
 
@@ -148,12 +148,12 @@ case ${step} in
     [[ ${NTHREADS_OCNANALECEN} -gt ${max_threads_per_task} ]] && export NTHREADS_OCNANALECEN=${max_threads_per_task}
     export APRUN_OCNANALECEN="${launcher} -n ${ntasks_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
 ;;
- "ocnanalchkpt")
+ "marineanlchkpt")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_MARINEANLCHKPT="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
  ;;
  "anal" | "analcalc")
 

env/JET.env

@@ -69,7 +69,7 @@ elif [[ "${step}" = "atmensanlsol" ]]; then
 
     export NTHREADS_ATMENSANLSOL=${NTHREADSmax}
     export APRUN_ATMENSANLSOL="${APRUN_default}"
-	
+
 elif [[ "${step}" = "atmensanlletkf" ]]; then
 
     export NTHREADS_ATMENSANLLETKF=${NTHREADSmax}
@@ -121,10 +121,10 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEBMAT="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 

env/ORION.env

@@ -130,18 +130,19 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export NTHREADS_MARINEBMAT=${NTHREADSmax}
     export APRUN_MARINEBMAT="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalchkpt" ]]; then
+elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
+
+    export APRUN_MARINEANLCHKPT="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY

@@ -1,6 +1,6 @@
 #!/bin/bash
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanalprep"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base ocnanal marineanlinit"
 
 
 ##############################################

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT → jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT

@@ -1,8 +1,9 @@
 #!/bin/bash
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalchkpt" -c "base ocnanal ocnanalchkpt"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlchkpt" -c "base marineanl marineanlchkpt"
 
 
 ##############################################
@@ -11,30 +12,18 @@
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export GDATE
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
+gPDY=${GDATE:0:8}
+gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
 
-export GPREFIX="${GDUMP}.t${gcyc}z."
-# Ignore possible spelling error (nothing is misspelled)
-# shellcheck disable=SC2153
-export APREFIX="${RUN}.t${cyc}z."
-
-# Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS
-
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
-
-
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNCHKPTSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_chkpt.sh}
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_checkpoint.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
@@ -50,9 +39,4 @@
   cat "${pgmout}"
 fi
 
-##########################################
-# Do not remove the Temporary working directory (do this in POST)
-##########################################
-cd "${DATAROOT}" || exit 1
-
 exit 0

jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE

@@ -0,0 +1,46 @@
+#!/bin/bash
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlfinal" -c "base marineanl marineanlfinal"
+
+##############################################
+# Set variables used in the script
+##############################################
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
+export GDUMP=${GDUMP:-"gdas"}
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
+
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+   COMOUT_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \
+   COMOUT_ICE_ANALYSIS:COM_ICE_ANALYSIS_TMPL \
+   COMOUT_ICE_RESTART:COM_ICE_RESTART_TMPL
+
+mkdir -p "${COMOUT_OCEAN_ANALYSIS}"
+mkdir -p "${COMOUT_ICE_ANALYSIS}"
+mkdir -p "${COMOUT_ICE_RESTART}"
+
+###############################################################
+# Run relevant script
+###############################################################
+
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_finalize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+#[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
+
+exit 0

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP → jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE

@@ -1,7 +1,9 @@
 #!/bin/bash
+
 source "${HOMEgfs}/ush/preamble.sh"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanalprep"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base marineanl marineanlinit"
 
 
 ##############################################
@@ -10,42 +12,30 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanal
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export GDATE
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
+gPDY=${GDATE:0:8}
+gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
 
-export OPREFIX="${RUN}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${RUN}.t${cyc}z."
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
 
 # Generate COM variables from templates
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-   COM_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
-   COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
-   COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
+   COMIN_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COMIN_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
+   COMIN_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
-##############################################
-
-# Add UFSDA to PYTHONPATH
-ufsdaPATH="${HOMEgfs}/sorc/gdas.cd/ush/"
-# shellcheck disable=SC2311
-pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python$(detect_py_ver)/"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${ufsdaPATH}:${pyiodaPATH}"
-export PYTHONPATH
-
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_prep.py}
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_initialize.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN → jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL

@@ -1,14 +1,16 @@
-#!/bin/bash
+#! /usr/bin/env bash
+
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
-
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlvar" -c "base marineanl marineanlvar"
 
 ##############################################
 # Set variables used in the script
 ##############################################
 
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
@@ -17,7 +19,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalr
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNRUNSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_run.sh}
+EXSCRIPT=${GDASMARINERUNSH:-${SCRgfs}/exglobal_marine_analysis_variational.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
@@ -33,9 +35,4 @@ if [[ -e "${pgmout}" ]] ; then
   cat "${pgmout}"
 fi
 
-##########################################
-# Do not remove the Temporary working directory (do this in POST)
-##########################################
-cd "${DATAROOT}" || exit 1
-
 exit 0