Merge branch 'develop' into bugfix/ocnanalprep

NOAA-EMC · Jul 8, 2024 · 21c753a · 21c753a
2 parents c2b1f8c + 58fca16
commit 21c753a
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diff --git a/ecf/scripts/gdas/atmos/gempak/jgdas_atmos_gempak.ecf b/ecf/scripts/gdas/atmos/gempak/jgdas_atmos_gempak.ecf
@@ -1,5 +1,5 @@
 #PBS -S /bin/bash
-#PBS -N %RUN%_atmos_gempak_%CYC%
+#PBS -N %RUN%_atmos_gempak_%FHR3%_%CYC%
 #PBS -j oe
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
@@ -31,9 +31,13 @@ module load gempak/${gempak_ver}
 
 module list
 
+#############################################################
+# environment settings
+#############################################################
 export cyc=%CYC%
 export cycle=t%CYC%z
 export USE_CFP=YES
+export FHR3=%FHR3%
 
 ############################################################
 # CALL executable job script here

diff --git a/ecf/scripts/gfs/atmos/gempak/jgfs_atmos_gempak.ecf b/ecf/scripts/gfs/atmos/gempak/jgfs_atmos_gempak.ecf
@@ -1,9 +1,9 @@
 #PBS -S /bin/bash
-#PBS -N %RUN%_atmos_gempak_%CYC%
+#PBS -N %RUN%_atmos_gempak_%FHR3%_%CYC%
 #PBS -j oe
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
-#PBS -l walltime=03:00:00
+#PBS -l walltime=00:30:00
 #PBS -l select=1:ncpus=28:mpiprocs=28:mem=2GB
 #PBS -l place=vscatter:shared
 #PBS -l debug=true
@@ -37,6 +37,7 @@ module list
 #############################################################
 export cyc=%CYC%
 export cycle=t%CYC%z
+export FHR3=%FHR3%
 
 ############################################################
 # CALL executable job script here

diff --git a/ecf/scripts/gfs/atmos/gempak/jgfs_atmos_pgrb2_spec_gempak.ecf b/ecf/scripts/gfs/atmos/gempak/jgfs_atmos_pgrb2_spec_gempak.ecf
@@ -1,9 +1,9 @@
 #PBS -S /bin/bash
-#PBS -N %RUN%_atmos_pgrb2_spec_gempak_%CYC%
+#PBS -N %RUN%_atmos_pgrb2_spec_gempak_%FHR3%_%CYC%
 #PBS -j oe
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
-#PBS -l walltime=00:30:00
+#PBS -l walltime=00:15:00
 #PBS -l select=1:ncpus=1:mem=1GB
 #PBS -l place=vscatter:shared
 #PBS -l debug=true
@@ -35,6 +35,7 @@ module list
 #############################################################
 export cyc=%CYC%
 export cycle=t%CYC%z
+export FHR3=%FHR3%
 
 ############################################################
 # CALL executable job script here

diff --git a/env/GAEA.env b/env/GAEA.env
@@ -12,24 +12,52 @@ step=$1
 export launcher="srun -l --export=ALL"
 export mpmd_opt="--multi-prog --output=mpmd.%j.%t.out"
 
+export OMP_STACKSIZE=2048000
+export NTHSTACK=1024000000
+
 ulimit -s unlimited
 ulimit -a
 
-if [[ "${step}" = "fcst" ]]; then
+if [[ "${step}" = "waveinit" ]]; then
+
+    export CFP_MP="YES"
+    if [[ "${step}" = "waveprep" ]]; then export MP_PULSE=0 ; fi
+    export wavempexec=${launcher}
+    export wave_mpmd=${mpmd_opt}
 
-    ppn="npe_node_${step}_${RUN}"
-    [[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
-    nprocs="npe_${step}_${RUN}"
-    [[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"
+elif [[ "${step}" = "fcst" ]]; then
 
+    if [[ "${CDUMP}" =~ "gfs" ]]; then
+        nprocs="npe_${step}_gfs"
+        ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
+    else
+        nprocs="npe_${step}"
+        ppn="npe_node_${step}"
+    fi
     (( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
     (( ntasks = nnodes*${!ppn} ))
     # With ESMF threading, the model wants to use the full node
     export APRUN_UFS="${launcher} -n ${ntasks}"
     unset nprocs ppn nnodes ntasks
 
+
 elif [[ "${step}" = "atmos_products" ]]; then
 
-    export USE_CFP="YES"  # Use MPMD for downstream product generation
+    export USE_CFP="YES"  # Use MPMD for downstream product generation on Hera
+
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+
+elif [[ "${step}" = "fit2obs" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_fit2obs))
+
+    export NTHREADS_FIT2OBS=${nth_fit2obs:-1}
+    [[ ${NTHREADS_FIT2OBS} -gt ${nth_max} ]] && export NTHREADS_FIT2OBS=${nth_max}
+    export MPIRUN="${launcher} -n ${npe_fit2obs} --cpus-per-task=${NTHREADS_FIT2OBS}"
 
 fi
diff --git a/env/HERCULES.env b/env/HERCULES.env
@@ -132,6 +132,16 @@ case ${step} in
     [[ ${NTHREADS_OCNANAL} -gt ${nth_max} ]] && export NTHREADS_OCNANAL=${nth_max}
     export APRUN_OCNANAL="${launcher} -n ${npe_ocnanalrun} --cpus-per-task=${NTHREADS_OCNANAL}"
  ;;
+"ocnanalecen")
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_ocnanalecen))
+
+    export NTHREADS_OCNANALECEN=${nth_ocnanalecen:-${nth_max}}
+    [[ ${NTHREADS_OCNANALECEN} -gt ${nth_max} ]] && export NTHREADS_OCNANALECEN=${nth_max}
+    export APRUN_OCNANALECEN="${launcher} -n ${npe_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
+;;
  "ocnanalchkpt")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

diff --git a/jobs/JGDAS_ATMOS_GEMPAK b/jobs/JGDAS_ATMOS_GEMPAK
@@ -3,27 +3,17 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak" -c "base gempak"
 
-# TODO (#1219) This j-job is not part of the rocoto suite
-
 ############################################
 # Set up model and cycle specific variables
 ############################################
-
-export fend=09
-export finc=3
-export fstart=00
-export GRIB=pgrb2f
+export model=${model:-gdas}
+export GRIB=${GRIB:-pgrb2f}
 export EXT=""
-export DBN_ALERT_TYPE=GDAS_GEMPAK
+export DBN_ALERT_TYPE=${DBN_ALERT_TYPE:-GDAS_GEMPAK}
 
 export SENDDBN=${SENDDBN:-NO}
 export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
 
-###################################
-# Specify NET and RUN Name and model
-####################################
-export model=${model:-gdas}
-
 ##############################################
 # Define COM directories
 ##############################################
@@ -40,26 +30,18 @@ for grid in 0p25 1p00; do
   fi
 done
 
-# TODO: These actions belong in an ex-script not a j-job
-if [[ -f poescript ]]; then
-   rm -f poescript
-fi
+########################################################
+# Execute the script for one degree grib
+########################################################
 
-{
-  ########################################################
-  # Execute the script.
-  echo "${SCRgfs}/exgdas_atmos_nawips.sh 1p00 009 GDAS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-  ########################################################
+"${SCRgfs}/exgdas_atmos_nawips.sh" "1p00" "${FHR3}" "GDAS_GEMPAK" "${COM_ATMOS_GEMPAK_1p00}"
 
-  ########################################################
-  # Execute the script for quater-degree grib
-  echo "${SCRgfs}/exgdas_atmos_nawips.sh 0p25 009 GDAS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  ########################################################
-} > poescript
+########################################################
+# Execute the script for quater-degree grib
+########################################################
 
-cat poescript
+"${SCRgfs}/exgdas_atmos_nawips.sh" "0p25" "${FHR3}" "GDAS_GEMPAK" "${COM_ATMOS_GEMPAK_0p25}"
 
-"${HOMEgfs}/ush/run_mpmd.sh" poescript
 export err=$?; err_chk
 
 ############################################

diff --git a/jobs/JGFS_ATMOS_GEMPAK b/jobs/JGFS_ATMOS_GEMPAK
@@ -6,27 +6,20 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak" -c "base gempak"
 ############################################
 # Set up model and cycle specific variables
 ############################################
-export finc=${finc:-3}
-export fstart=${fstart:-0}
 export model=${model:-gfs}
 export GRIB=${GRIB:-pgrb2f}
 export EXT=""
 export DBN_ALERT_TYPE=${DBN_ALERT_TYPE:-GFS_GEMPAK}
 
+export SENDDBN=${SENDDBN:-NO}
+export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
+
 # For half-degree P Grib files
 export DO_HD_PGRB=${DO_HD_PGRB:-YES}
 
-###################################
-# Specify NET and RUN Name and model
-####################################
-export model=${model:-gfs}
-
 ##############################################
 # Define COM directories
 ##############################################
-export SENDDBN=${SENDDBN:-NO}
-export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
-
 for grid in 0p25 0p50 1p00; do
   GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COM_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"
 done
@@ -40,73 +33,100 @@ for grid in 1p00 0p50 0p25 40km 35km_atl 35km_pac; do
   fi
 done
 
-# TODO: These actions belong in an ex-script not a j-job
-if [[ -f poescript ]]; then
-   rm -f poescript
-fi
-
+fhr=10#${FHR3}
 ocean_domain_max=180
 if (( ocean_domain_max > FHMAX_GFS )); then
   ocean_domain_max=${FHMAX_GFS}
 fi
 
-{
-  #################################################################
-  # Execute the script for the 384 hour 1 degree grib
-  ##################################################################
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 1p00 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 1p00 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 1p00 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 1p00 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 1p00 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 1p00 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}"
-
-  #################################################################
-  # Execute the script for the half-degree grib
-  ##################################################################
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p50 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p50}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p50 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p50}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p50 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p50}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p50 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p50}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p50 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p50}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p50 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p50}"
-
-  #################################################################
-  # Execute the script for the quater-degree grib
-  ####################################################################
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 0p25 ${FHMAX_GFS} GFS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}"
-
-  ####################################################################
-  # Execute the script to create the 35km Pacific grids for OPC
-  #####################################################################
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 35km_pac ${ocean_domain_max} GFS_GEMPAK_WWB ${COM_ATMOS_GEMPAK_35km_pac}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 35km_pac ${ocean_domain_max} GFS_GEMPAK_WWB ${COM_ATMOS_GEMPAK_35km_pac}"
-
-  ####################################################################
-  # Execute the script to create the 35km Atlantic grids for OPC
-  #####################################################################
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 35km_atl ${ocean_domain_max} GFS_GEMPAK_WWB ${COM_ATMOS_GEMPAK_35km_atl}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 35km_atl ${ocean_domain_max} GFS_GEMPAK_WWB ${COM_ATMOS_GEMPAK_35km_atl}"
-
-  #####################################################################
-  # Execute the script to create the 40km grids for HPC
-  ######################################################################
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 40km ${ocean_domain_max} GFS_GEMPAK_WWB ${COM_ATMOS_GEMPAK_40km}"
-  echo "time ${SCRgfs}/exgfs_atmos_nawips.sh 40km ${ocean_domain_max} GFS_GEMPAK_WWB ${COM_ATMOS_GEMPAK_40km}"
-} > poescript
-
-cat poescript
-
-"${HOMEgfs}/ush/run_mpmd.sh" poescript
+#################################################################
+# Execute the script for the 384 hour 1 degree grib
+##################################################################
+fhmin=0
+fhmax=240
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 3 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "1p00" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_1p00}"
+  fi
+fi
+
+fhmin=252
+fhmax=384
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 12 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "1p00" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_1p00}"
+  fi
+fi
+
+#################################################################
+# Execute the script for the half-degree grib
+##################################################################
+fhmin=0
+fhmax=240
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 3 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_0p50}"
+  fi
+fi
+
+fhmin=246
+fhmax=276
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 6 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_0p50}"
+  fi
+fi
+
+fhmin=288
+fhmax=384
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 12 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_0p50}"
+  fi
+fi
+
+#################################################################
+# Execute the script for the quater-degree grib
+####################################################################
+fhmin=0
+fhmax=120
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 1 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_0p25}"
+  fi
+fi
+
+fhmin=123
+fhmax=240
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 3 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_0p25}"
+  fi
+fi
+
+fhmin=252
+fhmax=384
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 12 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COM_ATMOS_GEMPAK_0p25}"
+  fi
+fi
+
+####################################################################
+# Execute the script to create the 35km and 40km grids
+#####################################################################
+fhmin=0
+fhmax="${ocean_domain_max}"
+if (( fhr >= fhmin && fhr <= fhmax )); then
+  if ((fhr % 3 == 0)); then
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "35km_pac" "${FHR3}" "GFS_GEMPAK_WWB" "${COM_ATMOS_GEMPAK_35km_pac}"
+
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "35km_atl" "${FHR3}" "GFS_GEMPAK_WWB" "${COM_ATMOS_GEMPAK_35km_atl}"
+
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "40km" "${FHR3}" "GFS_GEMPAK_WWB" "${COM_ATMOS_GEMPAK_40km}"
+  fi
+fi
+
 export err=$?; err_chk
 
 ############################################