Updates to run "base" s2s-prototype4

.gitignore

@@ -1,6 +1,6 @@
 __pycache__
 exec/
-fix/
+fix
 fix/0readme
 fix/fix_am
 fix/fix_chem

Externals_coupled.cfg

@@ -1,12 +1,12 @@
 [ufs-s2s-model]
-tag = v3.1
+tag = s2s_prototype4.0
 local_path = sorc/fv3_coupled.fd
 repo_url = https://github.com/ufs-community/ufs-s2s-model
 protocol = git
 required = True
 
 [EMC_post]
-hash = ba7e59b2
+tag = upp_gfsv16_release.v1.0.8
 local_path = sorc/gfs_post.fd
 repo_url = https://github.com/NOAA-EMC/EMC_post.git
 protocol = git

README.md

@@ -15,7 +15,10 @@ sh build_ncep_post.sh        #This command will build ncep_post.
 sh build_fv3_coupled.sh      #This command will build ufs-s2s-model
 
 To link fixed files and executable programs for the coupled application:
+On Hera: 
 sh link_fv3gfs.sh emc hera coupled
+On Orion: 
+sh link_fv3gfs.sh emc orion coupled
 ```
 
 ## Create CROW user file
@@ -56,6 +59,15 @@ mkdir -p $EXPROOT
 or
 
 ./setup_case.sh -p HERA ../cases/coupled_free_forecast.yaml test_3d
+
+
+For Orion: 
+First make sure you have python loaded: 
+module load contrib
+module load rocoto
+module load intelpython3
+and then replace ORION with HERA in the commands above. 
+
 ```
 This will create a experiment directory ($EXPERIMENT_DIRECTORY). In the current example, $EXPERIMENT_DIRECTORY=$EXPROOT/test_3d.
 

jobs/JWAVE_INIT

@@ -0,0 +1,93 @@
+#!/bin/bash
+
+date
+export PS4=' $SECONDS + '
+set -x -e
+
+#############################
+# Source relevant config files
+#############################
+configs="base wave waveinit"
+export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
+for config in $configs; do
+    . $config_path/config.$config
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+##########################################
+# Source machine runtime environment
+##########################################
+. $HOMEgfs/env/${machine}.env waveinit
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+# PATH for working directory
+export NET=${NET:-gfs}
+export RUN=${RUN:-gfs}
+export COMPONENTwave=${COMPONENTwave:-${RUN}wave}
+
+export HOMEgfs=${HOMEgfs:-$NWROOT/${NET}.${gfs_ver}}
+
+# Add default errchk = err_chk
+export errchk=${errchk:-err_chk}
+
+# Set HOMEwave to HOMEgfs
+HOMEwave=${HOMEwave:-${HOMEgfs}} 
+
+# Create and go to DATA directory
+export DATA=${DATA:-${DATAROOT:?}/${jobid}}
+mkdir -p $DATA
+cd $DATA
+
+cyc=${cyc:-00}
+export cycle=${cycle:-t${cyc}z}
+
+# Set PDY
+setpdy.sh
+sh ./PDY
+
+export pgmout=OUTPUT.$$
+
+export MP_PULSE=0
+
+# Set resources to propagate NTASKS across cfp call
+NTASKS=${NTASKS:-${npe_node_waveinit}}
+export NTASKS=${NTASKS:?NTASKS required to be set}
+
+# Path to HOME Directory
+export CODEwave=${CODEwave:-${HOMEfv3gfs}/WW3}
+export EXECwave=${EXECwave:-$HOMEwave/exec}
+export FIXwave=${FIXwave:-$HOMEwave/fix/fix_wave_${NET}}
+export PARMwave=${PARMwave:-$HOMEwave/parm/wave}
+export USHwave=${USHwave:-$HOMEwave/ush}
+export EXECcode=${EXECcode:-$CODEwave/exec}
+
+# Set COM Paths and GETGES environment
+export COMINwave=${COMINwave:-${ROTDIR:?}}
+export COMOUTwave=${COMOUTwave:-${ROTDIR:?}}
+export COMIN=${COMIN:-${COMINwave}/${COMPONENTwave}.${PDY}/${cyc}}
+export COMOUT=${COMOUT:-${COMOUTwave}/${COMPONENTwave}.${PDY}/${cyc}}
+[[ ! -d $COMOUT ]] && mkdir -m 775 -p $COMOUT
+
+if [ $SENDCOM = YES ]; then
+  mkdir -p $COMOUT/rundata
+fi
+
+export wavelog=${COMOUTwave}/wave.log
+
+# Set mpi serial command
+export wavempexec=${wavempexec:-"mpirun -n"}
+export wave_mpmd=${wave_mpmd:-"cfp"}
+
+# Execute the Script  
+$HOMEwave/scripts/exwave_init.sh
+
+# Remove temp directories
+if [ "$KEEPDATA" != "YES" ]; then
+  cd $DATAROOT
+  rm -rf $DATA
+fi
+date
+

jobs/JWAVE_POST_SBS

@@ -0,0 +1,117 @@
+#!/bin/bash
+
+date
+export PS4=' $SECONDS + '
+set -x -e
+
+#############################
+# Source relevant config files
+#############################
+configs="base wave wavepostsbs"
+export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
+for config in $configs; do
+    . $config_path/config.$config
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+##########################################
+# Source machine runtime environment
+##########################################
+. $HOMEgfs/env/${machine}.env wavepostsbs
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+# PATH for working directory
+export NET=${NET:-gfs}
+export RUN=${RUN:-gfs}
+export COMPONENTwave=${COMPONENTwave:-${RUN}wave}
+
+export HOMEgefs=${HOMEgefs:-$NWROOT/$NET.${gefs_ver}}
+export HOMEgfs=${HOMEgfs:-$NWROOT/$NET.${gfs_ver}}
+
+# Add default errchk = err_chk
+export errchk=${errchk:-err_chk}
+
+# Set HOMEwave to HOMEgefs
+HOMEwave=${HOMEwave:-${HOMEgfs}} 
+
+# Set resources to propagate NTASKS across cfp call
+NTASKS=${NTASKS:-${npe_node_waveprep}}
+export NTASKS=${NTASKS:?NTASKS required to be set}
+
+# Create and go to DATA directory
+export DATA=${DATA:-${DATAROOT:?}/${jobid}}
+mkdir -p $DATA
+cd $DATA
+
+export cyc=${cyc:-00}
+export cycle=${cycle:-t${cyc}z}
+
+# Set PDY
+setpdy.sh
+sh ./PDY
+
+export pgmout=OUTPUT.$$
+
+export MP_PULSE=0
+
+# Path to HOME Directory
+export CODEwave=${CODEwave:-${HOMEfv3gfs}/WW3}
+export EXECwave=${EXECwave:-$HOMEwave/exec}
+export FIXwave=${FIXwave:-$HOMEwave/fix/fix_wave_${NET}}
+export PARMwave=${PARMwave:-$HOMEwave/parm/wave}
+export USHwave=${USHwave:-$HOMEwave/ush}
+export EXECcode=${EXECcode:-$CODEwave/exec}
+
+# Set COM Paths and GETGES environment
+export COMINwave=${COMINwave:-${ROTDIR:?}}
+export COMOUTwave=${COMOUTwave:-${ROTDIR:?}}
+export COMIN=${COMIN:-${COMINwave}/${COMPONENTwave}.${PDY}/${cyc}}
+export COMOUT=${COMOUT:-${COMOUTwave}/${COMPONENTwave}.${PDY}/${cyc}}
+
+export COMINice=${COMINice:-${COMROOTp2}/omb/prod}
+export COMINwnd=${COMINwnd:-${COMROOT}/gfs/prod}
+export COMIN_WAV_CUR=${COMIN_WAV_CUR:-${COMROOTp2}/rtofs/prod}
+
+mkdir -p $COMOUT/gridded
+mkdir -p $COMOUT/station
+mkdir -p $COMOUT/stats
+
+export wavelog=${COMOUTwave}/wave.log
+
+# Set mpi serial command
+export wavempexec=${wavempexec:-"mpirun -n"}
+export wave_mpmd=${wave_mpmd:-"cfp"}
+
+env | sort
+
+# Set wave model ID tag to include member number 
+# if ensemble; waveMEMB var empty in deterministic
+# Set wave model ID tag to include member number
+# if ensemble; waveMEMB var empty in deterministic
+membTAG='p'
+if [ "${waveMEMB}" == "00" ]; then membTAG='c'; fi
+export membTAG
+export WAV_MOD_TAG=${COMPONENTwave}${waveMEMB}
+
+export CFP_VERBOSE=1
+
+# Execute the Script  
+$HOMEwave/scripts/exwave_post_sbs.sh
+err=$?
+if [ $err -ne 0 ]; then
+  msg="FATAL ERROR: ex-script of GWES_POST failed!"
+else
+  msg="$job completed normally!"
+fi
+postmsg "$jlogfile" "$msg"
+
+# Remove temp directories
+if [ "$KEEPDATA" != "YES" ]; then
+  cd $DATAROOT
+  rm -rf $DATA
+fi
+date
+

jobs/JWAVE_PREP

@@ -0,0 +1,126 @@
+#!/bin/bash
+
+date
+export PS4=' $SECONDS + '
+set -x -e
+
+#############################
+# Source relevant config files
+#############################
+configs="base wave waveprep"
+export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
+for config in $configs; do
+    . $config_path/config.$config
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+##########################################
+# Source machine runtime environment
+##########################################
+. $HOMEgfs/env/${machine}.env waveprep
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+# PATH for working directory
+export NET=${NET:-gfs}
+export RUN=${RUN:-gfs}
+export COMPONENTwave=${COMPONENTwave:-${RUN}wave}
+
+export HOMEgfs=${HOMEgfs:-$NWROOT/gfs.${gfs_ver}}
+
+# Add default errchk = err_chk
+export errchk=${errchk:-err_chk}
+
+# Set HOMEwave to HOMEgfs
+HOMEwave=${HOMEwave:-${HOMEgfs}} 
+
+# Set resources to propagate NTASKS across cfp call
+NTASKS=${NTASKS:-${npe_node_waveprep}}
+export NTASKS=${NTASKS:?NTASKS required to be set}
+
+# Create and go to DATA directory
+export DATA=${DATA:-${DATAROOT:?}/${jobid}}
+mkdir -p $DATA
+cd $DATA
+
+cyc=${cyc:-00}
+export cycle=${cycle:-t${cyc}z}
+
+# Set PDY
+setpdy.sh
+sh ./PDY
+# Set rtofs PDY
+export RPDY=$PDY
+
+export pgmout=OUTPUT.$$
+
+export MP_PULSE=0
+
+# CDO required for processing RTOFS currents
+# export CDO=${COMROOTp2}/nwprod/rtofs_glo.v1.2.0/bin/cdo
+export CDO=/gpfs/dell2/emc/verification/noscrub/Todd.Spindler/CDO/bin/cdo
+
+# Path to HOME Directory
+export CODEwave=${CODEwave:-${HOMEfv3gfs}/WW3}
+export EXECwave=${EXECwave:-$HOMEwave/exec}
+export FIXwave=${FIXwave:-$HOMEwave/fix/fix_wave_${NET}}
+export PARMwave=${PARMwave:-$HOMEwave/parm/wave}
+export USHwave=${USHwave:-$HOMEwave/ush}
+export EXECcode=${EXECcode:-$CODEwave/exec}
+
+###################################
+# Set COM Paths and GETGES environment
+###################################
+# Set COM Paths and GETGES environment
+export COMINwave=${COMINwave:-${ROTDIR:?}}
+export COMOUTwave=${COMOUTwave:-${ROTDIR:?}}
+export COMIN=${COMIN:-${COMINwave}/${COMPONENTwave}.${PDY}/${cyc}}
+export COMOUT=${COMOUT:-${COMOUTwave}/${COMPONENTwave}.${PDY}/${cyc}}
+[[ ! -d $COMOUT ]] && mkdir -m 775 -p $COMOUT
+
+if [ $RUN_ENVIR = "nco" ]; then
+  export COMIN_WAV_ICE=${COMIN_WAV_ICE:-$(compath.py gfs/prod)}/${CDUMP}.${PDY}/${cyc}
+  export COMIN_WAV_WND=${COMIN_WAV_WND:-$(compath.py gfs/prod)}/${CDUMP}.${PDY}/${cyc}
+  export COMIN_WAV_CUR=${COMIN_WAV_CUR:-$(compath.py ${WAVECUR_DID}/prod)}/${WAVECUR_DID}.${RPDY}
+  if [ ! -d $COMIN_WAV_CUR ]; then
+    export RPDY=`$NDATE -24 ${PDY}00 | cut -c1-8`
+    export COMIN_WAV_CUR=$(compath.py ${WAVECUR_DID}/prod)/${WAVECUR_DID}.${RPDY}
+  fi
+else 
+  if [ ! -d $DMPDIR/${WAVECUR_DID}.${RPDY} ]; then export RPDY=`$NDATE -24 ${PDY}00 | cut -c1-8`; fi
+  if [ ! -L $ROTDIR/${WAVECUR_DID}.${RPDY} ]; then # Check if symlink already exists in ROTDIR
+    $NLN $DMPDIR/${WAVECUR_DID}.${RPDY} $ROTDIR/${WAVECUR_DID}.${RPDY}
+  fi
+  $NLN $DMPDIR/$CDUMP.${PDY}/$cyc/${WAVICEFILE} $ROTDIR/$CDUMP.${PDY}/$cyc/${WAVICEFILE}
+  export COMIN_OBS=${COMIN_OBS:-$ROTDIR/$RUN.$PDY/$cyc}
+  export COMIN_WAV_ICE=${COMIN_OBS}
+  export COMIN_WAV_WND=${COMIN_OBS}
+  export COMIN_WAV_CUR=${ROTDIR}/${WAVECUR_DID}.${RPDY}
+fi
+
+if [ $SENDCOM = YES ]; then
+  mkdir -p $COMOUT
+fi
+
+export wavelog=${COMOUTwave}/wave.log
+
+# Set mpi serial command
+export wavempexec=${wavempexec:-"mpirun -n"}
+export wave_mpmd=${wave_mpmd:-"cfp"}
+
+# Set wave model ID tag to include member number 
+# if ensemble; waveMEMB var empty in deterministic
+export WAV_MOD_TAG=${COMPONENTwave}${waveMEMB}
+
+# Execute the Script  
+$HOMEwave/scripts/exwave_prep.sh
+
+# Remove temp directories
+if [ "$KEEPDATA" != "YES" ]; then
+  cd $DATAROOT
+  rm -rf $DATA
+fi
+date
+