add initial jobs and parm (#47)

* add initial jobs and parm

* update jobs yaml xml

* Update land_da_orion.yaml

* add run fcst script

* update jjobs yaml

jobs/JLAND_PREP_BMAT

@@ -0,0 +1,82 @@
+#!/bin/sh
+
+set -ex
+
+############################
+# copy restarts to workdir, convert to UFS tile for DA (all members) 
+
+if [[ ${EXP_NAME} == "openloop" ]]; then
+    do_jedi="NO"
+else
+    do_jedi="YES"
+    SAVE_TILE="YES"
+    LANDDADIR=${CYCLEDIR}/DA_update/
+fi
+
+TPATH=${LANDDA_INPUTS}/forcing/${ATMOS_FORC}/orog_files/
+YYYY=${CTIME:0:4}
+MM=${CTIME:4:2}
+DD=${CTIME:6:2}
+HH=${CTIME:8:2}
+
+mem_ens="mem000" 
+
+MEM_WORKDIR=${WORKDIR}/${mem_ens}
+MEM_MODL_OUTDIR=${OUTDIR}/${mem_ens}
+RSTRDIR=${MEM_WORKDIR}
+JEDIWORKDIR=${WORKDIR}/mem000/jedi
+FILEDATE=${YYYY}${MM}${DD}.${HH}0000
+
+cd $MEM_WORKDIR
+
+# load modulefiles
+module use modulefiles; module load modules.landda
+PYTHON=$(/usr/bin/which python)
+
+#fv3bundle_vn=psl_develop
+#DAtype=letkfoi_snow
+#SNOWDEPTHVAR=snwdph
+YAML_DA=construct
+GFSv17="NO"
+B=30 # back ground error std for LETKFOI
+cd $JEDIWORKDIR
+
+################################################
+# 4. CREATE BACKGROUND ENSEMBLE (LETKFOI)
+################################################
+
+if [[ ${DAtype} == 'letkfoi_snow' ]]; then
+
+    JEDI_EXEC="fv3jedi_letkf.x"
+
+    if [ $GFSv17 == "YES" ]; then
+        SNOWDEPTHVAR="snodl"
+        # field overwrite file with GFSv17 variables.
+        cp ${LANDDADIR}/jedi/fv3-jedi/yaml_files/${fv3bundle_vn}/gfs-land-v17.yaml ${JEDIWORKDIR}/gfs-land-v17.yaml
+    else
+        SNOWDEPTHVAR="snwdph"
+    fi
+    # FOR LETKFOI, CREATE THE PSEUDO-ENSEMBLE
+    for ens in pos neg
+    do
+        if [ -e $JEDIWORKDIR/mem_${ens} ]; then
+                rm -r $JEDIWORKDIR/mem_${ens}
+        fi
+        mkdir -p $JEDIWORKDIR/mem_${ens}
+        for tile in 1 2 3 4 5 6
+        do
+        cp ${JEDIWORKDIR}/${FILEDATE}.sfc_data.tile${tile}.nc  ${JEDIWORKDIR}/mem_${ens}/${FILEDATE}.sfc_data.tile${tile}.nc
+        done
+        cp ${JEDIWORKDIR}/${FILEDATE}.coupler.res ${JEDIWORKDIR}/mem_${ens}/${FILEDATE}.coupler.res
+    done
+
+    echo 'do_landDA: calling create ensemble'
+
+    # using ioda mods to get a python version with netCDF4
+    ${PYTHON} ${LANDDADIR}/letkf_create_ens.py $FILEDATE $SNOWDEPTHVAR $B
+    if [[ $? != 0 ]]; then
+        echo "letkf create failed"
+        exit 10
+    fi
+
+fi

jobs/JLAND_PREP_EXP

@@ -0,0 +1,174 @@
+#!/bin/sh
+
+set -ex
+
+############################
+# copy restarts to workdir, convert to UFS tile for DA (all members) 
+
+if [[ ${EXP_NAME} == "openloop" ]]; then
+    do_jedi="NO"
+else
+    do_jedi="YES"
+    SAVE_TILE="YES"
+    LANDDADIR=${CYCLEDIR}/DA_update/
+fi
+
+echo ${LANDDA_INPUTS}, ${ATMOS_FORC}
+TPATH=${LANDDA_INPUTS}/forcing/${ATMOS_FORC}/orog_files/
+YYYY=${CTIME:0:4}
+MM=${CTIME:4:2}
+DD=${CTIME:6:2}
+HH=${CTIME:8:2}
+YYYP=${PTIME:0:4}
+MP=${PTIME:4:2}
+DP=${PTIME:6:2}
+HP=${PTIME:8:2}
+mem_ens="mem000" 
+
+MEM_WORKDIR=${WORKDIR}/${mem_ens}
+MEM_MODL_OUTDIR=${OUTDIR}/${mem_ens}
+RSTRDIR=${MEM_WORKDIR}
+JEDIWORKDIR=${WORKDIR}/mem000/jedi
+FILEDATE=${YYYY}${MM}${DD}.${HH}0000
+
+if [[ ! -e ${MEM_WORKDIR} ]]; then
+    mkdir -p ${MEM_WORKDIR}
+fi
+if [[ ! -e ${MEM_MODL_OUTDIR} ]]; then
+    mkdir -p ${MEM_MODL_OUTDIR}
+fi
+
+mkdir -p $MEM_WORKDIR/modulefiles; cp ${CYCLEDIR}/modulefiles/landda_${MACHINE}.intel.lua $MEM_WORKDIR/modulefiles/modules.landda.lua
+cd $MEM_WORKDIR
+
+# load modulefiles
+module use modulefiles; module load modules.landda
+
+if [[ $do_jedi == "YES" && $ATMOS_FORC == "era5" ]]; then
+
+    # copy restarts into work directory
+	rst_in=${MEM_MODL_OUTDIR}/restarts/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+	if [[ ! -e ${rst_in} ]]; then
+	    rst_in=${LANDDA_INPUTS}/restarts/${ATMOS_FORC}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+	    fi
+	rst_out=${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+	cp ${rst_in} ${rst_out}
+
+    echo '************************************************'
+    echo 'calling vector2tile' 
+
+    export MEM_WORKDIR
+
+    # update vec2tile and tile2vec namelists
+    cp  ${CYCLEDIR}/template.vector2tile vector2tile.namelist
+
+    sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" vector2tile.namelist
+    sed -i -e "s/XXYYYY/${YYYY}/g" vector2tile.namelist
+    sed -i -e "s/XXMM/${MM}/g" vector2tile.namelist
+    sed -i -e "s/XXDD/${DD}/g" vector2tile.namelist
+    sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
+    sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
+    sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" vector2tile.namelist
+    sed -i -e "s/XXRES/${RES}/g" vector2tile.namelist
+    sed -i -e "s/XXTSTUB/${TSTUB}/g" vector2tile.namelist
+    sed -i -e "s#XXTPATH#${TPATH}#g" vector2tile.namelist
+
+    # submit vec2tile 
+    echo '************************************************'
+    echo 'calling vector2tile' 
+
+    ${BUILDDIR}/vector2tile_converter.exe vector2tile.namelist
+    if [[ $? != 0 ]]; then
+        echo "vec2tile failed"
+        exit
+    fi
+fi # vector2tile for DA
+
+if [[ $do_jedi == "YES" && $ATMOS_FORC == "gswp3" ]]; then
+
+	echo '************************************************'
+	echo 'calling tile2tile'    
+
+	export MEM_WORKDIR
+
+        # copy restarts into work directory
+	for tile in 1 2 3 4 5 6
+	do
+	    rst_in=${MEM_MODL_OUTDIR}/restarts/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+	    if [[ ! -e ${rst_in} ]]; then  
+		rst_in=${LANDDA_INPUTS}/restarts/${ATMOS_FORC}/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
+		fi
+	    rst_out=${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc
+	    cp ${rst_in} ${rst_out}
+	    done
+
+    # update tile2tile namelist
+    cp  ${CYCLEDIR}/template.ufs2jedi ufs2jedi.namelist
+
+    sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" ufs2jedi.namelist
+    sed -i -e "s/XXYYYY/${YYYY}/g" ufs2jedi.namelist
+    sed -i -e "s/XXMM/${MM}/g" ufs2jedi.namelist
+    sed -i -e "s/XXDD/${DD}/g" ufs2jedi.namelist
+    sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
+    sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
+    sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" ufs2jedi.namelist
+    sed -i -e "s/XXRES/${RES}/g" ufs2jedi.namelist
+    sed -i -e "s/XXTSTUB/${TSTUB}/g" ufs2jedi.namelist
+    sed -i -e "s#XXTPATH#${TPATH}#g" ufs2jedi.namelist
+
+    # submit tile2tile    
+    ${BUILDDIR}/tile2tile_converter.exe ufs2jedi.namelist
+    if [[ $? != 0 ]]; then
+        echo "tile2tile failed"
+        exit 
+    fi
+fi # tile2tile for DA
+
+if [[ $do_jedi == "YES" ]]; then
+    if [[ ! -e ${OUTDIR}/DA ]]; then
+	mkdir -p ${OUTDIR}/DA/jedi_incr
+	mkdir -p ${OUTDIR}/DA/logs
+	mkdir -p ${OUTDIR}/DA/hofx        
+    fi    
+    if [[ ! -e $JEDIWORKDIR ]]; then
+	mkdir -p $JEDIWORKDIR
+    fi    
+    cd $JEDIWORKDIR
+
+    if [[ ! -e ${JEDIWORKDIR}/output ]]; then
+	ln -s ${OUTDIR} ${JEDIWORKDIR}/output
+    fi
+
+    if  [[ $SAVE_TILE == "YES" ]]; then
+	for tile in 1 2 3 4 5 6
+	do
+	    cp ${RSTRDIR}/${FILEDATE}.sfc_data.tile${tile}.nc  ${RSTRDIR}/${FILEDATE}.sfc_data_back.tile${tile}.nc
+	done
+    fi
+
+    #stage restarts for applying JEDI update (files will get directly updated)
+    for tile in 1 2 3 4 5 6
+    do
+	ln -fs ${RSTRDIR}/${FILEDATE}.sfc_data.tile${tile}.nc ${JEDIWORKDIR}/${FILEDATE}.sfc_data.tile${tile}.nc
+    done
+
+    cres_file=${JEDIWORKDIR}/${FILEDATE}.coupler.res    
+
+    if [[ -e  ${RSTRDIR}/${FILEDATE}.coupler.res ]]; then
+	ln -sf ${RSTRDIR}/${FILEDATE}.coupler.res $cres_file
+    else #  if not present, need to create coupler.res for JEDI
+	cp ${LANDDADIR}/template.coupler.res $cres_file
+
+	sed -i -e "s/XXYYYY/${YYYY}/g" $cres_file
+	sed -i -e "s/XXMM/${MM}/g" $cres_file
+	sed -i -e "s/XXDD/${DD}/g" $cres_file
+	sed -i -e "s/XXHH/${HH}/g" $cres_file
+
+	sed -i -e "s/XXYYYP/${YYYP}/g" $cres_file
+	sed -i -e "s/XXMP/${MP}/g" $cres_file
+	sed -i -e "s/XXDP/${DP}/g" $cres_file
+	sed -i -e "s/XXHP/${HP}/g" $cres_file
+
+    fi    
+fi # do_jedi setup
+

jobs/JLAND_PREP_OBS

@@ -0,0 +1,68 @@
+#!/bin/sh
+
+set -ex
+
+############################
+# copy restarts to workdir, convert to UFS tile for DA (all members) 
+
+if [[ ${EXP_NAME} == "openloop" ]]; then
+    do_jedi="NO"
+else
+    do_jedi="YES"
+    SAVE_TILE="YES"
+    LANDDADIR=${CYCLEDIR}/DA_update/
+fi
+
+TPATH=${LANDDA_INPUTS}/forcing/${ATMOS_FORC}/orog_files/
+YYYY=${CTIME:0:4}
+MM=${CTIME:4:2}
+DD=${CTIME:6:2}
+HH=${CTIME:8:2}
+YYYP=${PTIME:0:4}
+MP=${PTIME:4:2}
+DP=${PTIME:6:2}
+HP=${PTIME:8:2}
+
+mem_ens="mem000" 
+
+MEM_WORKDIR=${WORKDIR}/${mem_ens}
+MEM_MODL_OUTDIR=${OUTDIR}/${mem_ens}
+RSTRDIR=${MEM_WORKDIR}
+JEDIWORKDIR=${WORKDIR}/mem000/jedi
+FILEDATE=${YYYY}${MM}${DD}.${HH}0000
+
+cd $JEDIWORKDIR
+
+# load modulefiles
+#module use modulefiles; module load modules.landda
+
+OBSDIR=${LANDDA_INPUTS}/DA
+################################################
+# 2. PREPARE OBS FILES
+################################################
+for obs in "${OBS_TYPES[@]}"; do
+    # get the. obs file name
+    if [ ${obs} == "GTS" ]; then
+	obsfile=$OBSDIR/snow_depth/GTS/data_proc/${YYYY}${MM}/adpsfc_snow_${YYYY}${MM}${DD}${HH}.nc4
+	# GHCN are time-stamped at 18. If assimilating at 00, need to use previous day's obs, so that
+	# obs are within DA window.
+    elif [ $ATMOS_FORC == "era5" ] && [ ${obs} == "GHCN" ]; then
+	obsfile=$OBSDIR/snow_depth/GHCN/data_proc/v3/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}.nc
+    elif [ $ATMOS_FORC == "gswp3" ] && [ ${obs} == "GHCN" ]; then
+	obsfile=$OBSDIR/snow_depth/GHCN/data_proc/v3/${YYYY}/fake_ghcn_snwd_ioda_${YYYP}${MP}${DP}.nc
+    elif [ ${obs} == "SYNTH" ]; then
+	obsfile=$OBSDIR/synthetic_noahmp/IODA.synthetic_gswp_obs.${YYYY}${MM}${DD}${HH}.nc
+    else
+	echo "do_landDA: Unknown obs type requested ${obs}, exiting"
+	exit 1
+    fi
+
+    # check obs are available
+    if [[ -e $obsfile ]]; then
+	echo "do_landDA: $i observations found: $obsfile"
+	ln -fs $obsfile  ${obs}_${YYYY}${MM}${DD}${HH}.nc
+    else
+	echo "${obs} observations not found: $obsfile"
+	#    JEDI_TYPES[$ii]="SKIP"
+    fi
+done