diff --git a/FV3GFSwfm/rt_ccpp-chem/config.base b/FV3GFSwfm/rt_ccpp-chem/config.base
index 09add67ef6..c284439a1b 100644
--- a/FV3GFSwfm/rt_ccpp-chem/config.base
+++ b/FV3GFSwfm/rt_ccpp-chem/config.base
@@ -108,10 +108,11 @@ if [[ "$CDATE" -ge "2019092100" && "$CDATE" -le "2019110700" ]]; then
export DUMP_SUFFIX="p" # Use dumps from NCO GFS v15.3 parallel
fi
export RUNDIR="$STMP/RUNDIRS/$PSLOT"
+export RUNDIR1="/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem"
export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
export ARCDIR="$NOSCRUB/archive/$PSLOT"
export ICSDIR="/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3ICS"
-export ATARDIR="/BMC/$HPSS_PROJECT/2year/rt-CCPP-Chem"
+export ATARDIR="/BMC/$HPSS_PROJECT/2year/rt_CCPP-Chem"
# Commonly defined parameters in JJOBS
export envir=${envir:-"prod"}
diff --git a/FV3GFSwfm/rt_ccpp-chem/rt_ccpp-chem.xml b/FV3GFSwfm/rt_ccpp-chem/rt_ccpp-chem.xml
index 5a139b72b0..fc18cb0060 100644
--- a/FV3GFSwfm/rt_ccpp-chem/rt_ccpp-chem.xml
+++ b/FV3GFSwfm/rt_ccpp-chem/rt_ccpp-chem.xml
@@ -30,10 +30,14 @@
-
+
+
+
+
-
+
+
@@ -71,7 +75,7 @@
- 1:ppn=4:tpp=1">
+ 1:ppn=24:tpp=1">
@@ -140,10 +144,14 @@
CDUMP&CDUMP;
ICSDIR&ICSDIR;
PUBDIR&PUBDIR;
+ RETRODIR&RETRODIR;
GDASDIR&GDASDIR;
ROTDIR&ROTDIR;
- @Y@m@d@H@M00
+
+ @Y@m@d@H@M00
+ &GDASDIR;/@y@j0000.gdas.t00z.atmanl.nemsio
+
@@ -173,11 +181,19 @@
ROTDIR&ROTDIR;
-
- &PUBDIR;/@y@j@H00.&CDUMP;.t@Hz.atmanl.nemsio
- &PUBDIR;/@y@j@H00.&CDUMP;.t@Hz.sfcanl.nemsio
- &ICSDIR;/@Y@m@d@H/&CDUMP;/gdas_available
-
+
+
+
+ &PUBDIR;/@y@j@H00.gfs.t@Hz.atmanl.nemsio
+ &PUBDIR;/@y@j@H00.gfs.t@Hz.sfcanl.nemsio
+
+
+ &RETRODIR;/@y@j@H00.gfs.t@Hz.atmanl.nemsio
+ &RETRODIR;/@y@j@H00.gfs.t@Hz.sfcanl.nemsio
+
+
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/gdas_available
+
@@ -207,10 +223,16 @@
-
- &ICSDIR;/@Y@m@d@H/&CDUMP;/&CASE;/INPUT/gfs_data.tile6.nc
- &ICSDIR;/@Y@m@d@H/&CDUMP;/&CASE;/INPUT/sfc_data.tile6.nc
-
+
+
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/&CDUMP;.t@Hz.atmanl.nemsio
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/&CDUMP;.t@Hz.sfcanl.nemsio
+
+
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/siganl.&CDUMP;.@Y@m@d@H
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/sfcanl.&CDUMP;.@Y@m@d@H
+
+
&ICSDIR;/@Y@m@d@H/&CDUMP;/&CASE;/INPUT/gfs_data.tile6.nc
@@ -250,13 +272,13 @@
- &ICSDIR;/@Y@m@d@H/&CDUMP;/gdas.t@Hz.atmanl.nemsio
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/gdas.t@Hz.atmanl.nemsio
&ROTDIR;/&CDUMP;.@Y@m@d/@H/&CDUMP;.t@Hz.atmf000.nemsio
- &ICSDIR;/@Y@m@d@H/&CDUMP;/gdas.t@Hz.atmanl.nemsio
- &ICSDIR;/@Y@m@d@H/&CDUMP;/siganl.&CDUMP;.@Y@m@d@H
- &ICSDIR;/@Y@m@d@H/&CDUMP;/sfcanl.&CDUMP;.@Y@m@d@H
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/gdas.t@Hz.atmanl.nemsio
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/siganl.&CDUMP;.@Y@m@d@H
+ &ICSDIR;/@Y@m@d@H/&CDUMP;/&CDUMP;.@Y@m@d/@H/sfcanl.&CDUMP;.@Y@m@d@H
&ROTDIR;/&CDUMP;.@Y@m@d/@H/&CDUMP;.t@Hz.atmf000.nemsio
@@ -287,7 +309,8 @@
cyc@H
- &RUNDIR;/@Y@m@d@H/&CDUMP;/regrid/atmanl.@Y@m@d@H
+
+ &RUNDIR1;/@Y@m@d@H/&CDUMP;/regrid/atmanl.@Y@m@d@H
&ROTDIR;/&CDUMP;.@Y@m@d/@H/&CDUMP;.t@Hz.atmf024.nemsio
diff --git a/jobs/rocoto/calcinc.sh b/jobs/rocoto/calcinc.sh
index a1f1b2a68e..1a9230e5f7 100755
--- a/jobs/rocoto/calcinc.sh
+++ b/jobs/rocoto/calcinc.sh
@@ -48,9 +48,6 @@ export DATA="$RUNDIR/$CDATE/$CDUMP"
[[ ! -d $DATA ]] && mkdir -p $DATA
cd $DATA
-
-#ln -sf /scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem/$CDATE/$CDUMP/regrid regrid #lzhang
-ln -sf $RUNDIR1/$CDATE/$CDUMP/regrid regrid #lzhang
mkdir -p calcinc
cd calcinc
diff --git a/jobs/rocoto/calcinc.sh-org b/jobs/rocoto/calcinc.sh_rt
similarity index 95%
rename from jobs/rocoto/calcinc.sh-org
rename to jobs/rocoto/calcinc.sh_rt
index a1f1b2a68e..45f8b41884 100755
--- a/jobs/rocoto/calcinc.sh-org
+++ b/jobs/rocoto/calcinc.sh_rt
@@ -49,7 +49,6 @@ export DATA="$RUNDIR/$CDATE/$CDUMP"
cd $DATA
-#ln -sf /scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem/$CDATE/$CDUMP/regrid regrid #lzhang
ln -sf $RUNDIR1/$CDATE/$CDUMP/regrid regrid #lzhang
mkdir -p calcinc
cd calcinc
diff --git a/jobs/rocoto/checkgdas.sh b/jobs/rocoto/checkgdas.sh
new file mode 100755
index 0000000000..be11f0e077
--- /dev/null
+++ b/jobs/rocoto/checkgdas.sh
@@ -0,0 +1,110 @@
+#!/bin/bash
+
+## this script checks to see if GDAS atmanal file exists on $GDASDIR
+## [/scratch2/BMC/public/data/grids/gdas/bufr]
+## and creates gdas_available file under $ICSDIR/${CDATE}/${CDUMP}/$CDUMP.$yyyymmdd/$hh
+##
+## if file is missing from $GDASDIR, pulls file from mass store
+##
+
+###############################################################
+## Abstract:
+## Get GFS intitial conditions
+## RUN_ENVIR : runtime environment (emc | nco)
+## HOMEgfs : /full/path/to/workflow
+## EXPDIR : /full/path/to/config/files
+## CDATE : current date (YYYYMMDDHH)
+## CDUMP : cycle name (gdas / gfs)
+## PDY : current date (YYYYMMDD)
+## cyc : current cycle (HH)
+###############################################################
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Source relevant configs
+configs="base"
+for config in $configs; do
+ . $EXPDIR/config.${config}
+ status=$?
+ [[ $status -ne 0 ]] && exit $status
+done
+
+
+###############################################################
+# Set script and dependency variablesyyyymmdd=`echo $CDATE | cut -c1-8`
+yyyymmdd=$(echo $CDATE | cut -c1-8)
+hh=$(echo $CDATE | cut -c9-10)
+yyyy=$(echo $CDATE | cut -c1-4)
+mm=$(echo $CDATE | cut -c5-6)
+dd=$(echo $CDATE | cut -c7-8)
+yyddd=$(date +%y%j -u -d $yyyymmdd)
+
+
+echo
+echo "CDATE = $CDATE"
+echo "CDUMP = $CDUMP"
+echo "ICSDIR = $ICSDIR"
+echo "PUBDIR = $PUBDIR"
+echo "RETROGDAS = $RETROGDAS"
+echo "GDASDIR = $GDASDIR"
+echo "ROTDIR = $ROTDIR"
+echo "PSLOT = $PSLOT"
+echo
+
+## initialize
+fv3ic_dir=$ICSDIR/${CDATE}/${CDUMP}/$CDUMP.$yyyymmdd/$hh
+
+mkdir -p $fv3ic_dir
+cd $fv3ic_dir
+
+echo "YYYYMMDDHH: ${yyyymmdd}${hh}"
+
+gdasfile=$GDASDIR/${yyddd}${hh}00.gdas.t${hh}z.atmanl.nemsio
+ls $gdasfile #ESRL
+status=$?
+if [[ $status -ne 0 ]]; then
+ echo "missing $gdasfile on /public; check in $RETROGDAS..."
+ ls $gdasfile #ESRL
+ status=$?
+elif [[ $status -ne 0 ]]; then
+
+ echo "missing $gdasfile in $RETROGDAS; check on mass store..."
+
+ # Operational archive
+ # /NCEPPROD/hpssprod/runhistory/rh${yyyy}/${yyyy}${mm}/${yyyy}${mm}${dd}/
+ # {$nameprefix}_gfs_prod_gdas.${yyyy}${mm}${dd}_${hh}.gdas_nemsio.tar
+ #
+ # where nameprefix=com 00Z 02/26/2020
+ # gpfs_dell1_nco_ios_com 12Z 06/12/2019
+ #
+
+ HPSSDIR="/NCEPPROD/hpssprod/runhistory/rh${yyyy}/${yyyy}${mm}/${yyyy}${mm}${dd}"
+ gdasfile="${HPSSDIR}/com_gfs_prod_gdas.${yyyy}${mm}${dd}_${hh}.gdas_nemsio.tar"
+ hsi -q list $gdasfile
+ status=$?
+ if [[ $status -ne 0 ]]; then
+ ### 12Z 12Jun2019 -- FV3GFS operational
+ echo "missing $gdasfile on mass store...; try gpfs_dell1 filename!"
+ gdasfile=${HPSSDIR}/gpfs_dell1_nco_ops_com_gfs_prod_gdas.${yyyy}${mm}${dd}_${hh}.gdas_nemsio.tar
+ hsi -q list $gdasfile
+ status=$?
+ if [[ $status -ne 0 ]]; then
+ echo "missing $gfsfile on mass store..."
+ exit 1
+ fi
+ else
+ cd $fv3ic_dir
+ htar xvf ${gdasfile} ./gdas.${yyyymmdd}/${hh}/gdas.t${hh}z.atmanl.nemsio
+ mv gdas.${yyyymmdd}/${hh}/gdas.t${hh}z.atmanl.nemsio ./
+ echo removing gdas.${yyyymmdd}/${hh}....
+ rmdir gdas.${yyyymmdd}/${hh} gdas.${yyyymmdd}
+ touch gdas_available
+ fi
+else
+ touch gdas_available
+fi
diff --git a/jobs/rocoto/getic_gsd_fv3gfs.sh b/jobs/rocoto/getic_gsd_fv3gfs.sh
index e8be17706c..a28ffea2e1 100755
--- a/jobs/rocoto/getic_gsd_fv3gfs.sh
+++ b/jobs/rocoto/getic_gsd_fv3gfs.sh
@@ -17,6 +17,7 @@ echo "CDUMP = $CDUMP"
echo "ICSDIR = $ICSDIR"
echo "PUBDIR = $PUBDIR"
echo "RETRODIR = $RETRODIR"
+echo "GDASDIR = $GDASDIR"
echo "ROTDIR = $ROTDIR"
echo "PSLOT = $PSLOT"
echo
@@ -25,7 +26,7 @@ echo
yyyymmdd=`echo $CDATE | cut -c1-8`
hh=`echo $CDATE | cut -c9-10`
yyddd=`date +%y%j -u -d $yyyymmdd`
-fv3ic_dir=$ICSDIR/${CDATE}/${CDUMP}
+fv3ic_dir=$ICSDIR/${CDATE}/${CDUMP}/$CDUMP.$yyyymmdd/$hh
## EMC archive on disk
## /scratch1/NCEPDEV/rstprod/com/gfs/prod
@@ -63,3 +64,14 @@ else
echo "missing input files!"
exit 1
fi
+
+echo "YYYYMMDDHH: ${yyyymmdd}${hh}"
+gdasfile=$GDASDIR/${yyddd}${hh}00.gdas.t${hh}z.atmanl.nemsio
+
+if [[ -f $gdasfile ]]
+then
+ ln -fs $gdasfile gdas.t${hh}z.atmanl.nemsio
+fi
+
+echo $GDASDIR
+echo $gdasfile
diff --git a/jobs/rocoto/getic_gsd_gfs.sh b/jobs/rocoto/getic_gsd_gfs.sh
index 6e30efc364..4320ead668 100755
--- a/jobs/rocoto/getic_gsd_gfs.sh
+++ b/jobs/rocoto/getic_gsd_gfs.sh
@@ -13,6 +13,7 @@ echo "CDUMP = $CDUMP"
echo "ICSDIR = $ICSDIR"
echo "PUBDIR = $PUBDIR"
echo "RETRODIR = $RETRODIR"
+echo "GDASDIR = $GDASDIR"
echo "ROTDIR = $ROTDIR"
echo "PSLOT = $PSLOT"
echo
@@ -21,7 +22,7 @@ echo
yyyymmdd=`echo $CDATE | cut -c1-8`
hh=`echo $CDATE | cut -c9-10`
yyddd=`date +%y%j -u -d $yyyymmdd`
-fv3ic_dir=$ICSDIR/${CDATE}/${CDUMP}
+fv3ic_dir=$ICSDIR/${CDATE}/${CDUMP}/$CDUMP.$yyyymmdd/$hh
## create links in FV3ICS directory
mkdir -p $fv3ic_dir
@@ -46,3 +47,14 @@ else
fi
fi
fi
+
+echo "YYYYMMDDHH: ${yyyymmdd}${hh}"
+gdasfile=$GDASDIR/${yyddd}${hh}00.gdas.t${hh}z.atmanl.nemsio
+
+if [[ -f $gdasfile ]]
+then
+ ln -fs $gdasfile gdas.t${hh}z.atmanl.nemsio
+fi
+
+echo $GDASDIR
+echo $gdasfile
diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index d1c6c026b3..10fa96930e 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -85,7 +85,7 @@ export NCP="/bin/cp -p"
export NMV="/bin/mv"
export NLN="/bin/ln -sf"
export VERBOSE="YES"
-export KEEPDATA="NO"
+export KEEPDATA="YES"
export CHGRP_CMD="chgrp rstprod"
export NEMSIOGET="$HOMEgfs/exec/nemsio_get"
export NCDUMP="$NETCDF/bin/ncdump"