Commit before test to see if it is working

ShunLiu-NOAA · Oct 23, 2020 · 860e0fd · 860e0fd
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diff --git a/ush/JEDI/readme.md b/ush/JEDI/readme.md
@@ -26,10 +26,6 @@ Things to change in submit_run_gsi.sh include:
 - jcap, jcap_b, levs: hopefully self explanatory, set to match your background files
 - dump: gdas or gfs
 
-Things specific to the IODA-converters portion
-- iodaconvbuild: path to the build directory of the ioda-converters
-- JEDImodule: path to a modulefile to source to get the JEDI environment
-
 Other things one can change
 - RootWork: defaults to stmp2 but can be anywhere
 - obsdir: default is glopara global dump
@@ -41,6 +37,19 @@ sbatch submit_run_gsi.sh
 
 ### To convert these GSI netCDF diag files to JEDI UFO GeoVaLs files and IODA observation files
 
+At the end of submit_run_gsi.sh, by default, the script will then submit submit_run_iodaconv.sh.
+This is to save resources, as the IODA-converters script does not require more than one node.
+
+Things specific to the IODA-converters portion
+- iodaconvbuild: path to the build directory of the ioda-converters
+- JEDImodule: path to a modulefile to source to get the JEDI environment
+Other things you will still need to change
+- adate: YYYYMMDDHH analysis date (or it gets this from $1)
+- rootwork: if you changed this before, need to be consistent!
+
+To run this again, without running GSI, just submit the file to slurm.
+sbatch submit_run_iodaconv.sh YYYYMMDDHH
+
 ### Summary of changes made between NOAA-EMC/GSI/release/gfsda.v16.0.0 and this branch feature/jedi_gfsv16
 
 ### Example of where/how to add additional fields to GSI/ioda-converters
diff --git a/ush/JEDI/run_gsi_iodaconv.sh b/ush/JEDI/run_gsi_iodaconv.sh
@@ -33,7 +33,24 @@ mkdir -p $IODA_data_iodaoutdir
 
 #
 # run script
-$IODA_iodaconv_iodaconvbin -n 20 -o $IODA_data_iodaoutdir $IODA_data_gsiindir
+python $IODA_iodaconv_iodaconvbin -n 20 -o $IODA_data_iodaoutdir -g $IODA_data_geovaloutdir $IODA_data_gsiindir
+
+# subset obs
+python $IODA_iodaconv_subsetbin -n 24 -m $IODA_data_iodaoutdir -g $IODA_data_geovaloutdir
+python $IODA_iodaconv_subsetbin -n 24 -s $IODA_data_iodaoutdir -g $IODA_data_geovaloutdir
+
+# combine conventional obs
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sfc_*m.nc4 -o $IODA_data_iodaoutdir/sfc_obs_"$adate"_m.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sfcship_*m.nc4 -o $IODA_data_iodaoutdir/sfcship_obs_"$adate"_m.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/aircraft_*m.nc4 -o $IODA_data_iodaoutdir/aircraft_obs_"$adate"_m.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sondes_ps*m.nc4 $IODA_data_iodaoutdir/sondes_q*m.nc4 $IODA_data_iodaoutdir/sondes_tsen*m.nc4 $IODA_data_iodaoutdir/sondes_uv*m.nc4 -o $IODA_data_iodaoutdir/sondes_obs_"$adate"_m.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sondes_ps*m.nc4 $IODA_data_iodaoutdir/sondes_q*m.nc4 $IODA_data_iodaoutdir/sondes_tv*m.nc4 $IODA_data_iodaoutdir/sondes_uv*m.nc4 -o $IODA_data_iodaoutdir/sondes_tvirt_obs_"$adate"_m.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sfc_*s.nc4 -o $IODA_data_iodaoutdir/sfc_obs_"$adate"_s.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sfcship_*s.nc4 -o $IODA_data_iodaoutdir/sfcship_obs_"$adate"_s.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/aircraft_*s.nc4 -o $IODA_data_iodaoutdir/aircraft_obs_"$adate"_s.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sondes_ps*s.nc4 $IODA_data_iodaoutdir/sondes_q*s.nc4 $IODA_data_iodaoutdir/sondes_tsen*s.nc4 $IODA_data_iodaoutdir/sondes_uv*s.nc4 -o $IODA_data_iodaoutdir/sondes_obs_"$adate"_s.nc4 -g $IODA_data_geovaloutdir/
+python $IODA_iodaconv_combineconvbin -i $IODA_data_iodaoutdir/sondes_ps*s.nc4 $IODA_data_iodaoutdir/sondes_q*s.nc4 $IODA_data_iodaoutdir/sondes_tv*s.nc4 $IODA_data_iodaoutdir/sondes_uv*s.nc4 -o $IODA_data_iodaoutdir/sondes_tvirt_obs_"$adate"_s.nc4 -g $IODA_data_geovaloutdir/
+
 
 if [[ "$IODA_iodaconv_cleanup" = "true" ]]; then
   cd $IODA_data_iodaoutdir

diff --git a/ush/JEDI/run_gsi_observer.sh b/ush/JEDI/run_gsi_observer.sh
@@ -35,7 +35,7 @@ export APRUN_GSI=$GSI_env_launcher
 
 ## variables for executables
 gsiexec=$GSIDIR/exec/global_gsi.x
-nccat=$GSIDIR/exec/nc_diag_cat_serial.x
+nccat=$GSIDIR/exec/ncdiag_cat.x
 NDATE=${NDATE:-`which ndate`}
 ncpc=/bin/cp
 ncpl="ln -fs"

diff --git a/ush/JEDI/submit_run_gsi.sh b/ush/JEDI/submit_run_gsi.sh
@@ -16,8 +16,6 @@ jcap=766
 jcap_b=1534
 levs=64
 dump='gdas'
-iodaconvbuild=/scratch1/NCEPDEV/da/Cory.R.Martin/JEDI/ioda-converters/build
-JEDImodule=/scratch1/NCEPDEV/da/Cory.R.Martin/JEDI/env_jedi_rh
 ##### things it is not necessary to change but you can
 RootWork=/scratch1/NCEPDEV/stmp2/$LOGNAME/GSI_forJEDI/
 obsdir=/scratch1/NCEPDEV/global/glopara/dump/
@@ -65,25 +63,5 @@ EOF
 # run GSI observer
 $MyDir/run_gsi_observer.sh $RootWork/GSI_observer_$adate.yaml || exit 1
 
-# create YAML for IODA converters
-rm -rf $RootWork/GSI_iodaconv_$adate.yaml
-cat > $RootWork/GSI_iodaconv_$adate.yaml << EOF
-data:
-  gsiindir: $RootWork/${adate}/GSI_out
-  iodaoutdir: $RootWork/${adate}/output
-  iodaworkdir: $RootWork/${adate}/iodaconv_work
-env:
-  launcher: srun --export=ALL
-  modulefile: $JEDImodule
-  nthreads: 1
-iodaconv:
-  iodaconvbin: $iodaconvbuild/bin/proc_gsi_ncdiag.py
-time:
-  cycle: '$Ha'
-  day: '$Da'
-  month: '$Ma'
-  year: '$Ya'
-EOF
-
-# run IODA converters
-$MyDir/run_gsi_iodaconv.sh $RootWork/GSI_iodaconv_$adate.yaml || exit 1
+# submit the IODA-converters script, comment out if you do not want to run this
+sbatch $MyDir/submit_run_iodaconv.sh $adate
diff --git a/ush/JEDI/submit_run_iodaconv.sh b/ush/JEDI/submit_run_iodaconv.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+#SBATCH --ntasks-per-node 40
+#SBATCH -A da-cpu
+#SBATCH -J run_gsi_iodaconv
+#SBATCH -t 00:30:00
+#SBATCH -q debug
+#SBATCH --nodes 1
+
+##### things you should change/confirm
+adate=$1
+iodaconvbuild=/scratch1/NCEPDEV/da/Cory.R.Martin/JEDI/ioda-converters/build
+JEDImodule=/scratch1/NCEPDEV/da/Cory.R.Martin/JEDI/env_jedi_rh
+##### things it is not necessary to change but you can
+RootWork=/scratch1/NCEPDEV/stmp2/$LOGNAME/GSI_forJEDI/
+cleanup='true'
+
+##### do not modify below here ####
+MyDir=$GSIDir/ush/JEDI
+Ya=`echo $adate | cut -c1-4`
+Ma=`echo $adate | cut -c5-6`
+Da=`echo $adate | cut -c7-8`
+Ha=`echo $adate | cut -c9-10`
+
+mkdir -p $RootWork
+
+# create YAML for IODA converters
+rm -rf $RootWork/GSI_iodaconv_$adate.yaml
+cat > $RootWork/GSI_iodaconv_$adate.yaml << EOF
+data:
+  gsiindir: $RootWork/${adate}/GSI_out
+  iodaoutdir: $RootWork/${adate}/ioda
+  geovaloutdir: $RootWork/${adate}/geovals
+  iodaworkdir: $RootWork/${adate}/iodaconv_work
+env:
+  launcher: srun --export=ALL
+  modulefile: $JEDImodule
+  nthreads: 1
+iodaconv:
+  iodaconvbin: $iodaconvbuild/bin/proc_gsi_ncdiag.py
+  subsetbin: $iodaconvbuild/bin/subset_files.py
+  combineconvbin: $iodaconvbuild/bin/combine_conv.py
+time:
+  cycle: '$Ha'
+  day: '$Da'
+  month: '$Ma'
+  year: '$Ya'
+EOF
+
+# run IODA converters
+$MyDir/run_gsi_iodaconv.sh $RootWork/GSI_iodaconv_$adate.yaml || exit 1