add in ioda converters step; need to still add geovals part

ush/JEDI/readme.md

@@ -25,6 +25,11 @@ Things to change in submit_run_gsi.sh include:
 - guessroot: path to $ROTDIR
 - 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

ush/JEDI/run_gsi_iodaconv.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+# run_gsincdiag_iodaconv.sh
+# run python ioda-iodaconverters
+# on GSI netCDF diag files to generate
+# IODA formatted observations for UFO H(x)
+# [email protected]
+set -x
+## variable definitions
+MYDIR=`dirname "$0"`
+YAMLFILE=$1
+## source helper functions
+source $MYDIR/helpers/parse_yaml.sh
+
+## read YAML config file
+if [[ -e $YAMLFILE ]]; then
+   eval $(parse_yaml $YAMLFILE "IODA_")
+else
+  echo "ERROR: YAML FILE $YAMLFILE DOES NOT EXIST, ABORT!"
+  exit 1
+fi
+
+# source modulefile to get proper python on environment
+source $IODA_env_modulefile
+
+# make working directory
+rm -rf $IODA_data_iodaworkdir
+mkdir -p $IODA_data_iodaworkdir
+cd $IODA_data_iodaworkdir
+
+# make output directory
+rm -rf $IODA_data_iodaoutdir
+mkdir -p $IODA_data_iodaoutdir
+
+#
+# run script
+$IODA_iodaconv_iodaconvbin -n 20 -o $IODA_data_iodaoutdir $IODA_data_gsiindir
+
+if [[ "$IODA_iodaconv_cleanup" = "true" ]]; then
+  cd $IODA_data_iodaoutdir
+  rm -rf $IODA_data_iodaworkdir
+fi
+date
+echo "GSI ncdiag ioda converter script completed"

ush/JEDI/submit_run_gsi.sh

@@ -16,10 +16,12 @@ 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/
-rstprod='false'
+rstprod='true'
 cleanup='true'
 
 ##### do not modify below here ####
@@ -31,6 +33,7 @@ Ha=`echo $adate | cut -c9-10`
 
 mkdir -p $RootWork
 
+# create YAML for GSI observer
 rm -rf $RootWork/GSI_observer_$adate.yaml
 cat > $RootWork/GSI_observer_$adate.yaml << EOF
 background:
@@ -50,13 +53,37 @@ observations:
 observer:
   cleanup: $cleanup
   gsidir: $GSIDir
-  outputdir: $RootWork/${adate}_out
-  workdir: $RootWork/${adate}_work
+  outputdir: $RootWork/${adate}/GSI_out
+  workdir: $RootWork/${adate}/GSI_work
 time:
   cycle: '$Ha'
   day: '$Da'
   month: '$Ma'
   year: '$Ya'
 EOF
 
-$MyDir/run_gsi_observer.sh $RootWork/GSI_observer_$adate.yaml
+# 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