get nco command from baselib

Author: weiyuan-jiang

GEOSldas_App/lenkf_j_template.py

@@ -63,6 +63,8 @@
 
 source $GEOSBIN/g5_modules
 
+setenv BASEBIN ${{BASEDIR}}/Linux/bin
+
 setenv MPI_STACK {DETECTED_MPI_STACK}
 
 if ( ${{MPI_STACK}} == "openmpi" ) then
@@ -103,11 +105,6 @@
 # reversed sequence for LADAS_COUPLING (Sep 2020)  (needed when coupling with ADAS using different BASEDIR)
 setenv LD_LIBRARY_PATH ${{BASEDIR}}/${{ARCH}}/lib:${{ESMADIR}}/lib:${{LD_LIBRARY_PATH}}
 
-module load nco
-# the nco module prepends to UDUNITS2_XML_PATH which Baselibs/g5_modules has already set
-# So here we reset to the one in Baselibs
-setenv UDUNITS2_XML_PATH ${{BASEDIR}}/${{ARCH}}/share/udunits/udunits2.xml
-
 setenv RUN_CMD "$GEOSBIN/esma_mpirun -np "
 
 #######################################################################
@@ -605,9 +602,9 @@
 
              sed -i -e "s/NT/$LEN_SUB/g" timestamp.cdl
              sed -i -e "s/DATAVALUES/$tstep2/g" timestamp.cdl
-             ncgen -k4 -o timestamp.nc4 timestamp.cdl
-             ncrcat -h $EXPID.$ThisCol.${{YYYY}}${{MM}}${{DD}}_* ${{EXPID}}.${{ThisCol}}.$YYYY$MM$DD.nc4
-             ncks -4 -h -v time_stamp timestamp.nc4 -A ${{EXPID}}.${{ThisCol}}.$YYYY$MM$DD.nc4
+             $BASEBIN/ncgen -k4 -o timestamp.nc4 timestamp.cdl
+             $BASEBIN/ncrcat -h $EXPID.$ThisCol.${{YYYY}}${{MM}}${{DD}}_* ${{EXPID}}.${{ThisCol}}.$YYYY$MM$DD.nc4
+             $BASEBIN/ncks -4 -h -v time_stamp timestamp.nc4 -A ${{EXPID}}.${{ThisCol}}.$YYYY$MM$DD.nc4
              /bin/rm timestamp.cdl
              /bin/rm timestamp.nc4
              # rudimentary check for desired nc4 file;  if ok, delete sub-daily files
@@ -748,7 +745,7 @@
           set tmp_file = $EXPDIR/output/$EXPDOMAIN/rs/$ENSDIR/Y${{eYEAR}}/M${{eMON}}/${{EXPID}}.${{rstf}}_internal_rst.${{eYEAR}}${{eMON}}${{eDAY}}_${{eHour}}${{eMin}}
 	  # copy generic restart file to final location/name but remove lat/lon variables
 	  #  (lat/lon variables are not correct when running in EASE-grid tile space)
-          ncks -4 -O -C -x -v lat,lon ${{rstf}}${{ENSID}}_internal_checkpoint $tmp_file
+          $BASEBIN/ncks -4 -O -C -x -v lat,lon ${{rstf}}${{ENSID}}_internal_checkpoint $tmp_file
           /bin/rm -f ${{rstf}}${{ENSID}}_internal_checkpoint
           set old_rst = `/usr/bin/readlink -f $EXPDIR/input/restart/${{rstf}}${{ENSID}}_internal_rst`
           /bin/rm -f $EXPDIR/input/restart/${{rstf}}${{ENSID}}_internal_rst
@@ -780,7 +777,7 @@
           set TM = `echo $ThisTime | cut -c5-6`
           set THISDIR = $EXPDIR/output/$EXPDOMAIN/rs/$ENSDIR/Y${{TY}}/M${{TM}}/
           if (! -e $THISDIR            ) mkdir -p $THISDIR
-             (ncks -4 -O -C -x -v lat,lon $rfile ${{THISDIR}}${{EXPID}}.landpert_internal_rst.${{ThisTime}}.nc4;\\
+             ($BASEBIN/ncks -4 -O -C -x -v lat,lon $rfile ${{THISDIR}}${{EXPID}}.landpert_internal_rst.${{ThisTime}}.nc4;\\
                /usr/bin/gzip ${{THISDIR}}${{EXPID}}.landpert_internal_rst.${{ThisTime}}.nc4; \\
                /bin/rm -f $rfile) &
        end