Introduce NCP and FCP in ush/hafs_runcmd.sh.inc. Under NCO environment,

NCP is set as cpreq, FCP is set as cpfs. Meanwhile, if desired, they can
be easily override at ecf or jjob levels.

ecf/post/jhafs_gempak.ecf

@@ -35,8 +35,6 @@ module load wgrib2/${wgrib2_ver}
 module load gempak/${gempak_ver}
 module list
 
-export NCP=cpfs 
-
 ${HOMEhafs}/jobs/JHAFS_GEMPAK
 
 %include <tail.h>

scripts/exhafs_analysis.sh

@@ -609,7 +609,7 @@ set -o pipefail
 ${APRUNC} ./hafs_gsi.x 2>&1 | tee ./stdout
 set +o pipefail
 
-${NCP} -p ./stdout ${GSISOUT}
+cat ./stdout > ${GSISOUT}
 
 # Cat runtime output files.
 cat fort.2* > ${GSISTAT}
@@ -836,8 +836,8 @@ fi # End diagnostic file generation block - if [ $GENDIAG = "YES" ]
 
 # Save satbias data for next cycle
 if [ ${online_satbias} = "yes" ]; then
-  ${NCP} satbias_out $DIAGanl/${out_prefix}.${RUN}.${gridstr}.analysis.abias
-  ${NCP} satbias_pc.out $DIAGanl/${out_prefix}.${RUN}.${gridstr}.analysis.abias_pc
+  ${FCP} satbias_out $DIAGanl/${out_prefix}.${RUN}.${gridstr}.analysis.abias
+  ${FCP} satbias_pc.out $DIAGanl/${out_prefix}.${RUN}.${gridstr}.analysis.abias_pc
 fi
 
 # If no processing error, remove $DIAG_DIR

scripts/exhafs_atm_post.sh

@@ -497,35 +497,35 @@ if [ -s ${INPdir}/${grid_spec} ] && [ ${INPdir}/${grid_spec} -nt ${INPdir}/RESTA
 fi
 if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
    [ -s ${INPdir}/RESTART/${grid_spec} ] && [ ${INPdir}/RESTART/${grid_spec} -nt ${RESTARTcom}/${grid_spec} ]; then
-  ${NCP} -pL ${INPdir}/RESTART/${grid_spec} ${RESTARTcom}/
+  ${FCP} ${INPdir}/RESTART/${grid_spec} ${RESTARTcom}/
 fi
 if [ -s ${INPdir}/${atmos_static} ] && [ ${INPdir}/${atmos_static} -nt ${INPdir}/RESTART/${atmos_static} ]; then
   ${NCP} -pL ${INPdir}/${atmos_static} ${INPdir}/RESTART/
 fi
 if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
    [ -s ${INPdir}/RESTART/${atmos_static} ] && [ ${INPdir}/RESTART/${atmos_static} -nt ${RESTARTcom}/${atmos_static} ]; then
-  ${NCP} -pL ${INPdir}/RESTART/${atmos_static} ${RESTARTcom}/
+  ${FCP} ${INPdir}/RESTART/${atmos_static} ${RESTARTcom}/
 fi
 if [ -s ${INPdir}/INPUT/${oro_data} ] && [ ${INPdir}/INPUT/${oro_data} -nt ${INPdir}/RESTART/${oro_data} ]; then
   ${NCP} -pL ${INPdir}/INPUT/${oro_data} ${INPdir}/RESTART/
 fi
 if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
    [ -s ${INPdir}/RESTART/${oro_data} ] && [ ${INPdir}/RESTART/${oro_data} -nt ${RESTARTcom}/${oro_data} ]; then
-  ${NCP} -pL ${INPdir}/RESTART/${oro_data} ${RESTARTcom}/
+  ${FCP} ${INPdir}/RESTART/${oro_data} ${RESTARTcom}/
 fi
 if [ -s ${INPdir}/INPUT/${oro_data_ls} ] && [ ${INPdir}/INPUT/${oro_data_ls} -nt ${INPdir}/RESTART/${oro_data_ls} ]; then
   ${NCP} -pL ${INPdir}/INPUT/${oro_data_ls} ${INPdir}/RESTART/
 fi
 if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
    [ -s ${INPdir}/RESTART/${oro_data_ls} ] && [ ${INPdir}/RESTART/${oro_data_ls} -nt ${RESTARTcom}/${oro_data_ls} ]; then
-  ${NCP} -pL ${INPdir}/RESTART/${oro_data_ls} ${RESTARTcom}/
+  ${FCP} ${INPdir}/RESTART/${oro_data_ls} ${RESTARTcom}/
 fi
 if [ -s ${INPdir}/INPUT/${oro_data_ss} ] && [ ${INPdir}/INPUT/${oro_data_ss} -nt ${INPdir}/RESTART/${oro_data_ss} ]; then
   ${NCP} -pL ${INPdir}/INPUT/${oro_data_ss} ${INPdir}/RESTART/
 fi
 if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
    [ -s ${INPdir}/RESTART/${oro_data_ss} ] && [ ${INPdir}/RESTART/${oro_data_ss} -nt ${RESTARTcom}/${oro_data_ss} ]; then
-  ${NCP} -pL ${INPdir}/RESTART/${oro_data_ss} ${RESTARTcom}/
+  ${FCP} ${INPdir}/RESTART/${oro_data_ss} ${RESTARTcom}/
 fi
 
 # grid_mspec files at the current and prior forecast hours
@@ -550,7 +550,7 @@ if [ $FHR -le 12 ] && [ -s ${INPdir}/${grid_mspec_old} ]; then
   if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
      [ -s ${INPdir}/RESTART/${grid_mspec_old} ] && \
      [ ${INPdir}/RESTART/${grid_mspec_old} -nt ${RESTARTcom}/${grid_mspec_old} ]; then
-    ${NCP} -pL ${INPdir}/RESTART/${grid_mspec_old} ${RESTARTcom}/
+    ${FCP} ${INPdir}/RESTART/${grid_mspec_old} ${RESTARTcom}/
   fi
 fi
 # Deliver grid_mspec at NHRS if NHRS less than 12
@@ -562,7 +562,7 @@ if [ $FHR -lt 12 ] && [ $FHR -eq $NHRS ] && [ -s ${INPdir}/${grid_mspec} ]; then
   if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && \
      [ -s ${INPdir}/RESTART/${grid_mspec} ] && \
      [ ${INPdir}/RESTART/${grid_mspec} -nt ${RESTARTcom}/${grid_mspec} ]; then
-    ${NCP} -pL ${INPdir}/RESTART/${grid_mspec} ${RESTARTcom}/
+    ${FCP} ${INPdir}/RESTART/${grid_mspec} ${RESTARTcom}/
   fi
 fi
 
@@ -578,7 +578,7 @@ if [ ! -z "${RESTARTcom}" ] && [ $SENDCOM = YES ] && [ $FHR -lt 12 ] && [ -s ${I
   while [ $(( $(date +%s) - $(stat -c %Y ${INPdir}/RESTART/${coupler_res}) )) -lt 30 ]; do sleep 10s; done
   for file_res in $fv_core $fv_core_tile $fv_tracer_tile $fv_srf_wnd_tile $sfc_data $phy_data $coupler_res ; do
     if [ -s ${INPdir}/RESTART/${file_res} ] && [ ${INPdir}/RESTART/${file_res} -nt ${RESTARTcom}/${file_res} ]; then
-      ${NCP} -pL ${INPdir}/RESTART/${file_res} ${RESTARTcom}/${file_res}
+      ${FCP} ${INPdir}/RESTART/${file_res} ${RESTARTcom}/${file_res}
     fi
   done
 fi
@@ -587,9 +587,9 @@ fi
 if [ $FHR -eq $NHRS ] && [ -s ${INPdir}/${fort_patcf} ]; then
   if [ -s ${INPdir}/${fort_patcf}_save ]; then
     cat ${INPdir}/${fort_patcf} >> ${INPdir}/${fort_patcf}_save
-    ${NCP} -pL ${INPdir}/${fort_patcf}_save ${COMOUTpost}/${trk_patcf}
+    ${FCP} ${INPdir}/${fort_patcf}_save ${COMOUTpost}/${trk_patcf}
   else
-    ${NCP} -pL ${INPdir}/${fort_patcf} ${COMOUTpost}/${trk_patcf}
+    ${FCP} ${INPdir}/${fort_patcf} ${COMOUTpost}/${trk_patcf}
   fi
 fi
 

scripts/exhafs_enkf_hx.sh

@@ -491,7 +491,7 @@ set -o pipefail
 ${APRUNC} ./hafs_gsi.x 2>&1 | tee ./stdout
 set +o pipefail
 
-${NCP} -p ./stdout ${GSISOUT}
+cat ./stdout > ${GSISOUT}
 
 # Cat runtime output files.
 cat fort.2* > ${GSISTAT}

scripts/exhafs_gempak.sh

@@ -122,8 +122,7 @@ ${GEMEXE}/gpend
 status=$?; [[ $status -ne 0 ]] && exit $status
 
 if [ "${SENDCOM^^}" = "YES" ]; then
-  ${NCP} $GDOUTF $GPOUTF
-# ${NCP} -p $GDOUTF $GPOUTF
+  ${FCP} $GDOUTF $GPOUTF
   if [ "${SENDDBN^^}" = "YES" ]; then
     $DBNROOT/bin/dbn_alert MODEL ${RUN^^}_GEMPAK $job $GPOUTF
   fi

scripts/exhafs_obs_prep.sh

@@ -69,11 +69,6 @@ cat ./hafs_change_prepbufr_qm_typ.out
 # Deliver to intercom
 ${NCP} -p ./prepbufr.qm_typ ${intercom}/${NET}.t${cyc}z.prepbufr
 
-# Deliver to com (no need to deliver to COMhafs). Will need modify permission properly if rstprod is involved
-#if [ $SENDCOM = YES ]; then
-#  ${NCP} -p ./prepbufr.qm_typ ${COMhafs}/${out_prefix}.${RUN}.prepbufr
-#fi
-
 cd $DATA
 
 NFTLDPLR=${NET}.t${cyc}z.tldplr.tm00.bufr_d
@@ -115,10 +110,10 @@ else
 fi
 if [ -s ./tldplr.ibm ]; then
   # Deliver to intercom
-  ${NCP} -p ./tldplr.ibm ${intercom}/${NFTLDPLR}
+  ${NCP} ./tldplr.ibm ${intercom}/${NFTLDPLR}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -p ./tldplr.ibm ${COMhafs}/${RFTLDPLR}
+    ${FCP} ./tldplr.ibm ${COMhafs}/${RFTLDPLR}
   fi
 fi
 
@@ -133,10 +128,10 @@ cat ./hdob.out
 set -e
 if [ -s ./hdob.ibm ]; then
   # Deliver to intercom
-  ${NCP} -p ./hdob.ibm ${intercom}/${NFHDOB}
+  ${NCP} ./hdob.ibm ${intercom}/${NFHDOB}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -p ./hdob.ibm ${COMhafs}/${RFHDOB}
+    ${FCP} ./hdob.ibm ${COMhafs}/${RFHDOB}
   fi
 fi
 
@@ -245,7 +240,7 @@ if [ -s ./nexrad.ibm ]; then
   ${NCP} -p ./nexrad.ibm ${intercom}/${NFNEXRAD}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -p ./nexrad.ibm ${COMhafs}/${RFNEXRAD}
+    ${FCP} ./nexrad.ibm ${COMhafs}/${RFNEXRAD}
   fi
 fi
 
@@ -260,7 +255,7 @@ if [[ -s ./dropsonde.${CDATE}.tar ]]; then
   ${NCP} -p ./dropsonde.${CDATE}.tar ${intercom}/${NFdropsonde}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -p ./dropsonde.${CDATE}.tar ${COMhafs}/${RFdropsonde}
+    ${FCP} ./dropsonde.${CDATE}.tar ${COMhafs}/${RFdropsonde}
   fi
 fi
 
@@ -273,7 +268,7 @@ if [ -s ${COMINhafs_OBS}/${NFTLDPLR} ]; then
   ${NCP} -L ${COMINhafs_OBS}/${NFTLDPLR} ${intercom}/${NFTLDPLR}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -L ${COMINhafs_OBS}/${NFTLDPLR} ${COMhafs}/${RFTLDPLR}
+    ${FCP} ${intercom}/${NFTLDPLR} ${COMhafs}/${RFTLDPLR}
   fi
 fi
 # HDOB data
@@ -282,7 +277,7 @@ if [ -s ${COMINhafs_OBS}/${NFHDOB} ]; then
   ${NCP} -L ${COMINhafs_OBS}/${NFHDOB} ${intercom}/${NFHDOB}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -L ${COMINhafs_OBS}/${NFHDOB} ${COMhafs}/${RFHDOB}
+    ${FCP} ${intercom}/${NFHDOB} ${COMhafs}/${RFHDOB}
   fi
 fi
 # NEXRAD data
@@ -291,7 +286,7 @@ if [ -s ${COMINhafs_OBS}/${NFNEXRAD} ]; then
   ${NCP} -L ${COMINhafs_OBS}/${NFNEXRAD} ${intercom}/${NFNEXRAD}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -L ${COMINhafs_OBS}/${NFNEXRAD} ${COMhafs}/${RFNEXRAD}
+    ${FCP} ${intercom}/${NFNEXRAD} ${COMhafs}/${RFNEXRAD}
   fi
 fi
 # TEMPdropsonde data
@@ -300,7 +295,7 @@ if [ -s ${COMINhafs_OBS}/${NFdropsonde} ]; then
   ${NCP} -L ${COMINhafs_OBS}/${NFdropsonde} ${intercom}/${NFdropsonde}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -L ${COMINhafs_OBS}/${NFdropsonde} ${COMhafs}/${RFdropsonde}
+    ${FCP} ${intercom}/${NFdropsonde} ${COMhafs}/${RFdropsonde}
   fi
 fi
 # TEMPdrop prepbufr
@@ -309,7 +304,7 @@ if [ -s ${COMINhafs_OBS}/${NFtempdrop} ]; then
   ${NCP} -L ${COMINhafs_OBS}/${NFtempdrop} ${intercom}/${NFtempdrop}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -L ${COMINhafs_OBS}/${NFtempdrop} ${COMhafs}/${RFtempdrop}
+    ${FCP} ${intercom}/${NFtempdrop} ${COMhafs}/${RFtempdrop}
   fi
 fi
 
@@ -349,7 +344,7 @@ if [ -s ./tempdrop.prepbufr ]; then
   ${NCP} -p ./tempdrop.prepbufr ${intercom}/${NFtempdrop}
   # Deliver to com
   if [ $SENDCOM = YES ]; then
-    ${NCP} -p ./tempdrop.prepbufr ${COMhafs}/${RFtempdrop}
+    ${FCP} ./tempdrop.prepbufr ${COMhafs}/${RFtempdrop}
   fi
 fi
 

scripts/exhafs_ocn_post.sh

@@ -107,7 +107,7 @@ done
 
 # Deliver to COMOUTpost
 if [ $SENDCOM = YES ]; then
-  ${NCP} -p ${INPdir}/${ocnout} ${COMOUTpost}/${ocnpost}
+  ${FCP} ${INPdir}/${ocnout} ${COMOUTpost}/${ocnpost}
 fi
 
 # Write out the ocnpostdone message file
@@ -135,7 +135,7 @@ oicout=oic_${YYYY}_${MM}_${DD}_${HH}.nc
 oicpost=${out_prefix}.${RUN}.mom6.f000.nc
 
 if [ $SENDCOM = YES ]; then
-  ${NCP} -p ${INPdir}/${oicout} ${COMOUTpost}/${oicpost}
+  ${FCP} ${INPdir}/${oicout} ${COMOUTpost}/${oicpost}
 fi
 
 cd ${DATA}

scripts/exhafs_product.sh

@@ -181,11 +181,11 @@ if [ "${tilestr}" = ".tile${nest_grids}" ]; then
 cat > ./deliver.sh<<EOF
 #!/bin/sh
 set -x
-${NCP} output.atcfunix ${COMOUTproduct}/${all_atcfunix_grid}
-${NCP} output.atcfunix ${COMOUTproduct}/${all_atcfunix}
+${FCP} output.atcfunix ${COMOUTproduct}/${all_atcfunix_grid}
+${FCP} output.atcfunix ${COMOUTproduct}/${all_atcfunix}
 if [[ \${1:-''} -le 12 ]]; then
-  ${NCP} output.atcfunix ${COMOUTproduct}/${fhr_atcfunix_grid}\$(printf "%03d" "\${1:-''}")
-  ${NCP} output.atcfunix ${COMOUTproduct}/${fhr_atcfunix}\$(printf "%03d" "\${1:-''}")
+  ${FCP} output.atcfunix ${COMOUTproduct}/${fhr_atcfunix_grid}\$(printf "%03d" "\${1:-''}")
+  ${FCP} output.atcfunix ${COMOUTproduct}/${fhr_atcfunix}\$(printf "%03d" "\${1:-''}")
 fi
 EOF
 
@@ -194,9 +194,9 @@ else
 cat > ./deliver.sh<<EOF
 #!/bin/sh
 set -x
-${NCP} output.atcfunix ${COMOUTproduct}/${all_atcfunix_grid}
+${FCP} output.atcfunix ${COMOUTproduct}/${all_atcfunix_grid}
 if [[ \${1:-''} -le 12 ]]; then
-  ${NCP} output.atcfunix ${COMOUTproduct}/${fhr_atcfunix_grid}\$(printf "%03d" "\${1:-''}")
+  ${FCP} output.atcfunix ${COMOUTproduct}/${fhr_atcfunix_grid}\$(printf "%03d" "\${1:-''}")
 fi
 EOF
 
@@ -339,15 +339,15 @@ if [ ${COMOUTproduct} = ${COMhafs} ] && [ -s ${COMhafs}/${trk_atcfunix} ]; then
      [ ${pubbasin2} = "SH" ] || [ ${pubbasin2} = "SP" ] || [ ${pubbasin2} = "SI" ]; then
     sed -i -e 's/NATIONAL HURRICANE CENTER/JOINT TYPHOON WARNING CENTER/g' fort.51 fort.61
   fi
-  ${NCP} fort.41 ${COMhafs}/${short}
+  ${FCP} fort.41 ${COMhafs}/${short}
   if [ "${SENDDBN^^}" = "YES" ]; then
     $DBNROOT/bin/dbn_alert MODEL ${RUN^^}_ASCII $job ${COMhafs}/${short}
   fi
-  ${NCP} fort.51 ${COMhafs}/${afos}
+  ${FCP} fort.51 ${COMhafs}/${afos}
   if [ "${SENDDBN^^}" = "YES" ]; then
     $DBNROOT/bin/dbn_alert MODEL ${RUN^^}_AFOS $job ${COMhafs}/${afos}
   fi
-  ${NCP} fort.61 ${COMhafs}/${tpc}
+  ${FCP} fort.61 ${COMhafs}/${tpc}
   if [ "${SENDDBN^^}" = "YES" ]; then
     $DBNROOT/bin/dbn_alert MODEL ${RUN^^}_STATS $job ${COMhafs}/${tpc}
   fi

ush/hafs_gempak_meta_grid.sh

@@ -226,8 +226,7 @@ status=$?; [[ $status -ne 0 ]] && exit $status
 
 GMETAF=${COMOUT}/gempak/${storm_id}/meta/${RUN}_${PDY}_${cyc}_${storm_id}
 if [ ${SENDCOM:-YES} = "YES" ]; then
-  ${NCP} grid.nmeta ${GMETAF}
-# ${NCP} -p grid.nmeta ${GMETAF}
+  ${FCP} grid.nmeta ${GMETAF}
   if [ ${SENDDBN:-NO} = "YES" ]; then
     $DBNROOT/bin/dbn_alert MODEL $(echo ${RUN} | tr [a-z] [A-Z])_METAFILE $job ${GMETAF}
   fi

ush/hafs_gempak_meta_nest.sh

@@ -452,8 +452,7 @@ if [ $attempts -gt 360 ] && [ ! -f ${COMIN}/${statfile} ]; then
   exit 1
 fi
 
-${NCP} ${COMIN}/${statfile} ./
-#${NCP} -p ${COMIN}/${statfile} ./
+${FCP} ${COMIN}/${statfile} ./
 
 numlines=$(cat $statfile | wc -l)
 cnt=1
@@ -546,8 +545,7 @@ status=$?; [[ $status -ne 0 ]] && exit $status
 
 GMETAF=${COMOUT}/gempak/${storm_id}/meta/${RUN}_${PDY}_${cyc}_${storm_id}_nest
 if [ ${SENDCOM:-YES} = "YES" ]; then
-  ${NCP} nest.nmeta ${GMETAF}
-# ${NCP} -p nest.nmeta ${GMETAF}
+  ${FCP} nest.nmeta ${GMETAF}
   if [ ${SENDDBN:-NO} = "YES" ]; then
     $DBNROOT/bin/dbn_alert MODEL $(echo ${RUN} | tr [a-z] [A-Z])_METAFILE $job ${GMETAF}
   fi

ush/hafs_make_orog.sh

@@ -87,20 +87,17 @@ echo "indir = $indir"
 
 cd $workdir
 
-cp ${indir}/thirty.second.antarctic.new.bin fort.15
-cp ${indir}/landcover30.fixed .
-#  uncomment next line to use the old gtopo30 data.
-#   cp ${indir}/gtopo30_gg.fine.nh  fort.235
-#  use gmted2020 data.
-cp -f ${indir}/gmted2010.30sec.int  fort.235
+${NLN} ${indir}/thirty.second.antarctic.new.bin fort.15
+${NLN} ${indir}/landcover30.fixed .
+${NLN} ${indir}/gmted2010.30sec.int  fort.235
 if [ $inorogexist -eq 1 ]; then
-   cp $inputorog .
+   ${NCP} $inputorog .
 fi
 
 if [ $is_latlon -eq 0 ]; then
-   cp ${griddir}/$OUTGRID .
+   ${NCP} ${griddir}/$OUTGRID .
 fi
-cp $executable .
+${NCP} $executable .
 
 echo  $mtnres $lonb $latb $efac $blat > INPS
 echo $OUTGRID >> INPS

ush/hafs_make_orog_gsl.sh

@@ -58,7 +58,7 @@ ln -sf ${griddir}/$OUTGRID .
 ln -sf ${topo_am}/"HGT.Beljaars_filtered.lat-lon.30s_res.nc" .
 ln -sf ${topo_am}/"geo_em.d01.lat-lon.2.5m.HGT_M.nc" .
 
-cp $executable .
+${NCP} -p $executable .
 
 echo $tile > grid_info.dat
 echo $res >> grid_info.dat
@@ -75,5 +75,3 @@ else
   exit 0
 fi
 
-exit
-

ush/hafs_runcmd.sh.inc

@@ -60,7 +60,14 @@ else
 fi
 
 # Some commonly used commands
-export NCP=${NCP:-"/bin/cp"}
+if [ "${RUN_ENVIR^^}" != "NCO" ]; then
+  export NCP=${NCP:-"/bin/cp"}
+  export FCP=${FCP:-"/bin/cp"}
+else
+  # Run by NCO on WCOSS2, use cpreq for NCP and cpfs for FCP
+  export NCP=${NCP:-"cpreq"}
+  export FCP=${FCP:-"cpfs"}
+fi
 export NMV=${NMV:-"/bin/mv"}
 export NLN=${NLN:-"/bin/ln -sf"}
 export TAR=${TAR:-tar}