Issue NOAA-EMC#5 - Sync merge branch 'feature/gfsv16b' into port2orion

* feature/gfsv16b: modified: run_gfsmos_master.sh.dell to still set range=both as the default for running the real-time parallel update checkout.sh to switch back to post version upp_gfsv16_release.v1.0.8. 1.0.9 still has issues. Issue #1 - sync Externals.cfg with checkout.sh update for FV3 GFSv16.0.6 tag modified: scripts/run_gfsmos_master.sh.dell to set default verification type o short. modified: sorc/checkout.sh updated to model tag GFS.v16.0.6 to fix contrib issue on HERA Issue #1 - update Externals.cfg to match updates to checkout.sh Update exwave_post_sbs.sh Adapting wavepostsbs for running on Hera
jkhender · Jun 17, 2020 · ff46607 · ff46607
2 parents ed6b279 + 1dd83b8
commit ff46607
Show file tree

Hide file tree

Showing 13 changed files with 111 additions and 92 deletions.
diff --git a/Externals.cfg b/Externals.cfg
@@ -1,28 +1,28 @@
 # External sub-modules of global-workflow
 
 [FV3GFS]
-tag = GFS.v16.0.1
+tag = GFS.v16.0.6
 local_path = sorc/fv3gfs.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
 required = True
 
 [GSI]
-tag = gfsda.v16.0.0
+branch = release/gfsda.v16.0.0
 local_path = sorc/gsi.fd
-repo_url = ssh://vlab.ncep.noaa.gov:29418/ProdGSI
+repo_url = https://github.com/NOAA-EMC/GSI.git
 protocol = git
 required = True
 
 [GLDAS]
-tag = gldas_gfsv16_release.v1.0.0
+tag = gldas_gfsv16_release.v1.2.0
 local_path = sorc/gldas.fd
 repo_url = https://github.com/NOAA-EMC/GLDAS.git
 protocol = git
 required = True
 
 [EMC_post]
-tag = upp_gfsv16_release.v1.0.5
+tag = upp_gfsv16_release.v1.0.9
 local_path = sorc/gfs_post.fd
 repo_url = https://github.com/NOAA-EMC/EMC_post.git
 protocol = git
@@ -36,7 +36,7 @@ protocol = git
 required = True
 
 [EMC_verif-global]
-tag = verif_global_v1.6.0
+tag = verif_global_v1.8.0
 local_path = sorc/verif-global.fd
 repo_url = https://github.com/NOAA-EMC/EMC_verif-global.git
 protocol = git

diff --git a/scripts/exwave_init.sh b/scripts/exwave_init.sh
@@ -14,6 +14,7 @@
 # Script history log:
 # 2019-05-06  J-Henrique Alves First Version.
 # 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported to R&D machine Hera
 #
 # $Id$
 #

diff --git a/scripts/exwave_post_sbs.sh b/scripts/exwave_post_sbs.sh
@@ -19,7 +19,8 @@
 #  wave_tar.sh               : tars the spectral and bulletin multiple files  
 #
 # Script history log:
-# 2019-12-06  J-Henrique Alves First Version adapted from HTolman post.sh 2007 
+# 2019-12-06  J-Henrique Alves: First Version adapted from HTolman post.sh 2007 
+# 2020-06-10  J-Henrique Alves: Porting to R&D machine Hera
 #
 # $Id$
 #
@@ -516,67 +517,7 @@
     export GRDIDATA=${DATA}/output_$YMDHMS
     ln -fs $DATA/mod_def.${waveuoutpGRD} mod_def.ww3
 
-    if [ $fhr = $fhrp ]
-    then
-      iwait=0
-      pfile=$COMIN/rundata/${WAV_MOD_TAG}.out_pnt.${waveuoutpGRD}.${YMD}.${HMS}
-      while [ ! -s ${pfile} ]; do sleep 10; ((iwait++)) && ((iwait==$iwaitmax)) && break ; echo $iwait; done
-      if [ $iwait -eq $iwaitmax ]; then 
-        echo " FATAL ERROR : NO RAW POINT OUTPUT FILE out_pnt.$waveuoutpGRD
-        echo ' '
-        [[ "$LOUD" = YES ]] && set -x
-        postmsg "$jlogfile" "FATAL ERROR : NO RAW POINT OUTPUT FILE out_pnt.$waveuoutpGRD
-        err=6; export err;${errchk}
-        exit $err
-      fi
-      ln -fs ${pfile} ./out_pnt.${waveuoutpGRD} 
-
-      if [ "$DOSPC_WAV" = 'YES' ]
-      then
-        export dtspec=3600.
-        if [ ${CFP_MP:-"NO"} = "YES" ]; then nm=0 ; fi # Counter for MP CFP
-        for buoy in $buoys
-        do
-          if [ ${CFP_MP:-"NO"} = "YES" ]; then
-            echo "$nm $USHwave/wave_outp_spec.sh $buoy $ymdh spec > spec_$buoy.out 2>&1" >> ${fcmdnow}
-            nm=`expr $nm + 1`
-          else
-            echo "$USHwave/wave_outp_spec.sh $buoy $ymdh spec > spec_$buoy.out 2>&1" >> ${fcmdnow}
-          fi
-        done
-      fi
-
-      if [ "$DOIBP_WAV" = 'YES' ]
-      then
-        export dtspec=3600.
-        if [ ${CFP_MP:-"NO"} = "YES" ]; then nm=0 ; fi # Counter for MP CFP
-        for buoy in $ibpoints
-        do
-          if [ ${CFP_MP:-"NO"} = "YES" ]; then
-            echo "$nm $USHwave/wave_outp_spec.sh $buoy $ymdh ibp > ibp_$buoy.out 2>&1" >> ${fcmdnow}
-            nm=`expr $nm + 1`
-          else
-            echo "$USHwave/wave_outp_spec.sh $buoy $ymdh ibp > ibp_$buoy.out 2>&1" >> ${fcmdnow}
-          fi
-        done
-      fi
-
-      if [ "$DOBLL_WAV" = 'YES' ]
-      then
-        export dtspec=3600.
-        if [ ${CFP_MP:-"NO"} = "YES" ]; then nm=0 ; fi # Counter for MP CFP
-        for buoy in $buoys
-        do
-          if [ ${CFP_MP:-"NO"} = "YES" ]; then
-            echo "$nm $USHwave/wave_outp_spec.sh $buoy $ymdh bull > bull_$buoy.out 2>&1" >> ${fcmdnow}
-            nm=`expr $nm + 1`
-          else
-            echo "$USHwave/wave_outp_spec.sh $buoy $ymdh bull > bull_$buoy.out 2>&1" >> ${fcmdnow}
-          fi
-        done
-      fi
-
-    fi
+# Gridded data (main part, need to be run side-by-side with forecast
 
     if [ $fhr = $fhrg ]
     then
@@ -607,25 +548,18 @@
             glo_15mxt) ymdh_int=`$NDATE -${WAVHINDH} $ymdh`; dt_int=3600.; n_int=9999 ;;
             glo_30mxt) ymdh_int=`$NDATE -${WAVHINDH} $ymdh`; dt_int=3600.; n_int=9999 ;;
           esac
-          if [ ${CFP_MP:-"NO"} = "YES" ]; then
-            echo "$nm $USHwave/wave_grid_interp_sbs.sh $grdID $ymdh_int $dt_int $n_int > grint_$grdID.out 2>&1" >> ${fcmdigrd}.${nigrd}
-          else
             echo "$USHwave/wave_grid_interp_sbs.sh $grdID $ymdh_int $dt_int $n_int > grint_$grdID.out 2>&1" >> ${fcmdigrd}.${nigrd}
-          fi
           if [ "$DOGRB_WAV" = 'YES' ]
           then
           gribFL=\'`echo ${OUTPARS_WAV}`\'
             case $grdID in
               glo_15mxt) GRDNAME='global' ; GRDRES=0p25 ; GRIDNR=255  ; MODNR=11 ;;
               glo_30mxt) GRDNAME='global' ; GRDRES=0p50 ; GRIDNR=255  ; MODNR=11 ;;
             esac
-            if [ ${CFP_MP:-"NO"} = "YES" ]; then
-              echo "$nm $USHwave/wave_grib2_sbs.sh $grdID $GRIDNR $MODNR $ymdh $fhr $GRDNAME $GRDRES $gribFL > grib_$grdID.out 2>&1" >> ${fcmdigrd}.${nigrd}
-            else
               echo "$USHwave/wave_grib2_sbs.sh $grdID $GRIDNR $MODNR $ymdh $fhr $GRDNAME $GRDRES $gribFL > grib_$grdID.out 2>&1" >> ${fcmdigrd}.${nigrd}
-            fi
           fi
-          echo "${fcmdigrd}.${nigrd}" >> ${fcmdnow}
+          echo "pwd" >> ${fcmdnow}
+          echo "${GRIBDATA}/${fcmdigrd}.${nigrd}" >> ${fcmdnow}
           chmod 744 ${fcmdigrd}.${nigrd}
           nigrd=$((nigrd+1)) 
           if [ ${CFP_MP:-"NO"} = "YES" ]; then nm=`expr $nm + 1` ; fi # Increment counter for fcmdigrd
@@ -649,17 +583,84 @@
               so_20m) GRDNAME='antarc' ; GRDRES=0p33 ; GRIDNR=255  ; MODNR=11   ;;
               glo_15mxt) GRDNAME='global' ; GRDRES=0p25 ; GRIDNR=255  ; MODNR=11   ;;
           esac
-          if [ ${CFP_MP:-"NO"} = "YES" ]; then
-            echo "$nm $USHwave/wave_grib2_sbs.sh $grdID $GRIDNR $MODNR $ymdh $fhr $GRDNAME $GRDRES $gribFL > grib_$grdID.out 2>&1" >> ${fcmdnow}
-            nm=`expr $nm + 1`
-          else
             echo "$USHwave/wave_grib2_sbs.sh $grdID $GRIDNR $MODNR $ymdh $fhr $GRDNAME $GRDRES $gribFL > grib_$grdID.out 2>&1" >> ${fcmdnow}
-          fi
         done
       fi
 
     fi
 
+# Point output part (can be split or become meta-task to reduce resource usage)
+    if [ $fhr = $fhrp ]
+    then
+      iwait=0
+      pfile=$COMIN/rundata/${WAV_MOD_TAG}.out_pnt.${waveuoutpGRD}.${YMD}.${HMS}
+      while [ ! -s ${pfile} ]; do sleep 10; ((iwait++)) && ((iwait==$iwaitmax)) && break ; echo $iwait; done
+      if [ $iwait -eq $iwaitmax ]; then
+        echo " FATAL ERROR : NO RAW POINT OUTPUT FILE out_pnt.$waveuoutpGRD
+        echo ' '
+        [[ "$LOUD" = YES ]] && set -x
+        postmsg "$jlogfile" "FATAL ERROR : NO RAW POINT OUTPUT FILE out_pnt.$waveuoutpGRD
+        err=6; export err;${errchk}
+        exit $err
+      fi
+      ln -fs ${pfile} ./out_pnt.${waveuoutpGRD}
+
+      if [ "$DOSPC_WAV" = 'YES' ]
+      then
+        export dtspec=3600.
+        for buoy in $buoys
+        do
+            echo "$USHwave/wave_outp_spec.sh $buoy $ymdh spec > spec_$buoy.out 2>&1" >> ${fcmdnow}
+        done
+      fi
+
+      if [ "$DOIBP_WAV" = 'YES' ]
+      then
+        export dtspec=3600.
+        for buoy in $ibpoints
+        do
+            echo "$USHwave/wave_outp_spec.sh $buoy $ymdh ibp > ibp_$buoy.out 2>&1" >> ${fcmdnow}
+        done
+      fi
+
+      if [ "$DOBLL_WAV" = 'YES' ]
+      then
+        export dtspec=3600.
+        for buoy in $buoys
+        do
+            echo "$USHwave/wave_outp_spec.sh $buoy $ymdh bull > bull_$buoy.out 2>&1" >> ${fcmdnow}
+        done
+      fi
+
+    fi
+
+    if [ ${CFP_MP:-"NO"} = "YES" ]; then
+      nfile=0
+      ifile=0
+      iline=1
+      ifirst='yes'
+      nlines=$( wc -l ${fcmdnow} | awk '{print $1}' )
+      while [ $iline -le $nlines ]; do
+        line=$( sed -n ''$iline'p' ${fcmdnow} )
+        if [ -z "$line" ]; then  
+          break
+        else
+          if [ "$ifirst" = 'yes' ]; then 
+            echo "#!/bin/sh" > cmdmfile.$nfile 
+            echo "$nfile cmdmfile.$nfile" >> cmdmprog
+            chmod 744 cmdmfile.$nfile
+          fi
+          echo $line >> cmdmfile.$nfile
+          nfile=$(( nfile + 1 ))
+          if [ $nfile -eq $NTASKS ]; then
+            nfile=0 
+            ifirst='no'
+          fi
+          iline=$(( iline + 1 ))
+        fi
+      done
+    fi
+
     wavenproc=`wc -l ${fcmdnow} | awk '{print $1}'`
     wavenproc=`echo $((${wavenproc}<${NTASKS}?${wavenproc}:${NTASKS}))`
 
@@ -673,7 +674,7 @@
     if [ "$wavenproc" -gt '1' ]
     then
       if [ ${CFP_MP:-"NO"} = "YES" ]; then
-        ${wavempexec} -n ${wavenproc} ${wave_mpmd} ${fcmdnow}
+        ${wavempexec} -n ${wavenproc} ${wave_mpmd} cmdmprog
       else
         ${wavempexec} ${wavenproc} ${wave_mpmd} ${fcmdnow}
       fi
@@ -738,20 +739,26 @@
 
 # 6.b Spectral data files
 
+  if [ ${CFP_MP:-"NO"} = "YES" ]; then nm=0; fi
+
   if [ "$DOIBP_WAV" = 'YES' ]
   then
     if [ ${CFP_MP:-"NO"} = "YES" ]; then
-      echo "0 $USHwave/wave_tar.sh $WAV_MOD_TAG ibp $Nibp > ${WAV_MOD_TAG}_ibp_tar.out 2>&1 "   >> cmdtarfile
+      echo "$nm $USHwave/wave_tar.sh $WAV_MOD_TAG ibp $Nibp > ${WAV_MOD_TAG}_ibp_tar.out 2>&1 "   >> cmdtarfile
+      nm=$(( nm + 1 ))
     else
       echo "$USHwave/wave_tar.sh $WAV_MOD_TAG ibp $Nibp > ${WAV_MOD_TAG}_ibp_tar.out 2>&1 "   >> cmdtarfile
     fi
   fi
   if [ "$DOSPC_WAV" = 'YES' ]
   then
     if [ ${CFP_MP:-"NO"} = "YES" ]; then
-      echo "1 $USHwave/wave_tar.sh $WAV_MOD_TAG spec $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
-      echo "2 $USHwave/wave_tar.sh $WAV_MOD_TAG bull $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
-      echo "3 $USHwave/wave_tar.sh $WAV_MOD_TAG cbull $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
+      echo "$nm $USHwave/wave_tar.sh $WAV_MOD_TAG spec $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
+      nm=$(( nm + 1 ))
+      echo "$nm $USHwave/wave_tar.sh $WAV_MOD_TAG bull $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
+      nm=$(( nm + 1 ))
+      echo "$nm $USHwave/wave_tar.sh $WAV_MOD_TAG cbull $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
+      nm=$(( nm + 1 ))
     else
       echo "$USHwave/wave_tar.sh $WAV_MOD_TAG spec $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile
       echo "$USHwave/wave_tar.sh $WAV_MOD_TAG bull $Nb > ${WAV_MOD_TAG}_spec_tar.out 2>&1 "   >> cmdtarfile

diff --git a/scripts/exwave_prep.sh b/scripts/exwave_prep.sh
@@ -30,6 +30,7 @@
 # Nov2012 JHAlves - Transitioning to WCOSS                                    #
 # Apr2019 JHAlves - Transitioning to GEFS workflow                            #
 # Nov2019 JHAlves - Merging wave scripts to global workflow                   #
+# Jun2020 JHAlves - Porting to R&D machine Hera                               #
 #                                                                             #
 #   WAV_MOD_ID and WAV_MOD_TAG replace modID. WAV_MOD_TAG                     # 
 #   is used for ensemble-specific I/O. For deterministic                      #

diff --git a/sorc/checkout.sh b/sorc/checkout.sh
@@ -59,7 +59,7 @@ if [[ ! -d gfs_post.fd ]] ; then
     rm -f ${topdir}/checkout-gfs_post.log
     git clone https://github.com/NOAA-EMC/EMC_post.git gfs_post.fd >> ${topdir}/checkout-gfs_post.log 2>&1
     cd gfs_post.fd
-    git checkout upp_gfsv16_release.v1.0.9
+    git checkout upp_gfsv16_release.v1.0.8
     cd ${topdir}
 else
     echo 'Skip.  Directory gfs_post.fd already exists.'

diff --git a/ush/wave_grib2_sbs.sh b/ush/wave_grib2_sbs.sh
@@ -11,6 +11,7 @@
 #
 # Script history log:
 # 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported to R&D machine Hera
 #
 # $Id$
 #

diff --git a/ush/wave_grid_interp.sh b/ush/wave_grid_interp.sh
@@ -11,6 +11,7 @@
 #
 # Script history log:
 # 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported to R&D machine Hera
 #
 # $Id$
 ###############################################################################

diff --git a/ush/wave_grid_interp_sbs.sh b/ush/wave_grid_interp_sbs.sh
@@ -11,6 +11,7 @@
 #
 # Script history log:
 # 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported to R&D machine Hera
 #
 # $Id$
 #

diff --git a/ush/wave_grid_moddef.sh b/ush/wave_grid_moddef.sh
@@ -11,6 +11,7 @@
 #
 # Script history log:
 # 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported to R&D machine Hera
 #
 # $Id$
 #                                                                             #
@@ -126,7 +127,7 @@
 # 3.  Clean up
 
   cd ..
-  #rm -rf moddef_$grdID
+  rm -rf moddef_$grdID
 
   set +x
   echo ' '

diff --git a/ush/wave_outp_spec.sh b/ush/wave_outp_spec.sh
@@ -11,6 +11,7 @@
 #
 # Script history log:
 # 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported to R&D machine Hera
 #
 # $Id$
 #
@@ -245,8 +246,8 @@
 
 # 3.b Clean up the rest
 
-#  rm -f ww3_outp.inp
-#  rm -f mod_def.ww3 out_pnt.ww3
+  rm -f ww3_outp.inp
+  rm -f mod_def.ww3 out_pnt.ww3
 
   cd ..
   rm -rf ${specdir}_${bloc}

diff --git a/ush/wave_prnc_cur.sh b/ush/wave_prnc_cur.sh
@@ -10,6 +10,9 @@
 # Abstract: Creates current binary data for forcing WW3
 #
 # Script history log:
+# 2019-10-02  J-Henrique Alves: origination, first version
+# 2019-11-02  J-Henrique Alves Ported to global-workflow.
+# 2020-06-10  J-Henrique Alves Ported R&D machine Hera   
 #
 # $Id$
 #

diff --git a/ush/wave_prnc_ice.sh b/ush/wave_prnc_ice.sh
@@ -16,6 +16,7 @@
 #  Update record :                                                            #
 #                                                                             #
 # - Origination: Hendrik Tolman                                01-Mar-2007    #
+# 2019-11-02  J-Henrique Alves Ported to global-workflow.
 #                                                                             #
 # Update log                                                                  #
 # Nov2019 JHAlves - Merging wave scripts to global workflow                   #

diff --git a/ush/wave_tar.sh b/ush/wave_tar.sh
@@ -17,6 +17,7 @@
 # Origination: Hendrik Tolman                                March 13, 2007   #
 # Update log                                                                  #
 # Nov2019 JHAlves - Merging wave scripts to global workflow                   #
+# 2020-06-10  J-Henrique Alves Ported R&D machine Hera   
 #                                                                             #
 ###############################################################################
 #
@@ -220,7 +221,7 @@
   cd $DATA
 
   set +x; [[ "$LOUD" = YES ]] && set -v
-  rm -f  ${STA_DIR}/${type}
+  rm -rf  ${STA_DIR}/${type}
   set +v
 
   echo ' '