run_nemo

#!/bin/bash
# ---------------------------

export NPROC=2000

#===============================================================
# SET SCRIPT VARIABLES
#===============================================================
export RUNNAME=EXP_harmIT
export YEARrun='2012'
export EXEC=nemo.exe					# Name of the exec file
export KHOMEDIR=/work/n01/n01/kariho40/NEMO/NEMOGCM_jdha/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/CONFIG/AMM60smago		# Home Directory
export HOMEDIR=/work/n01/n01/jelt/NEMO/NEMOGCM_jdha/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/CONFIG/XIOS_AMM60_nemo_harmIT              # Home Directory
#export DATADIR=/work/n01/n01/kariho40/NEMO/FORCINGS		# Where to get forcings
export DATADIR=/work/n01/n01/kariho40/NEMO/FORCINGS/2010_2013		# Where to get forcings
export GRIDDIR=/work/n01/n01/kariho40/NEMO/GRID		# Where to get forcings
export JOBDIR=$HOMEDIR/$RUNNAME			# Config directory
export SHAREDDIR=$HOMEDIR/../SHARED			# Config directory
export WDIR=$JOBDIR/WDIR			# Working directory
export OUTPUTDIR=$JOBDIR/OUTPUT		# Output directory
export LOGDIR=$JOBDIR/LOGS			# Logs directory
export RESTARTDIR=$JOBDIR/RESTART			# Logs directory
export BACKDIR=/home/n01/n01/jelt/NEMO/3.6		# Backup on home
export BACKJOBDIR=$BACKDIR/AMM60_$RUNNAME		# Backup on home
export CODEDIR=$HOMEDIR/BLD/
export XIOSDIR=/work/n01/n01/jdha/ST/xios-1.0/

export nrestart_max=2 #31 (For one submission this number must equal the number of lines in run_counter.txt)
export nrestart=`wc -l < $JOBDIR/run_counter.txt `

if [ "$nrestart" -le "$nrestart_max" ]; then

export nstart=`head -1 $JOBDIR/run_counter.txt | cut -d ' ' -f 4`
export nn_it000=`tail -1 $JOBDIR/run_counter.txt | cut -d ' ' -f 2`
export nitend=`tail -1 $JOBDIR/run_counter.txt | cut -d ' ' -f 3`

echo  ~~~~~~~~~~~~~~~~~~~
echo JOBDIR = $JOBDIR
echo WDIR = $WDIR
echo  ~~~~~~~~~~~~~~~~~~~

#===============================================================
# DO NOT CHANGE ANYTHING UNDER THIS LINE, EXCEPT FORCING PATHS
#===============================================================
#while true; do
#    read -p "Do you wish to remove $WDIR? [y/n]" yn
#    case $yn in
#        [Yy]* ) rm -r $WDIR; break;;
#        [Nn]* ) break;;
#        * ) echo "Please answer yes or no.";;
#    esac
#done

mkdir -p $WDIR
mkdir -p $OUTPUTDIR
mkdir -p $LOGDIR
echo $WDIR/AMM60_run* $LOGDIR
mv $WDIR/AMM60_run* $LOGDIR
rm -fr $WDIR/*	#Clean running directory
#mv $WDIR/* $LOGDIR	#Save logfiles
echo before cd WDIR:  `pwd`
cd $WDIR
echo after cd WDIR:  `pwd`

#===============================================================
# BACKUP of config files
#===============================================================
mkdir -p $BACKJOBDIR
echo `date`: BACKUP of config files
cp $JOBDIR/* $BACKJOBDIR/

#===============================================================
# EXECUTABLE
#===============================================================
rm  $JOBDIR/$EXEC
ln -s $CODEDIR/bin/$EXEC $JOBDIR/$EXEC
cp $JOBDIR/$EXEC $WDIR/$EXEC
rm  $JOBDIR/xios_server.exe
ln -s $XIOSDIR/bin/xios_server.exe $JOBDIR/xios_server.exe
cp $JOBDIR/xios_server.exe $WDIR

#===============================================================
# INPUT FILES
#===============================================================
#---------------------------------------------------------------
# Coordinates
#---------------------------------------------------------------
echo `date`: Link coordinates
ln -s $GRIDDIR/coordinates_AMM60.nc        ./coordinates.nc

#---------------------------------------------------------------
# Bathymetry
#---------------------------------------------------------------
echo `date`: Link Bathymetry
ln -s $GRIDDIR/bathyfile_AMM60_nosmooth.nc ./bathy_meter.nc

#---------------------------------------------------------------
# XML files
#---------------------------------------------------------------
ln -sf $JOBDIR/iodef.xml  ./iodef.xml 
ln -sf $JOBDIR/domain_def.xml  ./domain_def.xml
ln -sf $SHAREDDIR/field_def.xml  ./field_def.xml

#===============================================================
# INPUT FILES 
#===============================================================
#---------------------------------------------------------------
# BDY
#---------------------------------------------------------------
echo `date`: Link bdy data
TIDEDIR=$DATADIR
BDYDIR=/work/n01/n01/kariho40/NEMO/FORCINGS/2010_2013

for fic in `ls $TIDEDIR/NNA_AMM60bdy__bdytide*nc`; do
    ficdest=`basename $fic`
    ln -s $fic $WDIR/$ficdest
done

for yyyy in $YEARrun; do
  for fic in `ls $BDYDIR/AMM60bdy_NNA_R12_*${yyyy}*nc`; do
    ficdest=`basename $fic`
    ln -s $fic $WDIR/$ficdest
  done
done

ln -s $BDYDIR/coordinates.bdy.nc ./coordinates.bdy.nc
#ln -s $DATADIR/runoff_AMM60_allindex_bathynosmooth.nc ./rivers.nc

#---------------------------------------------------------------
# NAMELISTS
#---------------------------------------------------------------
#rm $JOBDIR/namelist_ref
#ln -s $SHAREDDIR/namelist_ref $JOBDIR/namelist_ref
cp $JOBDIR/namelist_ref $WDIR/namelist_ref

#---------------------------------------------------------------
# Restart file and/or initial condition and namelist
#---------------------------------------------------------------
if [[ $nn_it000 -eq 1 ]]; then
    echo INIT
    sed "\
    13c\
    ln_rstart   =   .false.   
    9c\
    nn_it000 = 1
    10c\
    nn_itend = "$nitend"
    11c\
    nn_date0 = "$nstart"
    17c\
    nn_stock = "$nitend"
    18c\
    nn_write = "$nitend" 
    306c\
    rn_sponge     = 30 " $JOBDIR/namelist_cfg > $WDIR/namelist_cfg
    ln -s $DATADIR/AMM60_inits_NNAR12_20100105.nc $WDIR/inits.nc
  else
    sed "\
    13c\
    ln_rstart   =   .true.   
    9c\
    nn_it000 = "$nn_it000"
    10c\
    nn_itend = "$nitend"
    11c\
    nn_date0 = "$nstart"
    17c\
    nn_stock = "$nitend"
    18c\
    nn_write = "$nitend"
    273c\
    nit000_han = "$nn_it000"
    274c\
    nitend_han = "$nitend" " $JOBDIR/namelist_cfg > $WDIR/namelist_cfg
    nit_rst1=`expr $nn_it000 - 1`
    nit_rst=`printf "%8.8d" $nit_rst1`
    for cnt in {0..1999}; do
      ind=`printf "%4.4d" $cnt`
      ln -s $RESTARTDIR/$nit_rst/restart_$ind.nc $WDIR/restart_$ind.nc
    done
  fi
#===============================================================
# LAUNCH JOB
#===============================================================
echo `date` Submit Run 
echo -V  $JOBDIR/submit_nemo.pbs 
qsub -V $JOBDIR/submit_nemo.pbs
qstat -u jelt

else #   from if statement --- if [ "$nrestart" -le "$nrestart_max" ]; then
echo Maximum number of restarts reached. Job not started
fi

exit