#!/bin/bash --login
#PBS -l select=8
#PBS -l walltime=12:00:00
#PBS -A n01-Shelf
####PBS -q short

# Set the number of threads to 1
#   This prevents any system libraries from automatically 
#   using threading.
export OMP_NUM_THREADS=1
#module load ddt
module load atp
export ATP_ENABLED=1

ulimit -s unlimited

## year and month are the formatted version of running month and year to be used for script launching
## y and m are the numeric one to be used in counting
iy1=$((y))
iy2=$((y+1))
iy2=$((y)) # just one year for now

# loop for years
yy=$iy1
while [  $yy -le $iy2 ]; do
# loop for years
year=${yy}

#loop for months
if [ $yy -eq $iy1 ]; then mm=$m; else mm=1; fi
while [ $mm -le 12 ]; do
#loop for months

if [ $mm -lt 10 ] ; then
   month=0$mm
else
   month=$mm
fi

tpd=288 # time steps per day
date
RUNDIR=/work/n01/n01/slwa/NEMO/src/NEMO_V3.6_STABLE_top_bdy/NEMO/NEMOGCM/CONFIG/XIOS_AMM7_top/EXP01/
echo "Running year $year, month $month ..."
#get run length in iterations (nit)
case $month in
	04|06|09|11) nit=$((30*tpd)) ;;
	#february considering leap years:
	02) if [ `expr $year % 4` -ne 0 -o `expr $year % 100` -eq 0 -a `expr $year % 400` -ne 0 ]; then nit=$((28*tpd)); else nit=$((29*tpd)); fi ;;
	#february not considering leap years:
	#02) nit=$((28*tpd)) ;;
	*) nit=$((31*tpd)) ;;
esac

nitend=`expr $nit0 + $nit`
nitend=`expr $nitend - 1`
if [ $nit0 -eq 1 ] ; then
   rstctl=0
   rstart=.true. 
   rsttrc=.false.   # no initial restart for tracer test
   euler=0
else
   rstctl=2
   rstart=.true.
   rsttrc=.true.
   euler=1
fi
wrt=$nit
m1=$((mm+1))
y1=$year
if [ $m1 -eq 13 ]; then 
	m1=1
	y1=$((year+1))
fi
if [ $m1 -lt 10 ] ; then
   month1=0$m1
else
   month1=$m1
fi
export EXEC=nemo.exe

cd $RUNDIR


rm NE-AMM-$IJ
cat namelist_cfg.template \
    | sed "s,__IT000__,$nit0,g" \
    | sed "s,__ITEND__,$nitend,g" \
    | sed "s,__DATE0__,${year}${month}01,g" \
    | sed "s,__STOCK__,$nit,g" \
    | sed "s,__WRITE__,$wrt,g" \
    | sed "s,__II__,$I,g" \
    | sed "s,__JJ__,$J,g" \
    | sed "s,__IIJJ__,$IJ,g" \
    | sed "s,__RSTCTL__,$rstctl,g" \
    | sed "s,__RSTART__,$rstart,g" \
    | sed "s,__EULER__,$euler,g" \
    > namelist_cfg
cat namelist_top_cfg.template \
    | sed "s,__RSTCTL__,$rstctl,g" \
    | sed "s,__RSTTR__,$rsttrc,g" \
    > namelist_top_cfg
echo "=== running nemo on $IJ cores (24 tasks per node)"

#link boundary files
#./setAnnualLinks.ROAM.sh $year

aprun -n$IJ ./$EXEC
 
date
RC=$? ; if test $RC -ne 0 ;  then echo   failed with error code = $RC ; exit ; fi

# submit post processing first - put daymean files in directories
OUTDIR=$RUNDIR/output_$year$month
mkdir $OUTDIR
mv ocean.output $OUTDIR/.
mv namelist_cfg $OUTDIR/.
mv solver.stat  $OUTDIR/.
mv tracer.stat $OUTDIR/.


# then deal with restart files
#slwa
rm restart.nc
rm restart_trc.nc
if [ $nitend -lt 10000 ] ; then
   nitrst=0000$nitend
elif [ $nitend -lt 100000 ] ; then
   nitrst=000$nitend
elif [ $nitend -lt 1000000 ] ; then
   nitrst=00$nitend
elif [ $nitend -lt 10000000 ] ; then
   nitrst=0$nitend
elif [ $nitend -lt 100000000 ] ; then
   nitrst=$nitend
else
   echo 'run too long'
   exit
fi


for i in {0..9}
do
 mv  'amm7_'$nitrst'_restart_trc_000'$i.nc 'restart_trc_000'$i.nc
 mv  'amm7_'$nitrst'_restart_000'$i.nc 'restart_000'$i.nc
 RC=$? ; if test $RC -ne 0 ;  then echo   failed with error code = $RC ; exit ; fi
done
for i in {10..99}
do
 mv  'amm7_'$nitrst'_restart_trc_00'$i.nc 'restart_trc_00'$i.nc
 mv  'amm7_'$nitrst'_restart_00'$i.nc 'restart_00'$i.nc
done
for i in {100..600}
do
 mv  'amm7_'$nitrst'_restart_trc_0'$i.nc 'restart_trc_0'$i.nc
 mv  'amm7_'$nitrst'_restart_0'$i.nc 'restart_0'$i.nc
done


# save restart files - takes a lot of time so only do once a year
if [ $mm -eq 12 ] ; then
OUTDIR=$RUNDIR/files_restart_$year$month
mkdir $OUTDIR
cp restart_* $OUTDIR/.
fi

nit0=`expr $nitend + 1`


mm=$((mm+1))
done # 1..12 months
yy=$((yy+1))
done # year and year+1

# submit next 2 years 
#if [ $y1 -lt 2100 ]; then
  #echo 'qsub -v I='$I',J='$J',IJ='$IJ',m='$m1',y='$y1',nit0='$nit0' -o /work/n01/n01/slwa/NEMO//src/NEMO_V3.6_STABLE_top_bdy/NEMO/NEMOGCM/CONFIG/XIOS_AMM7_top/EXP01/NE-AMM7-'$IJ'-'$y1'-'$month1' -N NE'$y1$month1' NE199501 annualrun.pbs'
  #qsub -v I=$I,J=$J,IJ=$IJ,m=$m1,y=$y1,nit0=$nit0 -o /work/n01/n01/slwa/NEMO//src/NEMO_V3.6_STABLE_top_bdy/NEMO/NEMOGCM/CONFIG/XIOS_AMM7_top/EXP01/NE-AMM7-$IJ-$y1-$month1 -N NE$y1$month1 NE199501 annualrun.pbs
#fi

exit