simulator_script_cluster

#!/bin/sh
# Sample simulator to Dakota system call script
# See Advanced Simulation Code Interfaces chapter in Users Manual

# $1 is params.in FROM Dakota
# $2 is results.out returned to Dakota

# Script sets up all the cases needed within the UQ case. Based in Askervein hill 1983, TU03b campaign measurements.
# Only 180 degres of wind direction are considered, so only 2 test cases are needed to set up the run, depending on a limiting angle (thetaLimit).
# This scripts computes all the variables and sets the cases automatically to be launched in a cluster using the script named "LaunchSimulationUQ".

# Local variable definition: 
NCORES=8
thetaLimit=210;
Href=10;
vkconstant=0.41;
# --------------
# PRE-PROCESSING
# --------------
# Incorporate the parameters from DAKOTA into the template, writing ros.in
# Use the following line if SNL's APREPRO utility is used instead of DPrePro.
# ../aprepro -c '*' -q --nowarning ros.template ros.in

dprepro $1 ABLConditions.template ABLConditions.in
# --------
# ANALYSIS
# --------
# choose the type of case depending on the wind direction
pi=`echo "4*a(1)" |bc -l`
cp ../templatedir/initialConditions.template initialConditions.in
a=$(grep 'AngleIn' ABLConditions.in | awk ' {print substr($2, 0, length($2))}');
theta=$(echo  ${a} | awk '{ print sprintf("%.9f", $1); }');
a1=$(grep 'AngleRef' ABLConditions.in | awk ' {print substr($2, 0, length($2))}');
thetaRef=$(echo  ${a1} | awk '{ print sprintf("%.9f", $1); }');
b=$(grep 'Uref' ABLConditions.in | awk ' {print substr($2, 0, length($2)-1)}')
U=$(echo  ${b} | awk '{ print sprintf("%.2f", $1); }');
Ucomp1=`echo "c(($thetaRef-$theta)*pi/180)*$U" | bc -l`
Ucomp2=`echo "s(($thetaRef-$theta)*pi/180)*$U" | bc -l`
if [ $(echo " ${theta} > $thetaLimit" | bc) -eq 1 ]; then
    cp -r ../casebase1/* .;
else
    cp -r ../casebase2/* .;
fi
c=$(grep 'z0' ABLConditions.in | awk ' {print substr($3, 0, length($3)-1)}')
z0=$(echo  ${c} | awk '{ print sprintf("%.15f", $1); }');
uStar=`echo "$U*$vkconstant/l(($Href+$z0)/$z0)" | bc -l`
tke=`echo "$uStar*$uStar/0.3" | bc -l`
eps=`echo "$uStar*$uStar*$uStar/($vkconstant*($Href+$z0))" | bc -l`
sed 's/tkeInitial/'${tke}'/g' initialConditions.template > initialConditions.1
sed 's/epsInitial/'${eps}'/g' initialConditions.1 > initialConditions.in
sed 's/tkeInitial/'${tke}'/g' ABLConditions.in > ABLConditions.1 
sed 's/Ucomp1/'${Ucomp1}'/g' ABLConditions.1 > ABLConditions.2
sed 's/Ucomp2/'${Ucomp2}'/g' ABLConditions.2 > ABLConditions.3
mv ABLConditions.3 ABLConditions.in
cp initialConditions.in 0/include/initialConditions
cp ABLConditions.in 0/include/ABLConditions
rm initialConditions.1
rm ABLConditions.1 ABCconditions.2
#------------------------------------------
#
#  WRITE THE SCRIPT TO RUN OPENFOAM
#
#-------------------------------------------
echo "#!/bin/bash" >> cluster_submissiono.pbs
echo "#PBS -N workdir$num " >> cluster_submissiono.pbs
echo "#PBS -e openfoam1.err " >> cluster_submissiono.pbs
echo "#PBS -o openfoam1.out " >> cluster_submissiono.pbs
echo "#PBS -m aeb " >> cluster_submissiono.pbs
echo "#PBS -M gsclara@stanford.edu " >> cluster_submissiono.pbs                          # giving the right name to the job to keep track of the simulations
echo "#PBS -l nodes=1:ppn=24 " >> cluster_submissiono.pbs
echo "#PBS -l walltime=08:00:00 " >> cluster_submissiono.pbs
echo "#PBS -V " >> cluster_submissiono.pbs
echo "#PBS -q medium " >> cluster_submissiono.pbs

echo "module load gnu/4.9.2 " >> cluster_submissiono.pbs
echo "module load openmpi/1.10.2-gnu-4.9.2 " >> cluster_submissiono.pbs
echo "source /your/installation/folder/OpenFOAM/OpenFOAM-4.0/etc/bashrc" >> cluster_submissiono.pbs
echo "cd $workdir" >> cluster_submissiono.pbs

echo "decomposePar >log.preRun " >> cluster_submissiono.pbs
echo "mpirun -np 24 scalarTransportBoundedSimpleFoam -parallel >log.run " >> cluster_submissiono.pbs
echo "wait" >> cluster_submissiono.pbs

#------------------------------------------
#
#  LAUCH OPENFOAM
#
#-------------------------------------------
chmod a+x cluster_submissiono.pbs
# ---------------------------
# OUTPUT FILE POST PROCESSING
# ---------------------------
# Need to write a results file so DAKOTA will proceed with the next
# job generation:
echo "1" > temp.txt # give dummy values to dakota
for i in {1..113};do
echo "1" >> temp.txt
done

mv temp.txt $2
# -------------
# CLEANUP
# -------------

# Do not want to cleanup in this case!
echo "case $num ready to be lauch"