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5fb9e6cd847e890abb566e1852f0aca42f19cde5
CFDEMcoupling-PFM/src/lagrangian/cfdemParticle/etc/functions.sh
cfdem 5fb9e6cd84 release on 2012-10-23_10-36-40
2012-10-23 10:36:40 +02:00

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#!/bin/bash
#===================================================================#
# test routine for cfdem project
# defining functions used by the shell scripts
# Christoph Goniva - June. 2011, DCS Computing GmbH
#===================================================================#
#==================================#
#- function to compile a cfdem library
compileLib()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
#doClean="$5"
#--------------------------------------------------------------------------------#
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $casePath
#- header
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- wclean and wmake
#if [ $doClean != "noClean" ]; then
rmdepall 2>&1 | tee -a $logpath/$logfileName
wclean 2>&1 | tee -a $logpath/$logfileName
#fi
wmake libso 2>&1 | tee -a $logpath/$logfileName
#- keep terminal open
#read
}
#==================================#
#==================================#
#- function to compile a cfdem solver
compileSolver()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
#doClean="$5"
#--------------------------------------------------------------------------------#
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $casePath
#- header
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- wclean and wmake
#if [ $doClean != "noClean" ]; then
rmdepall 2>&1 | tee -a $logpath/$logfileName
wclean 2>&1 | tee -a $logpath/$logfileName
#fi
wmake 2>&1 | tee -a $logpath/$logfileName
#- keep terminal open
#read
}
#==================================#
#==================================#
#- function to compile LIGGGHTS
compileLIGGGHTS()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
headerText="$3"
#--------------------------------------------------------------------------------#
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $CFDEM_LIGGGHTS_SRC_DIR
#- header
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- wclean and wmake
make clean-all 2>&1 | tee -a $logpath/$logfileName
make $CFDEM_LIGGGHTS_MAKEFILE_NAME -j $WM_NCOMPPROCS 2>&1 | tee -a $logpath/$logfileName
make makelib 2>&1 | tee -a $logpath/$logfileName
make -f Makefile.lib $CFDEM_LIGGGHTS_MAKEFILE_NAME 2>&1 | tee -a $logpath/$logfileName
}
#==================================#
#==================================#
#- function to compile a lammps lib
compileLMPlib()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
headerText="$3"
makeFileName="$4"
libraryPath="$5"
#--------------------------------------------------------------------------------#
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $libraryPath
#- header
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- clean up
echo "make clean" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
make -f $makeFileName clean 2>&1 | tee -a $logpath/$logfileName
#- compile
echo "make" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
make -f $makeFileName 2>&1 | tee -a $logpath/$logfileName
}
#==================================#
#==================================#
#- function to run a DEM case
DEMrun()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
solverName="$5"
#--------------------------------------------------------------------------------#
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $casePath/DEM
#- header
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- run applictaion
#liggghts < $solverName 2>&1 | tee -a $logpath/$logfileName
$CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME < $solverName 2>&1 | tee -a $logpath/$logfileName
#- keep terminal open (if started in new terminal)
#read
}
#==================================#
#==================================#
#- function to run a DEM case in parallel
parDEMrun()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
solverName="$5"
nrProcs="$6"
machineFileName="$7"
debugMode="$8"
#--------------------------------------------------------------------------------#
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $casePath/DEM
#- header
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- run applictaion
if [ $machineFileName == "none" ]; then
mpirun -np $nrProcs $debugMode $CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME < $solverName 2>&1 | tee -a $logpath/$logfileName
else
mpirun -machinefile $machineFileName -np $nrProcs $debugMode $CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME < $solverName 2>&1 | tee -a $logpath/$logfileName
fi
#- keep terminal open (if started in new terminal)
#read
}
#==================================#
#==================================#
#- function to run a CFD case
CFDrun()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
solverName="$5"
debugMode="$6"
#--------------------------------------------------------------------------------#
if [ $debugMode == "on" ]; then
debugMode="valgrind"
else
debugMode=""
fi
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $casePath/CFD
#- header
echo 2>&1 | tee -a /$logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- clean up case
rm couplingFiles/*
#- run applictaion
$debugMode $solverName 2>&1 | tee -a $logpath/$logfileName
#- keep terminal open (if started in new terminal)
#read
}
#==================================#
#==================================#
#- function to run a parallel CFD-DEM case
parCFDDEMrun()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
solverName="$5"
nrProcs="$6"
machineFileName="$7"
debugMode="$8"
#--------------------------------------------------------------------------------#
if [ $debugMode == "on" ]; then
debugMode="valgrind"
else
debugMode=""
fi
#- clean up old log file
rm $logpath/$logfileName
#- change path
cd $casePath/CFD
#- remove old data
rm -rf processor*
#- decompose case
decomposePar
#- header
echo 2>&1 | tee -a /$logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- write path
pwd 2>&1 | tee -a $logpath/$logfileName
echo 2>&1 | tee -a $logpath/$logfileName
#- clean up case
rm couplingFiles/*
#- run applictaion
if [ $machineFileName == "none" ]; then
mpirun -np $nrProcs $debugMode $solverName -parallel 2>&1 | tee -a $logpath/$logfileName
#- reconstruct case
#pseudoParallelRun "reconstructPar" $nrProcs
reconstructPar
else
mpirun -machinefile $machineFileName -np $nrProcs $debugMode $solverName -parallel 2>&1 | tee -a $logpath/$logfileName
#- reconstruct case
reconstructPar
fi
#- keep terminal open (if started in new terminal)
#read
}
#==================================#
#==================================#
#- function to collect results from
#- logfiles to one log file
collectLog()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
casePath="$3"
headerText="$4"
nrOfLines="$5"
#--------------------------------------------------------------------------------#
echo 2>&1 | tee -a $logpath/$logfileName
echo "// $headerText //" 2>&1 | tee -a $logpath/$logfileName
tail --lines=$nrOfLines $casePath |cut -d " " -f1- 2>&1 | tee -a $logpath/$logfileName
}
#==================================#
#==================================#
#- function to replace a line in a file where text consecutive
# the old line must look like: oldWord
# and will be replaced by: newWord
replaceLineInFile()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
filePath="$3"
oldWord="$4" # give text only until first "/"
newWord="$5"
#--------------------------------------------------------------------------------#
#- adapt /etc/bashrc
echo "replaceLineInFile $filePath" 2>&1 | tee -a $logpath/$logfileName
sed "/$oldWord/ c\ $newWord" $filePath > $filePath"2" 2>&1 | tee -a $logpath/$logfileName
cp $filePath"2" $filePath 2>&1 | tee -a $logpath/$logfileName
rm $filePath"2" 2>&1 | tee -a $logpath/$logfileName
}
#==================================#
#==================================#
#- function to replace a line in a file where text is separated by one blank
# the old line must look like: oldWord1 oldWord2
# and will be replaced by: newWord1 newWord2
replaceSeparatedLineInFile()
{
#--------------------------------------------------------------------------------#
#- define variables
logpath="$1"
logfileName="$2"
filePath="$3"
oldWord1="$4"
oldWord2="$5"
newWord1="$6"
newWord2="$7"
#--------------------------------------------------------------------------------#
#- adapt /etc/bashrc
echo "replaceLineInFile $filePath" 2>&1 | tee -a $logpath/$logfileName
sed "/$oldWord1 $oldWord2/ c\ $newWord1 $newWord2" $filePath > $filePath"2" 2>&1 | tee -a $logpath/$logfileName
cp $filePath"2" $filePath 2>&1 | tee -a $logpath/$logfileName
rm $filePath"2" 2>&1 | tee -a $logpath/$logfileName
}
#==================================#
#=======================================#
#- script to run a function in pseudo-parallel
# several runs of the function are started
# simultanously. Only makes sense on shared memory sys
# based on script by K. Wardle 6/22/09
# published at CFDonline forum
pseudoParallelRun()
{
#--------------------------------------------------------------------------------#
#- define variables
appname=$1
njobs=$2
outputfile="log.$appname"
#--------------------------------------------------------------------------------#
if [ -z "$njobs" ]; then
echo ""
echo " K. Wardle 6/22/09"
echo " bash script to run reconstructPar (or other fct) in pseudo-parallel mode"
echo " by breaking time directories into multiple ranges"
echo ""
echo " USAGE: appname <NP> <outputfile> [output file is optional] "
echo ""
exit
fi
appflag="-noZero"
#let njobs1=$njobs+1
echo "running $appname $appflag in pseudo-parallel mode on $njobs processors"
#count the number of time directories
nsteps=`ls -d processor0/[0-9]*/ | wc -l`
echo "do $appname on $nsteps time directories"
##nsteps=`ls processor0 | wc -l`
#echo "nsteps= $nsteps"
#let nsteps=$nsteps1-1
nchunk=`echo $nsteps/$njobs+1 | bc`
#echo "nchunk = $nchunk"
#find max time
tmin=`ls processor0 | sort -nr | tail -1`
#echo "tmin = $tmin"
tmax=`ls processor0 | sort -nr | head -1`
#echo "tmax = $tmax"
echo "making temp dir"
tempdir="temp.par$appname"
mkdir $tempdir
tstart=$tmin
p=p
for i in `seq $njobs`
do
nn=`echo $i*$nchunk | bc`
tstop=`ls processor0 | sed -n $nn$p`
if [ $i == $njobs ]
then
tstop=$tmax
fi
echo "Starting Job $i - $appname time = $tstart through $tstop"
`$appname $appflag -time "$tstart:$tstop" > $tempdir/output-$tstop &`
let nn=$nn+1
tstart=`ls processor0 | sed -n $nn$p`
done
#sleep until jobs finish
#if number of jobs > njobs, hold loop until job finishes
nmore_old=`echo 0`
until [ `ps -C $appname | wc -l` -eq 1 ];
do
sleep 10
## n1=`ps -C $appname | wc -l`
## n2=`echo $n1-1 | bc`
nnow=`ls -d [0-9]*/ | wc -l` ##count time directories in case root dir, this will include 0
nmore=`echo $nsteps-$nnow+1 | bc` ##calculate number left to reconstruct and subtract 0 dir
if [ $nmore != $nmore_old ]
then
echo "$nmore directories remaining..."
fi
nmore_old=$nmore
done
#combine and cleanup
if [ -n "$outputfile" ]
then
#check if output file already exists
if [ -e "$outputfile" ]
then
echo "output file $outputfile exists, moving to $outputfile.bak"
mv $outputfile $outputfile.bak
fi
echo "cleaning up temp files"
for i in `ls $tempdir`
do
cat $tempdir/$i >> $outputfile
done
fi
rm -rf $tempdir
echo "finished"
}
#==================================#
#- function make a tar.gz copy with date tag from a directory
# Remove the original directory
backupRemoveDir()
{
#--------------------------------------------------------------------------------#
#- define variables
filePath="$1"
backupPath="$2"
date="$3"
#--------------------------------------------------------------------------------#
echo "creating dirctory :\n $filePath""-until""$date\n"
mkdir $filePath"-until"$date
echo "move : $filePath/* to\n $filePath""-until""$date\n and tar.gz"
mv $filePath/* $filePath"-until"$date
tar czvf $filePath"-until"$date.tar.gz $filePath"-until"$date
rm -r $filePath"-until"$date
mv $filePath"-until"$date.tar.gz $backupPath
}
#==================================#
#- function make a tar.gz copy with date tag from a directory
# Keep the original directory
backupDir()
{
#--------------------------------------------------------------------------------#
#- define variables
filePath="$1"
backupPath="$2"
date="$3"
#--------------------------------------------------------------------------------#
echo "creating dirctory :\n $filePath""-until""$date\n"
mkdir $filePath"-until"$date
echo "move : $filePath/* to\n $filePath""-until""$date\n and tar.gz"
cp -r $filePath/* $filePath"-until"$date
tar czvf $filePath"-until"$date.tar.gz $filePath"-until"$date
rm -r $filePath"-until"$date
mv $filePath"-until"$date.tar.gz $backupPath
}
#========================================#
#- function to check if a directory exits
checkDir()
{
#--------------------------------------------------------------------------------#
#- define variables
filePath="$1"
#--------------------------------------------------------------------------------#
if [ -d "$filePath" ]; then
echo "true"
else
echo "false"
fi
}
#========================================#
#- function to check if a directory exits
checkDirComment()
{
#--------------------------------------------------------------------------------#
#- define variables
filePath="$1"
varName="$2"
critical="$3"
#--------------------------------------------------------------------------------#
if [ $(checkDir $filePath) == "true" ]; then
echo "valid:yes critical:$critical - $varName = $filePath"
else
echo "valid:NO critical:$critical - $varName = $filePath does not exist"
fi
}
#========================================#
#- track memory usage
trackMem()
{
#--------------------------------------------------------------------------------#
#- define variables
appname="$1"
fileName="$2"
#--------------------------------------------------------------------------------#
rm $fileName
echo "please use only the the first 15 strings of the command !!!"
/usr/bin/printf "%-6s %-9s %s\n" "PID" "Total" "Command" >> $fileName
/usr/bin/printf "%-6s %-9s %s\n" "---" "-----" "-------" >> $fileName
for PID in $(/bin/ps -e | /usr/bin/awk '$1 ~ /[0-9]+/ { print $1 }')
do
CMD=$(/bin/ps -o comm -p $PID | /usr/bin/tail -1)
if [ $CMD == $appname ]
then
TOTAL=$(/usr/bin/pmap $PID 2>/dev/null | /usr/bin/tail -1 | /usr/bin/awk '{ print $2 }')
[ -n "$TOTAL" ] && /usr/bin/printf "%-6s %-9s %s\n" "$PID" "$TOTAL" "$CMD"
fi
done | /usr/bin/sort -n -k2 >> $fileName
}
#========================================#
#- remove brackets from file
removeBracketsFromFile()
{
#--------------------------------------------------------------------------------#
#- define variables
oldFileName="$1"
newFileName="$oldFileName""_noBrackets"
#--------------------------------------------------------------------------------#
sed -e 's/[(,)]//g' $oldFileName > $newFileName
}
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