| 1 | #!@SHELL@
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| 2 | #
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| 3 | # Performs an molecular dynamics simulation with the BOSSANOVA method
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| 4 |
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| 5 | #MPIRUN="/opt/packages/mpichgm-1.2.7..15/bin/mpirun.ch_gm"
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| 6 | MPIRUN="/usr/bin/mpirun.mpich"
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| 7 | exec_prefix="@prefix@"
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| 8 | database="@bindir@"
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| 9 | MOLECUILDER="@bindir@/molecuilder"
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| 10 | JOINER="@bindir@/joiner"
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| 11 | CRUNCHER="/mount/bespin/heber/build/mpqc-2.3.0/bin/mpqc"
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| 12 | CONVERTER="/mount/bespin/heber/tmp/mpqc/espack2mpqc.py"
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| 13 | PREPARER="/mount/bespin/heber/tmp/mpqc/convertresults.sh"
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| 14 |
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| 15 | function check()
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| 16 | {
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| 17 | #1 MESSAGE
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| 18 | if [ $? -eq 0 ]; then
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| 19 | if [ -z $1 ]; then
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| 20 | echo "ok."
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| 21 | else
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| 22 | echo "ok: $1."
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| 23 | fi
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| 24 | else
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| 25 | if [ -z $1 ]; then
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| 26 | echo "failed."
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| 27 | else
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| 28 | echo "failed: $1."
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| 29 | fi
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| 30 | exit 1
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| 31 | fi
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| 32 | }
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| 33 |
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| 34 | #function MultiRunSim {
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| 35 | # # 1 is config file dir (with all files)
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| 36 | # # 2 is the machine file
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| 37 | #
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| 38 | # ${JOBRUNNER} --mpqc ${CRUNCHER} -nprocpernode 2 -nprocperjob 1 -nthreadperproc 2 --threadgrp=posix --messagegrp=proc --memorygrp=proc --nodefile $2 --readdir $1 --inputprefix=${1}/ --outputprefix=${1}/ --autoout --verbose --rerun 2>/dev/stdout | tee -a dynamic.log
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| 39 | #}
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| 40 |
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| 41 | function MultiRunSim {
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| 42 | # 1 is the number of groups
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| 43 | # 2 is the directory
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| 44 | # 3, ... are config files
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| 45 |
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| 46 | # find the next free proc group
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| 47 | divisor=$1
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| 48 | shift
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| 49 | DIR=$1
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| 50 | shift
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| 51 | started=0
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| 52 | pwd=`pwd`
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| 53 | while [ $started -eq 0 ]; do
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| 54 | groupnr=1
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| 55 | while [ $groupnr -le $divisor ]; do
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| 56 | if [ ! -e "${DIR}/ProcRuns${groupnr}" ]; then
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| 57 | #MaxNodes=`cat ${DIR}/ProcGroup${groupnr} | awk 'END{print NR}'`
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| 58 | #gamma=`grep ProcPEGamma $1 | awk -F"\t" {'print $2'}`
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| 59 | #psi=`grep ProcPEPsi $1 | awk -F"\t" {'print $2'}`
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| 60 | #let nodes=$gamma*$psi
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| 61 | #if [ $nodes -gt $MaxNodes ]; then
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| 62 | # echo "Process $1 needs too many nodes! Breaking." | tee -a dynamic.log
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| 63 | # exit 1
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| 64 | #fi
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| 65 | nodes=1
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| 66 | echo "touch ${DIR}/ProcRuns${groupnr}" >"${DIR}/ProcBatch${groupnr}"
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| 67 | if [ ! -z $1 ]; then
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| 68 | echo -n "rsh `cat <${DIR}/ProcGroup${groupnr}` 'cd ${pwd}/${DIR}" >>"${DIR}/ProcBatch${groupnr}"
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| 69 | fi
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| 70 | while [ ! -z $1 ]; do # add all config files as single lines
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| 71 | #echo -n "${MPIRUN} -machinefile ${DIR}/ProcGroup${groupnr} -np $nodes " >>"${DIR}/ProcBatch${groupnr}"
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| 72 | echo -n "; ${CRUNCHER} -o ${1/conf/out} ${1/conf/in}" >>"${DIR}/ProcBatch${groupnr}"
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| 73 | shift
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| 74 | done
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| 75 | echo "'" >>"${DIR}/ProcBatch${groupnr}"
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| 76 | echo "rm -f ${DIR}/ProcRuns${groupnr}" >>"${DIR}/ProcBatch${groupnr}"
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| 77 | /bin/sh "${DIR}/ProcBatch${groupnr}" &
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| 78 | started=1
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| 79 | let groupnr=${divisor}+1
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| 80 | else
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| 81 | let groupnr=$groupnr+1
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| 82 | fi
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| 83 | done
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| 84 | # wait a few seconds
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| 85 | #if [ $2 -gt 1 ]; then
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| 86 | # sleep 2
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| 87 | #fi
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| 88 | done
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| 89 | }
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| 90 |
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| 91 | # get command line options
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| 92 | if [ -z $3 ]; then
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| 93 | echo "Usage: $0 <config file> <Order> <max. bond distance> <MaxNodes> [MaxMDsteps]"
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| 94 | echo -e "\t<config file> the pcp config file of the total molecule"
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| 95 | echo -e "\t<Order> the highest bond order (i.e. the cutoff number in ANOVA series expansion)"
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| 96 | echo -e "\t<max. bond distance> maximum distance to look for bonds (bonds are associated by element covalent radii criterion)"
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| 97 | echo -e "\t[MaxMDSteps] overrides given MaxOuterStep in config file"
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| 98 | exit 1;
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| 99 | else
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| 100 | arg=$1
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| 101 | mainname=`grep mainname $arg | awk -F"\t" {'print $2'}`
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| 102 | order=$2
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| 103 | distance=$3
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| 104 | if [ -z $4 ]; then
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| 105 | MaxSteps=`grep MaxOuterStep $arg | awk -F"\t" {'print $2'}`
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| 106 | else
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| 107 | MaxSteps=$4
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| 108 | fi
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| 109 | echo "Going to run for a total of $MaxSteps steps, bond order $order and maximum distance $distance of config file $arg." | tee -a dynamic.log
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| 110 | fi
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| 111 |
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| 112 |
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| 113 | # get the directory
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| 114 | DIR=`dirname $arg`
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| 115 | if [ -z "`grep $DIR $arg`" ]; then
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| 116 | echo "Cannot find the directory $DIR in the config file." | tee -a dynamic.log
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| 117 | exit 1;
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| 118 | else
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| 119 | echo "Using $DIR as directory." | tee -a dynamic.log
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| 120 | fi
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| 121 |
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| 122 | PBS_NODEFILE="${DIR}/machines"
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| 123 | if [ ! -e $PBS_NODEFILE ]; then
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| 124 | i=1
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| 125 | cpus=`cat /proc/cpuinfo | grep processor | wc -l`
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| 126 | echo "localhost" >$PBS_NODEFILE
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| 127 | while [ $i -lt $cpus ]; do # add one localhost per cpu to machines file
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| 128 | echo "localhost" >>$PBS_NODEFILE
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| 129 | let i=$i+1
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| 130 | done
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| 131 | fi
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| 132 |
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| 133 | # delete old processor group files
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| 134 | rm ${DIR}/ProcGroup* -f
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| 135 | rm ${DIR}/ProcRuns* -f
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| 136 | rm ${DIR}/ProcBatch* -f
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| 137 |
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| 138 | # put nodes into groups
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| 139 | MaxNodes=0
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| 140 | for node in `cat <$PBS_NODEFILE`; do
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| 141 | let MaxNodes=$MaxNodes+1
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| 142 | done
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| 143 | gamma=`grep ProcPEGamma $arg | awk -F"\t" {'print $2'}`
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| 144 | psi=`grep ProcPEPsi $arg | awk -F"\t" {'print $2'}`
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| 145 | let nodes=$gamma*$psi
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| 146 | let divisor=$MaxNodes/$nodes
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| 147 | echo "Using $divisor processor groups." | tee -a dynamic.log
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| 148 | nodenr=0
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| 149 | groupnr=1
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| 150 | for node in `cat <$PBS_NODEFILE`; do
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| 151 | let nodenr=$nodenr+1
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| 152 | #echo "Current node $nodenr is $node." | tee -a dynamic.log
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| 153 | let currentgrouplimit=$groupnr*$nodes
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| 154 | if [ $currentgrouplimit -lt $nodenr ]; then
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| 155 | let groupnr=$groupnr+1
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| 156 | fi
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| 157 | #echo "Putting into group $groupnr." | tee -a dynamic.log
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| 158 | echo "$node" >>"${DIR}/ProcGroup${groupnr}"
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| 159 | done
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| 160 | i=0
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| 161 | while [ $i -lt $groupnr ]; do
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| 162 | let i=$i+1
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| 163 | echo "Group nr. $i" | tee -a dynamic.log
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| 164 | echo "===========" | tee -a dynamic.log
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| 165 | cat <"${DIR}/ProcGroup${i}"
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| 166 | cat <"${DIR}/ProcGroup${i}" >>dynamic.log
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| 167 | echo -e "\n" | tee -a dynamic.log
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| 168 | done
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| 169 |
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| 170 | # copy first conf
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| 171 | cp $arg ${arg}.MD
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| 172 |
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| 173 |
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| 174 | i=1;
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| 175 | while [ $i -le $MaxSteps ]; do
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| 176 | # break down the molecule with molecuilder
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| 177 | echo -n "Fragmenting ... " | tee -a dynamic.log
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| 178 | ${MOLECUILDER} ${arg}.MD -e ${database} -f $distance $order 2>/dev/null >/dev/null
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| 179 | check | tee -a dynamic.log
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| 180 | echo "done." | tee -a dynamic.log
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| 181 |
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| 182 | # get the number of digits of the fragment count
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| 183 | digits=1
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| 184 | while [ ! -e ${DIR}/BondFragment`printf "%0${digits}d" 0`.conf ]; do
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| 185 | let digits=$digits+1
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| 186 | done
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| 187 | echo "Found $digits digits for the fragment number." | tee -a dynamic.log
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| 188 |
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| 189 | # get the fragment count
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| 190 | frag=0
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| 191 | while [ -e ${DIR}/BondFragment`printf "%0${digits}d" $frag`.conf ]; do
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| 192 | # unset MaxOuterStep in config file
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| 193 | sed -i -e "s#MaxOuterStep.*\##MaxOuterStep\t0\t\##" ${DIR}/BondFragment`printf "%0${digits}d" $frag`.conf
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| 194 | rm -rf ${DIR}/BondFragment`printf "%0${digits}d" $frag`
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| 195 | let frag=$frag+1
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| 196 | done
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| 197 | echo "There are $frag fragments." | tee -a dynamic.log
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| 198 |
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| 199 |
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| 200 | # evaluate each fragment
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| 201 | # j=0
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| 202 | # while [ $j -lt $frag ]; do
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| 203 | # number=`printf "%0${digits}d" $j`
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| 204 | # # convert all configs
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| 205 | # echo -n "Converting ${DIR}/BondFragment${number}.conf ..." | tee -a dynamic.log
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| 206 | # sh $CONVERTER ${DIR}/BondFragment${number}.conf
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| 207 | # check | tee -a dynamic.log
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| 208 | # let j=$j+1
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| 209 | # done
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| 210 | #
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| 211 | # MultiRunSim ${DIR} $PBS_NODEFILE
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| 212 | #
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| 213 | # j=0
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| 214 | # while [ $j -lt $frag ]; do
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| 215 | # number=`printf "%0${digits}d" $j`
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| 216 | # # rename output files
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| 217 | # echo -n "Renaming `ls ${DIR}/BondFragment${number}.out.001.02.02` ..." | tee -a dynamic.log
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| 218 | # mv ${DIR}/BondFragment${number}.out.001.02.02 ${DIR}/BondFragment${number}.out
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| 219 | # check | tee -a dynamic.log
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| 220 | # let j=$j+1
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| 221 | # done
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| 222 |
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| 223 | # reset command arrays
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| 224 | grp=0;
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| 225 | while [ $grp -lt $divisor ]; do
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| 226 | command[$grp]=""
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| 227 | let grp=$grp+1
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| 228 | done
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| 229 |
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| 230 | # distribute the jobs among the groups
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| 231 | j=0;
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| 232 | while [ $j -lt $frag ]; do
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| 233 | number=`printf "%0${digits}d" $j`
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| 234 | # convert all configs
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| 235 | #echo -n "Converting ${DIR}/BondFragment${number}.conf ..." | tee -a dynamic.log
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| 236 | #sh $CONVERTER ${DIR}/BondFragment${number}.conf
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| 237 | #check | tee -a dynamic.log
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| 238 | # and distribute
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| 239 | let grp=${j}%${divisor}
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| 240 | #echo "BondFragment${number}.conf is evaluated by group $grp."
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| 241 | command[$grp]="${command[$grp]}BondFragment${number}.conf "
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| 242 | let j=$j+1
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| 243 | done
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| 244 |
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| 245 | # go through all groups and run the job
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| 246 | olddivisor=$divisor
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| 247 | if [ $divisor -gt $frag ]; then
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| 248 | divisor=$frag
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| 249 | fi
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| 250 | grp=0;
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| 251 | while [ $grp -lt $divisor ]; do
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| 252 | number=`printf "%0${digits}d" $j`
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| 253 | echo -n "Starting calculation of group $grp with fragments \"${command[$grp]}\" at step $i ... " | tee -a dynamic.log
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| 254 | MultiRunSim $divisor ${DIR} ${command[$grp]}
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| 255 | echo "done." | tee -a dynamic.log
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| 256 | let grp=$grp+1
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| 257 | done
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| 258 | divisor=$olddivisor
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| 259 |
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| 260 | # wait till all ProcRuns files are gone
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| 261 | # if [ $divisor -gt 1 ]; then
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| 262 | echo "Waiting for all running jobs at step $i to end ... " | tee -a dynamic.log
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| 263 | while [ ! -z "`find ${DIR} -name 'ProcRuns*'`" ]; do
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| 264 | #if [ ! -z "`find ${DIR} -name 'ProcRuns*'`" ]; then
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| 265 | # echo "still `ls ${DIR}/ProcRuns*` present"
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| 266 | #fi
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| 267 | sleep 1
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| 268 | done
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| 269 | echo "done." | tee -a dynamic.log
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| 270 | # fi
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| 271 |
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| 272 |
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| 273 | # convert results
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| 274 | sleep 1 # necessary for result files to close
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| 275 | echo -n "Converting all results ... " | tee -a dynamic.log
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| 276 | sh $PREPARER $DIR
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| 277 | check | tee -a dynamic.log
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| 278 |
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| 279 | # join the resulting forces into a single file
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| 280 | echo -n "Joining fragment energies ... " | tee -a dynamic.log
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| 281 | ${JOINER} ${DIR}/ $mainname >/dev/null 2>/dev/null
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| 282 | check | tee -a dynamic.log
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| 283 | echo "done." | tee -a dynamic.log
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| 284 |
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| 285 | # move the ions by calling pcp with this force file
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| 286 | sed -i -e "s#MaxOuterStep.*\##MaxOuterStep\t$i\t\##" ${arg}.MD
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| 287 | echo -n "Moving ions with obtained forces at step $i ... " | tee -a dynamic.log
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| 288 | $MOLECUILDER ${arg}.MD -e ${database} -P "${DIR}/pcp.Order${order}.forces.all" 2>/dev/null >/dev/null
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| 289 | echo "done" | tee -a dynamic.log
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| 290 |
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| 291 | # last of all, put "joined" energy and forces under this step
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| 292 | cp ${DIR}/pcp.Order${order}.energy.all ${DIR}/pcp.step${i}.energy.all
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| 293 | cp ${DIR}/pcp.Order${order}.forces.all ${DIR}/pcp.step${i}.forces.all
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| 294 |
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| 295 | # next step
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| 296 | let i=$i+1
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| 297 | done
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| 298 |
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| 299 | exit 0
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