molpro环境变量配置 - 计算化学公社

#!/bin/sh
MOLPRO_PREFIX='/home/hexin/molpro/molprop_2012_1_Linux_x86_64_i8'
exe="${MOLPRO_PREFIX}/bin/molpro.exe"
HOSTFILE_FORMAT="%u %N %n %x %d"
LAUNCHER="${MOLPRO_PREFIX}/parallel.x %x"
envlist="LD_LIBRARY_PATH"
LD_LIBRARY_PATH=":$LD_LIBRARY_PATH"
USER=${USER:-$LOGNAME}
if [ "x`hostname`" != x ] ; then
HOST="`hostname`"
else
# used previously, but sometimes the variables were not set correctly
HOST=${HOST:-${HOSTNAME:-`hostname`}}
HOST="`echo ${HOST} | sed -e 's/\..*//g'`"
fi
AIXTHREAD_SCOPE=${AIXTHREAD_SCOPE:-"s"}
if [ x"$MOLPRO_OPTIONS" != x ] ; then
set -- $MOLPRO_OPTIONS "$@"
MOLPRO_OPTIONS=""
fi
hostfile="${TMPDIR:-/tmp}/procgrp.$"
MOLPRO_OPTIONS_FILE="${TMPDIR:-/tmp}/molpro_options.$"
MOLPRO_NOARG="1"
logfile=1
MP_NODES=${MP_NODES:-0}
MP_PROCS=${MP_PROCS:-1}
if [ x"$PBS_NODEFILE" != x ] ; then
nodefile="$PBS_NODEFILE" # PBS
elif [ x"$QSUB_NODEINF" != x ] ; then
nodefile="$QSUB_NODEINF" # NQS
elif [ x"$PE_HOSTFILE" != x ] ; then
nodefile="$PE_HOSTFILE" # SunGridEngine
elif [ x"$LSB_DJOB_HOSTFILE" != x ]; then
nodefile="$LSB_DJOB_HOSTFILE" # LSF
elif [ x"$LSB_HOSTS" != x ]; then
nodefile="${TMPDIR:-/tmp}/nodefile.$" # Lava
rm -f "${nodefile}"
for h in $LSB_HOSTS ; do echo $h >> "${nodefile}" ; done
else
nodefile=""
fi
nodelist=
NODELIST=
OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
proc=0
RT_GRQ=${RT_GRQ:-"ON"}
verbose=0
envlist="$envlist AIXTHREAD_SCOPE MOLPRO_PREFIX MP_NODES MP_PROCS \
MP_TASKS_PER_NODE MOLPRO_NOARG MOLPRO_OPTIONS MOLPRO_OPTIONS_FILE \
MPI_MAX_CLUSTER_SIZE PROCGRP RT_GRQ TCGRSH TMPDIR XLSMPOPTS"
if [ "x${machine}" = xXT ] ; then
SHMEM_SWAP_BACKOFF="150"
CRAY_PORTALS_USE_BLOCKING_POLL="yes"
XT_SYMMETRIC_HEAP_SIZE="1G"
envlist="$envlist SHMEM_SWAP_BACKOFF CRAY_PORTALS_USE_BLOCKING_POLL XT_SYMMETRIC_HEAP_SIZE"
fi
molpro_help () {
cat << _EOF_
This help information relates to the shell script only, for details on
options processed by the Molpro executable please refer to the Molpro
manual.
The main purpose of this shell script is to enable launching of the
Molpro executable for parallel execution by setting up the environment,
host files etc. It is possible to run the Molpro executable directly
for serial builds, or launch with mpirun or equivalent for parallel
builds.
-h | --help : print this help information
--hostfile-format : override the default hostfile format
--launcher : override the default executable launcher
--nodefile : override the default location of the node file
-n | --tasks : specify number of processes
-N | --task-specification : specify processes, nodes, threads (see Molpro manual for details)
-t | --omp-num-threads : specify number of openmp threads (if enabled)
--tcgssh : for TCGMSG builds, use ssh instead of rsh
-v : verbose output (also passed onto the Molpro executable)
-x : specify a different Molpro executable to run
* : all other options passed on to the main Molpro executable
_EOF_
exit 0
}
while test "x$1" != x ; do
case $1 in
-h | --help ) molpro_help ;;
--hostfile-format ) shift; HOSTFILE_FORMAT="$1" ;;
--launcher ) shift; LAUNCHER="$1" ;;
--nodefile ) shift; nodefile="$1" ;;
-n | --tasks ) shift; nodelist="$1" ;;
-n* ) nodelist="`echo "$1" | sed -e 's/^-n//g'`" ;;
-N | --task-specification ) shift; NODELIST="$1" ;;
-t | --omp-num-threads ) shift; OMP_NUM_THREADS="$1" ;;
--tcgssh ) TCGRSH="`which ssh`" ;;
-v ) verbose=1; MOLPRO_OPTIONS="$MOLPRO_OPTIONS -v";;
-x ) shift; exe="$1" ;;
* ) MOLPRO_OPTIONS="$MOLPRO_OPTIONS $1" ;;
esac
shift
done
# add executable directory to PATH for finding mrcc executables
export PATH="`echo ${exe} | sed -e 's/\/[^\/]*$//g'`:${PATH}"
if [ "x$LAUNCHER" = x ] ; then
mode="serial"
if [ "x$verbose" = x1 ] ; then echo " # SERIAL mode"; fi
LAUNCHER="$exe"
else
mode="parallel"
if [ "x$verbose" = x1 ] ; then echo " # PARALLEL mode"; fi
# determine MP_PROCS
MP_PROCS=1
if [ "x$nodelist" != x ] ; then
MP_PROCS="`echo $nodelist | sed -e 's/\/.*$//g' -e '/:/d'`"
tasks_per_node="`echo $nodelist | sed -e 's/^.*\///g' -e 's/^[0-9]*$//g' -e 's/:.*$//g'`"
k="`echo $nodelist | sed -e '/:/!d' -e 's/^.*://g'`"
if [ "x$verbose" = x1 ] ; then
echo " nodelist=$nodelist"
echo " first =$MP_PROCS"
echo " second =$tasks_per_node"
echo " third =$k"
fi
if [ "x$k" != x ] ; then OMP_NUM_THREADS="$k"; fi
fi
XLSMPOPTS="parthds=$OMP_NUM_THREADS"
if [ "x${tasks_per_node}" = x ] ; then
LAUNCHER="`echo $LAUNCHER | sed -e 's/ -npernode %p//'`"
else
MPI_TASKS_PER_NODE="$tasks_per_node"
MPI_MAX_CLUSTER_SIZE="$tasks_per_node"
fi
# set up & write a hostfile
if [ "x$HOSTFILE_FORMAT" != x ] ; then
HOSTFILE_FORMAT="`echo $HOSTFILE_FORMAT | sed -e 's/%d/$working_dir/g'`"
HOSTFILE_FORMAT="`echo $HOSTFILE_FORMAT | sed -e 's/%N/$hostname/g'`"
HOSTFILE_FORMAT="`echo $HOSTFILE_FORMAT | sed -e 's/%n/1/g'`"
HOSTFILE_FORMAT="`echo $HOSTFILE_FORMAT | sed -e 's/%u/$user/g'`"
HOSTFILE_FORMAT="`echo $HOSTFILE_FORMAT | sed -e 's/%x/$exe/g'`"
if [ "x$verbose" = x1 ] ; then echo " HOSTFILE_FORMAT: $HOSTFILE_FORMAT"; fi
working_dir="`pwd`"
rm -f $hostfile
if [ -r "$nodefile" ] ; then # get nodes from PBS, this should over ride MP_PROCS etc.
user="$USER"
nodes_used=0
# some nodefiles contain other columns, assume node is in first column, nprocs in second
cat $nodefile | while read line; do
hostname="`echo $line | sed -e 's/ .*$//g'`"
count="`echo $line | sed -e 's/^[^ ]* *//g' -e 's/ .*$//g'`"
if [ x"$count" = x ] ; then count=1 ; fi
while [ $count -gt 0 ]; do
count=`expr $count - 1`
nodes_used=`expr $nodes_used + 1`
if [ "x$nodelist" != x ] ; then
if [ $nodes_used -le $MP_PROCS ] ; then
eval echo "$HOSTFILE_FORMAT" >> $hostfile
fi
else
eval echo "$HOSTFILE_FORMAT" >> $hostfile
fi
done
done
MP_PROCS=`cat "$hostfile" | wc -l`
elif [ "x$NODELIST" != x ] ; then # get nodes from -N option
hostname="$HOST"
user="$USER"
NODELIST="`echo $NODELIST | sed -e 's/,/ /g'`"
for i in $NODELIST; do
eval `echo $i | awk -v RS=: '{if (int($1)==$1) print "count="$1; else print "hostname="$1}'`
while [ $count -gt 0 ]; do
count=`expr $count - 1`
eval echo "$HOSTFILE_FORMAT" >> $hostfile
done
done
MP_PROCS=`cat "$hostfile" | wc -l`
else # local machine
hostname="$HOST"
user="$USER"
count=$MP_PROCS
> $hostfile
while [ $count -gt 0 ]; do
count=`expr $count - 1`
eval echo "$HOSTFILE_FORMAT" >> $hostfile
done
fi
# should sort hostfile somehow with sort on column with node names
if [ "x$verbose" = x1 ] ; then echo; cat $hostfile; echo; fi
# below is needed for tcgmsg, but really this should be treated more generally
PROCGRP="$hostfile"
fi
LAUNCHER="`echo $LAUNCHER | sed -e 's/%x/$exe/g'`"
LAUNCHER="`echo $LAUNCHER | sed -e 's/%h/$hostfile/g'`"
LAUNCHER="`echo $LAUNCHER | sed -e 's/%n/$MP_PROCS/g'`"
LAUNCHER="`echo $LAUNCHER | sed -e 's/%p/$tasks_per_node/g'`"
for i in $envlist ; do
eval j="$"$i
if [ "x${j}" != x ] ; then LAUNCHER="`echo $LAUNCHER | sed -e 's/%e/'$i='
$i' %e/g'`"; fi
done
LAUNCHER="`echo $LAUNCHER | sed -e 's/%e//g'`"
fi
for i in $envlist ; do
eval j="$"$i
if [ "x${j}" != x ] ; then
export $i
if [ "x$verbose" = x1 ] ; then echo " export $i='${j}'" ; fi
else
if [ "x$verbose" = x1 ] ; then echo " $i='${j}'" ; fi
fi
done
if [ "x${OMP_NUM_THREADS}" != x1 ] ; then
MOLPRO_OPTIONS="${MOLPRO_OPTIONS} -t ${OMP_NUM_THREADS}"
fi
LAUNCHER="`eval echo $LAUNCHER` $MOLPRO_OPTIONS"
if [ "x$verbose" = x1 ] ; then echo "$LAUNCHER" ; fi
if [ "x$mode" = xserial ] ; then
exec $LAUNCHER
else
echo "${MOLPRO_OPTIONS}" > ${MOLPRO_OPTIONS_FILE}
if [ x"`uname -s`" = xDarwin ] ; then
tt=`lsof -p $|egrep ' 0u *CHR'| sed -e 's/^.* *//'|grep '/dev/tty'`
if [ x"$tt" = x ] ; then
eval $LAUNCHER
rc=$?
else
eval $LAUNCHER </dev/null
rc=$?
fi
else
eval $LAUNCHER
rc=$?
fi
fi
if [ "x${LSB_HOSTS}" != x ] && [ "x${LSB_DJOB_HOSTFILE}" = x ]; then rm -f "${nodefile}" ; fi
rm -f ${hostfile} ${MOLPRO_OPTIONS_FILE}
exit ${rc}

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