Advanced Computing Research Centre

Script to use with MPICH2

MPICH2 is not installed on Bluecrystal however a number of commercial packages, e.g. Amber, are supplied with it pre-compiled and require it to run successfully. In order to run such codes under the queueing system you should copy the script below, edit the sections marked 1 and 2 and submit the script to the queue.

If you encounter any problems running your code, please contact hpc-help@bristol.ac.uk.

#!/bin/bash
#
#PBS -l walltime=360:00:00,nodes=2:ppn=4
#PBS -N CPB
#PBS -j oe
#
# 1. Set  working directory    EDIT THE FOLLOWING LINE
#

export MYDIR="$HOME/CPB"

#

# Change into the simulation run directory

cd $MYDIR

# 2. Set the executable name  EDIT THE FOLLOWING LINE
#

MYEXE="$AMBERHOME2/exe/sander.MPI -O -i md27.in -o md27.out -p t.top -c md26.rst -r md27.rst -x md27.mdcrd"

# ---------------------------------------------------------------
# DO NOT CHANGE ANYTHING BELOW THIS LINE ------------------------
#


# Get the JOBID
#

export JOBNO="`echo $PBS_JOBID | sed s/.master.ic.cluster//`"

# Create the mpd node file
#

`cat $PBS_NODEFILE |awk -F"." '{print($1)}' |sort |uniq > mpd.nodes.$JOBNO`

# CALCULATE THE TOTAL NUMBER OF NODES
#

export total=`cat mpd.nodes.$JOBNO |wc -l `

# BOOT THE MPD
#

mpdboot -n $total -f mpd.nodes.$JOBNO

# Wait for mpds to boot
#

sleep 5

export nnodes=`cat $PBS_NODEFILE |wc -l `

# Create the mpiexec node file
#

`cat $PBS_NODEFILE |awk -F"." '{print($1)}' |sort | uniq -c | awk '{ print($2":"$1);}' > mpi.nodes.$JOBNO`

# EXECUTE THE CODE
#

mpiexec -machinefile mpi.nodes.$JOBNO -n $nnodes $MYEXE gzip md27.mdcrd

#ON COMPLETION KILL THE MPDs
#

mpdallexit