From HPC

parallel queue

The parallel queue is for running two types of parallel job openMP and openMPI.

Contents 1 OpenMP 1.1 Compiling 1.2 Running OpenMP job 2 OpenMPI 2.1 Process that a parallel job goes through 2.2 Compiling OpenMPI 2.2.1 Intel 2.2.2 GNU 2.3 Submitting OpenMPI Job

OpenMP

Shared memory, single node. This is parallel across the cores on a single node, can often be archived by just compiling your code with openMP flags. However better performance can be achieve if you programs are written with openMP in mind.

Compiling

enabling openMP while compiling:

GNU: gfortran -fopenmp -o <exec> <src>

Intel: ifort -openmp -o <exec> <src>

Running OpenMP job

The enviroment OMP_NUM_THREADS must be set to define the number of threads the program should use. Use as many as you have processors i.e 8

The "#$ -pe smp 1" specifies the job should run on one complete node.

Example submission script

#!/bin/bash
#$ -cwd -V
#$ -l mem_free=7G,h_vmem=7.9G
#$ -pe smp 1
export OMP_NUM_THREADS=8
myOpenMPapp

To submit job to the queue

qsub script

OpenMPI

Distributed Memory, multiple nodes. This method of parallel requires you to write your programs to work with openMPI. Using openMPI the nodes will comunicate with each other via the infiniband network

Process that a parallel job goes through

• SGE produces a list of hosts $PE_HOSTFILE
• SGE executes a "start" script for the PE
• SGE runs the users job script
• On termination a "stop" script is executed

Scripts that are automatically used are in

/usr/local/sge6.0/streamline/mpi/

The ompi_start.sh script

#!/bin/sh
# Local info
# This is executed on the front end server
# SERVER=`hostname -s`
function ncpus() {
 n=`cat /proc/cpuinfo | grep processor | tail -1 | cut -f 2- -d :`
 echo $((n+1))
 return
}
SMP=${SMP:-`ncpus`}
. /etc/profile
#
pe_hostfile=$1
echo $pe_hostfile
cat $pe_hostfile
job_id=$2
user=`basename ${HOME}`
if [ -d /users/$user ]; then
  user_dir=/users/$user
else
  user_dir=${HOME}
fi
mpich_dir=${user_dir}/.mpich
mkdir -p $mpich_dir 

cat $pe_hostfile | cut -f 1 -d " " | sort > $mpich_dir/mpich_hosts.$job_id

Compiling OpenMPI

Setup up the system environment, using modules to load the OpenMPI libraries you want to use. This is likely to be a choice between GNU and Intel.

Compile using via wrapper scripts

Intel

With the module openmpi/1.2.6-1/intel loaded

/opt/openmpi-1.2.6-1/intel/bin/

mpic++, mpiCC, mpicc, mpicxx, mpif77, mpif90

GNU

With the module openmpi/1.2.6-1/gnu loaded

/opt/openmpi-1.2.6-1/gcc/bin/

mpic++, mpiCC, mpicc, mpicxx, mpif77, mpif90

Submitting OpenMPI Job

Run using batch scheduler

ompisub C <app> (C = cores)

ompisub 8 <prog> <args> (8 cores, which equals on node)

ompisub NxC <app> (N = Nodes C = Cores)

ompisub 4x3 <prog> <args> (4 nodes each setup to use 3 cores)