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Accueil du site > Informations pratiques > Guidelines to use the LPT computer cluster

Guidelines to use the LPT computer cluster

par Sylvain Capponi - 31 janvier 2007

Toutes les versions de cet article : English , français

Overview

Our Linux cluster can be used by LPT members. A separate login is needed and account can be opened by our system manager.

This cluster uses a standard queuing system, known as PBS, for which it is easy to find documentation on the web.

We provide here a simple script to run a monoprocessor job :

1) One needs to create a script file, say named "script.pbs", adjusting time, memory etc.

# !/bin/csh
#PBS -S /bin/csh
#PBS -q mono
#PBS -l nodes=1:ppn=1
#PBS -j eo
#PBS -l pcput=10:00:00
#PBS -l walltime=10:00:00
#PBS -l pmem=1gb
#PBS -M myemail@irsamc.ups-tlse.fr -m e

cd $PBS_O_WORKDIR

./a.out

2) Then this file should be executable : chmod u+x script.pbs

3) Finally, you must submit with the command qsub : qsub script.pbs

NB : we strongly encourage users to use parallelization either MPI on several nodes, or OpenMP on several cores (on a single node).

Queueing system

Details on the queues (time limit, number of simultaneous jobs etc.) can be obtained with the command : qstat -q

Compilers

We strongly recommend to use Intel compilers and dedicated MKL Lapack libraries. They can be found in directory : /opt/intel/

do source /opt/intel/bin/compilervars.sh to add environment variables.

In order to find the correct compiling options and environment variables, we strongly suggest to look at :

http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/