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Cluster System Cheat Sheet


This document is a quick reference for the cluster system.We’ve assembled some (hopefully) useful info and the mostfrequently used commands on a page that you can keep athand when working with the cluster system

Accessing the cluster system

Connect to e.g. via ssh for interactive work like editing files etc.

Do NOT try to start computations on the login nodes; the system will terminate anything using >30 minutes cputime (see ulimit -a) to keep nodes responsive for all users.

For computations, use the batch system to submit scripts: qsub <options> <jobscript_name>.

For file transfers, use (typical commands:scp, sftp, rsync).

Check for further information.

Batch system

An example script that can be submitted via qsub <job-script>:

#!/bin/bash -l
#PBS -N mysimulation
#PBS -M ich@mail.adresse
#PBS -l nodes=1:ppn=4
#PBS -l walltime=00:10:00
#PBS -l mem=3gb
# node the job ran on
echo "Job ran on:" $(hostname)
# load the relevant modules
module load icc
# change to working directory
cd $BIGWORK/mydir
# run the simulation

Batch system commands

Put job into the queue

$ qsub <options> <jobscript>

Interactive batch job with GUI

$ qsub -I -X

Show all jobs

$ qstat -a
$ showq

Show all jobs with node information

$ qstat -n1

Show full information for a given job

$ qstat -f <jobid>

Delete a job from the queue

$ qdel <jobid>

Queues & Partitions

The default queue is named all, which should be sufficient for most jobs. For jobs requiring a GPU accelerating unit,add the line #PBS -q gpu to your job script. To select a specific partition, use #PBS -W x=PARTITION:<partition> whereas <partition> is the name of a partition like lena, taurus, tane, haku, smp, dumbo. Partitions provided by institutes of the LUH are usually reserved Mo-Fr 08:00-20:00, but available to all accounts outside this time. Thus, jobs requesting less than 12 hours see additional resources weekday nights. On weekends, 60hours outside reservations are available. lcpuarchs -vv lists partitions including number of nodesand cpu architecture.

Further information about partitions.

The Modules Environment

Show all modules the cluster provides

$ module spider

Show currently loadable modules(this depends on the toolchain already loaded)

$ module avail

Load one or more modules

$ module load <modulname> <...>

Unload a module

$ module unload <modulname>

Show all currently loaded modules

$ module list

Show information about a given module

$ module show <modulname>

More information about software.

Linux Commands

man <command>: Show help for <command>

ls: List directory contents

cd <directory>: Change directory

rm : Delete file

mkdir <directory>: Create directory

passwd: Change password

Contact Information

guide/cheatsheet.txt · Last modified: 2021/05/09 12:30 (external edit)