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guide:cheatsheet

Cluster System Cheat Sheet


Introduction

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 login.cluster.uni-hannover.de 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 transfer.cluster.uni-hannover.de (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
./my_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

cluster-help@luis.uni-hannover.de

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