BwForCluster BinAC: Quickstart Guide

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1 Basics

Use the work file system and not your home directory for your calculations. Create a working directory using your username.

cd /beegfs/work/
mkdir <username>
cd <username>

Do not use the login nodes to carry out any calculations or heavy load file transfers.

2 Check the Queue

To check all running and queued jobs.


Just your own jobs.

qstat -u <username>

3 Simple Interactive Job

To start a 1 core job on a compute node providing a remote shell.

qsub -q short -l nodes=1:ppn=1 -I

The same but requesting the whole node.

qsub -q short -l nodes=1:ppn=28 -I

Standard Unix commands are directly available, for everything else use the modules.

module avail

Just an example

module load chem/gromacs/4.6.7-gnu-4.9

Be aware that we allow node sharing. Do not disturb the calculations of other users.

4 Simple Script Job

Use your favourite text editor to create a script.

#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:05:00
#PBS -S /bin/bash
#PBS -N Simple_Script_Job
#PBS -j oe
echo "my Username is:"
echo "My job is running on node:"
uname -a
module load chem/gromacs/4.6.7-gnu-4.9

Submit the job using

qsub -q short

Take a note of your jobID.

5 Killing a Job

Let's assume you build a Homer and want to stop/kill/remove a running job.

qdel <jobID>

6 Fancy Script Job

#PBS -l nodes=1:ppn=28:gpus=4:exclusive_process
#PBS -l walltime=36:00:00
#PBS -S /bin/bash
#PBS -N Gromacs_GPU
#PBS -j oe
#PBS -n
module purge
module load chem/gromacs/2016.4-gnu-5.2
gmx grompp -f NPT.mdp -c protein.pdb -n index.ndx -p
mdrun_s_gpu -v -deffnm NPT_protein -pin on -ntmpi 4 -ntomp 7 -gpu_id 0123 -s topol.tpr

Submit with

qsub -q gpu

There are tons of options, details and caveats. If there is anything not working, as you like, send an email to