BinAC/Quickstart Guide

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.

Check the Queue

To check all running and queued jobs.

qstat

Just your own jobs.

qstat -u <username>

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
g_luck

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

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
#PBS -o LOG
#PBS -n
cd $PBS_O_WORKDIR
echo "my Username is:"
whoami
echo "My job is running on node:"
uname -a
module load chem/gromacs/4.6.7-gnu-4.9
g_luck

Submit the job using

qsub -q short script.sh

Take a note of your jobID.

Killing a Job

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

qdel <jobID>

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 -o LOG
#PBS -n
module purge
module load devel/cuda/7.5 mpi/mvapich2/2.1-gnu-4.9 numlib/openblas/0.2.18-gnu-4.9
source /opt/bwhpc/common/chem/gromacs/2016_gnu-4.9/bin/GMXRC.bash
cd $PBS_O_WORKDIR
gmx grompp -f NPT.mdp -c protein.pdb -n index.ndx -p topol.top
mdrun_s_gpu -v -deffnm NPT_protein -pin on -ntmpi 4 -ntomp 7 -gpu_id 0123 -s topol.tpr

Submit with

qsub -q gpu script.sh

There are tons of options, details and caveats. If there is anything not working, as you like, send an email to [hpcmaster@uni-tuebingen.de hpcmaster].