JUSTUS2/Getting Started

General Workflow of Running a Calculation

On a compute cluster, you do not simply run log in and your software, but you write a "job script" that contains all commands to run and process your job and send this into a waiting queue to be run on one of several hundred computers.

How this is done is described in a little more detail here: Running Calculations

Get Access to the Cluster

Follow the registration process for the bwForCluster. → How to Register for a bwForCluster

Login to the Cluster

Setup service password and 2FA token and login to the cluster. → Login JUSTUS2

Using the Linux Commandline

HPC Wiki (external site) → Introduction to Linux Commandline

Training course → Linux course on training.bwhpc.de

also see: .bashrc Do's and Don'ts

Transfer your Data to the Cluster

Get familiar with available file systems on the cluster. → File Systems

Transfer your data to the cluster using appropriate tools. → Data Transfer

Find Information About Installed Software and Examples

Compiler, Libraries and application software are provided as software modules. Learn how to work with software modules. → Software

Run sample script from a pre-installed software (Software job examples in the page above)

Run your Software in a Batch Job

Get familiar with available nodes types on the cluster. → Hardware and Architecture

Submit and monitor your jobs with Slurm commands.

• → Running Your Calculations - a very brief introduction.
• → extensive Slurm HOWTO on specific tasks

Learn about Scaling your Job

How many compute-cores should my job use? This depends on the software and the problem you are trying to solve. But if you use too few cores, your computation may take much too long - if you use too many cores, they will not improve the speed of your computation and all you do by using more cores is wasting compute resources and energy.

If you run hundreds or thousands of similar calculations, you should look at this carefully before starting.

How to do this is described in: Scaling

Acknowledge the Cluster

Remember to mention the cluster in your publications. → Acknowledgement