Use of Marvin cluster and HPC systems

Duration: 8 hours / 2 days

Date: April 24-25

Time: 9:30 - 14:00

Level: Beginner

Format: Presential

ROOM: Dr. Aiguader 80, Barcelona - 24 April 61.107, 25 April 61.103 

Registration opening date: 20 of March

Deadline for registration: 3 of April 

Course Description

The course will describe the first steps working with a computing cluster, in our case, the UPF Marvin Cluster. We will learn what a cluster is, why we use it and how to work with it: How to submit jobs, to control these jobs and to improve our jobs’ configuration to take advantage of the cluster’s resources. We also will see how we can parallelize our jobs. 

Why should you attend the course?

Working with a cluster helps you do analyzes that wouldn’t be possible to process in your own computer (or they would last much longer). A correct use of the cluster also facilitates this task and saves a lot of time.

In summary, this course will help you to understand a cluster’s environment and to work with it effectively.

Prerequisites

Users with basic Linux environment knowledge or who attended the “Introduction to Linux” course.

Users should bring their own laptop.

Schedule

• Introduction to a cluster’s environment.

• Introduction to Marvin (computing and storage).

• Scripting in bash.

• How to connect to Marvin (Terminal / Visual Studio Code / Bitvise).

• Use of scientific software in a cluster.

• Introduction to SLURM.

• Ways to work with Marvin: sbatch, srun, interactive

• How to submit your first job.

• Gathering information about the job.

• Parallel working

Class Pace 

We encourage the participants to do as many questions as needed during the whole course. The hands-on practical session aims to enhance dynamic learning.  

References

https://www.upf.edu/web/sct-sit/marvin-cluster

https://slurm.schedmd.com/documentation.html

Short biography 

Marc Tormo is a Bioinformatics Technician at SCC and Genomics Core Facilities, at  UPF’s MELIS Department. Previously, he worked at the Centre for Research in Agricultural Genomics (CRAG, Bellaterra). He did a Postgraduate degree in Bioinformatics at Universitat Oberta de Catalunya and a Bachelor’s degree in Biology at Universitat Autònoma de Barcelona. His interests include NGS data analysis (specially Genomics, Transcriptomics and Metagenomics), Linux OS and HPC Systems.