PerMedCoE/BioExcel: Introduction to HPC for Life Scientists

Technical training

07 Mar 2023

Barcelona

Training course organised by the Barcelona Supercomputing Center

Objectives: High-performance computing (HPC) is a fundamental technology used to solve a wide range of scientific research problems. Many important challenges in science such as protein folding, drug discovery, and tumour evolution, all depend on simulations, models and analyses run on HPC facilities to make progress.

This course introduces HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in future. The course will cover basic concepts in HPC hardware, software, user environments, filesystems, and programming models. It also provides an opportunity to gain hands-on practical experience and assistance using an HPC system (MARENOSTRUM) through examples drawn from the life sciences, such as biomolecular simulation (GROMACS) and multicellular simulations (PhysiCell).

The course is organised and funded by PerMedCoE - the HPC/Exascale Centre of Excellence in Personalised Medicine (https://permedcoe.eu/) and BioExcel - the Centre of Excellence for Computational Biomolecular Research (http://bioexcel.eu) using the HPC infrastructure at the Barcelona Supercomputing Centre.

Prerequisites: Familiarity with basic Linux commands (at the level of being able to navigate a file system). You may find a Linux online course such as https://swcarpentry.github.io/shell-novice/ useful if you are less familiar with Linux.

No programming skills or previous HPC experience is required.

Participants will need to bring their own laptop to the course. Further instructions will be provided after registration.

Learning Outcomes: On completion of the course, we expect that attendees will be able to:

Explain the drivers and motivation to use HPC
Describe the European HPC landscape and HPC facilities available to researchers
Identify HPC hardware - Building blocks and architectures
Define Parallel computing - Programming models and implementations
Use HPC systems

More information in BSC website.

Venue

This course will take place face-to-face on the premises of the Universitat Politècnica de Catalunya - BarcelonaTech (UPC), right in front of the Barcelona Supercomputing Center.

Address: Vèrtex Building, Universitat Politècnica de Catalunya (UPC), Plaça d'Eusebi Güell, 6, 08034, Barcelona.

Location / How to arrive

For better location in an electronic map, the coordinates of Vèrtex Building can be used: 41.390416670796 N, 2.1143878004872 E.

Barcelona’s City Council route planner can be used to prepare the trip to the Venue by public transport (underground, bus, and tramway).

Reaching the area

In general, the easiest and fastest way of reaching the Venue from the Airport or other parts of the city is by using the underground.

There are two underground lines arriving to the Venue: L3 (green line) with direction Zona Universitària and L9S (orange line) with direction Zona Universitària. From the Airport (about 50 min), take the L9S line at Aeroport T1 or Aeroport T2 and get off at Zona Universitària. From the city centre (about 30 min), take the L3 line at the station that suits you the most -or take another line at your closest station and transfer to L3-, and get off at Palau Reial or Zona Universitària.

The nearest bus stops are stop number 1864 (Sor Eulàlia d’Anzizu – Dulcet stop) serving bus line 113 (going around the Venue’s neighbourhood); bus stop 297 (Av Pedralbes – Pg Manuel Girona stop) serving bus lines V5 (going to Mare de Déu del Port, a coastal neighbourhood), 63 (going to the centric Universitat square), and 78 (going to Barcelona-Sants international railway station); and bus stop 1413 (Av Pedralbes – Tòquio stop) serving as well -but in the reverse direction- bus lines V5 (going around the Venue’s neighbourhood), 63 (going to bordering Sant Joan Despí town), and 78 (going as well to Sant Joan Despí).

Pius XII is the closest tramway stop. This stop serves tramway lines T1, T2, and T3, mainly departing to towns bordering Barcelona by its south-east such as Sant Joan Despí.