PerMedCoE/BioExcel course on Introduction to HPC for Life scientists


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 will include lectures and hands-on exercises to introduce 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 the future. The course will cover basic concepts in HPC hardware, software, user environments, file systems, and programming models. It will also provide an opportunity to gain hands-on practical experience and assistance using an HPC system through examples drawn from the life sciences, such as biomolecular simulations and multicellular simulations.
The course is organised and funded by PerMedCoE – the HPC/Exascale Centre of Excellence in Personalised Medicine, and BioExcel – the Centre of Excellence for Computational Biomolecular Research, using the HPC infrastructure at the Barcelona Supercomputing Centre, part of the Spanish supercomputing network. 

Date: 7 – 8 March 2023.

Deadline for registration: 10 February.

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.

Places available: 40. Allocation of places will be based on a ‘first come – first served’ basis.

Registration is free. The course includes meals as detailed on the programme. Travel and accommodation are not included. A limited number of grants will be available for this event.

For prerequisites and registration visit the BSC website.

Learning outcomes

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

  • Explain the drivers and motivation to use HPC
  • Identify HPC hardware – Building blocks and architectures
  • Define Parallel computing – Programming models and implementations
  • Use HPC systems
    • Access
    • Batch schedulers & resource allocation
    • Running jobs
    • Dealing with errors
    • Using libraries
    • Performance


Day 1: Tuesday 7 March 2023
09:00 – 09:45             Welcome, introductions and expectations
09:45 – 10:05             LECTURE: Introduction to High Performance Computing (HPC)
10:05 – 10:30             PRACTICAL: Connecting to MareNostrum
10:30 – 11:00             Break
11:00 – 11:20             LECTURE: HPC Architectures
11:20 – 12:00             PRACTICAL: Overview of the MareNostrum system and modules
12:00 – 12:20             LECTURE: Batch systems and parallel application launchers
12:20 – 13:00             PRACTICAL: Batch Systems and MareNostrum Slurm Scheduler  
13:00 – 14:00             Lunch break
14:00 – 14:30             LECTURE: Computational Building Blocks (software + hardware)
14:30 – 15:00             LECTURE: Parallel Programming Models (OpenMP, MPI)
15:00 – 15:30             PRACTICAL: PhysiCell, OpenMP, MPI
15:30 – 16:00             Break
16:00 – 16:45             PRACTICAL: PhysiCell, OpenMP, MPI
16:45 – 17:45             Women in science session: From the Top Secret Rosies to women in HPC
17:45 – 18:30             Drinks and nibbles
Day 2: Wednesday 8 March 2023
09:00 – 09:05             Welcome
09:05 – 09:45             LECTURE: Mapping computation to HPC hardware: molecular simulation
09:45 – 10:30             PRACTICAL: GROMACS simulations on multicore CPUs
10:30 – 11:00             Break
11:00 – 11:45             PRACTICAL: GROMACS simulations on multi node clusters
11:45 – 12:15             LECTURE: GPU accelerators and heterogeneous architectures
12:15 – 12:55             PRACTICAL: GROMACS simulations on GPUs
13:00 – 14:00             Lunch break
14:00 – 14:30             LECTURE: Introduction to PyCOMPSs programming model
14:30 – 15:00             PRACTICAL: PyCOMPSs
15:00 – 15:30             LECTURE: PerMedCoE Building Blocks and Workflows
15:30 – 16:00             Break
16:00 – 16:30             PRACTICAL: PerMedCoE Building Blocks and Workflows
16:30 – 17:00             Course wrap-up, final questions and feedback