Overview
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 2023.
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.
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
Programme
| 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 |