All the PATC courses at BSC are free of charge.
Place: 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.
Target group: Life science researchers without previous experience in HPC.
Places available: 40. Allocation of places will be based on a ‘first come - first served’ basis.
Registration fee and grants: There is no registration fee. The course includes coffee breaks and lunch on the 7 and 8 of March. Accommodation and transport are not included.
A limited number of grants will be available for this event. If you would like to be considered for a grant:
-
Check the information in the PerMedCoE grants document.
-
Complete the registration form for the course.
-
Email Marta Lloret Llinares after the submission of your application explaining why you should be considered for a grant.
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 (MareNostrum) through examples drawn from the life sciences, such as biomolecular simulations (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 using the HPC infrastructure at the Barcelona Supercomputing Centre.
Requirements:
-
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
-
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
9:00 - 11:00 Running biomolecular simulations in GROMACS in different HPC architectures
11:00 - 11:30 Break
11:30 - 13:00 Running biomolecular simulations in GROMACS in different HPC architectures
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 & feedback
Academic staff:
Course convenors: Daniel Thomas López (EMBL-EBI, PerMedCoE), Marta Lloret Llinares (EMBL-EBI, PerMedCoE)
Lecturers: Jose Carbonell (BSC, PerMedCoE), Francisco Javier Conejero (BSC, PerMedCoE), Berk Hess (KTH, PerMedCoE), Szilárd Páll (KTH, PerMedCoE), Miguel Vazquez (BSC, PerMedCoE), David Vicente (BSC, PerMedCoE), Alessandra Villa (KTH, PerMedCoE), Thaleia Ntiniakou (BSC).
Materials: The materials used in the training use the licence Creative Commons CC BY 4.0.
