[ONSITE] PerMedCoE/BioExcel: Introduction to HPC for Life Scientists

Other Training

Fecha: 07/Mar/2023 Time: 09:00 - 08/Mar/2023 Time: 18:00

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.

Cost: There is no registration fee. Places available: 40. Allocation of places will be based on a ‘first come - first served’ basis. 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. (Please check the "further information" tab below)  

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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 (open session, registration required)
17:45 - 18:30        Drinks and nibbles

 

Day 2: Wednesday 8 March 2023

 
9:00 - 9:05            Welcome
9:05 - 9:45            Mapping computation to HPC hardware: molecular simulation
9:45 - 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        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 & feedback