[ONLINE] PATC: Introduction to HPC for Life Scientists

Date: 31/Jan/2022 Time: 10:00 - 02/Feb/2022 Time: 16:30

Place:

Online via Zoom

 

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.

Primary tabs

Programme

 

Time (CET)

Title

Day 1 (31/01/2022)

 

10:00 - 11:00

Welcome and introductions

11:00 - 11:20

LECTURE: High-Performance Computing (HPC)

11:20 - 11:40

PRACTICAL: Connecting to MareNostrum

11:40 - 12:00

BREAK

12:00 - 12:20

LECTURE: HPC Architectures

12:20 - 13:00

PRACTICAL: Overview of the MareNostrum system and modules

13:00 - 13:40

LUNCH

13:40 - 14:00

LECTURE: Batch systems and parallel application launchers

14:00 - 14:30

PRACTICAL: Batch Systems and MareNostrum Slurm Scheduler

14:30 - 14:50

BREAK

14:50 - 15:20

LECTURE: Parallel Computing Patterns

15:20 - 15:55

PRACTICAL: HMMER (condensed part 1 and part 2)

15:55 - 16:00

LECTURE: Review of Day 1

16:00

Finish

Day 2 (01/02/2022)

 

10:00 - 10:05

Welcome

10:05 - 10:35

LECTURE: Measuring Parallel Performance

10:35 - 11:20

PRACTICAL: Benchmarking Molecular Dynamics Performance Using GROMACS

11:20 - 11:40

BREAK

11:40 - 12:10

LECTURE: Computational Building Blocks: Software

12:10 - 12:40

LECTURE: Computational Building Blocks: Hardware

12:40 - 13:30

LUNCH

13:30 - 14:00

PRACTICAL: Benchmarking Molecular Dynamics Using GROMACS

14:00 - 14:30

LECTURE: Parallel Programming Models (OpenMP, MPI)

14:30 - 14:50

BREAK

14:50 - 16:00

PRACTICAL: PhysiCell, OpenMP, MPI

16:00 - 16:25

LECTURE: Building and compiling software: from algorithm to executable

16:25 - 16:30

LECTURE: Review of Day 2

16:30

Finish

Day 3 (02/02/2022)

 

10:00 - 10:05

Welcome

10:05 - 10:35

Lecture: Singularity containers

10:35 - 11:20

PRACTICAL: Containers

11:20 - 11:40

BREAK

11:40 - 12:40

Introduction to PyCOMPSs and task-based programming model.

Building blocks.

12:40 - 13:30

LUNCH

13:30 - 14:30

PRACTICAL: Workflows and building blocks

14:30 - 14:50

BREAK

14:50 - 15:20

LECTURE: The HPC landscape in Europe and the future of HPC. Course review and where next?

15:20 - 15:30

Final questions and end of the course