[ONLINE] PATC: Introduction to HPC for Life Scientists
Date: 31/Jan/2022 Time: 10:00 - 02/Feb/2022 Time: 16:30
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 |