Introduction to High Performance Computing for Life Scientists

Key Points

Welcome	We should all understand and follow the ARCHER2 Code of Conduct to ensure this course is conducted in the best teaching environment. The course will be flexible to best meet the learning needs of the attendees. Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees.
Who we are: Introducing BioExcel, PRACE, and EPCC training	To be determined
LECTURE: High-Performance Computing (HPC)	Computer clusters enable users to run larger, more complex jobs in a reasonable time HPC systems are state-of-the-art clusters composed of a large number of powerful computers linked by very fast interconnects.
PRACTICAL: Connecting to ARCHER2 and transferring data	ARCHER2’s login address is `login.archer2.ac.uk`. The password policy for ARCHER2 is well documented. There are a number of ways to transfer data to/from ARCHER2.
LECTURE: HPC Architectures [pre-recorded]	To be determined
PRACTICAL: Overview of the ARCHER2 system and modules	ARCHER2 consists of high performance login nodes, compute nodes, storage systems and interconnect. There is a wide range of software available on ARCHER2. The system is based on standard Linux with command line access. Software is available through modules.
LECTURE: Batch systems and parallel application launchers [pre-recorded]	To be determined
PRACTICAL: Batch Systems and ARCHER2 Slurm Scheduler	ARCHER2 uses the Slurm scheduler. `srun` is used to launch parallel executables in batch job submission scripts. There are a number of different partitions (queues) available.
LECTURE: Parallel Computing	To be determined
PRACTICAL: HMMER (1 of 2)
LECTURE: Review of Day 1	To be determined
Welcome	We should all understand and follow the ARCHER2 Code of Conduct to ensure this course is conducted in the best teaching environment. The course will be flexible to best meet the learning needs of the attendees. Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees.
LECTURE: Measuring Parallel Performance	To be determined
PRACTICAL: HMMER (2 of 2)
LECTURE: Computational Building Blocks: Software	To be determined
LECTURE: Computational Building Blocks: Hardware	To be determined
PRACTICAL: Benchmarking Molecular Dynamics Performance Using GROMACS 1	Larger systems scale better to large core-/node-counts than smaller systems.
LECTURE: Parallel Models to Exploit Parallelism	To be determined
PRACTICAL: Benchmarking Molecular Dynamics Using GROMACS 2	Hybrid MPI with OpenMP does affect performance. When running hybrid jobs, placement across NUMA regions is important.
LECTURE: Building and compiling software: from algorithm to executable	To be determined
LECTURE: Review of Day 2	To be determined
Welcome	We should all understand and follow the ARCHER2 Code of Conduct to ensure this course is conducted in the best teaching environment. The course will be flexible to best meet the learning needs of the attendees. Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees.
PRACTICAL: Benchmarking Molecular Dynamics Using GROMACS 3
LECTURE: Pipelines and Workflows	To be determined
QM/MM Simulations Using CP2K	To be determined
LECTURE: The future of HPC	To be determined
QM/MM Simulations Using CP2K	To be determined
LECTURE: The HPC landcsape in the EU and UK	To be determined
LECTURE: Course review and where next?	To be determined