REVIEW: Course review and where next?

Overview

Teaching: 20 min
Exercises: 0 min

Questions

• What have we learned over this course?

• Where do we go from here?

• What other training do BioExcel, PRACE, and EPCC offer?

Objectives

• Reviewing what has been taught this course.

• Describing what further training is offered by the course organisers.

• Answering any questions that course attendees might have about HPC and life science research.

Review of the course

The primary aim of this course was to teach you the basics of high-performance computing, and give a broad overview of how it can be be used for life science research. We hope that, during this course, we have answered the following questions:

• What is high-performance computing (HPC)?
• Why do people use HPC?
• What are the software and hardware components that make up a HPC (and a computer)?
  • How can these components affect the performance of applications?
• How do applications tackle problems in parallel?

Throughout this course, you will have had access to ARCHER2. We have aimed to provide you with a hands-on approach to using HPC facilities, and that you will now have a better idea of how to get the most out of the resources at your disposal. In particular, we hope that this course has given you:

• more experience of using a HPC machine and dealing with common stumbling blocks;
• a better notion of how to evaluate the parallel performance of an applications, and that you now know how to check that you are making good use of your HPC resources;
• Given you an understanding of current (and near-future) HPC facilities;
• an appreciation of the challenges of running life-science pipelines and workflows on HPC systems.
• Shown you how HPC can benefit your research, and where you can get access to HPC facilities in the EU and UK.

Where next?

This course was run in a collaboration between BioExcel, EPCC, and PRACE. Each of these partners has a great track-record at providing a variety of courses, from introductory courses like this one to much more expert courses.

BioExcel focuses primarily on the use of HPC for life sciences. They offer a number webinars and courses – most of these are recorded and free to watch after the fact. In particular, they run a Summer School that focuses on providing a hands-on experience of using BioExcel flagship software and tools (such as GROMACS, CP2K, HADDOCK, etc.).

Through ARCHER2, EPCC provides a wide range of courses and webinars that cover a wide variety of topics that all relate to HPC. These range from introductory courses about using HPC facilities and certain highly-used ARCHER2 software (e.g. LAMMPS and CP2K), to courses about programming for HPC environments. All of these courses and webinars are free to the public, and the recordings of these courses are always available to watch after the fact (you can find past EPCC courses here. EPCC also runs an M.Sc. programme .

PRACE predominantly focus on HPC and programming for HPC. PRACE offers a fantastic Summer of HPC programme that provides a one week training course to M.Sc. and B.Sc. students, followed by a 2-month placement at a European HPC centre. They also provide a number of short tutorial videos to teach the fundamentals of of working with parallel programming. Finally, they also run a number of courses related to HPC, many of which are available online afterwards.

Finally, for this course, you will have made ARCHER2 accounts – these accounts will remain in place, and the budget code ta017 will be available until 24th April 2021. Please make use of this to test your systems on ARCHER2 and to get a better grasp of using state-of-the-art HPC facilities.

Open consultation session

For the remainder of this course, the course organisers will be happy to answer any questions you have about your specific HPC need and uses. We’re also happy to clarify any points and answer any questions about the course.

Key Points