GROMACS GPU performance

In this workshop, we will examine how GROMACS uses GPUs and how you as a user can get the best value from that.

Prerequisites

Experience running production simulations with GROMACS. General concepts will be introduced with brief descriptions that should be familiar to experienced MD users. Links to the GROMACS documentation will be used frequently.

20 min

Introduction

20 min

Understanding Navigator GPU nodes

40 min

Getting performance from the MD algorithm

50 min

Performant PME simulations

15 min

General considerations for performance

Who is the course for?

This material is targeted towards researchers who already have experience with GROMACS and who would like to learn how to improve simulation performance when running on GPUs.

About the course

This lesson material is developed by the EuroCC National Competence Center Sweden (ENCCS) and taught in ENCCS workshops. It is aimed at researchers and developers who already have production experience with GROMACS. Each lesson episode has clearly defined learning objectives and includes multiple exercises along with solutions, and is therefore also useful for self-learning. The lesson material is licensed under CC-BY-4.0 and can be reused in any form (with appropriate credit) in other courses and workshops. Instructors who wish to teach this lesson can refer to the Instructor’s guide for practical advice.

Credits

The lesson file structure and browsing layout is inspired by and derived from work by CodeRefinery licensed under the MIT license. We have copied and adapted most of their license text.

Instructional Material

All ENCCS instructional material is made available under the Creative Commons Attribution license (CC-BY-4.0). The following is a human-readable summary of (and not a substitute for) the full legal text of the CC-BY-4.0 license. You are free:

  • to share - copy and redistribute the material in any medium or format

  • to adapt - remix, transform, and build upon the material for any purpose, even commercially.

The licensor cannot revoke these freedoms as long as you follow these license terms:

  • Attribution - You must give appropriate credit (mentioning that your work is derived from work that is Copyright (c) ENCCS and, where practical, linking to https://enccs.se), provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

  • No additional restrictions - You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:

    • You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.

    • No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.

Software

Except where otherwise noted, the example programs and other software provided by ENCCS are made available under the OSI-approved MIT license.