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Running MD applications efficiently in HPC, 26-27 April 2021

Running MD applications efficiently in HPC

The aim of the course is to provide MD users with a set of best practices to improve the performance of their simulations. This will be accomplished by tuning the appropriate SLURM switches and flags proper to the MD packages.

This course will be two half-days. It will have lectures interspersed with some hands-on sessions where you get to try out what you have just learned.

NOTE: The course will be online!

Topics to be covered are:

  1. Performance analysis of different versions of the packages (AMBER, NAMD, GROMACS, LAMMPS)
  2. Performance analysis on different architectures (CPU, GPU, KNL CPUs)
  3. General recommendations when using plugins.


Agenda, day 1

09:00-09:50   Lecture: Analysis of software performance I            
09:50-10:00   Coffee break
10:00-10:30   Lecture: Analysis of software performance II
10:30-12:00   Excercise: Time to run the provided examples and optimize your own scripts
Agenda, day 2
09:00-10:20  Setting a classical MD simulation (NAMD)
10:20-10:30  Coffee break
10:30-12:00  Setting a QM/MM simulation, Q&A (questions about different types of methods for MD, help in improving user's scripts)
Materials and recording
The presentations and materials can be downloaded here: https://github.com/hpc2n/CourseEfficientMD

The course was recorded (lectures) and can be seen on HPC2N's YouTube channel.

Participation is free. 

The hands-on will be done on HPC2N's systems, so you will need to have an account at HPC2N and at SUPR (or create such accounts) in order to participate in that part.

Course project: As part of the hands-on, you will be given temporary access to a course project, which will be used for running the hands-on examples. There are some policies regarding this, that we ask that you follow:

  • You may be given access to the project before the course; please do not use the allocation for running your own codes in. Usage of the project before the course means the priority of jobs submitted to it goes down, diminishing the opportunity for you and your fellow participants to run the examples during the course. You can read more detailed information about the job policies at HPC2N here.
  • The course project will be open 1-2 weeks after the course, giving the participants the opportunity to test run examples and shorter codes related to the course. During this time, we ask that you only use it for running course related jobs. Use your own discretion, but it could be: (modified) examples from the hands-on, short personal codes that have been modified to test things learned at the course, etc.
  • Anyone found to be misusing the course project, using up large amounts of the allocation for their own production runs, will be removed from the course project.

The course uses computing resources provided by the Swedish National Infrastructure for Computing (SNIC) at HPC2N partially funded by the Swedish Research Council through grant agreement no. 2018-05973.

Requirements: A previous knowledge of the MD packages (at least the one(s) you are interested in) is required for the day 1 only.

Instructors: Pedro Ojeda May

Helpers: Mirko Myllykoski, Birgitte Brydsö

Time and date: 26-27 April 2021, 09:00-12:00.

Location: ONLINE

Deadline for registration: 18 April 2021.

Please register using this form. All fields marked with * are mandatory. REGISTRATION CLOSED!

Updated: 2024-06-15, 11:05