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Efficient MD simulations at HPC2N, 28 February 2020

Efficient MD simulations at HPC2N

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THIS IS AN OLD COURSE AND THE EXAMPLE JOB SCRIPTS ARE NO LONGER VALID. THUS, THAT PART OF THE ORIGINAL MATERIAL IS NO LONGER AVAILABLE FOR DOWNLOAD!

You can find the material for a newer, similar course here: Efficient MD simulations in HPC


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)
  3. General recommendations when using plugins.

Agenda

09:00-10:30   Lecture: Analysis of software performance I            
10:30-10:45   Coffee break
10:45-11:30   Lecture: Analysis of software performance II
11:30-12:00   Excercise: Time to optimize your own scripts
 
The presentation can be downloaded here [.pptx].
 
Coffee/tea will be provided.

Participation is free. Bring your laptop for the hands-on!

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.

Note: Participants are kindly asked to limit the use of fragrances due to perfume intolerance issues.  Thank you.

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

Instructors: Pedro Ojeda May

Time and date: 28 February 2020, 09:00-12:00.

Location: MIT-Huset, room MC305 (Directions to MIT huset here).

Deadline for registration: 21 February 2020.

Please register using this form. All fields marked with * are mandatory. REGISTRATION IS CLOSED! Email bbrydsoe@hpc2n.umu.se to hear if it is still possible to join.

Updated: 2021-09-09, 15:12