RunningMD+QMMM-Spring2021

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:

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

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)