From d07323b748244d0eaf579b9cc122888e52b4e6bc Mon Sep 17 00:00:00 2001 From: Pedro Ojeda-May Date: Fri, 13 Sep 2024 10:15:35 +0200 Subject: [PATCH] GROMACS: usage --- docs/software.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/docs/software.md b/docs/software.md index 5a6fbb71..04b6ea91 100644 --- a/docs/software.md +++ b/docs/software.md @@ -663,6 +663,36 @@ AMD node that lacks that installation. plots from 15m to 1m for instance. It takes a few minutes before you can see the results on the plots. +## Gromacs + +Gromacs (GROningen MAchine for Chemical Simulations) is a versatile package to perform molecular +dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles + +### How to find Gromacs + +Gromacs is installed as a module on Kebnekaise. Notice that on the Intel nodes there are +more versions of this software installed than on the AMD nodes. Thus, if you are targeting one +version that is only installed on the Intel nodes, you will need to add the instruction +``#SBATCH -C skylake`` to your batch script, otherwise the job could arrive to an +AMD node that lacks that installation. + +### Exercises + +??? Note "Exercise 1: Running a MPI job" + + The input files for this exercise are located in [exercises/GROMACS/MPI](https://github.com/hpc2n/intro-course/tree/master/exercises/GROMACS/MPI){:target="_blank"}. + Go to this folder and run the script [job-mpi-gromacs.sh](https://github.com/hpc2n/intro-course/tree/master/exercises/GROMACS/MPI/job-mpi-gromacs.sh){:target="_blank"} by using different values of the + number of MPI tasks (-n). Submit this file to the batch queue (**sbatch job-mpi-gromacs.sh**). Use the + number you get from sbatch (this is called job ID) to get an URL on the command line by typing: + ``job-usage job_ID``. + + Then, copy and paste that URL on your local browser. After ~1 min. you will start + to see the usage of the resources. Tip: In the top-right corner change the updating + default 15m to 30s. + + In the plot for CPU usage, you can see how efficiently are the requested resources + being used (in percentage). How efficient is your simulation? + !!! Keypoints "Keypoints"