Benchmarking & Scaling Tutorial/Manual Benchmarking

Prepare your input

Its always a good idea to create some test input for your simulation. If you have a specific system you want to benchmark for a production run make sure you limit the time the simulation is run for. If you also want to test some code given different input sizes of data, prepare those systems (or data-sets) beforehand.

For this tutorials purpose we are using the Molecular Dynamics Code GROMACS as this is a common simulation program and readily available on most clusters. We prepared three test systems with increasing amounts of water molecules which you can download from here.

• TODO: Upload GROMACS test systems (5,10,15nm box dims)

Allocate an interactive session

As a first measure you should allocate a single node on your cluster and start and interactive session, i.e. login on the node. Often there are dedicated partitions/queues named "express" or "testing" or the like, for exactly this purpose with a time limit of a few hours. For a cluster running SLURM this could for example look like:

srun -p express -N 1 -n 72 -t 02:00:00 --pty bash

This will allocate 1 node with 72 tasks on the express partition for 2 hours and log you in (i.e. start a new bash shell) on the allocated node. Adjust this according to your clusters provided resources!

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