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:

• Download test input (tgz archive)
• SHA256 checksum: d1677e755bf5feac025db6f427a929cbb2b881ee4b6e2ed13bda2b3c9a5dc8b0

The unpacked tar archive contains a folder with three binary input files (.tpr), which can directly be used as an input file for GROMACS. Those input files should be compatible with all GROMACS versions equal to or later than 2016.5:

GROMACS Tutorial Systems

System	Sidelength of simulation box	No. of atoms
MD_5NM_WATER.tpr	5nm	12165
MD_10NM_WATER.tpr	10nm	98319
MD_15NM_WATER.tpr	15nm	325995

Allocate an interactive session

As a first measure you should allocate a single node on your cluster and start an 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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