Benchmarking & Scaling Tutorial/Manual Benchmarking

Prepare your input

It is 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	Simulation Type	Default simulation time
MD_5NM_WATER.tpr	5nm	12165	NVE	1ns (500000 steps à 2fs)
MD_10NM_WATER.tpr	10nm	98319	NVE	1ns (500000 steps à 2fs)
MD_15NM_WATER.tpr	15nm	325995	NVE	1ns (500000 steps à 2fs)

Download the tar archive to your local machine and upload it to an appropriate directory on your cluster.

Unpack the archive and change into the newly created folder:

tar xfa gromacs_benchmark_input.tgz
cd GROMACS_BENCHMARK_INPUT/

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!

First test run

Next, you want to navigate to your input data and load the environment module, which gives you access to GROMACS binaries. Since environment modules are organized differently on many cluster the steps to load the correct module might look different at your site.

module load GROMACS

We will make a first test run using the smallest system (5nm) and 18 cores to get a feeling for how long one simulation might take. Note that we are using the gmx_mpi executable which allows us to run the code on multiple compute nodes later. There might be a second binary available on your system just called "gmx", using a threadMPI parallelism, which is only suitable for shared memory systems (i.e. a single node).

mpirun -n 18 gmx_mpi mdrun -deffnm MD_5NM_WATER -nsteps 10000

mpirun -n 18 will spawn 18 processes calling the gmx_mpi executable. mdrun -deffnm MD_5NM_WATER tells GROMACS to run a molecular dynamics simulation and use the MD_5NM_WATER.tpr as its input. -nsteps 10000 tells it to only run 10000 steps of the simulation instead of the default 500000.

The simulation will presumably take a couple of seconds and the output will look similar to this:

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