azurehpc/apps/gromacs

Install and run gromacs Benchmarks

Prerequisites

Cluster is built with the desired configuration for networking, storage, compute etc. You can see the tutorial or examples folder in this repo for how to set this up.

Dependencies for binary version:

• None

Installation

NOTE: Update the gromacs version if needed in $azhpc_dir/apps/gromacs/install_gromacs.sh

First copy the apps directory to the cluster. The azhpc-scp can be used to do this:

azhpc-scp -r $azhpc_dir/apps hpcuser@headnode:.

Alternatively you can checkout the azurehpc repository but you will need to update the paths according to where you put it.

azhpc-run -u hpcuser  apps/gromacs/install_gromacs.sh 

Note: This will install into /apps.

Connect to the headnode

azhpc-connect -u hpcuser headnode

Running

NOTE: Update the gromacs version in $azhpc_dir/apps/gromacs/run_intelmpi.sh if needed

Now, you can run as follows:

qsub -v "package=<benchmark tar name>","casename=<casename>" -l select=2:ncpus=15:mpiprocs=30:ompthreads=1,place=scatter:excl apps/gromacs/run_intelmpi.sh

e.g. "package=GROMACS_TestCaseA.tar.gz","casename=ion_channel.tpr" 
		OR
	 "package=GROMACS_TestCaseB.tar.gz","casename=lignocellulose-tf.tpr"