Install

To install GROMACS on the cluster we are going to use SPACK. With the recent releases Spack introduced binary caches, so that an installation does not need to go through the lenghtly compilation, but rather downloads the compiled binaries for the specific target.

Connect to compute node

We are going to allocate a compute node to run a first installation.

salloc -N1 -p c5n --exclusive

Once the job is running, we can connect to the instance. Run this command until you see your job move to the running state (R) - should take about 5min.

squeue

ssh $SLURM_NODELIST

Install default GROMACS

We are using the AWS environment definition which was installed along with spack.

spack env list
spack env activate aws
spack env list

As a first pass, we are going to install GROMACS 2021.1 without special options.

spack install --no-check-signature --no-checksum gromacs@2021.1

Depending on how many packages are available in the binary cache (indicated by 1 in the screenshot above) this will take only a couple of minutes or up to an hour.

The hash highlighted in the screenshot is the unique identifier of the software installation. For easy reuse we put that into a environment variable.

read -p "Please paste the hash: " GROMACS_101_HASH

We commit the variable to our environment in case we need to log in again.

echo "export GROMACS_101_HASH=${GROMACS_101_HASH}" |tee -a ~/.bashrc