computing molecular dynamics skills

Setting up a GROMACS cluster

4. Installing SLURM

As I wrote before, this was the part that scared me most, but turned out to be the easiest. We’ve already installed SLURM using apt-get on all machines; this has also installed MUNGE which is needed for authentication. The first step is to setup MUNGE on all machines. First we need to create a MUNGE key on the headnode and distribute it to all the machines for authentication.

$ sudo /usr/sbin/create-munge-key

To copy it to the compute nodes, the easiest thing is to put a copy in your user home directory as this will be shared by NFS.

$ sudo cp /etc/munge/munge.key /home/fowler/

Then on each compute node we can copy the file into the right directory

/home/fowler/$ sudo cp munge.key /etc/munge/

There is a problem with permissions here; the original key is owned by munge which is part of the munge group. As we’ve been moving it around with sudo, it is now owned by root. So we also need to change the permissions back on each compute node.

$ sudo chown munge /etc/munge/munge.key
$ sudo chgrp munge /etc/munge/munge.key

There appears to be a bug with Ubuntu as well, this is fixed by adding the following line, on all machines, to /etc/default/munge


Now on each machine we can start the MUNGE service

$ sudo service munge start

and check it is running

$ ps -e | grep munge

Now we are in a position to setup SLURM.

/home/fowler$ cp /usr/share/doc/slurm-llnl/examples/slurm.conf.simple.gz .
/home/fowler$ gunzip slurm.conf.simple.gz
/home/fowler$ mv slurm.conf.simple slurm.conf
/home/fowler$ vim slurm.conf

This is an example, basic SLURM configuration file which you can just alter. All I did was change the following lines from their defaults to match my cluster, which is currently

NodeName=node0[1-2] Procs=16 State=UNKNOWN
PartitionName=production Nodes=node0[1-2] Default=YES MaxTime=INFINITE State=UP

This file needs to be copied to every machine, including the headnode.

/home/fowler/$ sudo cp slurm.conf /etc/slurm

Now we can start the SLURM controller on the headnode

$ sudo service slurm-llnl start

and the SLURM daemon on each compute note

$ slurrmd -c

For a simple check, run the following on the headnode

$ srun -N1 hostname

Or to try using two nodes

$ srun -N2 hostname

I’m going to assume you have a GROMACS TPR file called at-1-1.tpr that you’ve made using GROMPP. Let’s benchmark the cluster. So on the headnode, create and edit a SLURM job file

/home/fowler$ sudo vim

Mine looks like

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --time=00:15:00
#SBATCH --job-name=at-1-1

source /etc/profile.d/
module load gromacs/5.1.2

gmx mdrun -deffnm at-1-1 -ntmpi 1 -ntomp 1 -maxh 0.1 -resethway -noconfout -stepout 100 -v

This has some benchmarking specific flags. Make sure and at-1-1.tpr are both present, then submit it to the queue

$ sbatch
Submitted batch job 1

and then we can check the queue

$ squeue
1 productio at-1-1 fowler R 0:28 1 node02

Or, let’s run an MPI GROMACS job instead.

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1
#SBATCH --time=00:15:00
#SBATCH --job-name=at-1-1

source /etc/profile.d/
module load gromacs/5.1.2

mpirun -np 8 mdrun_mpi -deffnm at-1-1 -maxh 0.1 -resethway -noconfout -stepout 100 -v

Job done!

By Philip Fowler

Philip W Fowler is a computational biophysicist studying antimicrobial resistance working at the John Radcliffe Hospital in Oxford.

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