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If you only want to run your MPI job on a single node, then you don’t have to call mpirun before the singularity call. This will use MPI installed inside the container only and not use Artemis’s MPI at all, and will still have performance equivalent to “bare metal” on Artemis.

Example to run a Dockerfile on Artemis with Singularity

Start with a Dockerfile, like this one

To run this on your computer where you have root access, you probably only need to:

#In the directory where you have saved the Dockerfile
docker build Dockerfile

#Then this particular Dockerfile can be interfaced/run like so
sudo docker run --rm -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq Trinity --seqType fq --single `pwd`/reads.fq.gz --max_memory 1G --CPU 4 --output `pwd`/trinity_out_dir

But if we want to run it with Singularity we need to do a few more steps.

Firstly, we must convert the Dockerfile to a Singularity image, an easy way is to use the Python package Spython, https://vsoch.github.io/singularity-cli/recipes

Then as per Spython's instructions you can convert the Dockerfile by: 

spython recipe Dockerfile >> Singularity.trinity

Next, edit the newly created Singularity image. Add the Artemis-specific changes to your new singularity image, i.e.

Bootstrap: docker
From: ubuntu:16.04
%files
%Dockerfile $SRC/Dockerfile.$TRINITY_VERSION
%labels
MAINTAINER bhaas@broadinstitute.org
%post
mkdir /project /scratch

Next use Singularity to build the image (~30 minutes on my local laptop)

sudo singularity build Singularity.trinity.build Singularity.trinity

Now move the build to Artemis and run it with a PBS script

#!/bin/bash
#PBS -P PROJECT
#PBS -l select=1:ncpus=4:mem=4gb
#PBS -l walltime=0:10:00
 
module load singularity/2.6.1

cd "$PBS_O_WORKDIR"
singularity exec Singularity.trinity.build Trinity --seqType fq --single `pwd`/reads.fq.gz --max_memory 4G --CPU $NCPUS --output `pwd`/trinity_out_dir