RStan Container

Docker/Singularity image to run RStan on a Centos 6.10 kernel.

If you have used this work for a publication, you must acknowledge SIH, e.g: "The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney."

Quickstart for Artemis

Put this repo on Artemis e.g.

cd /project/<YOUR_PROJECT>
git clone https://github.com/Sydney-Informatics-Hub/rstan-contained.git

Then cd rstan-contained and modify the *.pbs scripts as needed and launch with qsub run_build.pbs to build the RStan Singularity image once, then afterwards use qsub run_artemis.pbs to run any workload.

Otherwise here are the full instructions for getting there....

How to recreate

Build with docker

Check out this repo then build the Docker file.

sudo docker build . -t sydneyinformaticshub/rstan:4.0.5

Run with docker.

To run this, mounting your current host directory in the container directory, at /project, and execute a run on the test images (that live in the container) run:

sudo docker run -it -v `pwd`:/project sydneyinformaticshub/rstan:4.0.5 /bin/bash -c "Rscript demostan.R"

Push to docker hub

sudo docker push nbutter/cellranger:ubuntu1604

See the repo at https://hub.docker.com/r/sydneyinformaticshub/rstan

Build with singularity

Use the run_build.pbs script to build on an Artemis compute node. The key details are:

export SINGULARITY_CACHEDIR=`pwd`
export SINGULARITY_TMPDIR=`pwd`

singularity build rstan.img docker://sydneyinformaticshub/rstan:4.0.5

Run with singularity

Use the run_artemis.pbs script to run an exampled workflow on an Artemis compute node. To run the singularity image (noting singularity mounts the current folder by default):

singularity run --bind /project:/project rstan.img /bin/bash -c "export TMPDIR="$PBS_O_WORKDIR" && Rscript code/test.R