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README.md

Run singularity containers on SDSC Comet with MPI support

https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg

Singularity is a project by Lawrence Berkeley Labs to bring container technology like Docker to High Performance Computing.

Comet at the San Diego Supercomputer Center is a Supercomputer funded by National Science Foundation that focuses on boosting computing resources of new HPC users.

In this repository I gathered some information on how to run Singularity on Comet computing nodes.

See an introduction to this tutorial on my blog: https://zonca.github.io/2017/01/singularity-hpc-comet.html

Use a pre-made Singularity container

Available on Comet at:

/oasis/scratch/comet/zonca/temp_project/ubuntu_anaconda_2018.simg

Available on DockerHub, see the Dockerfile in jupyter_datascience_docker/, see https://hub.docker.com/r/zonca/jupyter-datascience-comet/, you can transform it into a singularity container directly on Comet with:

module load singularity
singularity pull docker://zonca/jupyter-datascience-comet

Available on SingularityHub at https://www.singularity-hub.org/collections/1309:

module load singularity
singularity pull shub://zonca/singularity-comet

Build a Ubuntu 16.04 container

Requirements on the Host

First of all we need to build a container on a machine where we have root access, we cannot do this on Comet. I tested the following on Ubuntu 16.04.

If are interested in testing MPI locally on the Host, you'll need to install mvapich2 on the Host machine, you can follow the commands inside ubuntu.def.

How to build the container with singularity

Currently the kernel on Comet does not support Ubuntu 18.04.

Install the debootstrap package into the Host machine.

  • Install singularity, see http://singularity.lbl.gov/

  • Create an image of potentially 4GB:

      export IMAGE=/tmp/ubuntu_anaconda_2018.simg
      sudo singularity create -s 4096 $IMAGE
    
  • Clone this repository and cd into the folder

  • Bootstrap the image with the Ubuntu 16.04 OS and also install MPI support with mvapich2 version 2.1, the same currently available on Comet. See ubuntu_anaconda/Singularity in this repository for details (it is going to take some time):

      sudo singularity build $IMAGE ubuntu_anaconda
    
  • If you installed mvapich2 on the host, you can check that you can execute the hello world command using the Host MPI installation:

      mpirun -np 2 singularity exec $IMAGE /usr/bin/hellow
    

Test the container on Comet

  • Copy the container on your scratch folder:

      scp $IMAGE comet.sdsc.edu:/oasis/scratch/comet/$USER/temp_project/
    
  • SSH to Comet

  • Clone this repository and cd into the folder

  • Submit the job to the SLURM scheduler

      sbatch run_singularity.slurm
    
  • Check the output file singularity.*.out that the output shows all processes sending a "Hello World" string

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Run singularity containers on the Comet Supercomputer at San Diego Supercomputer Center

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