Singularity

Singularity

Article written by Markus Stöhr (VSC Team)

Containerization (historical, pre 1955)

(pictures from Wikipedia)

Containerization (historical, post 1955)

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HPC Situation

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Virtualization vs. Containerization

Docker vs. Singularity

Singularity:

container runs in user namespace
no privilege escalation
can be used in a multi-user environment

Container concepts

image: stored in a single file
build images with ‘recipes’
work interactively within container

Recipes in Singularity

section
setup	executed before post
post	install commands
files	executed after post
environment	add variables for runtime
runscript	commands when container is executed
labels	metadata
test
apps

OpenMPI example

Filename: OpenMPI-3.0.0

BootStrap: docker
From: centos:7.4.1708

%setup
     cp openmpi-3.0.0.tar.bz2 \
        ${SINGULARITY_ROOTFS}/usr/local/src/openmpi-3.0.0.tar.bz2

%post
    yum install -y gcc gcc-c++ gcc-gfortran 
    yum install -y wget tar make bzip2 gzip perl rsync zip
    yum install -y infinipath-psm-devel infinipath-psm 
    yum install -y libibverbs-devel libibverbs

    cd /usr/local/src 
    tar -xjf openmpi-3.0.0.tar.bz2
    cd openmpi-3.0.0  

    ./configure --prefix=/usr/local --with-hwloc --with-psm --with-verbs
    make -j 16
    make install
    ldconfig

Container build

on your local system as root user:

#singularity must be present
module load singularity/2.4.2

singularity build OpenMPI-3.0.0.img OpenMPI-3.0.0

Derive from existing container

Filename: MPI-Hello

BootStrap: localimage
From: .../OpenMPI-3.0.0.img

%post
    yum install -y git
    mkdir /usr/local/src/git 
    cd /usr/local/src/git  

    git clone https://github.com/wesleykendall/mpitutorial 
    cd mpitutorial/tutorials/mpi-hello-world/code 
    make 
    cp mpi_hello_world /usr/local/bin 

%runscript
    /usr/local/bin/mpi_hello_world $@

singularity build MPI-Hello.img MPI-Hello

Run Container

Copy image to VSC-3
Job script:

#!/bin/bash
#SBATCH -J singularity
#SBATCH -N 2


module purge
module load intel/18 openmpi/3.0.0 singularity/2.4.2

mpirun -np 32 ./MPI-Hello.img

Table of Contents

Singularity

Containerization (historical, pre 1955)

Containerization (historical, post 1955)

HPC Situation

Virtualization vs. Containerization

Docker vs. Singularity

Container concepts

Recipes in Singularity

OpenMPI example

Container build

Derive from existing container

Run Container

MPI call stack

Performance

Further reading