Containers for CyberShake

This page is to document the steps involved in enabling the CyberShake codebase to run in a container environment.

Selection of Containers

The available HPC Containers at the time of selection were Singularity, Charlie Cloud, and Shifter. Between the 3 of these container technologies, Singularity was widely adapted and had more open source tools. Because of this wide adaptation the module already existed in the Frontera system. Singularity has built-in support for different MPI libraries from OpenMPI, MPICH, IntelMPI to name a few. Shifter is highly reliant on MPICH ABI, which would require site-specific MPI libraries to be copied to the container at run time.

Setting up a serial container

(Explains the steps involved in building and running serial code in a container)

Image Prework: Convert Sandbox Director to image file: sudo singularity build new-sif.sif myUbuntu imageName sandbox directory

User Work: Install Dependencies sudo apt-get update && sudo apt-get install -y \

   build-essential \
   uuid-dev \
   libgpgme-dev \
   squashfs-tools \
   libseccomp-dev \
   wget \
   pkg-config \
   git \
   cryptsetup-bin

Download Go export VERSION=1.13.5 OS=linux ARCH=amd64 && \

   wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
   sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
   rm go$VERSION.$OS-$ARCH.tar.gz

Set Up Go echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \

   echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
   source ~/.bashrc

Install Singularity export VERSION=3.5.2 && # adjust this as necessary \

   wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
   tar -xzf singularity-${VERSION}.tar.gz && \
   cd singularity

Check if Singularity Works git clone https://github.com/sylabs/singularity.git && \

   cd singularity && \
   git checkout v3.5.2

Get Image singularity pull <source>

Execute Command in from Outside Container Singularity Commands singularity exec myPythonContainer.sif cat /etc/lsb-release imageName command

singularity exec myPythonContainer.sif python3 helloWorld.py imageName command

Find Size: singularity cache list

Containers on Frontera

Serial Containers

Explain how you got serial containers running on Frontera.

MPI Containers

Explain how you got MPI containers running on Frontera.