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. This 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>* singularity pull library://default/ubuntu:latest

• Sources include Singularity Container Library (library), Singularity Hub (shub) and Docker Hub (docker).

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

singularity exec image_name command singularity exec myPythonContainer.sif python3 helloWorld.py

Find Size of Container: singularity cache list

Basic Singularity Commands

Basic Singularity Commands Pull - pulls a container image from a remote source $ sudo singularity pull <remote source> <remote source> Singularity Container Services

   $ sudo singularity pull --name CONTAINER_NAME.sif library://USER/PULL_PATH:VERSION

Singularity Hub $ sudo singularity pull --name CONTAINER_NAME.sif shub://USER/PULL_PATH:VERSION (Note: the path only needs to match the pull card. please see the remote website for example.) Docker Hub $ sudo singularity build CONTAINER_NAME.sif docker://USER/PULL_PATH:VERSION (Note docker images have layers and it needs to be merged into 1 singularity image. For that to happen you MUST use: build)

Exec - executes an EXTERNAL COMMAND $ singularity exec IMAGE_NAME.sif EXTERNAL_COMMAND

Shell - shells into an existing container singularity shell IMAGE_NAME.sif

• Note: Your home directory is mounted by default

Run - runs an image. Run is based on the Run Script parameters that were placed into the container when the image was built based the recipe $ singularity run IMAGE_NAME.sif

Build (BIG TO DO: Very important) $ singularity build IMAGE_NAME.sif <source> Sources include Another Image either docker or singularity Singularity definition file (use to be known as a recipe file), usually denoted with name.def

Note: You can shell into a docker UI - explore different containers without pulling or building $ singularity shell docker://ubuntu

Creating Definition Files: Workflow: Set up complex workflows with Recipe File: Alternatively- Sandbox Directory Prototype Final Container: sudo singularity build --sandbox ubuntu_s docker://ubuntu

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.