Hands-on #2: Building containers from scratch

Singularity configuration file

We will build a container image for LAMMPS code using CentOS as the base image. A template Singularity configuration file is available in the /home directory.

Create/use the lammps template configuration file lammps.cfg

# Header
BootStrap: 
OSVersion: 
MirrorURL: 
Include:

# Sections
%setup

%post

%runscript

Header

We will BootStrap CentOS version 7 with package manager yum. The MirrorURL for downloading CentOS is http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/. Include: yum.

Sections

In this example, we will use %setup, %post and %runscript.

• Download and copy LAMMPS to /opt. Use $SINGULARITY_ROOTFS to access root file system in the container:

cd $SINGULARITY_ROOTFS/opt
wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz

• Install development tools: yum -y groupinstall "Development Tools"

• Configure and compile LAMMPS

mkdir -p /opt/lammps
cd /opt/lammps
tar xf ../lammps-stable.tar.gz --strip-components 1

cd src
make yes-granular |& tee log.make_yes_granular
make -j serial |& tee log.make_serial

• Configure the container to run lmp_serial on execution of the container:

/opt/lammps/src/lmp_serial "$@"

Creating the container image

• Create a container called lammps and modify the size to 2048 MiB.

singularity create --size 2048 /local/lammps.img`

• Bootstrap the lammps configuration file created in the previous step.

sudo singularity bootstrap /local/lammps.img lammps.cfg

Bootstrapping step requires root access.

Running the container image

To execute the container

singularity run /local/lammps.img -i in.granregion.mixer