Early experience with Singularity containers

Amr RadwanHPC Applications Specialist

Supercomputing Core Laboratory

Why containers?

Difference between VMs and Containers

Available Containers Systems

● Docker● Singularity● Shifter● Rkt

Components of container system

● Container engine● Recipe file ● Image● Container● Registry

Containers Workflow (Docker example)

Docker Vs SingularityDocker Singularity

Privilege model Root Daemon SUID

Access to host file system Yes Yes

Native support for GPU No Yes

Native support for infiniband

No Yes

Native support for MPI No Yes

Work with all schedulers No Yes

Design goal Microservices applications Scientific use cases

Containers are portable Yes ( Docker Hub ) Yes ( Docker Hub & Singularity Hub)

Use Cases

Deepvariant is an application we couldn't install on Ibex because of its dependence for newer underlying system packages such as Glibc

With Singularity, now we can run Deepvariant on Ibex!

Demo

Steps for the Demonstration:

● Build singularity image for OpenFoam application.● $singularity build openfoam.img openfoam.def

● Submit a batch job ● $ sbatch sing.sh

● Check the status ● $squeue -u radwanaa

● Move the image to another system and try the same steps ( Testing Portability)

Thank You