Is container-based technology a winner for high performance scientific applications?

High Performance Computing (HPC) applications require systems with environments for maximum use of limited resources to facilitate efficient computations. However, these systems are faced with a large trade-off between efficient resource allocation and minimum execution times for the applications executed on them. Also, deploying applications in newer environments is exacting. To alleviate this challenge, container-based systems are recently being deployed to reduce the trade-off. In this paper, we investigate container-based technology as an efficient virtualization technology for running high performance scientific applications. We select Docker as the container-based technology for our test bed. We execute autodock3, a molecular modeling simulation software mostly used for Protein-ligand docking, in Docker containers and VMs created using OpenStack. We compare the execution times of the docking process in both Docker containers and in VMs.