In this video from the Blue Waters 2018 Symposium, Maxim Belkin presents a tutorial on Containers: Shifter and Singularity on Blue Waters.
Container solutions are a great way to seamlessly execute code on a variety of platforms. Not only they are used to abstract away from the software stack of the underlying operating system, they also enable reproducible computational research. In this mini-tutorial, I will review the process of working with Shifter and Singularity on Blue Waters.
Maxim Belkin received his B.S. in Physics from the Nizhny Novgorod State University, Russia in 2005 and Ph.D. in Physics (with Honors) from the Illinois Institute of Technology, Chicago, IL in 2009. The research focus of his Ph.D. studies was on emergent behavior in ensembles of magnetic microparticles driven far from equilibrium. As the outcome of the work, they developed a hybrid continuum-particle model and carried out the simulations on CUDA-enabled GPU which gave a 100-fold speedup compared to the fastest CPU available at the moment. At UIUC, he switched my research focus to hybrid systems comprising novel inorganic materials and structures, such as graphene and plasmonic nanopores, mainly for molecular sequencing applications. In his research, he uses all-atom molecular dynamics (MD) and atomic-resolution Brownian dynamics (ARBD) simulations, which preserve atomic details by employing 3D potentials of mean force. He is currently working on Brownian dynamics toolkit plugin for VMD.
