Data-flow networks and using the Copernicus workflow system

Presenter: Peter Kasson, Associate Professor of Molecular Physiology and Biological Physics and of Biomedical Engineering, University of Virginia, Laboratory of Molecular Biophysics, Uppsala University

Date: June 14, 2017



I will provide an introduction to the concept of data-flow networks and their advantages in workflow systems. This introduction will use examples from several parallel data-flow packages. The second portion of this tutorial (second seminar) will focus on the Copernicus system and its use in molecular simulations. A brief introduction to Copernicus will be followed by a few high-level simulation algorithms facilitated by Copernicus and a tutorial session in composing simple and adaptive workflows with Copernicus. Basic Copernicus mechanics will be covered as well.

Target audience: Molecular simulation and related domain science areas.

Prerequisites: Familiarity with HPC environments, molecular dynamics simulation basics.

User Base: Copernicus: not tracked, users in molecular simulation domain science. Gromacs: 10,000+ users in molecular simulation domain science.

Software Availability: Open source LGPL2

Software Requirements: Linux-like environment (possibly Docker).

Use cases: Running many variations of a simulation in parallel; free-energy calculations; adaptive Markov State Model sampling.

Training and reference materials: