Data-flow networks and using the Copernicus workflow system


Peter Kasson

Associate Professor of Molecular Physiology and Biological Physics and of Biomedical Engineering, University of Virginia

Laboratory of Molecular Biophysics, Uppsala University


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.

Session details

When: 10:00 CST, June 14, 2017

Length of session: 1.5 hours: 30 minutes on data-flow generalities, 1 hour on Copernicus

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: