Data-flow networks and using the Copernicus workflow system
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.
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: http://copernicus.readthedocs.io