SC2002 Talks and Demonstrations

When: November 18-21 2002

Support: NAMD and VMD are developed by the Theoretical Biophysics Group at the Beckman Institute of the University of Illinois, supported by the NIH National Center for Research Resources and the National Science Foundation.

URL: http://www.sc2002.org/

Gordon Bell Award Finalist NAMD Paper

Title: NAMD: Biomolecular Simulation on Thousands of Processors
Location: Room 309-310
Time: 2:30 Wednesday
Authors: James C. Phillips, Gengbin Zheng, Sameer Kumar, Laxmikant V. Kale
Abstract: NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.

Theoretical Biophysics (TBG) and NCSA Itanium 2 Cluster and Display Wall Demo and Talk

Title: NAMD and VMD: Live Molecular Dynamics Simulation and Visualization on NCSA Itanium Linux Cluster and Tiled Display Wall
Location: NCSA booth
Times: 8pm Monday, 1pm Tuesday
Investigators: Klaus Schulten, Robert Skeel, Laxmikant Kale
Developers: James Phillips, John Stone, Justin Gullingsrud, Gengbin Zheng, Paul Grayson (all TBG)
Presenter: Jim Phillips, TBG
Contacts: Bill Bell, Bruce Loftis, and Rob Pennington at NCSA
TBG Support: Update display wall port of VMD, provide and present demo simulation.
What will be demonstrated: A NAMD simulation of GlpF (see below) will be running on the NCSA Itanium 2 Linux cluster at SC2002 VMD will be demonstrated on NCSA's tiled display wall powered by a cluster of low-cost graphics workstations built with commodity parts. VMD will be used to visualize the running simulation. The process of tuning NAMD for the Itanium processor will be discussed, and serial and parallel performance results will be presented. NAMD and VMD are developed by the Theoretical Biophysics Group at the University of Illinois. NAMD and VMD development is supported by the NIH National Center for Research Resources and the National Science Foundation.

Theoretical Biophysics (TBG) and Sun Microsystems XVR-4000 Demo

Title: NAMD and VMD: Interactive Molecular Dynamics Simulation
Location: Sun Microsystems booth
Times: various, unknown
Investigators: Klaus Schulten, Robert Skeel, Laxmikant Kale
Developers: James Phillips, John Stone, Justin Gullingsrud, Gengbin Zheng, Paul Grayson (all TBG)
Presenter: Sun personnel
Contacts: Travis Bryson at Sun Microsystems
TBG Support: Technical advice, NAMD and VMD inputs for demo simulation and display.
What will be demonstrated: A simulation of GlpF (see below) will be performed using NAMD on a 20 processor SunFire 6800 with ClusterTools 4.0 MPI parallel communication software. VMD will be running on the same machine and displayed by XVR-4000 graphics boards in two SunFire V880z systems. The V880z systems are connected to the 6800 via a high bandwidth multiple Myrinet connection. NAMD and VMD are developed by the Theoretical Biophysics Group at the University of Illinois. NAMD and VMD development is supported by the NIH National Center for Research Resources and the National Science Foundation.

About the GlpF Demo Simulation (In Both Sun and NCSA Booths)

Conduction in Aquaporins

Aquaporins are channel proteins abundantly present in all life forms, for example, bacteria, plants, and in the kidneys, the eyes, and the brain of humans. These proteins conduct water and small molecules, but no ions, across the cell walls. Their defective forms are known to cause diseases, e.g., diabetes insipidus, or cataracts. The molecular modeling program, NAMD, along with large parallel computers at the Pittsburgh and Illinois supercomputing centers permitted researchers now to model aquaporins in the natural environment of membrane and water in one of the largest molecular dynamics simulations ever (over 100,000 atoms). The simulations revealed in unprecedented detail how cells conduct water and glycerol, a molecule that serves cells' metabolism. The simulations provided a movie of the entire conduction process.

A greatly reduced model of a single GlpF channel, consisting of only 4210 atoms, 3295 of them fixed, will be used to demonstrate the power of NAMD to accelerate even small simulations on modest numbers of processors. The Tcl scripting capabilities of NAMD are used to apply a constant force, driving a single glycerol molecule back and forth through the channel. While the force biases the movement of the glycerol, it still takes over 100 ps of dynamics to find the proper alignment to pass through the specificity filter region of this remarkable molecule.