SC07 Talks and Demonstrations

When: November 11-16 2007

Support: NAMD, VMD, and BioCoRE are developed by the Theoretical and Computational 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.


Conference Tutorial Presentations

Title: High Performance Computing on GPUs with CUDA
Location: A3
Full Information:
Times: Sunday 8:30am-5pm
TCBG Presenters: John E. Stone and James C. Phillips
Other Presenters: Massimiliano Fatica, David P. Luebke, Ian A. Buck, John D. Owens, Mark J. Harris, Bernard Deschizeaux

NVIDIA's Compute Unified Driver Architecture (CUDA) platform is a co-designed hardware and software stack that expands the GPU beyond a graphics processor to a general-purpose parallel coprocessor with tremendous computational horsepower, and makes that horsepower accessible in a familiar environment - the C programming language. Scientists throughout industry and academia are already using CUDA to achieve dramatic speedups on production codes.

In this tutorial NVIDIA engineers will partner with academic and industrial researchers to present CUDA and discuss its advanced use for science and engineering domains. The morning session will introduce CUDA programming and the execution and memory models at its heart, motivate the use of CUDA with many brief examples from different HPC domains, and discuss fundamental algorithmic building blocks in CUDA. The afternoon will discuss advanced issues such as optimization and 'tips & tricks', and include real-world case studies from domain scientists using CUDA.

NIH National Center for Research Resources Booth Presentations

Title: Exploring Biomolecular Machines with Supercomputers
Location: Booth 3055, UCSD-National Biomedical Computation Resource
Full Information:
Times: Monday 7:40-9pm, Tuesday 10am-6pm, Thursday 10am-1pm
Presenters: James Phillips and John Stone
Contacts: Wilfred Li and Teri Simas at SDSC

The Theoretical and Computational Biophysics Group (TCBG), an NIH Resource for Macromolecular Modeling and Bioinformatics, is located at the Beckman Institute of the University of Illinois at Urbana-Champaign (UIUC). The Resource brings advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance through direct collaboration with experimental researchers, the distribution of user-friendly cutting-edge software, and a broad range of training and dissemination activities.

The flagship TCBG software packages NAMD, VMD, and BioCoRE, all distributed free of charge with source code, facilitate the discovery process from analysis, through modeling, to visualization of the molecular apparatus in biological cells:

  • NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code used regularly to simulate systems of 1,000,000 atoms and beyond on both large supercomputers and inexpensive Linux clusters.
  • VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using hardware-accelerated 3-D graphics and built-in scripting.
  • BioCoRE is a collaborative work environment that allows biomedical researchers to visualize information, to share resources, and to interact with each other and with research tools via a common infrastructure and across distance.

For improved VMD performance on the tiled display use "display cachemode on"; this is primarily useful for rotating static structures.