SGI technologies and grid visualisation advance membrane protein research at Henri Poincaré University

Nancy 07 November 2002The Computational Chemistry and Biochemistry Group at the Henri Poincaré University in Nancy, France, has become the first visualisation services client of the National Higher Education Computing Center (CINES) supercomputing facility at the University of Montpellier in southern France. The centre is newly equipped with a 512-processor SGI Origin 3800 server and an eight-processor Silicon Graphics Onyx2 visualisation system with four InfiniteReality2 subsystems.


In early June 2002, just prior to its decision to expand its already existing relationship with CINES to include visualisation services, the group collaborated with SGI and CINES in a demonstration of SGI's Visual Area Network concept. Held at CINES earlier this summer, this event was designed to show how geographically dispersed research teams could use Visual Area Networking to collaborate interactively on complex visualisations. During the demonstration, the research group in Nancy used Silicon Graphics visual workstations to manipulate visualisations generated by the Onyx2 system, located at the CINES facility in Montpellier, approximately 500 miles or 800 kilometers away.

This vivid demonstration of Visual Area Networking capabilities brought home to the Nancy group the many visualisation possibilities that the CINES facility offers beyond the computation services it was already providing. "CINES' computational resources enable us to tackle problems that we could not have dreamed of a couple of years ago", stated Henri Poincaré University's Dr. Christophe Chipot. "It enables us to move into the international forefront of our research areas. We appreciate having access to visualisation capabilities as well, as they allow us and others to see what's going on at the atomic-detail level in a single glimpse."

"The demonstration showed how effectively French institutions can access CINES as a scientific visualisation serving infrastructure and use our SGI supercomputing resources to accelerate research projects", stated Alain Quéré, director of CINES. "We are looking forward to frequent collaboration with Henri Poincaré University and to providing scientists at other institutions with the computing and visualisation resources they need to compete internationally."

"SGI was pleased to work with CINES and the Computational Chemistry and Biochemistry group at Nancy to conduct this dramatic demonstration of Visual Area Networking, a concept pioneered by SGI", added Paris-based SGI Country Manager Philippe Miltin. "In these and other demonstrations of Visual Area Networking, we have seen geographically dispersed teams sharing computational resources, using existing desktop systems to collaborate interactively over grid-like networks with centrally generated visualisations and substantially reducing time to insight. It is clear that Visual Area Networking is a powerful new tool for scientists and researchers."

For the grid visualisation demonstration, Nancy group researchers Mounir Tarek, Bernard Maigret, and Dr. Chipot generated a series of snapshots from a multi-nanosecond simulation of water molecules flowing into and through a peptide nanotube inserted in a model of a bacterial cell membrane. This simulation required a total of 200 lipid molecules and 6500 water molecules. Peptide nanotubes represent a potential alternative to classic antibiotics in fighting bacterial infections. The group also visualised the interaction of a cell membrane protein, a G-protein-coupled receptor, with a small peptide molecule. The visualisation enabled the team to see the orientation and motion of molecules in the membrane bilayer clearly.

"Biological systems like cell membranes are very difficult to investigate experimentally because very few cell membrane protein structures are known", explained Dr. Chipot. "For that reason, our investigations have been purely computational. Now, however, we can use the CINES service to visualise the results of our simulations directly. In terms of insight, I believe that a picture, especially an interactive, three-dimensional picture, is worth much more than a thousand words."

The data for the demonstration was generated on the SGI Origin 3800 system at Montpellier, where the molecular dynamics programme NAMD had been installed. Nancy scientists used an SGI workstation to communicate with the Onyx2 visualisation supercomputer at CINES, creating visualisations with Visual Molecular Dynamics (VMD) software. Images were grabbed, compressed, transmitted, and viewed using OpenGL Vizserver technology on both ends of a wide area network. SGI also provided demonstrations of Visual Area Networking technology, including SGI OpenGL Volumizer application programming interface and SGI OpenGL Vizserver software.

Time on the CINES SGI compute and visualisation system is allocated through a peer-reviewed application process. The Nancy group has been allocated approximately 110.000 hours of CPU time this year.

Leslie Versweyveld

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