SGI server and storage solutions help Robarts Research Institute create 3D models of functioning human organs

Mountain View 03 August 2004With help from high-performance computing and storage solutions from Silicon Graphics, scientists at Canada's Robarts Research Institute are modelling functioning human organs to aid in the development of minimally invasive surgery and therapy techniques. With a 20-processor SGI Altix 3000 server, a dual-processor SGI Altix 350 server, and a 6 terabyte SGI InfiniteStorage Storage Area Network (SAN) solution, the Virtual Augmentation & Simulation for Surgery & Therapy (VASST) laboratory at Robarts is working to advance a broad range of medical procedures in such areas as neurosurgery, prostate cancer therapy, breast cancer biopsy, and cardiac intervention and surgery.

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Based on Intel Itanium 2 processors and utilizing medical visualization software from Atamai Inc., the new 20-processor Altix system is equipped with 20GB of memory and is the largest computer ever installed at the institute. Integrated by SGI Professional Services, the two Altix systems are connected via an SGI SAN with SGI InfiniteStorage Shared Filesystem CXFS. Leveraging the Altix 350 server as a metadata server, the SAN makes up to 6 terabytes of research data immediately available to both Altix systems via CXFS, which provides instant, no-copy data sharing among systems on the SAN. And by combining fibre channel RAID with Serial ATA technology, Robarts can remove data access bottlenecks from its environment for faster problem solving.

"By creating an environment to model organs and simulate surgical procedures, we will accelerate the development of new minimally invasive therapies", stated Dr. Terry Peters, scientist and principal investigator at Robarts. "With SGI Professional Services providing integration expertise and SGI server and storage solutions, together with Itanium 2 processors and Atamai software, we have a powerful new weapon in the ongoing fight against a range of debilitating diseases, and a scalable platform for discovering new non-invasive surgical procedures and clinical treatments."

"Robarts Research Institute is working to significantly advance how our most lethal and debilitating diseases are diagnosed, treated, and even cured", stated Dr. Colin Holmes, sciences industry business development manager at SGI. "Real-time medical imaging demands close coupling of imaging modalities, new and existing compute platforms and high-performance storage in a hybrid computing environment. Our close working relationship with Intel, Atamai and Robarts researchers has helped produce just such a solution with the breadth and scalability required to generate, manage, and store massive 3D models and data sets while integrating smoothly into an already complex medical research infrastructure. We are excited to be a part of this effort to enable important new surgical techniques and treatments."

The VASST lab designs and implements the complex algorithms required for real-time 3D modelling of human organs, from the beating human heart to the functioning brain, for use in image-guided surgery and therapy procedures. These algorithms, both serial and parallel, run the gamut from generation of patient-specific models and 3D geometric alignment to interactive real-time soft tissue simulation.

The VASST laboratory selected SGI Altix over commodity clusters and all other systems because of the Altix platform's support for Intel Itanium 2 processors and compilers, its 64-bit Linux operating environment, and its global shared-memory architecture. "Our work requires significantly faster computation times in the simulation of organ function than is required in designing and refining image-guided surgical procedures", Dr. Peters stated. "This made SGI Altix the clear choice to run the applications developed by Atamai software. We also found Intel Itanium 2 compilers extensively helpful in optimizing processor performance and tuning applications."

As part of a two-year consulting project, Robarts will work closely with Atamai to develop software for the virtual patient simulation system. The system will leverage SGI's advanced graphics APIs and will incorporate world-class image processing and analysis techniques developed by Robarts. Atamai, a collaborative venture of former Robarts students with the University of Western Ontario and the London Health Sciences Centre, is based in London, Ontario, and provides custom medical visualization solutions to several research groups worldwide.

"The research underway at Robarts' VASST laboratory requires the leading floating-point performance, large cache, and instruction parallelism that are inherent in the Intel Itanium processor architecture", stated Richard Dracott, general manager of marketing and planning in Intel's Enterprise Platforms Group. "The resulting performance of the Itanium 2 processor-based SGI Altix system unleashes fundamentally new levels of research, and we look forward to the advances pursued by this team of medical innovators."

The Altix family leverages the built-in SGI NUMAlink interconnect fabric, which allows global addressing of all memory in the system and delivers data across nodes up to 200 times faster than conventional interconnects. For the first time, more complex data sets and complete work flows can be driven entirely out of memory, enabling the type of performance necessary for true innovation in surgical and physiological modelling that commodity clusters or repurposed enterprise UNIX servers cannot tackle.

Altix systems feature a fully supported, standard 64-bit Linux operating system and advanced development environment specifically optimized for data-intensive computations such as the registration and segmentation of multimodal medical imagery. SGI Altix has consistently set numerous records for sheer performance, and for its ability to efficiently run manufacturing, engineering and scientific applications across hundreds of processors in a Linux operating environment.

With InfiniteStorage, SGI is changing the rules in network storage by delivering hardware and software solutions specifically developed for the unique and demanding needs of data-intensive enterprises. The company's commitment to innovation enables timely availability of new technology, investment protection for existing technology, and a thriving partner community. SGI offers customers a complete family of network storage systems and software that enables customers to match solutions to their data-intensive enterprise needs while providing scalable capacity, management and performance in a cost-effective architecture.

SGI Altix 3000 systems are available today in configurations of 4 to 512 processors. For customers demanding even larger Altix systems, SGI plans to support configurations of 1024 and more processors over time. SGI InfiniteStorage Solutions are available directly from SGI or through SGI Solution Providers worldwide. Complementing InfiniteStorage are SGI Technology Solutions, that custom design, deliver and support storage solutions, and SGI Managed Services that provides comprehensive installation and configuration services to provide immediate return on storage investment.

More information on the Atamai-SGI-Roberts project is available in this VMW issue's article Joint project between SGI and Atamai creates 3D virtual patient simulation system at Robarts Research Institute


Leslie Versweyveld

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