National Cancer Institute and Merck select SGI servers for biomedical research

Mountain View 24 November 2003The National Cancer Institute's Advanced Biomedical Computing Center (ABCC) in Frederick, Maryland, has purchased from SCICOR an SGI Altix 3000 server, which was recently put into production. In addition, the Department of Bioinformatics at Merck & Co. Inc. has turned to SGI to support ongoing informatics efforts at its Merck Research Laboratories (MRL). The global, research-driven pharmaceutical company has installed two SGI Origin 3000 family of servers for complete integration of informatics and molecular profiling into basic and pre-clinical research.

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The new SGI Altix system, which contains 64 Intel Itanium 2 processors and runs the open-source Linux operating system, will serve as an important scientific computational resource that is part of a growing list of SGI servers supporting the United States' pre-eminent scientists at NCI and the National Institutes of Health.

Unlike some other high-performance computing centres, ABCC is focused exclusively on supporting research directed toward biological problems. Whether modelling anti-cancer drug interactions with known tumour targets or analysing genomic data, biomedical researchers can greatly benefit from the breakthrough capabilities of the SGI Altix 3000 family of servers, which deliver record-shattering performance and scalability running a 64-bit Linux OS in demanding computing environments such as the biosciences.

The SGI Altix 3000 family, fueled by the first high-performance Linux environment capable of scaling to 64 processors in a single node, represents a remarkable leap forward for scientists, biomedical researchers, programmers and other users of advanced technical computing systems. Advances of Altix 3000 systems include the ability to scale up to 64 processors and 4TB of memory in a single cluster node and to share memory globally across nodes, potentially involving hundreds of processors. The resulting combination delivers breakthrough performance and reduces the time and resources required to run such applications as AMBER and Gaussian, which are critical to research conducted at ABCC.

"For bioinformatics applications requiring large shared memory, large file support, or high code portability, the SGI Altix 3000 is the ideal combination of high-performance computing and industry-standard open source software, and should complement other bioinformatics platforms at the ABCC", stated Thomas Stanley, national director of civilian agencies, SGI.

The new 64-processor SGI Altix system increases the computational power of the ABCC, which already includes eight 8-processor SGI Origin 300 servers and one 64-processor SGI Origin 3800 server installed at the centre. The Altix server is connected to the ABCC Portable Batch System (PBS) Pro cluster, a workload and resource management system that includes the nine existing SGI servers at the ABCC.

In addition, those computing systems that are part of the PBS cluster will have access to nine terabytes of shared disk space on two SGI TP9400 Fibre Channel RAID arrays, the highest performance RAID storage subsystem in its class. This disk space is shared as an SGI CXFS clustered filesystem, the industry's fastest shared filesystem, which eliminates file duplication and the time necessary to move large files over the network.

At the Merck Research Laboratories, the high-performance computing systems support several projects in sequence informatics, molecular profiling, proteomics, research genetics and toxicology for Merck research programmes in the areas of metabolic disorders, neuroscience, infectious diseases and oncology.

The complete installation of new equipment last October included one 256-processor Origin system and one 32-processor Origin server. They were augmented by SGI InfiniteStorage with 10TB of disk, a mix of 10 Silicon Graphics Octane and Silicon Graphics Fuel workstations, four SGI Origin 300 servers, one SGI Altix 3000 server with 12 Intel Itanium processors and 300 seats of Platform LSF from SGI software partner Platform Computing.

MRL will use the servers, SGI TP9500 disk subsystems and large-memory bandwidth to enhance scientific computing, allowing Merck scientists to pursue solutions that were not previously possible. Bioinformatics scientists at the ten Merck research centres around the world, some of which have their own SGI systems, are running searches against the approximately 300 protein and nucleic acid databases mirrored on the department's high-speed disk storage arrays, including publicly available databases. Jobs run at the data centre range from simple searches that take a few seconds to major tasks that can take as long as 24 hours.

Merck & Co. Inc., headquartered in Whitehouse Station, New Jersey, conducts research at 10 major research centres in the United States, Europe, and Japan, manufactures products in 32 facilities and has operations in more than 60 countries. Merck's products worldwide are treatments for high blood pressure, cholesterol management, arthritis and pain, osteoporosis and asthma.

"We are pleased with Merck's selection of SGI technologies for these complex computational tasks, since SGI solutions are for the support of critical health care research and discovery processes", stated SGI Market Strategy Senior Director Bill Bartling, who oversees the company's sciences applications. "We've been working with Merck's Department of Bioinformatics since it was founded in 1994, and we look forward to continuing our close working relationship for many years to come."


Leslie Versweyveld

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