HPCwire: Q&A: Taking High Performance Computing Mainstream

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August 04, 2006

Q&A: Taking High Performance Computing Mainstream

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This week Microsoft announced the general availability of Microsoft Windows Compute Cluster Server 2003, the company's first product designed specifically for high performance computing (HPC). With Windows Compute Cluster Server 2003, Microsoft aims to make it easier to create, integrate and operate HPC clusters within organizations, thereby expanding the technology beyond traditional supercomputing centers by bringing the value of computational clusters within reach of more people.

To understand the impact of this event, PressPass convened a roundtable of customers who have been test driving Microsoft Windows Compute Cluster Server 2003 in demanding applications, including biomedical research and scientific modeling. Providing their insight are:

Ron Elber, professor of computer science at Cornell University

John Michalakes, senior software engineer at the National Center for Atmospheric Research (NCAR) in Boulder, Colorado

Matt Wortman, director of computational biology and IT at the Genome Research Institute, University of Cincinnati

PressPass: Would each of you begin by briefly describing the work you're doing as it relates to Microsoft Windows Compute Cluster Server?

Elber: At Cornell, we have a core facility called the Computational Biology Service Unit (CBSU) that's dedicated to computational biology and bioinformatics for Cornell researchers. We provide both research and computational support to biology groups. The cluster serves as a platform for computational biology applications used in a range of research activities in bioinformatics. We support many popular applications for sequence-based datamining, population genetics and protein structure prediction. Many of the projects require lengthy calculations, and massively parallel computing helps shorten the clock time and obtain results in a reasonable period. We have developed a Web-based interface that allows biologists to access the applications without any prior knowledge of cluster computing.

Michalakes: About eight years ago, NCAR and a number of partner organizations involved in atmospheric research and operational forecasting began working on a next-generation community weather model and data assimilation system to eventually replace aging model codes in use for forecasting and research. This new model, called the Weather Research and Forecast (WRF) model, is basically all new software, designed from the outset for HPC systems. WRF is maintained and freely distributed as a community model and is being run at hundreds of institutions across the range of systems, from individual workstations to large supercomputers. Thus, portability and portable performance has been a key concern in the design and implementation of WRF.

Wortman: One of our key focus areas at the Genome Research Institute is drug discovery. Early in the drug-discovery process, millions of chemical compounds are screened against disease targets to identify classes of molecules whose properties and activities guide researchers toward the discovery of new drugs. Our research focuses on applying computational tools to this process to reduce costs and save time. Specifically, we perform virtual in silico screening experiments that simulate the interactions between a disease target and those millions of chemical compounds to predict which compounds participate in desired interactions. The compounds predicted to have the most favorable properties are selected from the chemical library, and then proceed to in vitro testing to confirm the computational predictions. This combination of in silico and in vitro screening is much faster and less expensive than in vitro screening alone because the number of chemicals that need to be tested is reduced by several orders of magnitude. A typical job on our cluster begins when the disease target is sent to the scheduler along with a list of chemicals to be used during the simulation. The head node sends a copy of the disease target and a portion of the chemicals to each node where simulations occur independently. The head node analyzes and ranks the results of each simulation.

PressPass: What made you decide to use the Microsoft Windows Compute Cluster Server 2003, and what benefits do you think it offers to your organization and your work?

Michalakes: We strive to maintain WRF [NCAR's Weather Research and Forecast model] on as many systems deployed in our user community as possible. Until now, that meant systems running some flavor of UNIX or Linux. With the emergence of Microsoft Windows as a viable HPC operating system, and given that we receive on average one user request per month asking if WRF will work on Windows, we see Windows CCS as an opportunity for further broadening the range of computational resources available to the WRF user community.

Wortman: Our decision to use Windows Compute Cluster Server was motivated by the need to lower costs by reducing the complexity of our infrastructure. Windows Compute Cluster Server has several advantages to an organization like ours that uses Active Directory for identity management. First, our Windows technicians could apply their knowledge of Windows-based servers to it. This was evidenced by the fact that individuals with no HPC experience set up a Windows-based Compute Cluster Server HPC cluster without guidance or supervision. Second, using Active Directory and the Microsoft job scheduler enables our users to submit jobs from their workstations and reduces the number of user accounts.

Elber: Upgrading to Windows Compute Cluster Server was a natural step for us. We have been using a Windows-based HPC platform since the computational biology unit was started in 2001. Until recently, we used Windows-based systems adapted by the Cornell Theory Center (CTC) for HPC. We use Microsoft SQL Server for our database needs and Windows-based servers for hosting our Web interfaces. Therefore, Windows Compute Cluster Server allows for a homogeneous and easy-to develop environment. Our experience with the CTC's Windows-based HPC systems is very positive, and we expect Windows Compute Cluster Server to be even better.

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