HPCwire

The Leading Source for Global News and Information Covering the Ecosystem of High Productivity Computing

HPCwire >> Off the Wire

Q&A: Taking High Performance Computing Mainstream


Page:  1  of  3
1 | 2 | 3   All  »  

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.

Page:  1  of  3
1 | 2 | 3   All  »  

HPCwire on Twitter

Article Tools

  • Print This Page
  • Bookmark This Article

Share Options

(Digg, Technorati, more)


Subscribe

Discussion

There are 0 discussion items posted.  

HPC in the Cloud Part 2
People to Watch 2010


Feature Articles

The Week in Review

C-DAC announces plans for a petaflop system; IBM researchers are working on vertical integration techniques to extend Moore's Law another 15 years. We recap those stories and more in our weekly wrapup.
Read More...

Moscow State University Supercomputer Has Petaflop Aspirations

The Moscow State University supercomputer, Lomonosov, has been selected for a high-performance makeover, with the goal of tripling its processing power to achieve petaflop-level performance in 2010. T-Platforms, who developed and manufactured the supercomputer, is the odds-on favorite to lead the project.
Read More...

Intel Ups Performance Ante with Westmere Server Chips

Right on schedule, Intel has launched its Xeon 5600 processors, codenamed "Westmere EP." The 5600 represents the 32nm sequel to the Xeon 5500 (Nehalem EP) for dual-socket servers. Intel is touting better performance and energy efficiency, along with new security features, as the big selling points of the new Xeons.
Read More...

Top Headlines

Australia Commissions Cray Supercomputer

Mar 19 | OfficialWire | New super to support intelligence work Down Under. Read more...

Intel Partners See 'Easy' Upgrade Path With Xeon 5600 Chips

Mar 18 | ChannelWeb | Westmere parts already showing up in HPC machines. Read more...

AMD: OEMs primed for Opteron 6100s

Mar 17 | The Register | But what about the tier ones? Read more...

Arrival of the Desktop Supercomputer

Mar 17 | Cadalyst Magazine | A new generation of workstations is changing the nature of technical computing. Read more...

Scheduling HPC In The Cloud

Mar 17 | Linux Magazine | Latest iteration of Sun Grid Engine able to tap into Cloud. Read more...

Featured Whitepapers

Virtualization for Aggregation And The vSMP Architecture™

Jan 12 | | In-depth look at vSMP Foundation server virtualization technology, technical implementation, use cases and capabilities. The technical whitepaper provides an architectural overview and details on the three vSMP Foundation products: vSMP Foundation for SMP, vSMP Foundation for Cluster and vSMP Foundation for Cloud.

Copper Cable Technologies for High Performance Computing

Jan 18 | | This white paper discusses Gore’s copper cable assemblies, and how they continue to exceed the standards for providing reliable, cost-effective solutions for high-performance computer applications.

Multimedia

Webcast: Virtualized Data Center Roundtable

Join this online panel discussion for live Q&A with leading industry experts, analysts, and end-users to discuss the latest innovations, best practices, barriers to implementation, and measurable benefits of server virtualization with a particular focus on today's real world solutions.

Webcast: Watch SC09 Birds of a Feather Video: Scalable Fault-Tolerant HPC Supercomputers

Learn about scalable fault-tolerant architectures and examples of energy efficient and scalable supercomputing clusters using dual QDR InfiniBand to combine capacity computing with network failover capabilities with the help of programming languages such as MPI and a robust Linux cluster management package.

Webcast: High Performance Computing for a Smarter Planet

LIVE@SCO9: The IBM team discusses new innovations in hardware, software and services that help clients better understand their workloads and get insight from their R&D efforts. Technology demonstrations include the soon-to-be-released Power7 HPC processor, the DCS990 system with 2.4 petabytes of storage, the xCAT management tool, secure HPC cloud computing and more. Winners of two HPCwire Readers' and Editors’ Choice Awards! Take the IBM virtual tour at SC09 or more information go online to: http://www-03.ibm.com/systems/deepcomputing/sc09.html

SC09 HPC in the Cloud

Newsletters

Stay informed! Subscribe to HPCwire email Newsletters.






HPC Job Bank


Featured Events

HPC User Forum DICE
2010 High Performance Computing Linux Financial Markets
Cloud Computing Expo
Cloud Lab
ESC
DEISA PRACE Symposium