Skip to main content
Premium Trial:

Request an Annual Quote

Dell Steps into Biocluster Ring with Monster Linux Farm at Buffalo Center

Premium

Dell hasn't made a lot of noise in the life sciences market. Although plenty of bioinformatics departments use Dell servers in various configurations, Iobion recommends them as a low-cost option for its GeneTraffic system, and Time Logic soups them up to build its DeCypher accelerator, the company has kept a much lower profile than its competitors.

But with last week’s christening of a 4,000-processor Linux cluster at the Buffalo Center of Excellence in Bioinformatics, Dell made up for missed hype opportunities: At its press conference, CEO Michael Dell unveiled “what we believe [is] the largest cluster in the higher education universe.”

With more than 2,000 dual-processor Dell PowerEdge servers, up to 5.8 teraflops of compute power, and an estimated value of $13 million, this system very well could be. It is the second-largest cluster Dell has installed anywhere, according to Reza Rooholamini, director of operating systems and cluster development at Dell — but it’s certainly Dell’s largest life science win. Dell is also wrapping up another 2,000-processor serve farm scheduled to come online in a few weeks at the University of Buffalo’s Center for Computational Research, where the COE cluster is also housed.

Russ Miller, director CCR, said the center currently supports 100 research projects, and about one-third to one-half are in bioinformatics. An anticipated burst in bioinformatics activities associated with the newly-launched Center of Excellence prompted the decision to install the new CCR cluster before the order for the COE system was even placed, Miller said.

The COE cluster alone provides a 10-fold increase in the CCR’s computing power, and will be dedicated almost solely to protein folding computation. The system is already full, according to Jeff Skolnick, director of the COE, who added jokingly that it’s “time for a new computer.” Skolnick’s group is participating in the upcoming CASP5 protein structure prediction competition, so getting the system up and running as quickly as possible was a top priority.

Dell worked fast, getting the system in place within three months of the placement of the order, Miller said. The only delay was on the part of the COE, which had to construct a machine room to house the new clusters. In the meantime, Dell and its partners — including Platform Computing, EMC, TechConnect, and MSTI — built the cluster in a “staging area” in Long Island, and then moved everything to Buffalo once the machine room was ready.

Bundled Bioclusters

Dell currently offers bundled solutions from eight to 128 nodes, which include hardware, software, and professional services. Rooholamini said that the company has close to 150 clusters installed across four market segments. The Cornell Theory Center, the University of Alabama, the University of Pennsylvania, and the University of Missouri, St. Louis, are some of its other academic biocluster customers.

Rooholamini said he expects the number of bundled cluster solutions sold this year to double last year’s sales, with the largest growth areas being in the life sciences and energy. A larger push into bundled clusters, combined with the high-profile systems in Buffalo, should greatly increase Dell’s chances in the biosciences. ”Citing a recent IDC market research report that pinned the company with 40 percent of the clustered supercomputer or high-performance omputing market, Rooholamini noted that it’s difficult to break out how much of that number is derived from life sciences.”

But the company’s bundled cluster solutions aren’t exactly turnkey yet. Chris Dagdigian, a biocluster consultant with BioTeam, recently installed a 30-server Dell cluster at Harvard’s Center for Genomics Research, for which Dell “sent everything in individual boxes and then sent out local engineers to assist with the onsite assembly process.” While pleased with the price and performance of the hardware and networking equipment, he noted that the lack of a high-end storage offering might work to the company’s disadvantage.

In addition, Dagdigian pointed out, “Even if Dell can supply turnkey hardware and service options to customers in the life sciences, they still lack the domain- specific experience and professional services ability to integrate the clusters into production biocomputing environments.”

But Miller said Dell’s partnership strategy for the Buffalo project, which overcame its weaknesses in storage solutions and other areas, worked out well, with Dell serving as a single point of contact for requests and concerns on the part of Skolnick and Miller, who provided all the bioinformatics expertise necessary for the installation.

Dell’s Rooholamini has already set his sights on the next University of Buffalo order. With the 4,000-processor system already loaded to capacity, “I wouldn’t be surprised if it grows to 10,000 processors in the near future,” he said.

– BT

 

File Attachments

Filed under

The Scan

Renewed Gain-of-Function Worries

The New York Times writes that the pandemic is renewing concerns about gain-of-function research.

Who's Getting the Patents?

A trio of researchers has analyzed gender trends in biomedical patents issued between 1976 and 2010 in the US, New Scientist reports.

Other Uses

CBS Sunday Morning looks at how mRNA vaccine technology could be applied beyond SARS-CoV-2.

PLOS Papers Present Analysis of Cervicovaginal Microbiome, Glycosylation in Model Archaea, More

In PLOS this week: functional potential of the cervicovaginal microbiome, glycosylation patterns in model archaea, and more.