University of Pittsburgh
Reducing the Complexity in Complex Genetics
When Dr. Barmada first wrote his grant proposal to the NIH, he proposed a Linux cluster with 200 processors, 300GB of disk storage and installations services. “What I got from Apple was 250 processors, 2 ½ terabytes of Xserve RAID disk space — almost ten times the storage — plus installation and configuration, which wasn’t even in the original quote,” he says.
Productivity Times Five
With the Xserve G5s and Xserve RAID, Dr. Barmada can support the day-to-day demands of more than 30 professors and research teams involved in more than 120 complex research projects.
“With the Linux cluster we could run 48 jobs with 48 processors,” he says. “With the Xserve cluster we can get five times as much done. I was able to give the Apple cluster 750 jobs and run those for a day without any problems. And it can take a lot more work than we’re giving it.”
Scalable, Extensible Tools for Bioinformatics
To support bioinformatics research at the University, Barmada installed BioTeam’s iNquiry software on the Xserve G5 cluster. "Within two or three hours, we had the whole machine up and interconnected," Dr. Barmada says.
With all of the tools and web interfaces that come with the iNquiry package, “what was a statistical genetics cluster now also has the ability to serve as a comprehensive bioinformatics cluster,” he adds.
“With the Linux cluster we could run 48 jobs with 48 processors. With the Xserve cluster we can get five times as much done. I was able to give the Apple cluster 750 jobs and run those for a day without any problems. And it can take a lot more work than we’re giving it.”
Dr. Barmada also plans to use iNquiry to create web interfaces for the statistical genetic tools. “iNquiry is an extensible architecture, so we’re collecting web interfaces for our statistical genetics tools,” he says. “Where they don’t exist, we’re writing them ourselves.”
Cluster Administration Made Easy
With Mac OS X Server and Apple Remote Desktop, Dr. Barmada finds it much easier to manage the cluster. “All of the work Apple has done in terms of making graphical interfaces is reflected in the administration tools,” he says. “If I want to add people, I log onto the cluster — several miles away — from my desktop machine using Workgroup Manager. Then I click to add a new user. It’s much easier than logging into a Linux cluster and doing it manually.
“Apple Remote Desktop,” he adds, “also allows me to collect information about all of the machines or do large copies to all of the machines. It’s easier — and definitely much faster — because I don’t have to remember command line combinations.”
He also uses Mac OS X server administration tools for higher-level administrative tasks. “The administration tools include all of the configuration tools you’d find in any other system, only ‘Macified’,” he says. “It’s a lot easier to look at things in a graphical setup than it is to look at large tables of text, which you get through a command line tool.”
Easy management of the Xserve cluster has eliminated the need for a full-time administrator. “Other groups with Linux clusters need a full-time administrator to maintain the cluster,” he says. “We just have me, a faculty member and a technician who spends half his time on the cluster.” He uses the other half maintaining the other 120 desktop systems, which include both Macs and PCs.
Storage Without Bottlenecks
One aspect of the Xserve G5 cluster that particularly appealed to Barmada is its use of Xsan, Apple’s enterprise-class storage networking solution that eliminates bottlenecks of Ethernet-based network file servers.
“Xsan distributes the Xserve RAID storage load over the four head nodes instead of just one, so now I have four times the bandwidth accessing the same file system,” says Barmada. “Users can access terabytes of storage simultaneously, without running into bottlenecks.”
