Supercomputer Center Installs Flash-Powered Cluster

• By Dian Schaffhauser
• 03/08/11

The San Diego Supercomputer Center at the University of California, San Diego has a new member of the family. Named Trestles, the newcomer would rank No. 111 on the list of most powerful computers in the world and through 2013 is expected to serve members of TeraGrid, a distributed "cyberinfrastructure" for open scientific research.

Trestles is a dedicated TeraGrid cluster designed by the Supercomputing Center and Appro, a company that specializes in building high performance computing systems. It consists of 324 compute nodes, each with four sockets containing an eight-core 2.4 GHz AMD Opteron 6100 series processor. That makes for a total of 10,368 cores for the system. Loaded with 38 TB of flash memory, the cluster has a theoretical peak speed of 100 teraflops per second.

The cluster project was funded by a $2.8 million grant from the National Science Foundation. It took 10 weeks to get Trestles operational from the time the center took delivery of its hardware.

According to the center, the use of flash-based memory--the same kind of memory used in USB flash drives and cell phones--is fairly new to supercomputers. "UCSD and [the Supercomputing Center] are pioneering the use of flash in high-performance computing," said Allan Snavely, associate director of the center and a co-principal investigator for the new system. "Flash disks read data as much as 100 times faster than spinning disk, write data faster, and are more energy-efficient and reliable."

In mid-2011 the center will go into production with two other clusters running flash: Gordon, a 1,024-node supercomputer, and Dash, a smaller prototype of Gordon. Appro is involved with integration of both systems.

Trestles was designed with a single goal in mind: to enable as much productive science as possible, said Richard Moore, the center's deputy director and also a co-principal investigator. "Today's researchers are faced with sifting through tremendous amounts of digitally based data, and such data-intensive resources will give them the tools they need to do so." He added that that Trestles offers modest-scale and gateway users rapid job turnaround to increase researcher productivity, while also being able to host long-running jobs.

One early-user project focuses on establishing a portal on the TeraGrid for structural biology researchers to facilitate electron microscopy (EM) image processing. Bridget Carragher, director at the National Resource for Automated Molecular Microscopy at The Scripps Research Institute in La Jolla, CA, said she's enthusiastic about the potential of the new system for high performance structural biology projects. "Based on our initial experience, we're optimistic that this system will have a dramatic impact on the scale of projects we can undertake, and on the resolution that can be achieved for macromolecular structure."