Fusion-io's memory technology is being utilized by the SDSC, an organized research unit of UC San Diego, in its data-intensive computing initiatives. As part of these efforts, researchers are using the technology to advance research on the Protein Data Bank, the world's most comprehensive repository for
three-dimensional structures of large molecules and nucleic acids. The research carried out for the PDB serves as a foundation for accelerating the development of life-saving drugs, synthetic proteins used in medicine and other treatments for illnesses.
"As SDSC strives to serve as a center for research excellence, we focus heavily on evaluating how flash-based technologies can improve scientific discovery", stated Allan Snavely, Associate Director of SDSC and co-Principal Investigator of the Center's upcoming data-intensive high-performance computing (HPC) system, Gordon, which is currently in development. "Through our research, we are finding that storage memory products like those offered by Fusion-io are considerably faster than hard drive disks for many large memory and data-intensive problems, and that flash-based storage memory has the potential to make supercomputing-level results accessible outside the traditional user base."
Using Fusion-io's server-deployed technologies, researchers were able to reduce the time required to conduct complex MySQL database queries that determine relationships between proteins and the effects proteins can have on each other. Using traditional hard drive disks, a query analyzing more than 200 million protein structures took 30 minutes.
"With Fusion-io's shared data decentralization technologies - which place the storage memory medium right next to the processor to significantly reduce latency and increase processing speed - the same query took just three minutes", stated Robert Sinkovits, SDSC computational scientist and Gordon Applications Lead.
Spencer Bliven, a graduate student in the Bioinformatics and Systems Biology Department at UC San Diego working with Allen Snavely on the research, stated: "The PBD is helping us gain a more theoretical and practical understanding of the foundations of biological science. With the reduced query times I've seen in conducting tests with Fusion's ioMemory technology, I'm able to stay more focused on my research. This allows the scientific discovery process to be more spontaneous and greatly helps me in eliminating potential errors."
The computer used to realize the performance gains includes two quad-core Intel Xeon E5530 2.40 GHz processors and 48 GB of DDR3-1066 memory. It includes four 320 GB ioDrives mounted and configured as a single 1.2 TB RAID 0 device running an XFS file system.
"Storing crucial data in the server where it is processed can greatly accelerate the analysis of large data sets to enable new scientific discoveries", stated Neil Carson, Chief Technology Officer of Fusion-io. "It's inspiring to see how SDSC is leveraging the performance gains and reduced latency made possible by Fusion-io technology to advance complex biological research that serves as the foundation for many improvements in science and medicine."