Supercomputer Gordon for genomics research

I visited San Diego Supercomputing Center (SDSC) at the University of California, San Diego on Sept 13 (see photo taken at the entrance to the center). It was almost impossible to miss the brochure and poster of a new system that just came online at SDSC. Its was named Gordon.

Gordon is the latest Track 2 system awarded by the National Science Foundation and was built by Appro based on its name of the Xtreme-X architecture.

Gordon entered production in the first quarter of 2012, deploying a vast amount of flash storage to help speed solutions now hamstrung by the slower bandwidth and higher latencies of traditional hard disks. Gordon's "supernodes" exploit virtual shared-memory software to create large shared-memory systems that reduce solution times and yield results for applications that tax even the most advanced supercomputers.

The machine is configured as a 1,024-computer-node (16,384-core) supercomputer cluster architecture, which enables it to perform complex functions for data-intensive applications, including the study of genomics.

The Protein Data Bank (PDB) was among the early entities to apply Gordon's capabilities. The PDB is a worldwide repository of information about the 3D structures of large biological molecules. The PDB group performs predictive science with queries on pair-wise correlations and alignments of protein structures that predict fold space and other properties.

According to Appro article, in a test configuration of spinning disks and solid-state drives, Gordon was able to help the PDB determine that SSD improves query performance by a factor of three compared to spinning disks. Such insight should aid the PDB in its future research of proteins, nucleic acids and other biological molecules.


External Link:

• Gordon at SDSC

Cross-link:

• System - Gordon (jPage)
• Field - Genomics (jPage) 
• Institution - SDSC (jPage)
• HPC & Big Data (jBook)