Introducing Bio-X²

Featuring 20 teraflops of 8-core nodes with 4xDDR InfiniBand interconnect

What is Bio-X²

The Bio-X² cluster is the result of an NSF-funded research proposal submitted by 21 Bio-X affiliated faculty, representing 13 departments and 4 schools at Stanford. The purpose of the cluster is to facilitate biological research problems ranging in scale from molecules to organisms.

Bio-X² was funded by the National Science Foundation. The hardware represents generous donations by both Dell and Cisco. The new cluster is housed in James H. Clark Center, hub for the Bio-X Program.

The Bio-X² cluster has been ranked #54 in the June 2007 release of the Top500 supercomputers list.

What's new?

The latest cluster events can be found on the news page (RSS feed).

The next-generation supercomputing cluster has been installed in late January / early February 2007. While the spirit and scope of the original cluster live on, the new cluster utilizes cutting-edge technologies and ultra-fast interconnects.

What's old?

The original Bio-X cluster was retired on January 16, 2007. It has been de-comissioned and removed from Clark Center for reuse and recycling. Photos of the un-racking of the old cluster can be found here.

Why use this supercomputer?

Bio-X² is one of the existing most powerful supercomputers. With 20.6 teraflops, it's been ranked #54 in the June 2007 Top500 list. It contains 2,208 cores within 276 Dell PowerEdge 1950 compute nodes (dual-socket quad-core processors), featuring 16GB of memory each. The system storage includes a 50TB parallel Lustre file system, and a 4xDDR InfiniBand switch fabric, employing PCIe interfaces, interconnects the nodes (I/O and inter-process communication) with a 20Gb/s-per-link non-blocking tree topology. See the Hardware section of the documentation for more details.

Creating shared computing resources allows many groups to combine their hardware efforts into a central resource. The resulting system is larger than any individual lab could fund and manage on their own. Systems administration is greatly reduced, allowing you to focus on your research.

How can I get an account?

• if you're member of a registered lab, you can use the user application form
• if you're a PI, and want to register your lab, please use the lab application form
• if you already have an account, you can access your profile page.

More information

Please see our documentation for more details. Note that accounts are restricted to projects involving biological applications, broadly defined. Please contact Prof. Vijay Pande (pande at stanford dot edu) or Prof. Michael Levitt (michael dot levitt at stanford dot edu) if you have any questions or comments regarding scientific matters, or biox2-administrators at lists dot stanford dot edu for administrative, technical, or documentation questions.