Powerful new system allows phylogenetic researchers to conduct large-scale calculations

A new supercomputing cluster designed for the phylogenetic research community has been installed at the San Diego Supercomputer Center (SDSC). The Cluster, a 16 node, 8-way Fusion A8 by Western Scientific, features a total of 128 Opteron processors each with 4 GB memory, for a total of 0.5 TB memory. The cluster was purchased with a grant from the National Science Foundation in support of the CyberInfrastructure for Phylogenetic Research (CIPRES) project, a collaboration of biologists, computer scientists, statisticians and mathematicians at 19 institutions whose goal is to understand the evolutionary relationships between all living organisms.

SDSC is home to CIPRES’ Central Resource, a team of biologist/programmers implementing a new generation of software tools and databases in support of the National community of Phylogenetics researchers. The SDSC team creates production software releases and tools for database access and data deposition that are publicly available. The project is designing new data formats and data storage techniques and uniting these with new high end computing architectures to speed the prediction of evolutionary relationships. The cluster acquisition represents novel architecture that can provide additional computational muscle required by scientists.

“The goal of the CIPRES project is to push the size limits of phylogenetic reconstruction from evolutionary trees of 100 to 1,000 species to 100,000 species and more,” said SDSC project leader Mark Miller, “the problem is that the calculations for large trees are extremely intense in their demands both for computational power and memory bandwidth. We selected the Fusion A8 for its ability to deliver resources in both areas: the 64-bit 8 way architecture, together with the 32 GB memory allocation per node will provide the folks who model these large trees with plenty of power to push upwards on the size of the trees that can be simulated.”

CIPRES cluster installation team from left to right:
(back row) Mark Miller, Steve Meier, Alex Borchers
(front row) Terri Liebowitz, Bryan Banister, Kevin Fowler

“This new cluster will allow researchers to make significant steps forward in creating new solutions for the difficult computational problems that arise in studying evolutionary relationships, ” said Bernard Moret, CIPRES project leader and Professor of Computer Science and of Electrical and Computer Engineering at the University of New Mexico. “And, it will be an open resource for our entire phylogenetic community.”

Researchers within the community will be able to access the new cluster system through an allocation process. Formal announcement of the policies and procedures for obtaining such an allocation is scheduled on September 1, 2005, and will be posted on the CIPRES website.

About CIPRES
The Cyberinfrastructure for Phylogenetic Research (CIPRES) project is an open collaboration funded by the National Science Foundation. The goal of the CIPRES project (pronounced Cypress) is to enable large-scale phylogenetic reconstructions on a scale that will enable analyses of huge datasets containing hundreds of thousands of biomolecular sequences. To achieve this goal we have brought together a group of researchers involved in phylogeny estimation, statistics, and computer science to create new solutions for the difficult computational problems that arise in inferring evolutionary relationships. The project has a 5 year development plan (2003-2008) to create a national computational infrastructure for the international systematics community. The group is committed to providing open-source software.

About SDSC
SDSC is a world leader in using, innovating and providing information technology to enable advances and new discovery in science and engineering. Focusing on data-oriented and computational science and engineering applications, SDSC serves as an international resource for data cyberinfrastructure through the provision of software, hardware, and human resources in multi-disciplinary science and engineering, and serves as a leadership national cyberinfrastructure center to the NSF and broader community.

SDSC is an organized research unit of the University of California, San Diego with a professional staff of interdisciplinary scientists and engineers, software developers, service and support personnel. SDSC collaborates widely with national and international partners, federal agencies, private industry and others. For more information, see www.sdsc.edu.

Media contacts:

• Ashley Wood,
  SDSC Communications,
  858-534-8363
  awood@sdsc.edu

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, Florida State University, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css