The Palmetto Cluster: High Performance Computing at Clemson University

Jim Pepin, Chief Technology OfficerCLEMSON UNIVERSITY

Clemson University is using a next-generation high-performance computing cluster from Dell to enable a wide range of academic research.

The Palmetto cluster is a component of the campus cyberinfrastructure, which is also part of the Clemson University Academic Roadmap.

The cluster fulfills needs and leverages what individuals, departments and the University are doing as a whole in information technology, research and creative inquiry.

The Palmetto Cluster

The first phase of development, completed in December 2007, provided approximately 15 Teraflops (TF) of computing power and moved Clemson from outside the Top 500 to the Top 100 computing sites in the world.

A second phase was implemented during the week of May 5, adding another 16 TF to the cluster.

When fully developed , this cluster could operate at up to 100 TF.

Date Nodes TeraflopsRank in Worldwide

HPC SitesDec. 2007 250 15 TF Top 100May 2008 512 31 TF Top 60

Housed at Clemson’s Information Technology Center (ITC), the cluster is being developed by Clemson Computing and Information Technology (CCIT) in collaboration with Dell technicians and researchers across the university.

Computing Infrastructure

Jill Gemmill, Executive Director for Cyberinfrastructure Technology Integration, and Jim Pepin, Chief Technology Officer for Computing and Information Technology, in front of the Palmetto Cluster at the Information Technology Data Center

The cluster is built on LINUX with a tightly coupled 10GB/sec network. It is built with Myrinet, for cost-effective, high-performance, packet-communication and switching and MPI for messaging.

The cluster itself is connected into the campus network and takes advantage of the high-speed connection between the campus and ITC.

Networking Systems and Operations

The new Palmetto cluster allows me to undertake data- and computationally-intensive projects that would have otherwise been impossible. The new resources will be helpful for theoretical work aimed at developing new methods for estimation and inference about efficiency in production settings. In addition, I will now be able to apply these new methods while making more efficient use the very large amounts of data available on U.S. commercial banks to examine industry structure, etc. I will use the new cluster for research on computationally intensive methods for nonparametric estimation and inference.

Paul Wilson, Professor, John E. Walker Department of Economics, College of Business and Behavioral Science

We are conducting NIH-funded research to investigate how proteins in the body interact with the surfaces of synthetic materials, with the long-term goal of designing medical implants with improved biocompatibility.

The Palmetto cluster is a very exciting development for our entire research group as it provides us with the facilities and support that we need to move our projects forward and a competitive edge to continue our program in today's difficult funding environment.

My group will be primarily doing molecular dynamics simulations on proteins and polymers using the CHARMM program under 3 separate NIH grants. Our simulations will involve the need for a large number of CPUs for parallel processing runs using replical-exchange molecular dynamics (REMD) with a program called MMTSB for REMD control. Although I only have purchased 5 nodes at this time, I anticipate purchasing another 10 nodes over the coming year. We will heavily use these nodes as well as have needs for running jobs as a guest on between 30 to 50 nodes as resources are available on Palmetto.

Bob LaTour, Professor of Bioengineering, College of Engineering and Science

The new palmetto cluster will enable our research team to investigate how changes in school characteristics, arising from families moving across the more than 15,000 different school districts in the U.S., and changes in parents work behaviors affect the developmental outcomes of young children over time. In our earlier work on a smaller scale computer cluster, we were only able to examine a subset of these issues for much less informative sets of school characteristics and labor market opportunities.

The detailed forms of dynamic economic models we will now be able to analyze will help to define the new state of the art in computational microeconomic models. These new computational resources will make Clemson one of the primary places in the world for undertaking research in this rapidly developing field. I plan to use the "condo" computer cluster in my research on the effects of school characteristics and parents' work behaviors on children's performance in school and their intellectual development. A parent's choice of a school district to live in defines both a set of characteristics for the schools available to their children and a set of possible labor market opportunities for the parents. The interactions between these two possibly competing reasons for moving to any particular place can lead to spurious inferences about the impacts of school characteristics or parent's working on their children's development. By modeling the parents' choices of places of residence and their labor market behaviors (over 15,000 school districts), we hope to mitigate many of the potential biases that could have affected earlier studies.

Tom Mroz, Professor, The John E. Walker Department of Economics, College of Business and Behavioral Science

The capabilities of the new cluster allow us to consider wireless communication networks of a larger size using models of higher fidelity than was possible for us before. Our research computing emphasis is two-fold. We use Monte Carlo simulations based on high-fidelity models in research on cross-layer protocol design for mobile ad hoc packet radio networks. We also use novel computational-electromagnetic numerical-analysis algorithms for E&M characterization in problems concerning antenna design, E&M penetration, and electromagnetic compatibility

Dan Noneaker, Associate Professor and Associate Chair, Electrical and Computer Engineering, College of Engineering and Science

My group will be using the cluster to simulate the motion of various proteins and nucleic acid sequences in an effort to better understand how these molecules function and evolve in biological systems. First, by validating our dynamics calculations against experimental FRET analyses, we can derive a description of macromolecular dynamics that is simultaneously consistent with and more detailed than experimental measurements.

Next, calculations of flexibility and changes in flexibility due to mutation can be correlated to experimentally determined changes in activity, giving us a detailed atomic picture of the known relationship between dynamics and function. Further, molecular dynamics studies generate a statistical mechanical ensemble of conformational states from which thermodynamic properties (such as binding free energy) can be calculated and related to biomolecular function. In summary, we will be exploring conformational dynamic and thermodynamic properties of biomolecules in order to better understand their function and to better understand how these molecules evolve.

Brian Dominy, Assistant Professor, Chemistry, College of Engineering and Sciences

Faculty Researchers

CITIThe Cyberinfrastructure Technology Integration (CITI) team is a component of CCIT that is comprised of research scientists who support high-performance and high-throughput computing, collaborative software environments, scientific visualization, faculty development and training.  Please visit http://citi.clemson.edu for more information, including self-guided tutorials.

The Palmetto Cluster is being made possible through a strong partnership between faculty and IT administration, with faculty ‘owners’ providing a significant percentage of the funding for the compute nodes while the University provides the rest of the nodes plus the infrastructure to build the cluster (racks, switches, power, etc.)

The condominium model also provides commodity HPC to faculty and students who like to try new things.

Condominium Collaborative Partnership

Layout & Design by Suzie Medders