InsideTrack: SC08 Cluster Challenge Technical Brief

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As those of you attending SC08 this year begin to fill your calendars, we wanted to bring your attention back around to the second annual Cluster Challenge.  Last time, we introduced you to the teams and their respective vendor sponsors.  This time, we introduce you to the individual applications required during the performance qualification runs.  Brent Gorda graciously gave us access to his crack team of committee members working on this year’s application requirements.

.: Ricky Kendall from ORNL is managing the computational chemistry portion of the competition by introducing GAMESS into the mix. Ricky had this to say:

GAMESS is a great application for the participants because it demonstrates the needs of cluster resources for one rather demanding field computational chemistry.  Clusters configured to deal with the
GAMESS suite are able to run many applications.  GAMESS stresses all of the subsystems of the computational resource, in particular memory, interconnect, processor performance.  It also demonstrates some of the legacy aspects that computational scientists must deal with in the real world.

.: Tom Spelce of LLNL is managing two applications for this year’s competition.  The first, WPP, simulates ground motion during earthquakes.  According to Tom, it was recently in the spotlight during a simulation of the 1906 SDF earthquake.

WPP was chosen because one of the problems it simulates is the ground motion resulting from earthquakes. It is a relatively simple code which has some potential for source code modification to improve performance. WPP is the same code used by LLNL researches to reenact the 1906 San Francisco Earthquake on its 100 year anniversary.

Tom also had the task of bringing a CFD app [really a toolkit] into the competition.  He chose the widely used OpenFOAM [Open Field Operation and Manipulation] Toolkit.  According to Tom:

OpenFOAM is an OpenSource, parallel Computational Toolkit that can simulate a wide range of physical phenomena, from chemical kinetics, fluid flow and heat transger, to solid dynamics, electromagnetics and
even financial engineering.

.: Doug Fuller of ASU is the bio guru of the group.  Bioinformatics codes is still an emerging sector of HPC.  Doug chose two bio-centric applications for the competition, POY and RAxML.

POY and RAxML are two separate, related bioinformatics applications that will expose students to newly developed parallel software that is on the frontier of this young and exciting field of computationally intensive research.  In particular, the datasets and results produced by these applications will be readily understood by the students and the audience: from genetic sequences, the students will use these applications to analyze the genetic differences among organisms and their relationships to each other.

We were also able to get an inside look at this year’s Cluster Challenge theme.  If you recall, last year’s theme featured air racing.  Keeping in line with the competitive atmosphere, the Cluster Challenge theme for 2008 will be cycling.  Austin has a large contingency of cyclists, not to mention its the home of Lance Armstrong.  Trek bicycles graciously donated plenty of eye candy for the event.  This, being the perfect forum for such an organization.  Where better to recruit the latest crop of CFD specialists right out of school?

Make sure to peddle your beach cruiser over to the Cluster Challenge showcase and check out the exciting competition.