Research & U: ‘Cluster’


By Joshua Ostrer

The IBM supercomputer, donated by IBM Senior Vice President John Kelly and installed over the past summer, is finally being put to use.

The cluster, which holds 88 iDataPlex servers with Intel Xeon 5600 series processors, providing 1056 processor cores, was used this past week for calculations by Janet Anderson, the Florence B. Sherwood Professor of Physical Sciences and Professor of Chemistry.

“We ran molecular dynamics calculations which simulate the motion of a protein molecule in a ‘box’ of water molecules and salt ions. We will use the trajectory of the dynamics calculation to predict the hydrogen exchange rate of amide groups in the protein,”  said Anderson.

The new cluster represents a significant improvement in processing power as compared to any previous option available at Union. Before , doing calculations like those performed by Anderson was far more difficult.

“This summer my research student Steve Scoglio ‘12 and I used the 8-core Mac Pros in the Kelly lab to do similar calculations. The cluster and the Macs run a program called NAMD (Not ‘just’ Another Molecular Dynamics) from the University of Illinois at Urbana-Champaign which has been designed to use multiple processors to speed up the simulations,” said Anderson.

The cluster’s processing power has proved itself extremely beneficial. The cluster was able to perform certain calculations in .0003 seconds, as opposed to in .03 seconds using previous setups.

“The cluster is at least four times faster than the Macs. Most of that is due to the number of processors we are using, 110 on the cluster vs. eight on the Mac Pros,” said Anderson.

With the cluster already in use, there is hope for even easier computing using the cluster.

“The cluster should be getting better at using its many processors once the Infiniband software is installed to accelerate communication between the processors,” said Anderson. Infiniband is a high-speed interconnect designed especially for high-performance computers, and it’s used in most of the world’s most powerful supercomputers.

For those interested in taking advantage of the cluster’s advanced computing power, you’re going to need familiarity with Linux or UNIX systems, since the cluster runs Red Hat Enterprise Linux. In particular, you’ll need to be experienced with the command line.

According to Anderson, “As long as the user knows enough Linux/UNIX to be able to function without a desktop GUI…you have to be able to do everything you need to do using the command line. Only software which has been written for multiprocessor use will benefit from the cluster. Even then, the number of processors to use has been somewhat trial and error for us, because the time doesn’t scale linearly with the number of processors. The optimal number of processors is a function of how the computational problem has been broken up into smaller pieces.”

In regards to future use of the cluster, the Liaison Committee on Academic Computing and Technology, which is comprised of faculty, students and ITS administrators, is still discussing guidelines for use of the cluster.

For those students with their hearts set on using the cluster, Anderson has some advice: “In the meantime, brush up on your Linux!”


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