My Other Computer Is a Supercomputer
Computational Biology on Iceberg
The Iceberg Dell Supercluster has been a complete revolution to our research. We have been using supercomputing centers for decades, but we always felt limited by relatively restrictive queues, too-small runtime quotas and difficulties in adopting the system to our needs. The last couple of years we have been building our own Linux clusters with 50–100 CPUs, but off-the-shelf hardware leads to higher support and administration costs, not to mention the fact that the cluster is sometimes idling, such as when we are busy writing papers. The new Dell cluster at Stanford is an extremely cost-effective solution to this; by having a shared resource, there are hundreds of nodes available when we want to test a new model overnight, but our cost is only the average number of nodes we are using. We are not only in complete charge of the hardware, but the resources also are an order of magnitude more powerful than anything we've used before or after the installation; we spend only about an hour a week on administration.
Computational biology usually involves extremely heavy calculations on sequences or protein structures. Some of the most common applications involve finding matching patterns between families of sequences or structures and simulating the motions of atoms in biomolecules. Pattern matching it is no big deal for a handful of sequences, but our current project, together with the Department of Energy, relies on large-scale prediction of accurate models for the proteins in the Shewanella bacterium (famous for its ability to eat radioactivity and toxic waste). This involves hundreds of thousands of sequence profiles of which we need to make all-vs.-all comparisons. It used to take weeks of carefully planned runs on our local cluster, but now we literally are able to test an idea overnight and submit a new version of the experiment the next day.
The molecular dynamics simulations of atomic motions are also as impressive. The simple idea is to calculate the forces atoms exert on each other and then use Newton's equation of motion to determine new positions a very short time later (a step is usually 2 femtoseconds, that is 2 × 10-15 of a second). A single iteration in the simulation is fast, but billions of steps are required to study biological reactions. For this reason, we have optimized our code manually to use Intel's Streaming SIMD Extensions instructions, available on the Pentium 4 Xeon CPUs to speed up our programs Gromacs and Encad by a factor of 2–4, which made it possible to simulate proteins like the Villin headpiece (Figure I) for more than a microsecond, using only two weeks of time on ten of Iceberg's nodes. Actually, with the optimized code, even the individual Dell/Intel Xeon processors are faster than the top-of-the-line IBM Power4 or Alpha CPUs (chips that are found in other supercomputers), at less than one-tenth of the cost. This is by far the best computer investment we ever made, and we will not hesitate to expand it in the future.
The Villin headpiece is a very small protein consisting of about 600 atoms. However, the cell is always surrounded by water (red/white rods), which brings the atom count up to about 10,000. Every single atom interacts with the closest 100–200 neighbors; the interactions have to be calculated every single step, and then we repeat this for a half-billion steps to generate a microsecond of simulation data. The data for Figure I was generated from a two-week run on ten of Iceberg's nodes.
—Michael Levitt and Erik Lindahl of the Department of Structural Biology, Stanford University School of Medicine
The goal of any high-performance computing cluster should be to bring it to a stable and working state as quickly as possible, and then run it until the hardware dies. This allows the users of the system performing research to have a stable system to use on demand. Making changes to the system for the sake of making changes is not how to handle a computing system of this scale. In my mind, this is what is provided by using the cluster distribution that we've chosen on which to standardize. The only administration work should be monitoring queues, filesystem sizes, reviewing logs for errors and/or activity and monitoring hardware to determine whether replacement is needed. With the combination of Rocks and a support plan from Dell, using Silver support on the compute nodes and Gold on the front end, we will enjoy three years of worry-free performance and parts replacement. Our goal is to generate funds by billing for compute time that will allow for the replacement of the cluster within the three-year period. And when the new cluster arrives, we'll install Rocks, and we will be off and running for another three-year cycle.
The current plan is to charge for usage on Iceberg with the idea that the revenue generated will cover the purchase of a replacement cluster in three years. This replacement most likely will be Iceberg-II, with the same node count, but a 1U form factor rather than 2U in order to maximize our floor space. Iceberg will stay on-line as separate cluster and decrease in size as hardware fails.
Additionally, we are in the planning stages of acquiring a new 600-node cluster that we plan to bring up in the next 6–12 months. This cluster will be housed at an off-site location. We are in negotiations with a research institute that has expressed interest in housing the cluster and providing specialized services (generated power, UPS, power, HVAC and so on) free of charge, in exchange for processing time on the cluster. Other options are being considered as well. Outside the scope of Iceberg, I'm looking into building yet another cluster for commercial purposes. I'd like to think this would be the largest Rocks cluster when completed, in addition to claiming a top-20 seat on the TOP500.
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