Tag Archives: SimBioSys

Petaflops and Cell Processors

An interesting article regarding the world’s fastest computer was in C&E News today when it hit my desktop. At a time where there is so much focus on High Performance Computing it was interesting to read about the RoadRunner system delivered by IBM to the Los Alamos National Laboratory.

Quoting Wikipedia “Roadrunner differs from many contemporary supercomputers in that it is a hybrid system, using two different processor architectures for the heavy lifting. Usually supercomputers only use one, since it would be easier to design and program for. To tap the full potential of Roadrunner, all software will have to be written specially for this hybrid architecture which is uniquely complex. The hybrid design consists of dual-core Opteron server processors manufactured by AMD utilizing the standard x86 architecture. Attached to each Opteron core is a Cell processor manufactured by IBM using Power Architecture technology. ”

I have blogged previously about Cell Processors being applied for Virtual Screening/Docking (1,2) and have been helping SimBioSys in their marketing and business development of their eHITS Lightning software as discussed here.

With the fastest computer in the world using the Cell processor as part of its architecture, and with the processor now proving itself for docking, the question is whether we will see this processor become even more mainstream in the foreseeable future. It’s NOT easy to port…but it can be done.

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Posted by on June 19, 2008 in Uncategorized


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A Green Solution for Virtual Screening Using the IBM Cell Broadband Processor

I spent a few days this week in Boston at the Bio-IT conference. I was there for two reasons – to support one of the companies I have been consulting with of late and to present on ChemSpider.

The ChemSpider presentation seemed to be well received and I’m grateful for the opportunity to expose the ongoing work we are doing on ChemSpider.

I have spent the past few months supporting the efforts of SimBioSys to bring a potentially revolutionary platform to market. The intention was to deliver the platform to Boston Bio-It and under the leadership of Zsolt Zsoldos, the Chief Technology Officer for SimBioSys, the deadline was met. Zsolt’s already blogged about the WOW FACTOR at Bio-IT. Check it out…it was a true phenomenon.

I’ve blogged previously about the possibility to derive processing power from a gaming system (1,2). By the time that eHITS Lightning was unveiled at Bio-IT the Cell Processor had managed to deliver up to 120X performance improvements for certain examples.A White Paper about the technology has been online for a while now. The technology delivered was enough to garner a position as a finalist for the Best in Show award. It was enough to have some of the other domain players question how much work it was to port eHITS to the Cell. It was essentially a full rewrite and over two man years of effort to deal with coding for the special nature of the processor.

Zsolt’s presentation to the Best in Show judges is online here. You MUST look at slides 8 and 9 to really “get it”. The cost savings associated with the electricity, cooling, space and, in theory, network administration, are enormous. A 100 CPU Intel cluster could be replaced with three PlayStations for the same eHITS throughput. It’s definitely a  “Green Solution”.

With so much attention being given to coding on Graphic Processing Units it’s quite surprising that no one is yet talking about the advantages of the Cell processor. Well, maybe they will now!

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Posted by on May 2, 2008 in Consulting


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