zidane1strife said:
Hmmm, Do you think that processors like cell will make a difference(IOW significantly hasten/increase the speed) for this kind of thing in the near future, or will such processors be unsuitable for such purposes?
Absolutely, I couldn't help but chuckle when I saw this. Protein Folding is perhaps one of the most computationally expensive tasks that have yet been attempted and requires computational power that’s an order of magnitude greater (at least) than the ASCI series the DoE runs at massive costs. These people are wasting their time and resources that could better be allocated towards more established and less complicated tasks. (E.g. United Devices and their Anthrax/Cancer program)
an IBM researcher originally designed the
Cellular concept for RT Ray-tracing, which never got the funding needed due to the small demand for such a device. Later, IBM resurrected the concept for it's
Blue Gene Program which would leverage a pFLOP (in it's initial incarnation) of raw computing power based on the cellular architecture (e.g. along with it's eDRAM and speedy cache access) to explore Protein Folding - which is the true work-horse of the biological world.
Probably it will work well, but the challenge will be program it (low level side). The high level algorithms work is already done.
The problem is the immense computational resources necessary for folding protein. For example, I remember hearing in one lecture that a pFLOP devoted to just Protein Folding would take 2.5 years to simulate just 100microsec of folding mechanics/kinetics. The Stanford site states that a super computer would need "hundreds of thousands" of processors to keep-up with the PC users at home who are running a plethora of other background tasks and are using the same architecture with the same bottlenecks as any traditional Von Neumann architecture... I find this comment ignorant.
The programming of it will be relatively easy as there has been over 30 years of research on massive parallel computing to leverage.
The stuff IBM, SUN and the like will be putting out in a little more than a year will make all you've done during this time frame look like a waste. IBM alone is gearing up for a pFLOP+ scale system devoted to Folding in 2005.
IIRC at any given time they have 35,000 CPUs available to do the work.
And this is nothing compared to what will be done in the 2004-2006 timeframe. This is going to be like the Human Genome Project PartII where the 3 years of work put in at first can be computed by the end of the project in a month.
