This was originally intended to be micro-blogged talk. Probably on friendfeed. But when I walked into the old Chevron building on the Pitt campus to listen to Professor Wilfred van Gunsteren the wireless was spotty, so I saved my notes for a triumphant return to normal blogging. The talk is part of a lecture series presented by the CMMS at the University of Pittsburgh. Since it was probably the intended purpose when I started Bleeding Edge Biotech; this is my notepad of the distinguished lecturer’s slides and talking points.
Continue reading ‘Thirty Years of (Bio)Molecular Simulation: How Far Have We Come?’
There’s a new podcast on Futures in Biotech with Dr. Pande from Folding@Home. Macresearch summarized it well:
How a bunch of Sony PS3s have become the largest component of the world’s fastest computer
The challenges of distributed computing, and in particular how data storage and CPU usage can actually complement each other
After the hype in the 80s around computational modeling of protein structure, the computational power available today could finally make that hype a reality
How to take a non-parallel task and transform it into a series of computational chunks (a.k.a. how to make a baby in 1 day with 270 women)
How modeling of protein structure will be able to get more into the dynamics of protein conformational changes
What would you do if you had 250,000 CPUs?
I really like the final point, “What would you do with 250,000 CPU’s”, because it’s an important question. Petascale computing has arrived but most applications aren’t ready to scale to thousands or millions of cores. Folding@Home is as a distributed computing project as it is biomedical. What they’ve been able to do is treat simulations as data and use bayesian data mining techniques to put together the whole picture with suprising efficiency. A clever workaround for Folding@Home’s “supercomputer”, which is severely limited by network latencies and individual agents with slow hardware compared to ‘real’ supercomputers. Finally he reports that PS3’s and GPU’s are achieving 20-30x acceleration. Exciting stuff!
image taken from Flikr, CC licence
The PSC and NRBSC have made the news again, this time in HPCwire. They’ve posted the Readers and Editors Choice awards for SC07 and the WiiMD demo earned us “Most Innovative Use of HPC in Life Sciences”.
Further Reading:
WiiMD: Bowling on Big Ben
Engadget: wiimote used in buckyball bowling and other educational simulations
Nintendo’s latest video console the Wii is doing very well. What I’ve found interesting is the exploration people are doing with the Wiimote controller itself. It’s already been used for video editing, playing Half-life, and even business presentations. A couple of months ago we were using it as a mouse in VMD and Chimera. Some interest has peaked in having an application designed specifically for the use of the wiimote and scientific visualization.
Wii Linux
Wiimote playing Half-life
