Visit additional Tabor Communication Publications
August 04, 2010
A paper published in Nature this week shows that human creativity trumps computer software, at least in the protein folding arena. A protein folding game, called Foldit, that allows people to puzzle together protein structures, is proving to be quite successful. The game was conceived by scientists at the University of Washington after they got the idea that mere mortals could use their intuition to tweak protein structures in novel ways.
Protein folding has been the domain of supercomputing for some time, given that it's basically an exercise in molecular dynamics. But the FLOPS needed to simulate proteins of any size is considerable, so even petascale machines have to take some computational short-cuts to predict the molecular structures. Humans, though, can use creativity as a short-cut when problem solving. From the University of Washington announcement:
It turns out that people can, indeed, compete with supercomputers in this arena. Analysis shows that players bested the computers on problems that required radical moves, risks and long-term vision – the kinds of qualities that computers do not possess.
Ars Technica does a deeper dive into why the protein folding software often comes up short when it starts crunching on really big structures:
It sounds simple, but with anything more than a short chain of amino acids, there are a tremendous number of potential configurations to be sampled in 3D space, which can bring powerful computers to their knees. The Rosetta algorithm handles the huge energy landscape it needs to scan by taking big leaps between different configurations, then attempting to minimize the energy by making smaller tweaks. This lets it sample large portions of the structural landscape, but sometimes leaves it stuck: the path between its current location and an energy minimum may take it through a high energy state, which would keep Rosetta from finding the solution.
But it may be only a matter of time before the supers regain the upper hand. The University of Washington researchers are trying to analyze the approaches used by more successful Foldit players, with the idea of trying to replicate those strategies in software.
Full story at Ars Technica
In quieter times, sounding the bell of funding big science with big systems tends to resonate further than when ears are already burning with sour economic and national security news. For exascale's future, however, the time could be ripe to instill some sense of urgency....
In a recent solicitation, the NSF laid out needs for furthering its scientific and engineering infrastructure with new tools to go beyond top performance, Having already delivered systems like Stampede and Blue Waters, they're turning an eye to solving data-intensive challenges. We spoke with the agency's Irene Qualters and Barry Schneider about..
Large-scale, worldwide scientific initiatives rely on some cloud-based system to both coordinate efforts and manage computational efforts at peak times that cannot be contained within the combined in-house HPC resources. Last week at Google I/O, Brookhaven National Lab’s Sergey Panitkin discussed the role of the Google Compute Engine in providing computational support to ATLAS, a detector of high-energy particles at the Large Hadron Collider (LHC).
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.