Highlights of our Work
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The most powerful compute engine in your laptop and home computer is
what? The central processing unit, of course. Wrong, it is the
graphics processing unit (GPU)! Since GPUs are specialized for
graphics and games, popular uses of modern computers, their
development benefitted from strong market forces. Modern GPUs reach
Teraflop speed, passing entire computer clusters filling a room.
Unfortunately, GPUs lie dormant when computers are employed for
intensive biological computing like biomolecular simulations. GPUs
are now getting a wake-up call from biomedical researchers who then
enjoy many-fold speed-ups of their laptop computations
(see the Oct 2007 highlight),
vendors already now hawking GPU-powered "desktop
supercomputers." The next challenge is to bring the GPU from the
laptop to computer centers, speeding up the world's fastest
supercomputers. Building on previous development experience of
NAMD
and
VMD, a
recent report
describes NAMD running at impressive speed
on a GPU cluster. The report suggests techniques, useful also for
programmers of other applications to efficiently accelerate computer
clusters through GPUs. The report is particularly timely with a new,
large GPU-accelerated computer cluster coming on-line. The reported
GPU-based speed-ups will permit biomolecular simulations largely
unfeasible so far for studies of entire virus particles and cellular
organelles. More information here.