Biomedical Engineering Reference
In-Depth Information
The application is multi-thread safe, and benchmarks show that the algorithm delivers
the full theoretical output of which the hardware is capable.
Parallelization is achieved on multiple levels by taking advantage of the structure of
the Debye formula. The first level divides the SAXS evaluation in multiple independent
computations according to the binning of the scattering momenta. A nested level then
makes full use of the work-groups in the hardware by splitting the inner summation
of the Debye formula into separate partial sums. The resulting program runs orders of
magnitude faster than an optimized single core CPU implementation.
A caching algorithm on the inner contributions allows for the efficient re-evaluation
of SAXS profiles from partially updated structures, delivering even greater performance
benefits.
The GPGPU algorithm was integrated into an energy term within the PHAISTOS
software framework for protein structure determination, inference and simulation. This
yielded a 16-fold speed increase of the Markov chain Monte Carlo simulation, com-
pared to the best multi-threaded CPU implementation, enabling its application to im-
portant biological targets. An open source implementation is now available.
Acknowledgements.
This research was funded by the Danish Council for Indepen-
dent Research (FTP, 274-09-0184). CA acknowledges partial funding from the Danish
Strategic Research Council (contract number 10-092299), for the HIPERFIT research
center (http://hiperfit.dk).
Source Code Availability
The source code of our implementation can be found online at: http://www.phaistos.org
and http://sourceforge.net/projects/phaistos/files.
References
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