PyGBe: Python on the surface, GPUs at the heart. BEM solver for Electrostatics of Biomolecules

2013-03-13T23:24:59Z (GMT) by Christopher Cooper Lorena A. Barba
<p>Poster presented at the GPU Technology Conference, March 2013, San Jose, CA.</p> <p>It presents the PyGBe code (pronounced 'pig-bee'), which solves the linearized Poisson-Boltzmann equation using a boundary element method, BEM. The underlying dense systems are solved using a Krylov-subspace method, accelerated with a treecode to achieve O(N log N) complexity. </p> <p>The code presents a Python environment for the user, while computing all kernels in CUDA (interfaced with PyCuda), for maximum ease of use, combined with high performance on GPUs.</p> <p><strong>Acknowledgement</strong></p> <p>This research is made possible by a grant from the Office of Naval Research, Applied Computational Analysis Program (N00014-11-1-0356). LAB also acknowledges support from NSF CAREER award OCI-1149784.</p>