Amber

Amber Molecular Modeling with ClearSpeed Acceleration

ClearSpeed acceleration of Amber 9 has been shown to deliver a speedup of between 3.4x and 9.4x for compute intensive sections of the code using a single Advance X620 accelerator board.

The Amber 9 methods that include the effective radius and force calculation of AMBER’s Generalized Born (GB) models, 1, 2, and 6 have been modified to take advantage of ClearSpeed’s Advance™ accelerator board. Supported options include constant pH7 and analytical linearized Poission Boltzmann (ALPB) as well as options that do not directly change the force calculation, including NMR restraints.

While the genborn module of Amber is a small part of the sander executable, it typically amounts for 95-97% of the CPU compute time for GB simulations. The CPU compute time is mainly spent in three loops: effective radii calculations, diagonal and off-diagonal force calculations.

The overall structure of the code was maintained. A thin layer written in C, using ClearSpeed’s CSAPI library, was added to handle the communication between the host and board.

Host: 2.8GHz Pentium 4 EMT64, OS: RHEL4-64, CSXL: version 2.50

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