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J Chem Theory Comput. 2012 Jul 10;8(7):2272-81. doi: 10.1021/ct3001798. Epub 2012 Jun 7.

Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

Author information

1
Max-Planck-Institut für Kohlenforschung , Kaiser-Wilheim-Platz 1, 45470 Mülheim an der Ruhr, Germany.

Abstract

In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

PMID:
26588960
DOI:
10.1021/ct3001798

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