GPU accelerated implementation of NCI calculations using promolecular density.
The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand-protein binding. A custom implementation for NCI using promolecular density is presented. It is designed to leverage the computational power of NVIDIA graphics processing unit (GPU) accelerators through the CUDA programming model. The code performances of three versions are examined on a test set of 144 systems. NCI calculations are particularly well suited to the GPU architecture, which reduces drastically the computational time. On a single compute node, the dual-GPU version leads to a 39-fold improvement for the biggest instance compared to the optimal OpenMP parallel run (C code, icc compiler) with 16 CPU cores. Energy consumption measurements carried out on both CPU and GPU NCI tests show that the GPU approach provides substantial energy savings. © 2017 Wiley Periodicals, Inc.
Parallel Computing division, ATOS Company, 1 rue de Provence, Echirolles, 38130, France.|Departmant of Computer Science, CReSTIC (Centre de Recherche en STIC) EA3804, University of Reims Champagne-Ardenne, Moulin de la Housse, Reims, 51687, France.|Department of Chemistry, ICMR, UMR CNRS 7312, University of Reims Champagne-Ardenne, Moulin de la Housse, Reims, 51687, France.
Gaëtan
G
Rubez
Departmant of Computer Science, CReSTIC (Centre de Recherche en STIC) EA3804, University of Reims Champagne-Ardenne, Moulin de la Housse, Reims, 51687, France.
Jean-Matthieu
JM
Etancelin
Parallel Computing division, ATOS Company, 1 rue de Provence, Echirolles, 38130, France.
Xavier
X
Vigouroux
Departmant of Computer Science, CReSTIC (Centre de Recherche en STIC) EA3804, University of Reims Champagne-Ardenne, Moulin de la Housse, Reims, 51687, France.
Michael
M
Krajecki
Departmant of Computer Science, CReSTIC (Centre de Recherche en STIC) EA3804, University of Reims Champagne-Ardenne, Moulin de la Housse, Reims, 51687, France.
Jean-Charles
JC
Boisson
Department of Chemistry, ICMR, UMR CNRS 7312, University of Reims Champagne-Ardenne, Moulin de la Housse, Reims, 51687, France.
Eric
0000-0001-9308-6947
E
Hénon
CUDA; NCI; electron density; graphics processing unit; high performance computing; noncovalent interactions