Massively parallel and linear-scaling algorithm for second-order Moller-Plesset perturbation theory applied to the study of supramolecular wires

被引:20
作者
Kjaergaard, Thomas [1 ]
Baudin, Pablo [1 ]
Bykov, Dmytro [1 ]
Eriksen, Janus Juul [1 ]
Ettenhuber, Patrick [1 ]
Kristensen, Kasper [1 ]
Larkin, Jeff [4 ]
Liakh, Dmitry [2 ]
Pawlowski, Filip [1 ]
Vose, Aaron [3 ]
Wang, Yang Min [1 ]
Jorgensen, Poul [1 ]
机构
[1] Aarhus Univ, Dept Chem, qLEAP Ctr Theoret Chem, Langelandsgade 140, DK-8000 Aarhus C, Denmark
[2] Oak Ridge Natl Lab, Sci Comp Grp, Natl Ctr Computat Sci, Oak Ridge, TN 37831 USA
[3] Cray Inc, Seattle, WA USA
[4] NVIDIA Inc, Santa Clara, CA USA
基金
欧洲研究理事会;
关键词
Linear Scaling Quantum Chemistry; Massively Parallel Quantum Chemistry Implementation; Supramolecular wires; Method development; ELECTRON CORRELATION METHODS; ATOMIC ORBITAL BASIS; COUPLED-CLUSTER; LARGE MOLECULES; CORRELATION-ENERGY; AB-INITIO; FRAGMENTATION APPROACH; LOCAL TREATMENT; RI-MP2; METHOD; FOCK MATRIX;
D O I
10.1016/j.cpc.2016.11.002
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
We present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide Expand-Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide-Expand-Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, Where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the "resolution of the identity second-order Moller-Plesset perturbation theory" (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24440 basis functions and 91280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods. (C) 2016 Elsevier B.V. All rights reserved.
引用
收藏
页码:152 / 160
页数:9
相关论文
共 107 条
[1]   The Dalton quantum chemistry program system [J].
Aidas, Kestutis ;
Angeli, Celestino ;
Bak, Keld L. ;
Bakken, Vebjorn ;
Bast, Radovan ;
Boman, Linus ;
Christiansen, Ove ;
Cimiraglia, Renzo ;
Coriani, Sonia ;
Dahle, Pal ;
Dalskov, Erik K. ;
Ekstrom, Ulf ;
Enevoldsen, Thomas ;
Eriksen, Janus J. ;
Ettenhuber, Patrick ;
Fernandez, Berta ;
Ferrighi, Lara ;
Fliegl, Heike ;
Frediani, Luca ;
Hald, Kasper ;
Halkier, Asger ;
Hattig, Christof ;
Heiberg, Hanne ;
Helgaker, Trygve ;
Hennum, Alf Christian ;
Hettema, Hinne ;
Hjertenaes, Eirik ;
Host, Stinne ;
Hoyvik, Ida-Marie ;
Iozzi, Maria Francesca ;
Jansik, Branislav ;
Jensen, Hans Jorgen Aa. ;
Jonsson, Dan ;
Jorgensen, Poul ;
Kauczor, Joanna ;
Kirpekar, Sheela ;
Kjrgaard, Thomas ;
Klopper, Wim ;
Knecht, Stefan ;
Kobayashi, Rika ;
Koch, Henrik ;
Kongsted, Jacob ;
Krapp, Andreas ;
Kristensen, Kasper ;
Ligabue, Andrea ;
Lutnaes, Ola B. ;
Melo, Juan I. ;
Mikkelsen, Kurt V. ;
Myhre, Rolf H. ;
Neiss, Christian .
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2014, 4 (03) :269-284
[2]   ELIMINATION OF ENERGY DENOMINATORS IN MOLLER-PLESSET PERTURBATION-THEORY BY A LAPLACE TRANSFORM APPROACH [J].
ALMLOF, J .
CHEMICAL PHYSICS LETTERS, 1991, 181 (04) :319-320
[3]   Fast noniterative orbital localization for large molecules [J].
Aquilante, Francesco ;
Pedersen, Thomas Bondo ;
Sanchez de Meras, Alfredo ;
Koch, Henrik .
JOURNAL OF CHEMICAL PHYSICS, 2006, 125 (17)
[4]   Unbiased auxiliary basis sets for accurate two-electron integral approximations [J].
Aquilante, Francesco ;
Lindh, Roland ;
Pedersen, Thomas Bondo .
JOURNAL OF CHEMICAL PHYSICS, 2007, 127 (11)
[5]   Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency [J].
Aquilante, Francesco ;
Gagliardi, Laura ;
Pedersen, Thomas Bondo ;
Lindh, Roland .
JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (15)
[6]   Linear scaling second-order Moller-Plesset theory in the atomic orbital basis for large molecular systems [J].
Ayala, PY ;
Scuseria, GE .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (08) :3660-3671
[7]   Efficient linear-scaling second-order Moller-Plesset perturbation theory: The divide-expand-consolidate RI-MP2 model [J].
Baudin, Pablo ;
Ettenhuber, Patrick ;
Reine, Simen ;
Kristensen, Kasper ;
Kjaergaard, Thomas .
JOURNAL OF CHEMICAL PHYSICS, 2016, 144 (05)
[8]   Large-scale correlated electronic structure calculations: The RI-MP2 method on parallel computers [J].
Bernholdt, DE ;
Harrison, RJ .
CHEMICAL PHYSICS LETTERS, 1996, 250 (5-6) :477-484
[10]   CALCULATION OF SMALL MOLECULAR INTERACTIONS BY DIFFERENCES OF SEPARATE TOTAL ENERGIES - SOME PROCEDURES WITH REDUCED ERRORS [J].
BOYS, SF ;
BERNARDI, F .
MOLECULAR PHYSICS, 1970, 19 (04) :553-&