1
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Shi T, Wang Z, Aldossary A, Liu Y, Li XS, Head-Gordon M. Local Second Order Mo̷ller-Plesset Theory with a Single Threshold Using Orthogonal Virtual Orbitals: A Distributed Memory Implementation. J Chem Theory Comput 2024. [PMID: 39221855 DOI: 10.1021/acs.jctc.4c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
In order to alleviate the computational burden associated with superlinear compute scalings with molecular size in electron correlation methods, researchers have developed local correlation methods that wisely treat relatively small contributions as zeros but still yield accurate energy approximation. Such local correlation techniques can also be combined with parallel computing resources to obtain further efficiency and scalability. This work focuses on the distributed memory parallel implementation of a local correlation method for second order Mo̷ller-Plesset (MP2) theory. This method also only has a single threshold to control the dropping of terms and accuracy of different computing kernels in the algorithm. The process partitioning strategy and distributed parallel implementation with the message passing interface (MPI) are discussed. In particular, the algorithm relies on a fixed sparsity pattern matrix multiplication and a corresponding distributed conjugate gradient solver, which exhibits almost linear scaling in both strong and weak scaling analyses. Numerical experiments on a range of molecules, including linear chains and molecules with 2 and 3-dimensional characters, are reported. For example, with only 32 MPI ranks, this MP2 implementation can calculate the correlation energy of vancomycin in def2-TZVP basis within 0.003% accuracy (10-6.5 threshold) in half an hour, where the same problem is unfeasible to solve with sequential or pure shared memory implementations.
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Affiliation(s)
- Tianyi Shi
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zhenling Wang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Yang Liu
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xiaoye S Li
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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2
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Petrov K, Csóka J, Kállay M. Analytic Gradients for Density Fitting MP2 Using Natural Auxiliary Functions. J Phys Chem A 2024; 128:6566-6580. [PMID: 39074307 PMCID: PMC11317987 DOI: 10.1021/acs.jpca.4c02822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024]
Abstract
The natural auxiliary function (NAF) approach is an approximation to decrease the size of the auxiliary basis set required for quantum chemical calculations utilizing the density fitting technique. It has been proven efficient to speed up various correlation models, such as second-order Møller-Plesset (MP2) theory and coupled-cluster methods. Here, for the first time, we discuss the theory of analytic derivatives for correlation methods employing the NAF approximation on the example of MP2. A detailed algorithm for the gradient calculation with the NAF approximation is proposed in the framework of the method of Lagrange multipliers. To assess the effect of the NAF approximation on gradients and optimized geometric parameters, a series of benchmark calculations on small and medium-sized systems was performed. Our results demonstrate that, for MP2, sufficiently accurate gradients and geometries can be achieved with a moderate time reduction of 15-20% for both small and medium-sized molecules.
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Affiliation(s)
- Klára Petrov
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN−BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA−BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - József Csóka
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN−BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA−BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN−BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA−BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
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3
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Zheng Y, Ni Z, Wang Y, Li W, Li S. Analytical Gradient Using Cluster-in-Molecule RI-MP2 Method for the Geometry Optimizations of Large Systems. J Chem Theory Comput 2024; 20:3626-3636. [PMID: 38626287 DOI: 10.1021/acs.jctc.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
We present an efficient analytical energy gradient algorithm for the cluster-in-molecule resolution-of-identity second-order Møller-Plesset perturbation (CIM-RI-MP2) method based on the Lagrange multiplier method. Our algorithm independently constructs the Lagrangian formalism within each cluster, avoiding the solution of the coupled-perturbed Hartree-Fock (CPHF) equation for the whole system. Due to this feature, the computational cost of the CIM-RI-MP2 gradients is much lower than that of other local MP2 algorithms. Benchmark calculations of several molecules containing up to 312 atoms demonstrate the general applicability of our CIM-RI-MP2 gradient algorithm. The optimized structure of a 244-atom molecule using the CIM-RI-MP2 method with the cc-pVDZ basis set is in good agreement with the corresponding crystal structure. A single-point gradient calculation conducted for a molecular cage containing 972 atoms and 9612 basis functions takes 48 h on 25 nodes, utilizing a total of 600 CPU cores. The present CIM-RI-MP2 gradient program is applicable for obtaining the optimized geometries of large systems with hundreds of atoms.
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Affiliation(s)
- Yang Zheng
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Zhigang Ni
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Yuqi Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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4
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Stocks R, Palethorpe E, Barca GMJ. High-Performance Multi-GPU Analytic RI-MP2 Energy Gradients. J Chem Theory Comput 2024; 20:2505-2519. [PMID: 38456899 DOI: 10.1021/acs.jctc.3c01424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
This article presents a novel algorithm for the calculation of analytic energy gradients from second-order Møller-Plesset perturbation theory within the Resolution-of-the-Identity approximation (RI-MP2), which is designed to achieve high performance on clusters with multiple graphical processing units (GPUs). The algorithm uses GPUs for all major steps of the calculation, including integral generation, formation of all required intermediate tensors, solution of the Z-vector equation and gradient accumulation. The implementation in the EXtreme Scale Electronic Structure System (EXESS) software package includes a tailored, highly efficient, multistream scheduling system to hide CPU-GPU data transfer latencies and allows nodes with 8 A100 GPUs to operate at over 80% of theoretical peak floating-point performance. Comparative performance analysis shows a significant reduction in computational time relative to traditional multicore CPU-based methods, with our approach achieving up to a 95-fold speedup over the single-node performance of established software such as Q-Chem and ORCA. Additionally, we demonstrate that pairing our implementation with the molecular fragmentation framework in EXESS can drastically lower the computational scaling of RI-MP2 gradient calculations from quintic to subquadratic, enabling further substantial savings in runtime while retaining high numerical accuracy in the resulting gradients.
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Affiliation(s)
- Ryan Stocks
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Elise Palethorpe
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Giuseppe M J Barca
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
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5
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Pham BQ, Carrington L, Tiwari A, Leang SS, Alkan M, Bertoni C, Datta D, Sattasathuchana T, Xu P, Gordon MS. Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller-Plesset perturbation method. J Chem Phys 2023; 158:2887208. [PMID: 37114705 DOI: 10.1063/5.0143424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller-Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ∼0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | | | | | - Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Colleen Bertoni
- Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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6
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Aroeira GJR, Davis MM, Turney JM, Schaefer HF. Fermi.jl: A Modern Design for Quantum Chemistry. J Chem Theory Comput 2022; 18:677-686. [PMID: 34978451 DOI: 10.1021/acs.jctc.1c00719] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Approximating molecular wave functions involves heavy numerical effort; therefore, codes for such tasks are written completely or partially in efficient languages such as C, C++, and Fortran. While these tools are dominant throughout quantum chemistry packages, the efficient development of new methods is often hindered by the complexity associated with code development. In order to ameliorate this scenario, some software packages take a dual approach where a simpler, higher-level language, such as Python, substitutes the traditional ones wherever performance is not critical. Julia is a novel, dynamically typed, programming language that aims to solve this two-language problem. It gained attention because of its modern and intuitive design, while still being highly optimized to compete with "low-level" languages. Recently, some chemistry-related projects have emerged exploring the capabilities of Julia. Herein, we introduce the quantum chemistry package Fermi.jl, which contains the first implementations of post-Hartree-Fock methods written in Julia. Its design makes use of many Julia core features, including multiple dispatch, metaprogramming, and interactive usage. Fermi.jl is a modular package, where new methods and implementations can be easily added to the existing code. Furthermore, it is designed to maximize code reusability by relying on general functions with specialized methods for particular cases. The feasibility of the project is explored through evaluating the performance of popular ab initio methods. It is our hope that this project motivates the usage of Julia within the community and brings new contributions into Fermi.jl.
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Affiliation(s)
- Gustavo J R Aroeira
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Matthew M Davis
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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7
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Szabó PB, Csóka J, Kállay M, Nagy PR. Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications. J Chem Theory Comput 2021; 17:2886-2905. [PMID: 33819030 PMCID: PMC8154337 DOI: 10.1021/acs.jctc.1c00093] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A linear-scaling
local second-order Møller–Plesset
(MP2) method is presented for high-spin open-shell molecules based
on restricted open-shell (RO) reference functions. The open-shell
local MP2 (LMP2) approach inherits the iteration- and redundancy-free
formulation and the completely integral-direct, OpenMP-parallel, and
memory and disk use economic algorithms of our closed-shell LMP2 implementation.
By utilizing restricted local molecular orbitals for the demanding
integral transformation step and by introducing a novel long-range
spin-polarization approximation, the computational cost of RO-LMP2
approaches that of closed-shell LMP2. Extensive benchmarks were performed
for reactions of radicals, ionization potentials, as well as spin-state
splittings of carbenes and transition-metal complexes. Compared to
the conventional MP2 reference for systems of up to 175 atoms, local
errors of at most 0.1 kcal/mol were found, which are well below the
intrinsic accuracy of MP2. RO-LMP2 computations are presented for
challenging protein models of up to 601 atoms and 11 000 basis
functions, which involve either spin states of a complexed iron ion
or a highly delocalized singly occupied orbital. The corresponding
runtimes of 9–15 h obtained with a single, many-core CPU demonstrate
that MP2, as well as spin-scaled MP2 and double-hybrid density functional
methods, become widely accessible for open-shell systems of unprecedented
size and complexity.
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Affiliation(s)
- P Bernát Szabó
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - József Csóka
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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8
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Lew-Yee JFH, Piris M, M Del Campo J. Resolution of the identity approximation applied to PNOF correlation calculations. J Chem Phys 2021; 154:064102. [PMID: 33588540 DOI: 10.1063/5.0036404] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this work, the required algebra to employ the resolution of the identity approximation within the Piris Natural Orbital Functional (PNOF) is developed, leading to an implementation named DoNOF-RI. The arithmetic scaling is reduced from fifth-order to fourth-order, and the memory scaling is reduced from fourth-order to third-order, allowing significant computational time savings. After the DoNOF-RI calculation has fully converged, a restart with four-center electron repulsion integrals can be performed to remove the effect of the auxiliary basis set incompleteness, quickly converging to the exact result. The proposed approach has been tested on cycloalkanes and other molecules of general interest to study the numerical results, as well as the speed-ups achieved by PNOF7-RI when compared with PNOF7.
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Affiliation(s)
- Juan Felipe Huan Lew-Yee
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City C.P. 04510, Mexico
| | - Mario Piris
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain; Euskal Herriko Unibertsitatea (UPV/EHU), PK 1072, 20080 Donostia, Euskadi, Spain; and Basque Foundation for Science (IKERBASQUE), 48009 Bilbao, Euskadi, Spain
| | - Jorge M Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City C.P. 04510, Mexico
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9
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Calvin JA, Peng C, Rishi V, Kumar A, Valeev EF. Many-Body Quantum Chemistry on Massively Parallel Computers. Chem Rev 2020; 121:1203-1231. [DOI: 10.1021/acs.chemrev.0c00006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Justus A. Calvin
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chong Peng
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Varun Rishi
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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10
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Gordon MS, Windus TL. Editorial: Modern Architectures and Their Impact on Electronic Structure Theory. Chem Rev 2020; 120:9015-9020. [DOI: 10.1021/acs.chemrev.0c00700] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Theresa L. Windus
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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11
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Poole D, Galvez Vallejo JL, Gordon MS. A New Kid on the Block: Application of Julia to Hartree–Fock Calculations. J Chem Theory Comput 2020; 16:5006-5013. [DOI: 10.1021/acs.jctc.0c00337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Jorge L. Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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12
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Barca GMJ, McKenzie SC, Bloomfield NJ, Gilbert ATB, Gill PMW. Q-MP2-OS: Møller-Plesset Correlation Energy by Quadrature. J Chem Theory Comput 2020; 16:1568-1577. [PMID: 31972086 DOI: 10.1021/acs.jctc.9b01142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a quadrature-based algorithm for computing the opposite-spin component of the MP2 correlation energy which scales quadratically with basis set size and is well-suited to large-scale parallelization. The key ideas, which are rooted in the earlier work of Hirata and co-workers, are to abandon all two-electron integrals, recast the energy as a seven-dimensional integral, approximate that integral by quadrature, and employ a cutoff strategy to minimize the number of intermediate quantities. We discuss our implementation in detail and show that it parallelizes almost perfectly on 840 cores for cyclosporine (a molecule with roughly 200 atoms), exhibits [Formula: see text] scaling for a sequence of polyglycines, and is principally limited by the accuracy of its quadrature.
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Affiliation(s)
- Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Simon C McKenzie
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia.,Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nathaniel J Bloomfield
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Andrew T B Gilbert
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Peter M W Gill
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
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13
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Yoshikawa T, Komoto N, Nishimura Y, Nakai H. GPU-Accelerated Large-Scale Excited-State Simulation Based on Divide-and-Conquer Time-Dependent Density-Functional Tight-Binding. J Comput Chem 2019; 40:2778-2786. [PMID: 31441083 DOI: 10.1002/jcc.26053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 01/09/2023]
Abstract
The present study implemented the divide-and-conquer time-dependent density-functional tight-binding (DC-TDDFTB) code on a graphical processing unit (GPU). The DC method, which is a linear-scaling scheme, divides a total system into several fragments. By separately solving local equations in individual fragments, the DC method could reduce slow central processing unit (CPU)-GPU memory access, as well as computational cost, and avoid shortfalls of GPU memory. Numerical applications confirmed that the present code on GPU significantly accelerated the TDDFTB calculations, while maintaining accuracy. Furthermore, the DC-TDDFTB simulation of 2-acetylindan-1,3-dione displays excited-state intramolecular proton transfer and provides reasonable absorption and fluorescence energies with the corresponding experimental values. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Nana Komoto
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto, 615-8520, Japan
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14
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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15
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Maitra R. Dynamically adjustable spin component scaled second order Møller-Plesset perturbation theory for strongly correlated molecular systems. J Chem Phys 2018; 149:204107. [PMID: 30501233 DOI: 10.1063/1.5051516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a novel spin-component scaled Møller-Plesset second order (MP2) perturbation theory [S. Grimme, J. Chem. Phys. 118, 9095 (2003)] in which the singlet and triplet correlation channels are dressed in a dynamical manner over the entire molecular potential energy surface. In order to strike the right balance between the short and long range correlation, the different correlation channels are scaled by two complementary functions without introducing any external parameter: while the singlet channel contribution to correlation energy is attenuated with increasing strong correlation of the system, the triplet channel contribution is amplified. We have justified our approach from physical reasoning as well as a few numerical examples with some difficult systems, like symmetric stretching of water and nitrogen molecules, which clearly demonstrate the efficacy of this method in describing the molecular potential energy surface, even in the strongly correlated regions where the conventional MP2 and its other variants disastrously fail.
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Affiliation(s)
- Rahul Maitra
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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16
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Liu KY, Herbert JM. Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs. J Chem Phys 2017; 147:161729. [DOI: 10.1063/1.4986110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kuan-Yu Liu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Cooper B, Girdlestone S, Burovskiy P, Gaydadjiev G, Averbukh V, Knowles PJ, Luk W. Quantum Chemistry in Dataflow: Density-Fitting MP2. J Chem Theory Comput 2017; 13:5265-5272. [PMID: 29019679 DOI: 10.1021/acs.jctc.7b00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the use of dataflow technology in the computation of the correlation energy in molecules at the Møller-Plesset perturbation theory (MP2) level. Specifically, we benchmark density fitting (DF)-MP2 for as many as 168 atoms (in valinomycin) and show that speed-ups between 3 and 3.8 times can be achieved when compared to the MOLPRO package run on a single CPU. Acceleration is achieved by offloading the matrix multiplications steps in DF-MP2 to Dataflow Engines (DFEs). We project that the acceleration factor could be as much as 24 with the next generation of DFEs.
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Affiliation(s)
- Bridgette Cooper
- Department of Physics, Blackett Laboratory, Imperial College London , Prince Consort Road, SW7 2AZ London, United Kingdom
| | | | | | | | - Vitali Averbukh
- Department of Physics, Blackett Laboratory, Imperial College London , Prince Consort Road, SW7 2AZ London, United Kingdom
| | - Peter J Knowles
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Wayne Luk
- Department of Computing, Imperial College London , 180 Queen's Gate, SW7 2AZ London, United Kingdom
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Kjærgaard T, Baudin P, Bykov D, Kristensen K, Jørgensen P. The divide–expand–consolidate coupled cluster scheme. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1319] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Pablo Baudin
- Department of ChemistryAarhus UniversityAarhusDenmark
| | - Dmytro Bykov
- Department of ChemistryAarhus UniversityAarhusDenmark
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Eriksen JJ. Efficient and portable acceleration of quantum chemical many-body methods in mixed floating point precision using OpenACC compiler directives. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1271155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Janus J. Eriksen
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, D-55128 Mainz, Germany
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20
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Bykov D, Kjaergaard T. The GPU-enabled divide-expand-consolidate RI-MP2 method (DEC-RI-MP2). J Comput Chem 2016; 38:228-237. [DOI: 10.1002/jcc.24678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/27/2016] [Accepted: 11/01/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Dmytro Bykov
- Department of Chemistry; qLeap Center for Theoretical Chemistry, University of Aarhus; DK-8000 Århus C Denmark
| | - Thomas Kjaergaard
- Department of Chemistry; qLeap Center for Theoretical Chemistry, University of Aarhus; DK-8000 Århus C Denmark
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