skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller–Plesset perturbation method

Journal Article · · Journal of Chemical Physics
DOI:https://doi.org/10.1063/5.0143424· OSTI ID:1986175
ORCiD logo [1];  [2];  [2];  [2];  [1]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Ames Lab., and Iowa State Univ., Ames, IA (United States)
  2. EP Analytics 2, San Diego, CA (United States)
  3. Argonne National Laboratory (ANL), Argonne, IL (United States)
+ Show Author Affiliations

Here, 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.

Research Organization:
Ames Laboratory (AMES), Ames, IA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-07CH11358; AC02-06CH11357
OSTI ID:
1986175
Report Number(s):
IS-J-11,078; TRN: US2402978
Journal Information:
Journal of Chemical Physics, Vol. 158, Issue 16; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English

References (46)

Reduced scaling in electronic structure calculations using Cholesky decompositions journal June 2003
Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Møller-Plesset perturbation theory journal July 2012
Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods † journal August 2010
Simplifications in the generation and transformation of two-electron integrals in molecular calculations journal October 1977
Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions journal April 2023
Tensor hypercontraction. II. Least-squares renormalization journal December 2012
A Massively Parallel Implementation of the CCSD(T) Method Using the Resolution-of-the-Identity Approximation and a Hybrid Distributed/Shared Memory Parallelization Model journal July 2021
Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid-Distributed/Shared Memory Programming Model journal January 2020
Massively parallel algorithm and implementation of RI-MP2 energy calculation for peta-scale many-core supercomputers journal September 2016
Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications book January 2011
An effective fragment method for modeling solvent effects in quantum mechanical calculations journal August 1996
Use of approximate integrals in ab initio theory. An application in MP2 energy calculations journal June 1993
Fast linear scaling second-order Møller-Plesset perturbation theory (MP2) using local and density fitting approximations journal May 2003
Coulombic potential energy integrals and approximations journal May 1973
Analytic Gradients for the Effective Fragment Molecular Orbital Method journal September 2016
Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations journal August 2017
Fully Integrated Effective Fragment Molecular Orbital Method journal April 2013
Accelerating Resolution-of-the-Identity Second-Order Møller−Plesset Quantum Chemistry Calculations with Graphical Processing Units † journal March 2008
The Fragment Molecular Orbital Method book January 2009
Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry journal April 2013
MPI/OpenMP Hybrid Parallel Algorithm of Resolution of Identity Second-Order Møller–Plesset Perturbation Calculation for Massively Parallel Multicore Supercomputers journal November 2013
Application of resolution of identity approximation of second-order Møller–Plesset perturbation theory to three-body fragment molecular orbital method journal August 2011
Hybrid RHF/MP2 Geometry Optimizations with the Effective Fragment Molecular Orbital Method journal February 2014
The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds journal July 2012
Compressing the Four-Index Two-Electron Repulsion Integral Matrix using the Resolution-of-the-Identity Approximation Combined with the Rank Factorization Approximation journal February 2019
Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD) journal January 2010
MPI/OpenMP hybrid parallel algorithm for resolution of identity second-order Møller-Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers journal January 2017
Tensor Hypercontraction Equation-of-Motion Second-Order Approximate Coupled Cluster: Electronic Excitation Energies in O(N4) Time journal July 2013
Fragment molecular orbital method: application to polypeptides journal March 2000
Pair interaction molecular orbital method: an approximate computational method for molecular interactions journal October 1999
Application of second-order Møller–Plesset perturbation theory with resolution-of-identity approximation to periodic systems journal November 2010
Hybrid Distributed/Shared Memory Model for the RI-MP2 Method in the Fragment Molecular Orbital Framework journal September 2019
RI-MP2: optimized auxiliary basis sets and demonstration of efficiency journal September 1998
Self-consistent molecular-orbital methods. 22. Small split-valence basis sets for second-row elements journal May 1982
Theoretical development of the fragment molecular orbital (FMO) method book January 2006
Fragmentation Methods: A Route to Accurate Calculations on Large Systems journal August 2011
PDG: A Composite Method Based on the Resolution of the Identity journal October 2021
On the Beebe-Linderberg two-electron integral approximation journal December 1986
Communication: Tensor hypercontraction. III. Least-squares tensor hypercontraction for the determination of correlated wavefunctions journal December 2012
Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method journal March 2013
On the Correlation Problem in Atomic and Molecular Systems. Calculation of Wavefunction Components in Ursell‐Type Expansion Using Quantum‐Field Theoretical Methods journal December 1966
Quartic scaling second-order approximate coupled cluster singles and doubles via tensor hypercontraction: THC-CC2 journal March 2013
Note on an Approximation Treatment for Many-Electron Systems journal October 1934
RI-MP2: first derivatives and global consistency journal October 1997
Integral approximations for LCAO-SCF calculations journal October 1993
Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules journal March 1972

Similar Records

Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions
Journal Article · Mon Apr 03 00:00:00 EDT 2023 · Journal of Chemical Theory and Computation · OSTI ID:1986175
Systematically Improvable Tensor Hypercontraction: Interpolative Separable Density-Fitting for Molecules Applied to Exact Exchange, Second- and Third-Order Møller–Plesset Perturbation Theory
Journal Article · Tue Dec 03 00:00:00 EST 2019 · Journal of Chemical Theory and Computation · OSTI ID:1986175
Improving efficiency of semi‐direct møller–plesset second‐order perturbation methods through oversubscription on multiple nodes
Journal Article · Tue Jun 04 00:00:00 EDT 2019 · Journal of Computational Chemistry · OSTI ID:1986175
+1 more

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY