Novel Computer Architectures and Quantum Chemistry.

Electronic structure theory (especially quantum chemistry) has thrived and has become increasingly relevant to a broad spectrum of scientific endeavors as the sophistication of both computer architectures and software engineering has advanced. This article provides a brief history of advances in both hardware and software, from the early days of IBM mainframes to the current emphasis on accelerators and modern programming practices.

[1]  Yihan Shao,et al.  Accelerating resolution-of-the-identity second-order Møller-Plesset quantum chemistry calculations with graphical processing units. , 2008, The journal of physical chemistry. A.

[2]  Ivan S. Ufimtsev,et al.  An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units. , 2015, The Journal of chemical physics.

[3]  Kazuya Ishimura,et al.  A new parallel algorithm of MP2 energy calculations , 2006, J. Comput. Chem..

[4]  Benjamin G. Levine,et al.  Nanoscale multireference quantum chemistry: full configuration interaction on graphical processing units. , 2015, Journal of chemical theory and computation.

[5]  Theresa L. Windus,et al.  Components for integral evaluation in quantum chemistry , 2008, J. Comput. Chem..

[6]  Alan Edelman,et al.  Julia: A Fresh Approach to Numerical Computing , 2014, SIAM Rev..

[7]  Ivan S. Ufimtsev,et al.  Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs). , 2011, Journal of chemical theory and computation.

[8]  FRANCESCO AQUILANTE,et al.  MOLCAS 7: The Next Generation , 2010, J. Comput. Chem..

[9]  Mark S. Gordon,et al.  Mixed-precision evaluation of two-electron integrals by Rys quadrature , 2012, Comput. Phys. Commun..

[10]  Rolf Hempel,et al.  The MPI Message Passing Interface Standard , 1994 .

[11]  Sandeep Sharma,et al.  PySCF: the Python‐based simulations of chemistry framework , 2018 .

[12]  T. Martínez,et al.  Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction. , 2017, The Journal of chemical physics.

[13]  Weiguo Liu,et al.  Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA , 2008, Comput. Phys. Commun..

[14]  M. Mitchell Waldrop,et al.  The chips are down for Moore’s law , 2016, Nature.

[15]  Alán Aspuru-Guzik,et al.  Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units , 2010, Computing in Science & Engineering.

[16]  Yoshifumi Nishimura,et al.  GPU‐Accelerated Large‐Scale Excited‐State Simulation Based on Divide‐and‐Conquer Time‐Dependent Density‐Functional Tight‐Binding , 2019, J. Comput. Chem..

[17]  Ilya Kaliman,et al.  LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library , 2013, J. Comput. Chem..

[18]  Torvald Riegel,et al.  Evaluation of AMD's advanced synchronization facility within a complete transactional memory stack , 2010, EuroSys '10.

[19]  Yong Dou,et al.  FPGA Implementation of Variable-Precision Floating-Point Arithmetic , 2011, APPT.

[20]  György Cserey,et al.  The BRUSH algorithm for two-electron integrals on GPU , 2015 .

[21]  Robert J. Harrison,et al.  Portable tools and applications for parallel computers , 1991 .

[22]  Edmond Chow,et al.  Horizontal vectorization of electron repulsion integrals , 2016, J. Comput. Chem..

[23]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system , 2008, IBM J. Res. Dev..

[24]  Jing Zhang,et al.  Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences , 2013 .

[25]  Thom H. Dunning,et al.  Gaussian basis sets for use in correlated molecular calculations. V. Core-valence basis sets for boron through neon , 1995 .

[26]  J. Daniel Gezelter.  Open Source and Open Data Should Be Standard Practices. , 2015, The journal of physical chemistry letters.

[27]  Peter R. Taylor,et al.  Chemical Calculations on Cray Computers , 1990 .

[28]  Martin C. Herbordt,et al.  FPGA HPC using OpenCL: Case Study in 3D FFT , 2018, HEART.

[29]  Richard M. Russell,et al.  The CRAY-1 computer system , 1978, CACM.

[30]  F. Matthias Bickelhaupt,et al.  Chemistry with ADF , 2001, J. Comput. Chem..

[31]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation. , 2008, Journal of chemical theory and computation.

[32]  Matthew L. Leininger,et al.  Psi4: an open‐source ab initio electronic structure program , 2012 .

[33]  Pascal Bouvry,et al.  Performance Evaluation and Energy Efficiency of High-Density HPC Platforms Based on Intel, AMD and ARM Processors , 2013, EE-LSDS.

[34]  Zvonko G. Vranesic,et al.  Field-Programmable Gate Arrays , 1992 .

[35]  A heterogeneous CPU + GPU algorithm for variational two-electron reduced-density matrix driven complete active space self-consistent field theory. , 2019, Journal of chemical theory and computation.

[36]  Jörg Kussmann,et al.  Pre-selective screening for matrix elements in linear-scaling exact exchange calculations. , 2013, The Journal of chemical physics.

[37]  Felipe Zapata,et al.  Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table , 2016, J. Comput. Chem..

[38]  Angela K. Wilson,et al.  Gaussian basis sets for use in correlated molecular calculations. X. The atoms aluminum through argon revisited , 2001 .

[39]  Brian E. Smith,et al.  Performance Effects of Node Mappings on the IBM BlueGene/L Machine , 2005, Euro-Par.

[40]  Jörg Kussmann,et al.  Preselective Screening for Linear-Scaling Exact Exchange-Gradient Calculations for Graphics Processing Units and General Strong-Scaling Massively Parallel Calculations. , 2015, Journal of chemical theory and computation.

[41]  Örjan Ekeberg,et al.  Brain-scale simulation of the neocortex on the IBM Blue Gene/L supercomputer , 2008, IBM J. Res. Dev..

[42]  Brad Gallagher,et al.  Terascale turbulence computation using the FLASH3 application framework on the IBM Blue Gene/L system , 2008, IBM J. Res. Dev..

[43]  David,et al.  Gaussian basis sets for use in correlated molecular calculations . Ill . The atoms aluminum through argon , 1999 .

[44]  T. H. Dunning.  Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[45]  Martin Head-Gordon,et al.  A method for two-electron Gaussian integral and integral derivative evaluation using recurrence relations , 1988 .

[46]  Kirk A. Peterson,et al.  Accurate correlation consistent basis sets for molecular core–valence correlation effects: The second row atoms Al–Ar, and the first row atoms B–Ne revisited , 2002 .

[47]  Roland Lindh,et al.  2MOLCAS as a development platform for quantum chemistry software , 2004 .

[48]  David E. Woon,et al.  Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties , 1994 .

[49]  Robert J. Harrison,et al.  FPGA acceleration of a quantum Monte Carlo application , 2008, Parallel Comput..

[50]  Benjamin G. Levine,et al.  A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units. , 2017, The Journal of chemical physics.

[51]  Richard A Friesner,et al.  Phaseless Auxiliary-Field Quantum Monte Carlo on Graphical Processing Units. , 2018, Journal of chemical theory and computation.

[52]  György Cserey,et al.  Calculation of quantum chemical two-electron integrals by applying compiler technology on GPU. , 2019, Journal of chemical theory and computation.

[53]  Mark S. Gordon,et al.  A new approach for second‐order perturbation theory , 2016, J. Comput. Chem..

[54]  Alistair P. Rendell,et al.  Distributed data parallel coupled‐cluster algorithm: Application to the 2‐hydroxypyridine/2‐pyridone tautomerism , 1993, J. Comput. Chem..

[55]  Benjamin G. Levine,et al.  Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors. , 2017, The Journal of chemical physics.

[56]  Jarek Nieplocha,et al.  Advances, Applications and Performance of the Global Arrays Shared Memory Programming Toolkit , 2006, Int. J. High Perform. Comput. Appl..

[57]  Xavier Andrade,et al.  Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods. , 2013, Journal of chemical theory and computation.

[58]  Peter Pulay,et al.  What Is the Price of Open-Source Software? , 2015, The journal of physical chemistry letters.

[59]  Vladimir Mironov,et al.  An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture , 2019, Int. J. High Perform. Comput. Appl..

[60]  Mark S. Gordon,et al.  New Multithreaded Hybrid CPU/GPU Approach to Hartree-Fock. , 2012, Journal of chemical theory and computation.

[61]  Laxmikant V. Kalé,et al.  Fine-grained parallelization of the Car - Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer , 2008, IBM J. Res. Dev..

[62]  Mark S. Gordon,et al.  Performance and energy efficiency analysis of 64-bit ARM using GAMESS , 2015, Co-HPC@SC.

[63]  Angela K. Wilson,et al.  Gaussian basis sets for use in correlated molecular calculations. VII. Valence, core-valence, and scalar relativistic basis sets for Li, Be, Na, and Mg , 2011 .

[64]  Christine M. Isborn,et al.  Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units , 2011, Journal of chemical theory and computation.

[65]  Thomas Müller,et al.  Columbus—a program system for advanced multireference theory calculations , 2011 .

[66]  Weiguo Liu,et al.  Molecular Dynamics Simulations on Commodity GPUs with CUDA , 2007, HiPC.

[67]  Takeshi Yoshikawa,et al.  Linear‐scaling self‐consistent field calculations based on divide‐and‐conquer method using resolution‐of‐identity approximation on graphical processing units , 2015, J. Comput. Chem..

[68]  Jean-François Méhaut,et al.  Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures. , 2009, The Journal of chemical physics.

[69]  A Eugene DePrince,et al.  Coupled Cluster Theory on Graphics Processing Units I. The Coupled Cluster Doubles Method. , 2011, Journal of chemical theory and computation.

[70]  Koji Yasuda,et al.  Two‐electron integral evaluation on the graphics processor unit , 2008, J. Comput. Chem..

[71]  Jörg Kussmann,et al.  Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units. , 2017, Journal of chemical theory and computation.

[72]  Koji Yasuda,et al.  Accelerating Density Functional Calculations with Graphics Processing Unit. , 2008, Journal of chemical theory and computation.

[73]  Thomas R. Furlani,et al.  A Parallel Direct SCF Method for Large Molecular Systems , 1996 .

[74]  Masha Sosonkina,et al.  Core and Uncore Joint Frequency Scaling Strategy , 2018 .

[75]  Todd J Martínez,et al.  Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity. , 2016, The Journal of chemical physics.

[76]  Lorenz S. Cederbaum,et al.  Accurate Quantum Chemistry in Single Precision Arithmetic: Correlation Energy. , 2011, Journal of chemical theory and computation.

[77]  So Hirata,et al.  Monte Carlo MP2 on Many Graphical Processing Units. , 2016, Journal of chemical theory and computation.

[78]  Maged M. Michael,et al.  Quantitative comparison of Hardware Transactional Memory for Blue Gene/Q, zEnterprise EC12, Intel Core, and POWER8 , 2015, 2015 ACM/IEEE 42nd Annual International Symposium on Computer Architecture (ISCA).

[79]  Ajay K. Royyuru,et al.  Blue Gene: A vision for protein science using a petaflop supercomputer , 2001, IBM Syst. J..

[80]  S. F. Nugent,et al.  The iPSC/2 direct-connect communications technology , 1988, C3P.

[81]  L. Dagum,et al.  OpenMP: an industry standard API for shared-memory programming , 1998 .

[82]  John M. Dennis,et al.  Scaling climate simulation applications on the IBM Blue Gene/L system , 2008, IBM J. Res. Dev..

[83]  Thomas Müller,et al.  High-level multireference methods in the quantum-chemistry program system COLUMBUS: Analytic MR-CISD and MR-AQCC gradients and MR-AQCC-LRT for excited states, GUGA spin–orbit CI and parallel CI density , 2001 .

[84]  Christoph R Jacob.  How Open Is Commercial Scientific Software? , 2016, The journal of physical chemistry letters.

[85]  Masha Sosonkina,et al.  Energy-Efficient Computational Chemistry: Comparison of x86 and ARM Systems. , 2015, Journal of chemical theory and computation.

[86]  Robert W. Numrich,et al.  Co-arrays in the next Fortran Standard , 2005, FORF.

[87]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics. , 2009, Journal of chemical theory and computation.

[88]  Kenneth M Merz,et al.  Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations. , 2013, Journal of chemical theory and computation.

[89]  Andrey Asadchev,et al.  Fast and Flexible Coupled Cluster Implementation. , 2013, Journal of chemical theory and computation.

[90]  Mark S Gordon,et al.  Quantum Chemical Calculations Using Accelerators: Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi. , 2014, Journal of chemical theory and computation.

[91]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation. , 2009, Journal of chemical theory and computation.

[92]  Jarek Nieplocha,et al.  Component‐based integration of chemistry and optimization software , 2004, Journal of computational chemistry.

[93]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[94]  Jörg Kussmann,et al.  Hybrid CPU/GPU Integral Engine for Strong-Scaling Ab Initio Methods. , 2017, Journal of chemical theory and computation.

[95]  Yuri Alexeev,et al.  Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method. , 2016, Journal of chemical theory and computation.

[96]  Koji Yasuda,et al.  Efficient calculation of two‐electron integrals for high angular basis functions , 2014 .

[97]  Beverly A. Sanders,et al.  Final Report: Super Instruction Architecture for Scalable Parallel Computations , 2013 .

[98]  Tjerk P. Straatsma,et al.  NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..