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ACS symposium series

Parallel Implementation of the Electronic Structure Code GAMESS

Theresa L. Windus, Michael W. I. Schmidt, Mark S. Gordon

Published May 17, 1995• 7 citations
Publisher

Abstract

This paper outlines various tools and techniques for the parallelization of quantum chemistry codes; in particular, for the electronic structure code GAMESS. A general overview of the parallel capabilities of GAMESS are also presented. The parallelization of quantum chemistry codes has become a very active area of research over the last decade( 1, 2, 3, 4 ). Until recently, most of this research has dealt with self-consistent field (SCF) theory( 1 ). However, in the last few years parallel implementations of post-SCF methods have been presented ( 2 ). Most of the post-SCF methods and analytic Hessians for SCF wavefunctions face the substantial problem of parallelizing the atomic orbital (AO) integral to molecular orbital (MO) integral transformation ( 3 ). The objective of this paper is to provide general information about the parallel implementation of GAMESS. The following sections are presented in this paper: (A) a brief overview of the functionality of the ab initio code GAMESS (General Atomic and Molecular Electronic Structure System); (B) a short discussion of the model, software, and general ideas used to parallelize GAMESS; (C) spécifics concerning the parallelization of the SCF; (D) discussion concerning the AO to MO integral transformation; (E) the transformation as applied to multi-configuration SCF (MCSCF); (F) the transformation as applied to analytic Hessians; (G) a brief overview of the parallel MP2 code; and (H) conclusions and future areas of research will be discussed.

DOI
10.1021/bk-1995-0592.ch002

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This paper outlines various tools and techniques for the parallelization of quantum chemistry codes; in particular, for the electronic structure code GAMESS. A general overview of the parallel capabilities of GAMESS are also presented. The parallelization of quantum chemistry codes has become a very active area of research over the last decade( 1, 2, 3, 4 ). Until recently, most of this research has dealt with self-consistent field (SCF) theory( 1 ). However, in the last few years parallel implementations of post-SCF methods have been presented ( 2 ). Most of the post-SCF methods and analytic Hessians for SCF wavefunctions face the substantial problem of parallelizing the atomic orbital (AO) integral to molecular orbital (MO) integral transformation ( 3 ). The objective of this paper is to provide general information about the parallel implementation of GAMESS. The following sections are presented in this paper: (A) a brief overview of the functionality of the ab initio code GAMESS (General Atomic and Molecular Electronic Structure System); (B) a short discussion of the model, software, and general ideas used to parallelize GAMESS; (C) spécifics concerning the parallelization of the SCF; (D) discussion concerning the AO to MO integral transformation; (E) the transformation as applied to multi-configuration SCF (MCSCF); (F) the transformation as applied to analytic Hessians; (G) a brief overview of the parallel MP2 code; and (H) conclusions and future areas of research will be discussed.
Advances in computer hardware have pushed forward the size of chemical investigations that are accessible using quantum chemistry. However, because state-of-the-art quantum chemistry methods scale as N 5 - N7, the hardware advances can only take us so far. A key advance in the past decade has been the development of scalable (parallel) codes for highly correlated wavefunctions. Following a summary of the methods used in our approach to parallelism in GAMESS (General Atomic and Molecular Electronic Structure System), several applications that emphasize the efficiacy of scalable codes will be discussed. These include the prediction of potential new fuels, the study of new materials with desirable properties and the study of species of biological importance
ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.
We demonstrate the use of graphical processing units (GPUs) to carry out complete self-consistent-field calculations for molecules with as many as 453 atoms (2131 basis functions). Speedups ranging from 28× to 650× are achieved as compared to a mature third-party quantum chemistry program (GAMESS) running on a traditional CPU. The computational organization used to construct the Coulomb and exchange operators is discussed. We also present results using three GPUs in parallel, combining coarse and fine-grained parallelism.
We present here a set of algorithms that completely rewrites the Hartree-Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS-US, GAMESS-UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6-31G Self-Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one- and two-electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc.
The first chapter in this thesis describes the theoretical framework that underlies much of electronic structure theory. The second chapter provides a review of the modern state of the intersection between electronic structure theory and high-performance computing. The next four chapters describe the development and implementation of new code into the GAMESS software package that utilizes Graphics Processing Units (GPUs) to achieve optimal performance. Chapter Three discusses an initial implementation of the GPU-driven Fock build step for the Restricted Hartree-Fock (RHF) method and the subsequent performance analysis on the Summit supercomputer. Chapter Four describes further developments to the aforementioned GPU-driven RHF Fock build code. Chapter Five discusses the extension of the GPU-driven RHF Fock build algorithm to the entirety of the Self-Consistent Field (SCF) process, which enables multiple steps of the SCF process to utilize GPUs. Chapter Six discusses the development of a new, GPU-driven algorithm for the Møller-Plesset Second-Order Perturbation Theory method (MP2) using the Resolution of the Identity (RI) and a subsequent performance analysis of the new RI-MP2 algorithm on the Summit Supercomputer. The next two chapters discuss the development of JuliaChem, a new electronic structure theory software package implemented in the Julia programming language. Chapter Seven provides an initial performance assessment of the RHF SCF algorithm implemented in Julia compared to GAMESS. Chapter Eight describes further algorithmic developments to the JuliaChem RHF algorithm and provides a performance analysis compared to modern developments in the GAMESS code. Chapter Nine provides an analysis of the ethylenedione molecule and its inherently unstable nature using multiple theoretical methods. Chapter Ten, the final chapter of the dissertation, provides final concluding thoughts.
Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree-Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency.