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化学学报

Single-precision CCSD and CCSD(T) Calculations with Density Fitting Approximations on Graphics Processing Units

Zhifan Wang, Bing He, Yanzhao Lu, Fan Wang

Published Jan 1, 2022• 5 citations
Publisher

Abstract

b ( a 成都师范学院 化学与生命科学学院/功能分子结构优化与应用四川省高校重点实验室 成都 611130) ( b 四川大学 原子与分子物理研究所 成都 610064) 摘要 作者此前工作表明, 在耦合簇 CCSD (Coupled-Cluster approaches within the singles and doubles approximation)与 CCSD(T) (CCSD approaches augmented by a perturbative treatment of triple excitations)计算中结合单精度数与消费型图形 处理单元(GPU), 可以显著提高计算速度.然而由于 CCSD(T)计算对内存的巨大需求以及消费型 GPU 的内存限制, 在 利用消费型 GPU 进行加速时, 不考虑利用空间对称性的情况下, 此前开发的 CCSD(T)程序仅能用于计算 300~400 个 基函数的体系.利用密度拟合(Density-Fitting, DF)处理双电子积分可以显著降低 CCSD(T)计算过程中的内存需求, 本 工作发展了基于密度拟合近似并结合单精度数进行运算的 DF-CCSD(T)程序, 该程序可用于包含 700 个基函数的无对 称性体系的单点能计算, 以及包含 1700 个基函数的有对称性体系.

DOI
10.6023/a22070313

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Efficient scalable implementations are presented for two single-reference coupled-cluster (CC) methods with non-iterative corrections for triple excitations, which accurately describe single bond dissociations in molecules in contrast to the standard CCSD(T) approach. These methods are (a) the completely renormalized coupled-cluster theory, CR-CC(2,3), and (b) the ΛCCSD(T) approach, the triples energy corrections in both of which are formulated using the left eigenvector of the CC similarity transformed Hamiltonian. The density fitting approximation is employed for factorizing the two-electron repulsion integrals (ERIs), which eliminates memory bottlenecks associated with the storage of the four-index ERIs by allowing an integral-direct algorithm. Massively parallel algorithms have been developed for the above methods within the GAMESS quantum chemistry program using a hybrid MPI and OpenMP based parallelization model. All compute-intensive steps in the CCSD amplitude and the left eigenvector equations, as well as the triples corrections in both methods, have been adapted to execute on graphical processing units (GPUs) using the OpenMP target directives. Performance of these codes is demonstrated on petascale supercomputers equipped with NVIDIA A100 GPUs. While the CR-CC(2,3) and ΛCCSD(T) computations take roughly twice as much time as the standard CCSD(T) method, the GPU-offloaded codes are shown to impart 3.5-5× accelerations relative to the CPU-only parallel codes, thereby significantly reducing the time-to-solution for the CR-CC(2,3) and ΛCCSD(T) methods.
Abstract A high‐performance implementation of the coupled‐cluster singles, doubles, and perturbative triples [CCSD(T)] is developed in the Massively Parallel Quantum Chemistry program. Novel features include: (1) reduced memory requirements via a density‐fitting (DF) CCSD implementation utilizing distributed lazy evaluation for tensors with more than two unoccupied indices and (2) the ability to utilize efficiently many‐core nodes (Intel Xeon Phi) and heterogeneous nodes with multiple NVIDIA GPUs on each node. All data that are greater than quadratic in the system size are distributed among processes. Excellent strong scaling is observed on distributed‐memory computers equipped with conventional CPUs, Intel Xeon Phi processors, and heterogeneous nodes with multiple NVIDIA GPUs Canonical CCSD(T) energies can be evaluated for systems containing 200 electrons and 1000 basis functions in a few days using a small size commodity cluster, with even larger computations possible on leadership‐class computing resources.
높아지는 Graphic Processing Unit(GPU)의 연산 성능과 GPU에서의 범용 프로그래밍을 위한 개발 환경의 개발, 보급으로 인해 GPU를 일반연산에 활용하는 연구가 활발히 진행되고 있다. 이와 같이 일반 연산에 활용되고 있는 GPU로 nVidia Tesla와 AMD/ATI의 FireStream 들이 있다. 특수 목적 연산 장치인 GPU를 일반 연산을 위해 프로그래밍하기 위해서는 그에 맞는 프로그램 개발 환경이 필요한데 nVidia에서 개발한 CUDA(Compute Unified Device Architecture) 환경은 자사의 GPU 프로그램 개발을 위해 제공되는 개발 환경이다. CUDA 개발 환경은 nVidia GPU 프로그래밍 뿐만 아니라 차세대 이종 병렬 프로그램 개발 환경의 공개 표준으로 논의되고 있는 OpenCL(Open Computing Language)와 유사한 특징을 보일 것으로 예상되기 때문에 그 중요성은 특정 GPU 에만 국한되지 않는다. 본 논문에서는 경로 적분 몬테 카를로 (Path Integral Monte Carlo) 방법을 CUDA 개발 환경을 사용하여 nVidia GPU 상에서 병렬화한 결과를 제시하였다.
An algorithm is presented for the coupled-cluster singles, doubles, and perturbative triples correction [CCSD(T)] method based on the density fitting or the resolution-of-the-identity (RI) approximation for performing calculations on heterogeneous computing platforms composed of multicore CPUs and graphics processing units (GPUs). The directive-based approach to GPU offloading offered by the OpenMP application programming interface has been employed to adapt the most compute-intensive terms in the RI-CCSD amplitude equations with computational costs scaling as O ( N O 2 N V 4 ), O ( N O 3 N V 3 ), and O ( N O 4 N V 2 ) (where N O and N V denote the numbers of correlated occupied and virtual orbitals, respectively) and the perturbative triples correction to execute on GPU architectures. The pertinent tensor contractions are performed using an accelerated math library such as cuBLAS or hipBLAS. Optimal strategies are discussed for splitting large data arrays into tiles to fit them into the relatively small memory space of the GPUs, while also minimizing the low-bandwidth CPU–GPU data transfers. The performance of the hybrid CPU–GPU RI-CCSD(T) code is demonstrated on pre-exascale supercomputers composed of heterogeneous nodes equipped with NVIDIA Tesla V100 and A100 GPUs and on the world’s first exascale supercomputer named “Frontier”, the nodes of which consist of AMD MI250X GPUs. Speedups within the range 4–8× relative to the recently reported CPU-only algorithm are obtained for the GPU-offloaded terms in the RI-CCSD amplitude equations. Applications to polycyclic aromatic hydrocarbons containing 16–66 carbon atoms demonstrate that the acceleration of the hybrid CPU–GPU code for the perturbative triples correction relative to the CPU-only code increases with the molecule size, attaining a speedup of 5.7× for the largest circumovalene molecule (C 66 H 20 ). The GPU-offloaded code enables the computation of the perturbative triples correction for the C 60 molecule using the cc-pVDZ/aug-cc-pVTZ-RI basis sets in 7 min on Frontier when using 12,288 AMD GPUs with a parallel efficiency of 83.1%.