Acceleration of the Relativistic Dirac-Kohn-Sham Method with GPU: A Pre-Exascale Implementation of BERTHA and PyBERTHA.

IF 5.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Journal of Chemical Theory and Computation Pub Date : 2025-04-08 Epub Date: 2025-03-21 DOI:10.1021/acs.jctc.4c01759
Loriano Storchi, Laura Bellentani, Jeff Hammond, Sergio Orlandini, Leonardo Pacifici, Nicoló Antonini, Leonardo Belpassi
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Abstract

In this paper, we present the recent advances in the computation of the Dirac-Kohn-Sham (DKS) method of the BERTHA code. We show here that the simple underlined structure of the FORTRAN code also favors efficient porting of the code to GPUs, leading to a particularly efficient hybrid CPU/GPU implementation (OpenMP/OpenACC), where the most computationally intensive part for DKS matrix evaluation (three-center two-electron integrals evaluated via the McMurchie-Davidson scheme) is efficiently offloaded to the GPU via compiler directives based on the OpenACC programming model. This scheme in combination with the use of a linear algebra library optimized for GPUs (cuBLAS, cuSOLVER) significantly accelerates the DKS calculations. In addition, the low-level integral kernel developed here at FORTRAN level was used to port our real-time DKS (RT-TDDKS) implementation based on Python (PyBERTHART) for the utilization of the GPU. The results obtained on the new Tier-0 EuroHPC supercomputer (LEONARDO) of the CINECA Supercomputing Centre with a single NVIDIA A100 card are very satisfactory. We achieve a speedup up to 30 for Au16 in a single-point DKS energy calculation and up to 10 for the Au8 systems in an RT-TDDKS calculation, compared to our OpenMP (i.e., CPU only) parallel implementation (with 32 cores). The approach presented here is very general and, to our knowledge, represents the first port of a Python API to GPUs based on a FORTRAN kernel for the evaluation of two-electron integrals. The implementation is currently limited to the use of a single GPU accelerator, but future paths to an actual exascale implementation are discussed.

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用GPU加速相对论Dirac-Kohn-Sham方法:BERTHA和PyBERTHA的前百亿亿次实现。
本文介绍了BERTHA码的Dirac-Kohn-Sham (DKS)方法计算的最新进展。我们在这里展示了FORTRAN代码的简单带线结构也有利于有效地将代码移植到GPU,从而导致特别高效的CPU/GPU混合实现(OpenMP/OpenACC),其中DKS矩阵计算最密集的部分(通过mcmurkie - davidson方案评估的三中心双电子积分)通过基于OpenACC编程模型的编译器指令有效地卸载到GPU。该方案与针对gpu优化的线性代数库(cuBLAS, cuSOLVER)的使用相结合,显着加速了DKS计算。此外,在FORTRAN级别开发的低级积分内核用于移植基于Python (PyBERTHART)的实时DKS (RT-TDDKS)实现,以利用GPU。在CINECA超级计算中心的新一代Tier-0 EuroHPC超级计算机(LEONARDO)上使用单张NVIDIA A100卡获得了令人满意的结果。与我们的OpenMP(即仅CPU)并行实现(32核)相比,我们在单点DKS能量计算中实现了Au16的加速高达30,在RT-TDDKS计算中实现了Au8系统的加速高达10。这里提出的方法非常通用,据我们所知,它代表了基于FORTRAN内核的Python API到gpu的第一个端口,用于评估双电子积分。实现目前仅限于使用单个GPU加速器,但未来的路径,以实际的百亿亿级的实现进行了讨论。
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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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