用GPU加速相对论Dirac-Kohn-Sham方法:BERTHA和PyBERTHA的前百亿亿次实现。

IF 5.7 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
{"title":"用GPU加速相对论Dirac-Kohn-Sham方法:BERTHA和PyBERTHA的前百亿亿次实现。","authors":"Loriano Storchi, Laura Bellentani, Jeff Hammond, Sergio Orlandini, Leonardo Pacifici, Nicoló Antonini, Leonardo Belpassi","doi":"10.1021/acs.jctc.4c01759","DOIUrl":null,"url":null,"abstract":"<p><p>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 Au<sub>16</sub> in a single-point DKS energy calculation and up to 10 for the Au<sub>8</sub> 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.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"3460-3475"},"PeriodicalIF":5.7000,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Acceleration of the Relativistic Dirac-Kohn-Sham Method with GPU: A Pre-Exascale Implementation of BERTHA and PyBERTHA.\",\"authors\":\"Loriano Storchi, Laura Bellentani, Jeff Hammond, Sergio Orlandini, Leonardo Pacifici, Nicoló Antonini, Leonardo Belpassi\",\"doi\":\"10.1021/acs.jctc.4c01759\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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 Au<sub>16</sub> in a single-point DKS energy calculation and up to 10 for the Au<sub>8</sub> 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.</p>\",\"PeriodicalId\":45,\"journal\":{\"name\":\"Journal of Chemical Theory and Computation\",\"volume\":\" \",\"pages\":\"3460-3475\"},\"PeriodicalIF\":5.7000,\"publicationDate\":\"2025-04-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Theory and Computation\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jctc.4c01759\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/3/21 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Theory and Computation","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jctc.4c01759","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/3/21 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0

摘要

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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Acceleration of the Relativistic Dirac-Kohn-Sham Method with GPU: A Pre-Exascale Implementation of BERTHA and PyBERTHA.

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.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
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.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信