Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
skip to main content
10.1145/3458817.3476160acmconferencesArticle/Chapter ViewAbstractPublication PagesscConference Proceedingsconference-collections
research-article
Open access

Accelerating all-electron ab initio simulation of raman spectra for biological systems

Published: 13 November 2021 Publication History

Abstract

Raman spectroscopy provides chemical and compositional information that can serve as a structural fingerprint for various materials. Therefore, simulations of Raman spectra, including both quantum perturbation analyses and ground-state calculations are of significant interest. However, highly accurate full quantum mechanical (QM) simulations of Raman spectra have previously been confined to small systems. For large systems such as biological materials, the computational cost of full QM simulations is extremely high, and their extension to such systems remains challenging. In the work described here, by employing robust new algorithms and advances in implementation for the many-core architectures, we are able to perform fast, accurate, and massively parallel full ab initio simulations of the Raman spectra of biological systems with excellent strong and weak scaling, thereby providing a starting point for applying QM approaches to structural studies of such systems.

Supplementary Material

MP4 File (Accelerating All-Electron Ab Initio Simulation of Raman Spectra for Biological Systems.mp4.mp4)
Presentation video

References

[1]
Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, Ville Havu, Xinguo Ren, Karsten Reuter, and Matthias Scheffler. Ab initio molecular simulations with numeric atom-centered orbitals. Comput. Phys. Commun., 180(11):2175--2196, November 2009.
[2]
Honghui Shang, Christian Carbon, Patrick Rinke, and Matthias Scheffler. Lattice dynamics calculations based on density-functional perturbation theory in real space. Computer Physics Communications, 215:26--46, jun 2017.
[3]
Honghui Shang, Nathaniel Raimbault, Patrick Rinke, Matthias Scheffler, Mariana Rossi, and Christian Carbogno. All-electron, real-space perturbation theory for homogeneous electric fields: theory, implementation, and application within DFT. New Journal of Physics, 20(7):073040, jul 2018.
[4]
Paolo Giannozzi, Stefano Baroni, Nicola Bonini, Matteo Calandra, Roberto Car, Carlo Cavazzoni, Davide Ceresoli, Guido L Chiarotti, Matteo Cococcioni, Ismaila Dabo, Andrea Dal Corso, Stefano de Gironcoli, Stefano Fabris, Guido Fratesi, Ralph Gebauer, Uwe Gerstmann, Christos Gougoussis, Anton Kokalj, Michele Lazzeri, Layla Martin-Samos, Nicola Marzari, Francesco Mauri, Riccardo Mazzarello, Stefano Paolini, Alfredo Pasquarello, Lorenzo Paulatto, Carlo Sbraccia, Sandro Scandolo, Gabriele Sclauzero, Ari P Seitsonen, Alexander Smogunov, Paolo Umari, and Renata M Wentzcovitch. Quantum espresso: a modular and open-source software project for quantum simulations of materials. Journal of Physics: Condensed Matter, 21(39):395502 (19pp), 2009.
[5]
G. Kresse and J. Hafner. Ab initio molecular dynamics for liquid metals. Phys. Rev. B, 47:558--561, Jan 1993.
[6]
Aldo H. Romero, Douglas C. Allan, Bernard Amadon, Gabriel Antonius, Thomas Applencourt, Lucas Baguet, Jordan Bieder, François Bottin, Johann Bouchet, Eric Bousquet, Fabien Bruneval, Guillaume Brunin, Damien Caliste, Michel Côté, Jules Denier, Cyrus Dreyer, Philippe Ghosez, Matteo Giantomassi, Yannick Gillet, Olivier Gingras, Donald R. Hamann, Geoffroy Hautier, François Jollet, Gérald Jomard, Alexandre Martin, Henrique P.C. Miranda, Francesco Naccarato, Guido Petretto, Nicholas A. Pike, Valentin Planes, Sergei Prokhorenko, Tonatiuh Rangel, Fabio Ricci, Gian Marco Rignanese, Miquel Royo, Massimiliano Stengel, Marc Torrent, Michiel J. Van Setten, Benoit Van Troeye, Matthieu J. Verstraete, Julia Wiktor, Josef W. Zwanziger, and Xavier Gonze. ABINIT: Overview and focus on selected capabilities. Journal of Chemical Physics, 152(12), 2020.
[7]
Thomas D. Kühne, Marcella Iannuzzi, Mauro Del Ben, Vladimir V. Rybkin, Patrick Seewald, Frederick Stein, Teodoro Laino, Rustam Z. Khaliullin, Ole Schütt, Florian Schiffmann, Dorothea Golze, Jan Wilhelm, Sergey Chulkov, Mohammad Hossein Bani-Hashemian, Valéry Weber, Urban Borštnik, Mathieu Taillefumier, Alice Shoshana Jakobovits, Alfio Lazzaro, Hans Pabst, Tiziano Müller, Robert Schade, Manuel Guidon, Samuel Andermatt, Nico Holmberg, Gregory K. Schenter, Anna Hehn, Augustin Bussy, Fabian Belleflamme, Gloria Tabacchi, Andreas Glöß, Michael Lass, Iain Bethune, Christopher J. Mundy, Christian Plessl, Matt Watkins, Joost VandeVondele, Matthias Krack, and Jürg Hutter. CP2K: An electronic structure and molecular dynamics software package -Quickstep: Efficient and accurate electronic structure calculations. Journal of Chemical Physics, 152(19), 2020.
[8]
Kurt Lejaeghere, Gustav Bihlmayer, T. Bjorkman, Peter Blaha, S. Blugel, Volker Blum, Damien Caliste, Ivano E Castelli, Stewart J Clark, Andrea Dal Corso, Stefano de Gironcoli, Thierry Deutsch, John Kay Dewhurst, Igor Di Marco, Claudia Draxl, M. Du ak, Olle Eriksson, José A Flores-Livas, Kevin F Garrity, Luigi Genovese, Paolo Giannozzi, Matteo Giantomassi, Stefan Goedecker, Xavier Gonze, O. Granas, E K U Gross, Andris Gulans, François Gygi, D R Hamann, Phil J Hasnip, N A W Holzwarth, D. Iu an, Dominik B Jochym, François Jollet, Daniel Jones, Georg Kresse, Klaus Koepernik, E. Kucukbenli, Yaroslav O Kvashnin, Inka L M Locht, Sven Lubeck, Martijn Marsman, Nicola Marzari, Ulrike Nitzsche, L. Nordstrom, Taisuke Ozaki, Lorenzo Paulatto, Chris J Pickard, Ward Poelmans, Matt IJ Probert, Keith Refson, Manuel Richter, G.-M. Rignanese, Santanu Saha, Matthias Scheffler, Martin Schlipf, Karlheinz Schwarz, Sangeeta Sharma, Francesca Tavazza, P. Thunstrom, Alexandre Tkatchenko, Marc Torrent, David Vanderbilt, Michiel J van Setten, Veronique Van Speybroeck, John M Wills, Jonathan R Yates, G.-X. Zhang, and Stefaan Cottenier. Reproducibility in density functional theory calculations of solids. Science, 351(6280):aad3000--aad3000, mar 2016.
[9]
Michael Frisch, Martin Head-Gordon, and John Pople. Direct analytic scf second derivatives and electric field properties. Chem. Phys., 141(2--3):189 -- 196, 1990.
[10]
Roberto Dovesi, Fabien Pascale, Bartolomeo Civalleri, Klaus Doll, Nicholas M. Harrison, Ian Bush, Philippe D'Arco, Yves Noël, Michel Rérat, Philippe Carbonnière, Mauro Causà, Simone Salustro, Valentina Lacivita, Bernard Kirtman, Anna Maria Ferrari, Francesco Silvio Gentile, Jacopo Baima, Mauro Ferrero, Raffaella Demichelis, and Marco De La Pierre. The CRYSTAL code, 1976--2020 and beyond, a long story. The Journal of chemical physics, 152(20):204111, 2020.
[11]
B Delley. An all-electron numerical method for solving the local density functional for polyatomic molecules. J. Chem. Phys., 92(1):508, 1990.
[12]
Sandra Luber and Markus Reiher. Theoretical raman optical activity study of the ß domain of rat metallothionein. Journal of Physical Chemistry B, 114(2):1057--1063, 2010.
[13]
Simone Salustro, Anna Maria Ferrari, Roberto Orlando, and Roberto Dovesi. Comparison between cluster and supercell approaches: the case of defects in diamond. Theoretical Chemistry Accounts, 136(4):1--13, 2017.
[14]
Petr Bouř, Jana Sopková, Lucie Bednárová, Petr Maloň, and Timothy A Keiderling. Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra. Journal of Computational Chemistry, 18(5):646--659, apr 1997.
[15]
Shigeki Yamamoto and Petr Bouř. Calculation of Vibrational Spectra of Large Molecules from Their Fragments, pages 181--197. Springer Singapore, Singapore, 2018.
[16]
Fabien Pascale, Simone Salustro, Anna Maria, Ferrari Michel, Rérat Philippe, and D Arco Roberto. The Infrared spectrum of very large (periodic) systems : global versus fragment strategies --- the case of three defects in diamond. Theoretical Chemistry Accounts, 137(12):1--7, 2018.
[17]
Noah S Bieler, Moritz P Haag, Christoph R Jacob, and Markus Reiher. Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. Journal of Chemical Theory and Computation, 7(6):1867--1881, jun 2011.
[18]
Shigeki Yamamoto, Xiaojun Li, Kenneth Ruud, and Petr Bouř. Transferability of Various Molecular Property Tensors in Vibrational Spectroscopy. Journal of Chemical Theory and Computation, 8(3):977--985, mar 2012.
[19]
Péter Pulay. Convergence acceleration of iterative sequences. the case of scf iteration. Chem. Phys. Lett., 73(2):393--398, 1980.
[20]
A. D. Becke. A multicenter numerical integration scheme for polyatomic molecules. J. Chem. Phys., 88(4):2547--2553, 1988.
[21]
Jon Baker, Jan Andzelm, Andrew Scheiner, and Bernard Delley. The effect of grid quality and weight derivatives in density functional calculations. J. Chem. Phys., 101(10):8894--8902, 1994.
[22]
Bernard Delley. High order integration schemes on the unit sphere. J. Comput. Chem., 17(9):1152--1155, 1996.
[23]
V. Havu, V. Blum, P. Havu, and M. Scheffler. Efficient integration for all-electron electronic structure calculation using numeric basis functions. J. Comput. Phys., 228(22):8367--8379, December 2009.
[24]
Bernard Delley. Fast calculation of electrostatics in crystals and large molecules. The Journal of Physical Chemistry, 100(15):6107--6110, 1996.
[25]
M. S. Lam and M. Wolf. A data locality optimizing algorithm. In Proceedings of the ACM SIGPLAN 1991 Conference on Programming Language Design and Implementation, PLDI 91, pages 30--44, New York, NY, USA, 1991. ACM.
[26]
S. Coleman and K. S. McKinley. Tile size selection using cache organization and data layout. In Proceedings of the ACM SIGPLAN 1995 Conference on Programming Language Design and Implementation, PLDI 95, pages 279--290, New York, NY, USA, 1995. ACM.
[27]
J. Liu, Y. Zhang, W. Ding, and M. T. Kandemir. On-chip cache hierarchy-aware tile scheduling form ulticore machines. In Proceedings of the 9th Annual IEEE/ACM International Symposium on Code Generation and Optimization, CGO 11, page 161--170, Chamonix, France, 2011. ACM.
[28]
S. Mehta, R. Garg, N. Trivedi, and P. Yew. Leveraging prefetching to boost performance of tiled codes. In Proceedings of the 2016 International Conference on Supercomputing, ISC 16, New York, NY, USA, 2016. ACM.
[29]
Mingchuan Wu, Ying Liu, Huimin Cui, Qingfu Wei, Quanfeng Li, Limin Li, Fang Lv, Jingling Xue, and Xiaobing Feng. Bandwidth-aware loop tiling for dma-supported scratchpad memory. In Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques, PACT '20, page 97--109, New York, NY, USA, 2020. Association for Computing Machinery.
[30]
W. Zhao, H. Fu, J. Fang, W. Zheng, L. Gan, and G. Yang. Optimizing convolutional neural networks on the sunway taihulight supercomputer. ACM Transactions on Architecture and Code Optimization (TACO), 15(1):1--26, 2018.
[31]
B. Khailany and B. Khailany. Cudadma: Optimizing gpu memory bandwidth via warp specialization. In High Performance Computing, Networking, Storage and Analysis, 2011.
[32]
A. Rygula, K. Majzner, K. M. Marzec, A. Kaczor, M. Pilarczyk, and M. Baranska. Raman spectroscopy of proteins: A review. Journal of Raman Spectroscopy, 44(8):1061--1076, 2013.
[33]
Holly J. Butler, Lorna Ashton, Benjamin Bird, Gianfelice Cinque, Kelly Curtis, Jennifer Dorney, Karen Esmonde-White, Nigel J. Fullwood, Benjamin Gardner, Pierre L. Martin-Hirsch, Michael J. Walsh, Martin R. McAinsh, Nicholas Stone, and Francis L. Martin. Using Raman spectroscopy to characterize biological materials. Nature Protocols, 11(4):664--687, 2016.
[34]
Manli Wang, Ruiyuan Cao, Leike Zhang, Xinglou Yang, Jia Liu, Mingyue Xu, Zhengli Shi, Zhihong Hu, Wu Zhong, and Gengfu Xiao. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, (January):2019--2021, 2020.

Cited By

View all
  • (2023)OpenCL-accelerated first-principles calculations of all-electron quantum perturbations on HPC resourcesFrontiers in Chemistry10.3389/fchem.2023.115689111Online publication date: 26-May-2023
  • (2023)Scalability and efficiency challenges for the exascale supercomputing system: practice of a parallel supporting environment on the Sunway exascale prototype system面对E级超算系统的可扩展性和效率挑战: 神威E级原型系统并行支撑环境的实践Frontiers of Information Technology & Electronic Engineering10.1631/FITEE.220041224:1(41-58)Online publication date: 23-Jan-2023
  • (2023)Portable and Scalable All-Electron Quantum Perturbation Simulations on Exascale SupercomputersProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3581784.3607085(1-13)Online publication date: 12-Nov-2023

Index Terms

  1. Accelerating all-electron ab initio simulation of raman spectra for biological systems
              Index terms have been assigned to the content through auto-classification.

              Recommendations

              Comments

              Information & Contributors

              Information

              Published In

              cover image ACM Conferences
              SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
              November 2021
              1493 pages
              ISBN:9781450384421
              DOI:10.1145/3458817
              Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

              Sponsors

              In-Cooperation

              • IEEE CS

              Publisher

              Association for Computing Machinery

              New York, NY, United States

              Publication History

              Published: 13 November 2021

              Permissions

              Request permissions for this article.

              Check for updates

              Author Tags

              1. all-electron
              2. biological systems
              3. many-core processor
              4. quantum mechanics
              5. scalability

              Qualifiers

              • Research-article

              Funding Sources

              Conference

              SC '21
              Sponsor:

              Acceptance Rates

              Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

              Upcoming Conference

              Contributors

              Other Metrics

              Bibliometrics & Citations

              Bibliometrics

              Article Metrics

              • Downloads (Last 12 months)259
              • Downloads (Last 6 weeks)22
              Reflects downloads up to 23 Dec 2024

              Other Metrics

              Citations

              Cited By

              View all
              • (2023)OpenCL-accelerated first-principles calculations of all-electron quantum perturbations on HPC resourcesFrontiers in Chemistry10.3389/fchem.2023.115689111Online publication date: 26-May-2023
              • (2023)Scalability and efficiency challenges for the exascale supercomputing system: practice of a parallel supporting environment on the Sunway exascale prototype system面对E级超算系统的可扩展性和效率挑战: 神威E级原型系统并行支撑环境的实践Frontiers of Information Technology & Electronic Engineering10.1631/FITEE.220041224:1(41-58)Online publication date: 23-Jan-2023
              • (2023)Portable and Scalable All-Electron Quantum Perturbation Simulations on Exascale SupercomputersProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3581784.3607085(1-13)Online publication date: 12-Nov-2023

              View Options

              View options

              PDF

              View or Download as a PDF file.

              PDF

              eReader

              View online with eReader.

              eReader

              Login options

              Media

              Figures

              Other

              Tables

              Share

              Share

              Share this Publication link

              Share on social media