Porting ONETEP to Graphical Processing Unitbased Coprocessors
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GPAW, Gpus, and LUMI
GPAW, GPUs, and LUMI Martti Louhivuori, CSC - IT Center for Science Jussi Enkovaara GPAW 2021: Users and Developers Meeting, 2021-06-01 Outline LUMI supercomputer Brief history of GPAW with GPUs GPUs and DFT Current status Roadmap LUMI - EuroHPC system of the North Pre-exascale system with AMD CPUs and GPUs ~ 550 Pflop/s performance Half of the resources dedicated to consortium members Programming for LUMI Finland, Belgium, Czechia, MPI between nodes / GPUs Denmark, Estonia, Iceland, HIP and OpenMP for GPUs Norway, Poland, Sweden, and how to use Python with AMD Switzerland GPUs? https://www.lumi-supercomputer.eu GPAW and GPUs: history (1/2) Early proof-of-concept implementation for NVIDIA GPUs in 2012 ground state DFT and real-time TD-DFT with finite-difference basis separate version for RPA with plane-waves Hakala et al. in "Electronic Structure Calculations on Graphics Processing Units", Wiley (2016), https://doi.org/10.1002/9781118670712 PyCUDA, cuBLAS, cuFFT, custom CUDA kernels Promising performance with factor of 4-8 speedup in best cases (CPU node vs. GPU node) GPAW and GPUs: history (2/2) Code base diverged from the main branch quite a bit proof-of-concept implementation had lots of quick and dirty hacks fixes and features were pulled from other branches and patches no proper unit tests for GPU functionality active development stopped soon after publications Before development re-started, code didn't even work anymore on modern GPUs without applying a few small patches Lesson learned: try to always get new functionality to the -
Light-Matter Interaction and Optical Spectroscopy from Infrared to X-Rays
24th ETSF Workshop on Electronic Excitations Light-Matter Interaction and Optical Spectroscopy from Infrared to X-Rays Jena, Germany 16 – 20 September 2019 Welcome The workshop series of the European Theoretical Spectroscopy Facility (ETSF) provides a fo- rum for excited states and spectroscopy in condensed-matter physics, chemistry, nanoscience, materials science, and molecular physics attracting theoreticians, code developers, and experi- mentalists alike. Light-matter interaction will be at core of the 2019 edition of the ETSF workshop. Cutting-edge spectroscopy experiments allow to probe electrons, plasmons, excitons, and phonons across different energy and time scales with unprecedented accuracy. A deep physical understanding of the underlying quantum many-body effects is of paramount importance to analyze exper- imental observations and render theoretical simulations predictive. The workshop aims at discussing the most recent advances in the theoretical description of the interaction between light and matter focusing on first-principles methods. This broad subject will be covered in its diverse declinations, from core-level spectroscopy to collective low-energy excitations, dis- cussing also matter under extreme conditions, and systems driven out of equilibrium by strong laser pulses. Exchange between theorists and experimentalists is fostered to open new horizons towards the next generation of novel spectroscopy techniques. The workshop will also face the challenges posed by the formidable complexity of heterogeneous and nanostructured systems such as those of interest for light harvesting and energy generation, prompting to bridge the gap be- tween experimental and in silico spectroscopy. Workshop topics include: Linear and nonlinear optical spectroscopy • Core-level spectroscopies • Ultrafast excitation dynamics • Electron-phonon coupling • Light harvesting in natural and synthetic systems • We are glad to welcome you in Jena, the city of light, and wish you an inspiring workshop with lots of interesting science and fruitful discussions. -
D6.1 Report on the Deployment of the Max Demonstrators and Feedback to WP1-5
Ref. Ares(2020)2820381 - 31/05/2020 HORIZON2020 European Centre of Excellence Deliverable D6.1 Report on the deployment of the MaX Demonstrators and feedback to WP1-5 D6.1 Report on the deployment of the MaX Demonstrators and feedback to WP1-5 Pablo Ordejón, Uliana Alekseeva, Stefano Baroni, Riccardo Bertossa, Miki Bonacci, Pietro Bonfà, Claudia Cardoso, Carlo Cavazzoni, Vladimir Dikan, Stefano de Gironcoli, Andrea Ferretti, Alberto García, Luigi Genovese, Federico Grasselli, Anton Kozhevnikov, Deborah Prezzi, Davide Sangalli, Joost VandeVondele, Daniele Varsano, Daniel Wortmann Due date of deliverable: 31/05/2020 Actual submission date: 31/05/2020 Final version: 31/05/2020 Lead beneficiary: ICN2 (participant number 3) Dissemination level: PU - Public www.max-centre.eu 1 HORIZON2020 European Centre of Excellence Deliverable D6.1 Report on the deployment of the MaX Demonstrators and feedback to WP1-5 Document information Project acronym: MaX Project full title: Materials Design at the Exascale Research Action Project type: European Centre of Excellence in materials modelling, simulations and design EC Grant agreement no.: 824143 Project starting / end date: 01/12/2018 (month 1) / 30/11/2021 (month 36) Website: www.max-centre.eu Deliverable No.: D6.1 Authors: P. Ordejón, U. Alekseeva, S. Baroni, R. Bertossa, M. Bonacci, P. Bonfà, C. Cardoso, C. Cavazzoni, V. Dikan, S. de Gironcoli, A. Ferretti, A. García, L. Genovese, F. Grasselli, A. Kozhevnikov, D. Prezzi, D. Sangalli, J. VandeVondele, D. Varsano, D. Wortmann To be cited as: Ordejón, et al., (2020): Report on the deployment of the MaX Demonstrators and feedback to WP1-5. Deliverable D6.1 of the H2020 project MaX (final version as of 31/05/2020). -
Introducing ONETEP: Linear-Scaling Density Functional Simulations on Parallel Computers Chris-Kriton Skylaris,A) Peter D
THE JOURNAL OF CHEMICAL PHYSICS 122, 084119 ͑2005͒ Introducing ONETEP: Linear-scaling density functional simulations on parallel computers Chris-Kriton Skylaris,a) Peter D. Haynes, Arash A. Mostofi, and Mike C. Payne Theory of Condensed Matter, Cavendish Laboratory, Madingley Road, Cambridge CB3 0HE, United Kingdom ͑Received 29 September 2004; accepted 4 November 2004; published online 23 February 2005͒ We present ONETEP ͑order-N electronic total energy package͒, a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and the number of processors. ONETEP is based on our reformulation of the plane wave pseudopotential method which exploits the electronic localization that is inherent in systems with a nonvanishing band gap. We summarize the theoretical developments that enable the direct optimization of strictly localized quantities expressed in terms of a delocalized plane wave basis. These same localized quantities lead us to a physical way of dividing the computational effort among many processors to allow calculations to be performed efficiently on parallel supercomputers. We show with examples that ONETEP achieves excellent speedups with increasing numbers of processors and confirm that the time taken by ONETEP as a function of increasing number of atoms for a given number of processors is indeed linear. What distinguishes our approach is that the localization is achieved in a controlled and mathematically consistent manner so that ONETEP obtains the same accuracy as conventional cubic-scaling plane wave approaches and offers fast and stable convergence. We expect that calculations with ONETEP have the potential to provide quantitative theoretical predictions for problems involving thousands of atoms such as those often encountered in nanoscience and biophysics. -
5 Jul 2020 (finite Non-Periodic Vs
ELSI | An Open Infrastructure for Electronic Structure Solvers Victor Wen-zhe Yua, Carmen Camposb, William Dawsonc, Alberto Garc´ıad, Ville Havue, Ben Hourahinef, William P. Huhna, Mathias Jacqueling, Weile Jiag,h, Murat Ke¸celii, Raul Laasnera, Yingzhou Lij, Lin Ling,h, Jianfeng Luj,k,l, Jonathan Moussam, Jose E. Romanb, Alvaro´ V´azquez-Mayagoitiai, Chao Yangg, Volker Bluma,l,∗ aDepartment of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA bDepartament de Sistemes Inform`aticsi Computaci´o,Universitat Polit`ecnica de Val`encia,Val`encia,Spain cRIKEN Center for Computational Science, Kobe 650-0047, Japan dInstitut de Ci`enciade Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain eDepartment of Applied Physics, Aalto University, Aalto FI-00076, Finland fSUPA, University of Strathclyde, Glasgow G4 0NG, UK gComputational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA hDepartment of Mathematics, University of California, Berkeley, CA 94720, USA iComputational Science Division, Argonne National Laboratory, Argonne, IL 60439, USA jDepartment of Mathematics, Duke University, Durham, NC 27708, USA kDepartment of Physics, Duke University, Durham, NC 27708, USA lDepartment of Chemistry, Duke University, Durham, NC 27708, USA mMolecular Sciences Software Institute, Blacksburg, VA 24060, USA Abstract Routine applications of electronic structure theory to molecules and peri- odic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries arXiv:1912.13403v3 [physics.comp-ph] 5 Jul 2020 (finite non-periodic vs. -
CESMIX: Center for the Exascale Simulation of Materials in Extreme Environments
CESMIX: Center for the Exascale Simulation of Materials in Extreme Environments Project Overview Youssef Marzouk MIT PSAAP-3 Team 18 August 2020 The CESMIX team • Our team integrates expertise in quantum chemistry, atomistic simulation, materials science; hypersonic flow; validation & uncertainty quantification; numerical algorithms; parallel computing, programming languages, compilers, and software performance engineering 1 Project objectives • Exascale simulation of materials in extreme environments • In particular: ultrahigh temperature ceramics in hypersonic flows – Complex materials, e.g., metal diborides – Extreme aerothermal and chemical loading – Predict materials degradation and damage (oxidation, melting, ablation), capturing the central role of surfaces and interfaces • New predictive simulation paradigms and new CS tools for the exascale 2 Broad relevance • Intense current interest in reentry vehicles and hypersonic flight – A national priority! – Materials technologies are a key limiting factor • Material properties are of cross-cutting importance: – Oxidation rates – Thermo-mechanical properties: thermal expansion, creep, fracture – Melting and ablation – Void formation • New systems being proposed and fabricated (e.g., metallic high-entropy alloys) • May have relevance to materials aging • Yet extreme environments are largely inaccessible in the laboratory – Predictive simulation is an essential path… 3 Demonstration problem: specifics • Aerosurfaces of a hypersonic vehicle… • Hafnium diboride (HfB2) promises necessary temperature -
Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids
Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Tancogne-Dejean, Nicolas et al. “Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids.” Physical Review Letters 118.8 (2017): n. pag. © 2017 American Physical Society As Published http://dx.doi.org/10.1103/PhysRevLett.118.087403 Publisher American Physical Society Version Final published version Citable link http://hdl.handle.net/1721.1/107908 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. week ending PRL 118, 087403 (2017) PHYSICAL REVIEW LETTERS 24 FEBRUARY 2017 Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids † Nicolas Tancogne-Dejean,1,2,* Oliver D. Mücke,3,4 Franz X. Kärtner,3,4,5,6 and Angel Rubio1,2,3,5, 1Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany 2European Theoretical Spectroscopy Facility (ETSF), Luruper Chaussee 149, 22761 Hamburg, Germany 3Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany 4The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany 5Physics Department, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany 6Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA (Received 29 September 2016; published 24 February 2017) An accurate analytic model describing the microscopic mechanism of high-harmonic generation (HHG) in solids is derived. -
Popular GPU-Accelerated Applications
LIFE & MATERIALS SCIENCES GPU-ACCELERATED APPLICATIONS | CATALOG | AUG 12 LIFE & MATERIALS SCIENCES APPLICATIONS CATALOG Application Description Supported Features Expected Multi-GPU Release Status Speed Up* Support Bioinformatics BarraCUDA Sequence mapping software Alignment of short sequencing 6-10x Yes Available now reads Version 0.6.2 CUDASW++ Open source software for Smith-Waterman Parallel search of Smith- 10-50x Yes Available now protein database searches on GPUs Waterman database Version 2.0.8 CUSHAW Parallelized short read aligner Parallel, accurate long read 10x Yes Available now aligner - gapped alignments to Version 1.0.40 large genomes CATALOG GPU-BLAST Local search with fast k-tuple heuristic Protein alignment according to 3-4x Single Only Available now blastp, multi cpu threads Version 2.2.26 GPU-HMMER Parallelized local and global search with Parallel local and global search 60-100x Yes Available now profile Hidden Markov models of Hidden Markov Models Version 2.3.2 mCUDA-MEME Ultrafast scalable motif discovery algorithm Scalable motif discovery 4-10x Yes Available now based on MEME algorithm based on MEME Version 3.0.12 MUMmerGPU A high-throughput DNA sequence alignment Aligns multiple query sequences 3-10x Yes Available now LIFE & MATERIALS& LIFE SCIENCES APPLICATIONS program against reference sequence in Version 2 parallel SeqNFind A GPU Accelerated Sequence Analysis Toolset HW & SW for reference 400x Yes Available now assembly, blast, SW, HMM, de novo assembly UGENE Opensource Smith-Waterman for SSE/CUDA, Fast short -
Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems Louis P
WWW.C-CHEM.ORG FULL PAPER Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems Louis P. Lee,*[a] Daniel J. Cole,[a] Mike C. Payne,[a] and Chris-Kriton Skylaris[b] First principles electronic structure calculations are typically Generalized Wannier Functions of ONETEP to natural atomic performed in terms of molecular orbitals (or bands), providing a orbitals, NBO analysis can be performed within a localized straightforward theoretical avenue for approximations of region in such a way that ensures the results are identical to an increasing sophistication, but do not usually provide any analysis on the full system. We demonstrate the capabilities of qualitative chemical information about the system. We can this approach by performing illustrative studies of large derive such information via post-processing using natural bond proteins—namely, investigating changes in charge transfer orbital (NBO) analysis, which produces a chemical picture of between the heme group of myoglobin and its ligands with bonding in terms of localized Lewis-type bond and lone pair increasing system size and between a protein and its explicit orbitals that we can use to understand molecular structure and solvent, estimating the contribution of electronic delocalization interactions. We present NBO analysis of large-scale calculations to the stabilization of hydrogen bonds in the binding pocket of with the ONETEP linear-scaling density functional theory package, a drug-receptor complex, and observing, in situ, the n ! p* which we have interfaced with the NBO 5 analysis program. In hyperconjugative interactions between carbonyl groups that ONETEP calculations involving thousands of atoms, one is typically stabilize protein backbones. -
The CECAM Electronic Structure Library and the Modular Software Development Paradigm
The CECAM electronic structure library and the modular software development paradigm Cite as: J. Chem. Phys. 153, 024117 (2020); https://doi.org/10.1063/5.0012901 Submitted: 06 May 2020 . Accepted: 08 June 2020 . Published Online: 13 July 2020 Micael J. T. Oliveira , Nick Papior , Yann Pouillon , Volker Blum , Emilio Artacho , Damien Caliste , Fabiano Corsetti , Stefano de Gironcoli , Alin M. Elena , Alberto García , Víctor M. García-Suárez , Luigi Genovese , William P. Huhn , Georg Huhs , Sebastian Kokott , Emine Küçükbenli , Ask H. Larsen , Alfio Lazzaro , Irina V. Lebedeva , Yingzhou Li , David López- Durán , Pablo López-Tarifa , Martin Lüders , Miguel A. L. Marques , Jan Minar , Stephan Mohr , Arash A. Mostofi , Alan O’Cais , Mike C. Payne, Thomas Ruh, Daniel G. A. Smith , José M. Soler , David A. Strubbe , Nicolas Tancogne-Dejean , Dominic Tildesley, Marc Torrent , and Victor Wen-zhe Yu COLLECTIONS Paper published as part of the special topic on Electronic Structure Software Note: This article is part of the JCP Special Topic on Electronic Structure Software. This paper was selected as Featured ARTICLES YOU MAY BE INTERESTED IN Recent developments in the PySCF program package The Journal of Chemical Physics 153, 024109 (2020); https://doi.org/10.1063/5.0006074 An open-source coding paradigm for electronic structure calculations Scilight 2020, 291101 (2020); https://doi.org/10.1063/10.0001593 Siesta: Recent developments and applications The Journal of Chemical Physics 152, 204108 (2020); https://doi.org/10.1063/5.0005077 J. Chem. Phys. 153, 024117 (2020); https://doi.org/10.1063/5.0012901 153, 024117 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp The CECAM electronic structure library and the modular software development paradigm Cite as: J. -
Programming Models for Quantum Many-Body Methods on Multicore and Manycore Processors
Programming models for quantum many-body methods on multicore and manycore processors Jeff Hammond1 and Eugene DePrince2 1 Argonne 2 Georgia Tech 6 February 2011 Jeff Hammond Electronic Structure Calculation Methods on Accelerators Abstract The growing diversity in computer processor architectures poses a serious challenge to the computational chemistry community. This talk considers some of the key issues, including disjoint address spaces, non-standard architectures and execution models, and the different APIs required to use them. Specifically, we will describe our experiences in developing coupled-cluster methods for Intel multicore, Intel MIC, NVIDIA Fermi and Blue Gene/Q in both a clean-sheet implementation and NWChem. Of fundamental interest is the development of codes that scale not only within the node but across thousands of nodes; hence, the interaction between the processor and the network will be analyzed in detail. Jeff Hammond Electronic Structure Calculation Methods on Accelerators Software Automation Jeff Hammond Electronic Structure Calculation Methods on Accelerators The practical TCE { NWChem many-body codes What does it do? 1 GUI input quantum many-body theory e.g. CCSD. 2 Operator specification of theory. 3 Apply Wick's theory to transform operator expressions into array expressions. 4 Transform input array expression to operation tree using many types of optimization. 5 Produce Fortran+Global Arrays+NXTVAL implementation. Developer can intercept at various stages to modify theory, algorithm or implementation. Jeff Hammond Electronic Structure Calculation Methods on Accelerators The practical TCE { Success stories First parallel implementation of many (most) CC methods. First truly generic CC code (not string-based): fRHF,ROHF,UHF}×CCfSD,SDT,SDTQ}×{T /Λ,EOM,LR/QRg Most of the largest calculations of their kind employ TCE: CR-EOMCCSD(T), CCSD-LR α, CCSD-QR β, CCSDT-LR α Reduces implementation time for new methods from years to hours, TCE codes are easy to verify. -
Improvements of Bigdft Code in Modern HPC Architectures
Available on-line at www.prace-ri.eu Partnership for Advanced Computing in Europe Improvements of BigDFT code in modern HPC architectures Luigi Genovesea;b;∗, Brice Videaua, Thierry Deutscha, Huan Tranc, Stefan Goedeckerc aLaboratoire de Simulation Atomistique, SP2M/INAC/CEA, 17 Av. des Martyrs, 38054 Grenoble, France bEuropean Synchrotron Radiation Facility, 6 rue Horowitz, BP 220, 38043 Grenoble, France cInstitut f¨urPhysik, Universit¨atBasel, Klingelbergstr.82, 4056 Basel, Switzerland Abstract Electronic structure calculations (DFT codes) are certainly among the disciplines for which an increasing of the computa- tional power correspond to an advancement in the scientific results. In this report, we present the ongoing advancements of DFT code that can run on massively parallel, hybrid and heterogeneous CPU-GPU clusters. This DFT code, named BigDFT, is delivered within the GNU-GPL license either in a stand-alone version or integrated in the ABINIT software package. Hybrid BigDFT routines were initially ported with NVidia's CUDA language, and recently more functionalities have been added with new routines writeen within Kronos' OpenCL standard. The formalism of this code is based on Daubechies wavelets, which is a systematic real-space based basis set. The properties of this basis set are well suited for an extension on a GPU-accelerated environment. In addition to focusing on the performances of the MPI and OpenMP parallelisation the BigDFT code, this presentation also relies of the usage of the GPU resources in a complex code with different kinds of operations. A discussion on the interest of present and expected performances of Hybrid architectures computation in the framework of electronic structure calculations is also adressed.