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  • 1.
    Krahn, Natalie
    et al.
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    Zhang, Jingji
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
    Melnikov, Sergey V.
    Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
    Tharp, Jeffery M.
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    Villa, Alessandra
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Patel, Armaan
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    Howard, Rebecca J.
    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 65, Sweden.
    Gabir, Haben
    Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
    Patel, Trushar R.
    Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 2E1, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
    Stetefeld, Jörg
    Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
    Puglisi, Joseph
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
    Söll, Dieter
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
    tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut2024In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 52, no 2, p. 513-524Article in journal (Refereed)
    Abstract [en]

    Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G-U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G-C base pairs (G3:C70 and G5:C68).

  • 2.
    Massaro, Daniele
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics, Turbulent simulations laboratory.
    Karp, Martin
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. Institute of Fluid Mechanics (LSTM), Friedrich--Alexander--Universität (FAU) Erlangen--Nürnberg, Erlangen 91058, Germany.
    Direct numerical simulation of the turbulent flow around a Flettner rotor2024In: Scientific Reports, E-ISSN 2045-2322, Vol. 14, no 1, article id 3004Article in journal (Refereed)
    Abstract [en]

    The three-dimensional turbulent flow around a Flettner rotor, i.e. an engine-driven rotating cylinder in an atmospheric boundary layer, is studied via direct numerical simulations (DNS) for three different rotation speeds (α). This technology offers a sustainable alternative mainly for marine propulsion, underscoring the critical importance of comprehending the characteristics of such flow. In this study, we evaluate the aerodynamic loads produced by the rotor of height h, with a specific focus on the changes in lift and drag force along the vertical axis of the cylinder. Correspondingly, we observe that vortex shedding is inhibited at the highest α values investigated. However, in the case of intermediate α, vortices continue to be shed in the upper section of the cylinder (y/h>0.3). As the cylinder begins to rotate, a large-scale motion becomes apparent on the high-pressure side, close to the bottom wall. We offer both a qualitative and quantitative description of this motion, outlining its impact on the wake deflection. This finding is significant as it influences the rotor wake to an extent of approximately one hundred diameters downstream. In practical applications, this phenomenon could influence the performance of subsequent boats and have an impact on the cylinder drag, affecting its fuel consumption. This fundamental study, which investigates a limited yet significant (for DNS) Reynolds number and explores various spinning ratios, provides valuable insights into the complex flow around a Flettner rotor. The simulations were performed using a modern GPU-based spectral element method, leveraging the power of modern supercomputers towards fundamental engineering problems.

  • 3.
    Jansson, Niclas
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Karp, Martin
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Podobas, Artur
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Software and Computer systems, SCS.
    Markidis, Stefano
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics, Turbulent simulations laboratory.
    Neko: A modern, portable, and scalable framework for high-fidelity computational fluid dynamics2024In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 275, p. 106243-106243, article id 106243Article in journal (Refereed)
    Abstract [en]

    Computational fluid dynamics (CFD), in particular applied to turbulent flows, is a research area with great engineering and fundamental physical interest. However, already at moderately high Reynolds numbers the computational cost becomes prohibitive as the range of active spatial and temporal scales is quickly widening. Specifically scale-resolving simulations, including large-eddy simulation (LES) and direct numerical simulations (DNS), thus need to rely on modern efficient numerical methods and corresponding software implementations. Recent trends and advancements, including more diverse and heterogeneous hardware in High-Performance Computing (HPC), are challenging software developers in their pursuit for good performance and numerical stability. The well-known maxim “software outlives hardware” may no longer necessarily hold true, and developers are today forced to re-factor their codebases to leverage these powerful new systems. In this paper, we present Neko, a new portable framework for high-order spectral element discretization, targeting turbulent flows in moderately complex geometries. Neko is fully available as open software. Unlike prior works, Neko adopts a modern object-oriented approach in Fortran 2008, allowing multi-tier abstractions of the solver stack and facilitating hardware backends ranging from general-purpose processors (CPUs) down to exotic vector processors and FPGAs. We show that Neko’s performance and accuracy are comparable to NekRS, and thus on-par with Nek5000’s successor on modern CPU machines. Furthermore, we develop a performance model, which we use to discuss challenges and opportunities for high-order solvers on emerging hardware

  • 4.
    Khan, Monsurul
    et al.
    Purdue Univ, Dept Mech Engn, Indiana, PA 47905 USA..
    More, Rishabh V.
    Purdue Univ, Dept Mech Engn, Indiana, PA 47905 USA.;MIT, Dept Mech Engn, Cambridge, MA 02139 USA..
    Banaei, Arash Alizad
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Ardekani, Arezoo M.
    Purdue Univ, Dept Mech Engn, Indiana, PA 47905 USA..
    Rheology of concentrated fiber suspensions with a load-dependent friction coefficient2023In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 8, no 4, article id 044301Article in journal (Refereed)
    Abstract [en]

    We investigate the effects of fiber aspect ratio, roughness, flexibility, and volume fraction on the rheology of concentrated suspensions in a steady shear flow using direct numerical simulations. We model the fibers as inextensible continuous flexible slender bodies with the Euler-Bernoulli beam equation governing their dynamics suspended in an incompressible Newtonian fluid. The fiber dynamics and fluid flow coupling is achieved using the immersed boundary method. In addition, the fiber surface roughness might lead to interfiber contacts, resulting in normal and tangential forces between the fibers, which follow Coulomb's law of friction. The surface roughness is modeled as hemispherical pro-trusions on the fiber surfaces. Their deformation results in a normal load-dependent friction coefficient. Our simulations accurately predict the experimentally observed shear thinning in fiber suspensions. Furthermore, we find that the suspension viscosity eta increases with increasing the volume fraction, roughness, fiber rigidity, and aspect ratio. The increase in eta is the macroscopic manifestation of a similar increase in the microscopic contact contribution to the total stress with these parameters. In addition, we observe positive and negative first N1 and second N2 normal stress differences, respectively, with |N2| < |N1|, in agreement with previous experiments. Last, we propose a modified Maron-Pierce law to quantify the reduction in the jamming volume fraction by increasing the fiber aspect ratio and roughness. Our results and analysis establish the use of fiber surface tribology to tune the suspension flow behavior.

  • 5.
    Karp, Martin
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). Division of Computational Science and Technology, EECS, KTH Royal Institute of Technology, Stockholm, Sweden.
    Massaro, Daniele
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. SimEx/FLOW, Engineering Mechanics, KTH Royal Institute of Technology, Stockholm, Sweden.
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. PDC Centre for High Performance Computing, EECS, KTH Royal Institute of Technology, Stockholm, Sweden.
    Hart, Alistair
    Hewlett Packard Enterpise (HPE), UK.
    Wahlgren, Jacob
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). Division of Computational Science and Technology, EECS, KTH Royal Institute of Technology, Stockholm, Sweden.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. SimEx/FLOW, Engineering Mechanics, KTH Royal Institute of Technology, Stockholm, Sweden.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). Division of Computational Science and Technology, EECS, KTH Royal Institute of Technology, Stockholm, Sweden.
    Large-scale direct numerical simulations of turbulence using GPUs and modern Fortran2023In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846Article in journal (Refereed)
    Abstract [en]

    We present our approach to making direct numerical simulations of turbulence with applications in sustainable shipping. We use modern Fortran and the spectral element method to leverage and scale on supercomputers powered by the Nvidia A100 and the recent AMD Instinct MI250X GPUs, while still providing support for user software developed in Fortran. We demonstrate the efficiency of our approach by performing the world’s first direct numerical simulation of the flow around a Flettner rotor at Re = 30,000 and its interaction with a turbulent boundary layer. We present a performance comparison between the AMD Instinct MI250X and Nvidia A100 GPUs for scalable computational fluid dynamics. Our results show that one MI250X offers performance on par with two A100 GPUs and has a similar power efficiency based on readings from on-chip energy sensors.

  • 6.
    Vistoli, Giulio
    et al.
    Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Milano, Italy.
    Manelfi, Candida
    EXSCALATE, Dompé Farmaceutici S.p.A, Napoli, Italy.
    Talarico, Carmine
    EXSCALATE, Dompé Farmaceutici S.p.A, Napoli, Italy.
    Fava, Anna
    EXSCALATE, Dompé Farmaceutici S.p.A, Napoli, Italy.
    Warshel, Arieh
    Department of Chemistry, University of Southern California, Los Angeles, USA.
    Tetko, Igor V.
    BIGCHEM GmbH, Valerystr, Germany; Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich-Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
    Apostolov, Rossen
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Ye, Yang
    Natural Products Chemistry Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
    Latini, Chiara
    High Performance Computing Dept, CINECA, Casalecchio di Reno, Bologna, Italy.
    Ficarelli, Federico
    High Performance Computing Dept, CINECA, Casalecchio di Reno, Bologna, Italy.
    Palermo, Gianluca
    DEIB–Politecnico di Milano, Milano, Italy.
    Gadioli, Davide
    DEIB–Politecnico di Milano, Milano, Italy.
    Vitali, Emanuele
    DEIB–Politecnico di Milano, Milano, Italy.
    Varriale, Gaetano
    SAS Institute Srl, Roma, Italy.
    Pisapia, Vincenzo
    SAS Institute Srl, Roma, Italy.
    Scaturro, Marco
    SAS Institute Srl, Milano, Italy.
    Coletti, Silvano
    Chelonia SA (AG), Allschwil, Switzerland.
    Gregori, Daniele
    E4 Computer Engineering S.p.A, Scandiano (RE), Italy, RE.
    Gruffat, Daniel
    Nanome Inc, San Diego, CA, USA.
    Leija, Edgardo
    Nanome Inc, San Diego, CA, USA.
    Hessenauer, Sam
    Nanome Inc, San Diego, CA, USA.
    Delbianco, Alberto
    EnI, San Donato Milanese, Italy.
    Allegretti, Marcello
    Dompé Farmaceutici S.p.A, L’Aquila, Italy.
    Beccari, Andrea R.
    EXSCALATE, Dompé Farmaceutici S.p.A, Napoli, Italy.
    MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions2023In: Expert Opinion on Drug Discovery, ISSN 1746-0441, E-ISSN 1746-045X, Vol. 18, no 8, p. 821-833Article in journal (Refereed)
    Abstract [en]

    Introduction: Collaborative computing has attracted great interest in the possibility of joining the efforts of researchers worldwide. Its relevance has further increased during the pandemic crisis since it allows for the strengthening of scientific collaborations while avoiding physical interactions. Thus, the E4C consortium presents the MEDIATE initiative which invited researchers to contribute via their virtual screening simulations that will be combined with AI-based consensus approaches to provide robust and method-independent predictions. The best compounds will be tested, and the biological results will be shared with the scientific community. Areas covered: In this paper, the MEDIATE initiative is described. This shares compounds’ libraries and protein structures prepared to perform standardized virtual screenings. Preliminary analyses are also reported which provide encouraging results emphasizing the MEDIATE initiative’s capacity to identify active compounds. Expert opinion: Structure-based virtual screening is well-suited for collaborative projects provided that the participating researchers work on the same input file. Until now, such a strategy was rarely pursued and most initiatives in the field were organized as challenges. The MEDIATE platform is focused on SARS-CoV-2 targets but can be seen as a prototype which can be utilized to perform collaborative virtual screening campaigns in any therapeutic field by sharing the appropriate input files.

  • 7.
    Majdolhosseini, Maryam
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Zhou, Zhou
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Kleiven, Svein
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Villa, Alessandra
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Which part of axonal membrane is the most vulnerable: A molecular dynamics/Finite Element study2023In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 52, no SUPPL 1, p. S39-S39Article in journal (Other academic)
  • 8.
    Williams, Jeremy J.
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Tskhakaya, David
    Institute of Plasma Physics of the CAS, Prague, Czech Republic.
    Costea, Stefan
    LeCAD, University of Ljubljana, Ljubljana, Slovenia.
    Peng, Ivy Bo
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Garcia-Gasulla, Marta
    Barcelona Supercomputing Center, Barcelona, Spain.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Leveraging HPC Profiling & Tracing Tools to Understand the Performance of Particle-in-Cell Monte Carlo Simulations2023In: arXiv:2306.16512 / [ed] Demetris Zeinalipour, Limassol, Cyprus: Springer Nature, 2023, article id arXiv:2306.16512Conference paper (Refereed)
    Abstract [en]

    Large-scale plasma simulations are critical for designing and developing next-generation fusion energy devices and modeling industrial plasmas. BIT1 is a massively parallel Particle-in-Cell code designed for specifically studying plasma material interaction in fusion devices. Its most salient characteristic is the inclusion of collision Monte Carlo models for different plasma species. In this work, we characterize single node, multiple nodes, and I/O performances of the BIT1 code in two realistic cases by using several HPC profilers, such as perf, IPM, Extrae/Paraver, and Darshan tools. We find that the BIT1 sorting function on-node performance is the main performance bottleneck. Strong scaling tests show a parallel performance of 77% and 96% on 2,560 MPI ranks for the two test cases. We demonstrate that communication, load imbalance and self-synchronization are important factors impacting the performance of the BIT1 on large-scale runs.

  • 9.
    Ju, Yi
    et al.
    Max Planck Computing and Data Facility, Max Planck Computing and Data Facility.
    Li, Mingshuai
    Technical University of Munich, Technical University of Munich.
    Perez, Adalberto
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Bellentani, Laura
    CINECA, Cineca.
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. Friedrich-Alexander-Universität Erlangen-Nürnberg.
    Laure, Erwin
    Max Planck Computing and Data Facility, Max Planck Computing and Data Facility.
    In-Situ Techniques on GPU-Accelerated Data-Intensive Applications2023In: Proceedings 2023 IEEE 19th International Conference on e-Science, e-Science 2023, Institute of Electrical and Electronics Engineers (IEEE) , 2023Conference paper (Refereed)
    Abstract [en]

    The computational power of High-Performance Computing (HPC) systems is constantly increasing, however, their input/output (IO) performance grows relatively slowly, and their storage capacity is also limited. This unbalance presents significant challenges for applications such as Molecular Dynamics (MD) and Computational Fluid Dynamics (CFD), which generate massive amounts of data for further visualization or analysis. At the same time, checkpointing is crucial for long runs on HPC clusters, due to limited walltimes and/or failures of system components, and typically requires the storage of large amount of data. Thus, restricted IO performance and storage capacity can lead to bottlenecks for the performance of full application workflows (as compared to computational kernels without IO). In-situ techniques, where data is further processed while still in memory rather to write it out over the I/O subsystem, can help to tackle these problems. In contrast to traditional post-processing methods, in-situ techniques can reduce or avoid the need to write or read data via the IO subsystem. They offer a promising approach for applications aiming to leverage the full power of large scale HPC systems. In-situ techniques can also be applied to hybrid computational nodes on HPC systems consisting of graphics processing units (GPUs) and central processing units (CPUs). On one node, the GPUs would have significant performance advantages over the CPUs. Therefore, current approaches for GPU-accelerated applications often focus on maximizing GPU usage, leaving CPUs underutilized. In-situ tasks using CPUs to perform data analysis or preprocess data concurrently to the running simulation, offer a possibility to improve this underutilization.

  • 10.
    Karp, Martin
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Liu, Felix
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). Raysearch Laboratories..
    Stanly, Ronith
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Rezaeiravesh, Saleh
    The University of Manchester, Manchester, United Kingdom.
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Uncertainty Quantification of Reduced-Precision Time Series in Turbulent Channel Flow2023In: Proceedings of 2023 SC Workshops of the International Conference on High Performance Computing, Network, Storage, and Analysis, SC Workshops 2023, Association for Computing Machinery (ACM) , 2023, p. 387-390Conference paper (Refereed)
    Abstract [en]

    With increased computational power through the use of arithmetic in low-precision, a relevant question is how lower precision affects simulation results, especially for chaotic systems where analytical round-off estimates are non-trivial to obtain. In this work, we consider how the uncertainty of the time series of a direct numerical simulation of turbulent channel flow at Ret = 180 is affected when restricted to a reduced-precision representation. We utilize a non-overlapping batch means estimator and find that the mean statistics can, in this case, be obtained with significantly fewer mantissa bits than conventional IEEE-754 double precision, but that the mean values are observed to be more sensitive in the middle of the channel than in the near-wall region. This indicates that using lower precision in the near-wall region, where the majority of the computational efforts are required, may benefit from low-precision floating point units found in upcoming computer hardware.

  • 11.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    We present the implementation of an efficient matrix-folded formalism for the evaluation of complex response functions and the calculation of transition properties at the level of the second-order algebraic-diagrammatic construction (ADC(2)) scheme. The underlying algorithms, in combination with the adopted hybrid MPI/OpenMP parallelization strategy, enabled calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1032 contracted basis functions, thereby utilizing vast computational resources from up to 32,768 CPU cores. Further analysis of the convergence behavior of the involved iterative subspace algorithms revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window, including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electronic circular dichroism spectrum calculated with a complex polarization propagator approach at the ADC(2) level of theory.

  • 12.
    Nocerino, Elisabetta
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Stuhr, U.
    Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    San Lorenzo, I.
    Nanoscience Center, Niels Bohr Institute, University of Copenhagen, Noerre Alle 59, DK-2100 Copenhagen O, Denmark, Nørre Allé 59; Department of Applied Science and Technology, Politecnico di Torino, corso Duca degli abruzzi 24 10129 Torino, Italy.
    Mazza, F.
    Institute of Solid State Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria, Wiedner Hauptstraße 8–10.
    Mazzone, D. G.
    Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Hellsvik, Johan
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Hasegawa, S.
    Neutron Science Laboratory, Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
    Asai, S.
    Neutron Science Laboratory, Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
    Masuda, T.
    Neutron Science Laboratory, Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan, Chiba; Trans-scale Quantum Science Institute, The University of Tokyo, Tokyo 113-0033, Japan; Institute of Materials Structure Science, High Energy Accelerator Research Organization, Ibaraki 305-0801, Japan.
    Itoh, S.
    Institute of Materials Structure Science, High Energy Accelerator Research Organization, Ibaraki 305-0801, Japan.
    Minelli, A.
    Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom.
    Hossain, Z.
    Department of Physics, Indian Institute of Technology, Kanpur 208016, India.
    Thamizhavel, A.
    DCMPMS, Tata Institute of Fundamental Research, Mumbai 400005, India.
    Lefmann, K.
    Nanoscience Center, Niels Bohr Institute, University of Copenhagen, Noerre Alle 59, DK-2100 Copenhagen O, Denmark.
    Sassa, Y.
    Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
    Månsson, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Q-dependent electron-phonon coupling induced phonon softening and non-conventional critical behavior in the CDW superconductor LaPt2Si22023In: Journal of Science: Advanced Materials and Devices, ISSN 2468-2284, Vol. 8, no 4, article id 100621Article in journal (Refereed)
    Abstract [en]

    This paper reports the first experimental observation of phonons and their softening on single crystalline LaPt2Si2 via inelastic neutron scattering. From the temperature dependence of the phonon frequency in close proximity to the charge density wave (CDW) q-vector, we obtain a CDW transition temperature of TCDW = 230 K and a critical exponent β = 0.28 ± 0.03. This value is suggestive of a non-conventional critical behavior for the CDW phase transition in LaPt2Si2, compatible with a scenario of CDW discommensuration (DC). The DC would be caused by the existence of two CDWs in this material, propagating separately in the non equivalent (Si1–Pt2–Si1) and (Pt1–Si2–Pt1) layers, respectively, with transition temperatures TCDW−1 = 230 K and TCDW−2 = 110 K. A strong q-dependence of the electron-phonon coupling has been identified as the driving mechanism for the CDW transition at TCDW−1 = 230 K while a CDW with 3-dimensional character, and Fermi surface quasi-nesting as a driving mechanism, is suggested for the transition at TCDW−2 = 110 K. Our results clarify some aspects of the CDW transition in LaPt2Si2 which have been so far misinterpreted by both theoretical predictions and experimental observations and give direct insight into its actual temperature dependence.

  • 13.
    Chien, Steven W.D.
    et al.
    University of Edinburgh, United Kingdom.
    Sato, Kento
    RIKEN Center for Computational Science Japan.
    Podobas, Artur
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Software and Computer systems, SCS.
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Honda, Michio
    University of Edinburgh, United Kingdom.
    Improving Cloud Storage Network Bandwidth Utilization of Scientific Applications2023In: Proceedings of the 7th Asia-Pacific Workshop on Networking, APNET 2023, Association for Computing Machinery (ACM) , 2023, p. 172-173Conference paper (Refereed)
    Abstract [en]

    Cloud providers began to provide managed services to attract scientific applications, which have been traditionally executed on supercomputers. One example is AWS FSx for Lustre, a fully managed parallel file system (PFS) released in 2018. However, due to the nature of scientific applications, the frontend storage network bandwidth is left completely idle for the majority of its lifetime. Furthermore, the pricing model does not match the scalability requirement. We propose iFast, a novel host-side caching mechanism for scientific applications that improves storage bandwidth utilization and end-to-end application performance: by overlapping compute and data writeback through inexpensive local storage. iFast supports the Massage Passing Interface (MPI) library that is widely used by scientific applications and is implemented as a preloaded library. It requires no change to applications, the MPI library, or support from cloud operators. We demonstrate how iFast can accelerate the end-to-end time of a representative scientific application Neko, by 13-40%.

  • 14.
    Smail, R. E.
    et al.
    CSSM, Department of Physics, University of Adelaide, Adelaide, South Australia 5005, Australia.
    Batelaan, M.
    CSSM, Department of Physics, University of Adelaide, Adelaide, South Australia 5005, Australia.
    Horsley, R.
    School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom.
    Nakamura, Y.
    RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
    Perlt, H.
    Institut für Theoretische Physik, Universität Leipzig, 04103 Leipzig, Germany.
    Pleiter, Dirk
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Rakow, P. E.L.
    Theoretical Physics Division, Department of Mathematical Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom.
    Schierholz, G.
    Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
    Stüben, H.
    Universität Hamburg, Regionales Rechenzentrum, 20146 Hamburg, Germany.
    Young, R. D.
    CSSM, Department of Physics, University of Adelaide, Adelaide, South Australia 5005, Australia; Center for Theoretical Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
    Zanotti, J. M.
    CSSM, Department of Physics, University of Adelaide, Adelaide, South Australia 5005, Australia.
    Constraining beyond the standard model nucleon isovector charges2023In: Physical Review D: covering particles, fields, gravitation, and cosmology, ISSN 2470-0010, E-ISSN 2470-0029, Vol. 108, no 9, article id 094511Article in journal (Refereed)
    Abstract [en]

    At the TeV scale, low-energy precision observations of neutron characteristics provide unique probes of novel physics. Precision studies of neutron decay observables are susceptible to beyond the Standard Model (BSM) tensor and scalar interactions, while the neutron electric dipole moment, dn, also has high sensitivity to new BSM CP-violating interactions. To fully utilize the potential of future experimental neutron physics programs, matrix elements of appropriate low-energy effective operators within neutron states must be precisely calculated. We present results from the QCDSF/UKQCD/CSSM Collaboration for the isovector charges gT, gA and gS of the nucleon, ς and Ξ baryons using lattice QCD methods and the Feynman-Hellmann theorem. We use a flavor symmetry breaking method to systematically approach the physical quark mass using ensembles that span five lattice spacings and multiple volumes. We extend this existing flavor-breaking expansion to also account for lattice spacing and finite volume effects in order to quantify all systematic uncertainties. Our final estimates of the nucleon isovector charges are gT=1.010(21)stat(12)sys,gA=1.253(63)stat(41)sys and gS=1.08(21)stat(03)sys renormalized, where appropriate, at μ=2 GeV in the MS¯ scheme.

  • 15.
    Hasan, Md Nur
    et al.
    Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector-III, SaltLake, Kolkata 700 106, India.
    Bharati, Ritadip
    School of Physical Sciences, National Institute of Science Education and Research HBNI, Jatni - 752050, Odisha, India.
    Hellsvik, Johan
    KTH, School of Engineering Sciences (SCI), Physics, Condensed Matter Theory. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pal, Samir Kumar
    Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector-III, SaltLake, Kolkata 700 106, India.
    Bergman, Anders
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Sharma, Shivalika
    Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea.
    Di Marco, Igor
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden; Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea; Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
    Pereiro, Manuel
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Thunström, Patrik
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Oppeneer, Peter M.
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Eriksson, Olle
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Karmakar, Debjani
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden; Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
    Magnetism in A V3Sb5 (A=Cs, Rb, and K): Origin and Consequences for the Strongly Correlated Phases2023In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 131, no 19, article id 196702Article in journal (Refereed)
    Abstract [en]

    The V-based kagome systems AV3Sb5 (A=Cs, Rb, and K) are unique by virtue of the intricate interplay of nontrivial electronic structure, topology, and intriguing fermiology, rendering them to be a playground of many mutually dependent exotic phases like charge-order and superconductivity. Despite numerous recent studies, the interconnection of magnetism and other complex collective phenomena in these systems has yet not arrived at any conclusion. Using first-principles tools, we demonstrate that their electronic structures, complex fermiologies and phonon dispersions are strongly influenced by the interplay of dynamic electron correlations, nontrivial spin-polarization and spin-orbit coupling. An investigation of the first-principles-derived intersite magnetic exchanges with the complementary analysis of q dependence of the electronic response functions and the electron-phonon coupling indicate that the system conforms as a frustrated spin cluster, where the occurrence of the charge-order phase is intimately related to the mechanism of electron-phonon coupling, rather than the Fermi-surface nesting.

  • 16.
    Karmakar, Debjani
    et al.
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden; Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
    Pereiro, Manuel
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Hasan, Md Nur
    Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector-III, SaltLake, Kolkata 700 106, India.
    Bharati, Ritadip
    School of Physical Sciences, National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Jatni, 752050 Odisha, India.
    Hellsvik, Johan
    KTH, School of Engineering Sciences (SCI), Physics, Condensed Matter Theory. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pal, Samir Kumar
    Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector-III, SaltLake, Kolkata 700 106, India.
    Bergman, Anders
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Sharma, Shivalika
    Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea.
    Di Marco, Igor
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden; Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea; Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
    Thunström, Patrik
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Oppeneer, Peter M.
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Eriksson, Olle
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Magnetism in A V3Sb5 (A=Cs, Rb, K): Complex landscape of dynamical magnetic textures2023In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 108, no 17, article id 174413Article in journal (Refereed)
    Abstract [en]

    We have investigated the dynamical magnetic properties of the V-based kagome stibnite compounds by combining the ab initio-extracted magnetic parameters of a spin-Hamiltonian, like inter-site exchange parameters, magnetocrystalline anisotropy and site projected magnetic moments, with full-fledged simulations of atomistic spin- dynamics. Our calculations reveal that, in addition to a ferromagnetic order along the [001] direction, the system hosts a complex landscape of magnetic configurations comprised of commensurate and incommensurate spin spirals along the [010] direction. The presence of such chiral magnetic textures may be the key toward solving the mystery about the origin of the experimentally observed inherent breaking of the C6 rotational, mirror, and the time-reversal symmetry.

  • 17.
    Netzer, Gilbert
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    QHDL: a Low-Level Circuit Description Language for Quantum Computing2023In: Proceedings of the 20th ACM International Conference on Computing Frontiers 2023, CF 2023, Association for Computing Machinery (ACM) , 2023, p. 201-204Conference paper (Refereed)
    Abstract [en]

    This paper proposes a descriptive language called QHDL, akin to VHDL, to program gate-based quantum computing systems. Unlike other popular quantum programming languages, QHDL targets low-level quantum computing programming and aims to provide a common framework for programming FPGAs and gate-based quantum computing systems. The paper presents an initial implementation and design principles of the QHDL framework, including a compiler and quantum computer simulator. We discuss the challenges of low-level integration of streaming models and quantum computing for programming FPGAs and gate-based quantum computing systems.

  • 18.
    Jansson, Niclas
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Karp, Martin
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Perez, Adalberto
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Mukha, Timofey
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Ju, Yi
    Max Planck Computing and Data Facility, Garching, Germany.
    Liu, Jiahui
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Pall, Szilard
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Laure, Erwin
    Max Planck Computing and Data Facility, Garching, Germany.
    Weinkauf, Tino
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Schumacher, Jörg
    Technische Universität Ilmenau, Ilmenau, Germany.
    Schlatter, Philipp
    Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Germany.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Exploring the Ultimate Regime of Turbulent Rayleigh–Bénard Convection Through Unprecedented Spectral-Element Simulations2023In: SC '23: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Association for Computing Machinery (ACM) , 2023, p. 1-9, article id 5Conference paper (Refereed)
    Abstract [en]

    We detail our developments in the high-fidelity spectral-element code Neko that are essential for unprecedented large-scale direct numerical simulations of fully developed turbulence. Major inno- vations are modular multi-backend design enabling performance portability across a wide range of GPUs and CPUs, a GPU-optimized preconditioner with task overlapping for the pressure-Poisson equation and in-situ data compression. We carry out initial runs of Rayleigh–Bénard Convection (RBC) at extreme scale on the LUMI and Leonardo supercomputers. We show how Neko is able to strongly scale to 16,384 GPUs and obtain results that are not pos- sible without careful consideration and optimization of the entire simulation workflow. These developments in Neko will help resolv- ing the long-standing question regarding the ultimate regime in RBC. 

  • 19.
    Sadhukhan, Banasree
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Bergman, Anders
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Kvashnin, Yaroslav O.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Hellsvik, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. NORDITA, Hannes Alfvens Vag 12, SE-10691 Stockholm, Sweden.;Stockholm Univ, Hannes Alfvens Vag 12, SE-10691 Stockholm, Sweden..
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Spin-lattice couplings in two-dimensional CrI3 from first-principles computations2022In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 105, no 10, article id 104418Article in journal (Refereed)
    Abstract [en]

    Since thermal fluctuations become more important as dimensions shrink, it is expected that low-dimensional magnets are more sensitive to atomic displacement and phonons than bulk systems are. Here we present a fully relativistic first-principles study on the spin-lattice coupling, i.e., how the magnetic interactions depend on atomic displacement, of the prototypical two-dimensional ferromagnet CrI3. We extract an effective measure of the spin-lattice coupling in CrI3, which is up to ten times larger than what is found for bcc Fe. The magnetic exchange interactions, including Heisenberg and relativistic Dzyaloshinskii-Moriya interactions, are sensitive both to the in-plane motion of Cr atoms and out-of-plane motion of ligand atoms. We find that significant magnetic pair interactions change sign from ferromagnetic (FM) to antiferromagnetic (AFM) for atomic displacements larger than 0.16 (0.18) angstrom for Cr (I) atoms. We explain the observed strong spin-lattice coupling by analyzing the orbital decomposition of isotropic exchange interactions, involving different crystal-field-split Cr-3d orbitals. The competition between the AFM t(2g)-t(2g) and FM t(2g)-e(g) contributions depends on the bond angle formed by Cr and I atoms as well as Cr-Cr distance. In particular, if a Cr atom is displaced, the FM-AFM sign changes when the I-Cr-I bond angle approaches 90 degrees. The obtained spin-lattice coupling constants, along with the microscopic orbital analysis, can act as a guiding principle for further studies of the thermodynamic properties and combined magnon-phonon excitations in two-dimensional magnets.

  • 20.
    Karp, Martin
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Podobas, Artur
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Kenter, Tobias
    Paderborn University.
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Plessl, Christian
    Paderborn University.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    A High-Fidelity Flow Solver for Unstructured Meshes on Field-Programmable Gate Arrays: Design, Evaluation, and Future Challenges2022In: HPCAsia2022: International Conference on High Performance Computing in Asia-Pacific Region, Association for Computing Machinery (ACM) , 2022, p. 125-136Conference paper (Refereed)
    Abstract [en]

    The impending termination of Moore’s law motivates the search for new forms of computing to continue the performance scaling we have grown accustomed to. Among the many emerging Post-Moore computing candidates, perhaps none is as salient as the Field-Programmable Gate Array (FPGA), which offers the means of specializing and customizing the hardware to the computation at hand.

    In this work, we design a custom FPGA-based accelerator for a computational fluid dynamics (CFD) code. Unlike prior work – which often focuses on accelerating small kernels – we target the entire Poisson solver on unstructured meshes based on the high-fidelity spectral element method (SEM) used in modern state-of-the-art CFD systems. We model our accelerator using an analytical performance model based on the I/O cost of the algorithm. We empirically evaluate our accelerator on a state-of-the-art Intel Stratix 10 FPGA in terms of performance and power consumption and contrast it against existing solutions on general-purpose processors (CPUs). Finally, we propose a data movement-reducing technique where we compute geometric factors on the fly, which yields significant (700+ Gflop/s) single-precision performance and an upwards of 2x reduction in runtime for the local evaluation of the Laplace operator.

    We end the paper by discussing the challenges and opportunities of using reconfigurable architecture in the future, particularly in the light of emerging (not yet available) technologies.

  • 21.
    Kliuchnikov, Evgenii
    et al.
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Klyshko, Eugene
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA.;Univ Toronto, Dept Phys, Toronto, ON M5S 1A7, Canada..
    Kelly, Maria S.
    Univ Cincinnati, Dept Chem, Cincinnati, OH 45221 USA..
    Zhmurov, Artem
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Dima, Ruxandra, I
    Univ Cincinnati, Dept Chem, Cincinnati, OH 45221 USA..
    Marx, Kenneth A.
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Barsegov, Valeri
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue2022In: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, p. 953-974Article in journal (Refereed)
    Abstract [en]

    Microtubules (MTs), a cellular structure element, exhibit dynamic instability and can switch stochastically from growth to shortening; but the factors that trigger these processes at the molecular level are not understood. We developed a 3D Microtubule Assembly and Disassembly DYnamics (MADDY) model, based upon a bead-per-monomer representation of the alpha beta-tubulin dimers forming an MT lattice, stabilized by the lateral and longitudinal interactions between tubulin subunits. The model was parameterized against the experimental rates of MT growth and shortening, and pushing forces on the Dam1 protein complex due to protofilaments splaying out. Using the MADDY model, we carried out GPU-accelerated Langevin simulations to access dynamic instability behavior. By applying Machine Learning techniques, we identified the MT characteristics that distinguish simultaneously all four kinetic states: growth, catastrophe, shortening, and rescue. At the cellular 25 mu M tubulin concentration, the most important quantities are the MT length L, average longitudinal curvature kappa(long), MT tip width w, total energy of longitudinal interactions in MT lattice U-long, and the energies of longitudinal and lateral interactions required to complete MT to full cylinder U-long(add) and U-lat(add) . At high 250 mu M tubulin concentration, the most important characteristics are L, kappa(long), number of hydrolyzed alpha beta-tubulin dimers n(hyd) and number of lateral interactions per helical pitch n(lat) in MT lattice, energy of lateral interactions in MT lattice U-lat, and energy of longitudinal interactions in MT tip u(long). These results allow greater insights into what brings about kinetic state stability and the transitions between states involved in MT dynamic instability behavior.

  • 22.
    Asquith, Nathan L.
    et al.
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Sch Med, Discovery & Translat Sci Dept, Leeds, England.;Boston Childrens Hosp, Harvard Med Sch, Vasc Biol Program, Karp Res Labs, Boston, MA USA..
    Duval, Cedric
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Sch Med, Discovery & Translat Sci Dept, Leeds, England..
    Zhmurov, Artem
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. EuroCC Natl Competence Ctr Sweden, Stockholm, Sweden.
    Baker, Stephen R.
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Sch Med, Discovery & Translat Sci Dept, Leeds, England..
    McPherson, Helen R.
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Sch Med, Discovery & Translat Sci Dept, Leeds, England..
    Domingues, Marco M.
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Sch Med, Discovery & Translat Sci Dept, Leeds, England.;Univ Lisbon, Inst Mol Med, Fac Med, Lisbon, Portugal..
    Connell, Simon D. A.
    Univ Leeds, Sch Phys & Astron, Mol & Nanoscale Phys Grp, Leeds, England..
    Barsegov, Valeri
    Univ Massachusetts, Dept Chem, Lowell, MA USA..
    Ariens, Robert A. S.
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Sch Med, Discovery & Translat Sci Dept, Leeds, England.;Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Discovery & Translat Sci Dept, Leeds LS2 9JT, England..
    Fibrin protofibril packing and clot stability are enhanced by extended knob-hole interactions and catch-slip bonds2022In: Blood Advances, ISSN 2473-9529, Vol. 6, no 13, p. 4015-4027Article in journal (Refereed)
    Abstract [en]

    Fibrin polymerization involves thrombin-mediated exposure of knobs on one monomer that bind to holes available on another, leading to the formation of fibers. In silico evidence has suggested that the classical A:a knob-hole interaction is enhanced by surrounding residues not directly involved in the binding pocket of hole a, via noncovalent interactions with knob A. We assessed the importance of extended knob-hole interactions by performing biochemical, biophysical, and in silico modeling studies on recombinant human fibrinogen variants with mutations at residues responsible for the extended interactions. Three single fibrinogen variants, yD297N, yE323Q, and yK356Q, and a triple variant yDEK (yD297N/yE323Q/yK356Q) were produced in a CHO (Chinese Hamster Ovary) cell expression system. Longitudinal protofibril growth probed by atomic force microscopy was disrupted for yD297N and enhanced for the yK356Q mutation. Initial polymerization rates were reduced for all variants in turbidimetric studies. Laser scanning confocal microscopy showed that yDEK and yE323Q produced denser clots, whereas yD297N and yK356Q were similar to wild type. Scanning electron microscopy and light scattering studies showed that fiber thickness and protofibril packing of the fibers were reduced for all variants. Clot viscoelastic analysis showed that only yDEK was more readily deformable. In silico modeling suggested that most variants displayed only slip-bond dissociation kinetics compared with biphasic catch-slip kinetics characteristics of wild type. These data provide new evidence for the role of extended interactions in supporting the classical knob-hole bonds involving catch-slip behavior in fibrin formation, clot structure, and clot mechanics.

  • 23.
    Kliuchnikov, Evgenii
    et al.
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Zhmurov, Artem
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Marx, Kenneth A.
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Mogilner, Alex
    NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10003 USA.;NYU, Dept Biol, 251 Mercer St, New York, NY 10003 USA..
    Barsegov, Valeri
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    CellDynaMo-stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly2022In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 18, no 6, article id e1010165Article in journal (Refereed)
    Abstract [en]

    We introduce a Stochastic Reaction-Diffusion-Dynamics Model (SRDDM) for simulations of cellular mechanochemical processes with high spatial and temporal resolution. The SRDDM is mapped into the CellDynaMo package, which couples the spatially inhomogeneous reaction-diffusion master equation to account for biochemical reactions and molecular transport within the Langevin Dynamics (LD) framework to describe dynamic mechanical processes. This computational infrastructure allows the simulation of hours of molecular machine dynamics in reasonable wall-clock time. We apply SRDDM to test performance of the Search-and-Capture of mitotic spindle assembly by simulating, in three spatial dimensions, dynamic instability of elastic microtubules anchored in two centrosomes, movement and deformations of geometrically realistic centromeres with flexible kinetochores and chromosome arms. Furthermore, the SRDDM describes the mechanics and kinetics of Ndc80 linkers mediating transient attachments of microtubules to the chromosomal kinetochores. The rates of these attachments and detachments depend upon phosphorylation states of the Ndc80 linkers, which are regulated in the model by explicitly accounting for the reactions of Aurora A and B kinase enzymes undergoing restricted diffusion. We find that there is an optimal rate of microtubule-kinetochore detachments which maximizes the accuracy of the chromosome connections, that adding chromosome arms to kinetochores improve the accuracy by slowing down chromosome movements, that Aurora A and kinetochore deformations have a small positive effect on the attachment accuracy, and that thermal fluctuations of the microtubules increase the rates of kinetochore capture and also improve the accuracy of spindle assembly. Author summary The CellDynaMo package models, in 3D, any cellular subsystem where sufficient detail of the macromolecular players and the kinetics of relevant reactions are available. The package is based on the Stochastic Reaction-Diffusion-Dynamics model that combines the stochastic description of chemical kinetics, Brownian diffusion-based description of molecular transport, and Langevin dynamics-based representation of mechanical processes most pertinent to the system. We apply the model to test the Search-and-Capture mechanism of mitotic spindle assembly. We find that there is an optimal rate of microtubule-kinetochore detachments which maximizes the accuracy of chromosome connections, that chromosome arms improve the attachment accuracy by slowing down chromosome movements, that Aurora A kinase and kinetochore deformations have small positive effects on the accuracy, and that thermal fluctuations of the microtubules increase the rates of kinetochore capture and also improve the accuracy.

  • 24.
    Karp, Martin
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Podobas, Artur
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Reducing Communication in the Conjugate Gradient Method: A Case Study on High-Order Finite Elements2022In: Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2022, Association for Computing Machinery (ACM) , 2022, article id 2Conference paper (Refereed)
    Abstract [en]

    Currently, a major bottleneck for several scientific computations is communication, both communication between different processors, so-called horizontal communication, and vertical communication between different levels of the memory hierarchy. With this bottleneck in mind, we target a notoriously communication-bound solver at the core of many high-performance applications, namely the conjugate gradient method (CG). To reduce the communication we present lower bounds on the vertical data movement in CG and go on to make a CG solver with reduced data movement. Using our theoretical analysis we apply our CG solver on a high-performance discretization used in practice, the spectral element method (SEM). Guided by our analysis, we show that for the Poisson equation on modern GPUs we can improve the performance by 30% by both rematerializing the discrete system and by reformulating the system to work on unique degrees of freedom. In order to investigate how horizontal communication can be reduced, we compare CG to two communication-reducing techniques, namely communication-avoiding and pipelined CG. We strong scale up to 4096 CPU cores and showcase performance improvements of upwards of 70% for pipelined CG compared to standard CG when applied on SEM at scale. We show that in addition to improving the scaling capabilities of the solver, initial measurements indicate that the convergence of SEM is largely unaffected by pipelined CG.

  • 25. Smail, R. E.
    et al.
    Horsley, R.
    Nakamura, Y.
    Perlt, H.
    Pleiter, Dirk
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Rakow, P. E. L.
    Schierholz, G.
    Stüben, H.
    Young, R. D.
    Zanotti, J. M.
    Tensor Charges and their Impact on Physics Beyond the Standard Model2022In: Proceedings of Science, Sissa Medialab Srl , 2022Conference paper (Refereed)
    Abstract [en]

    The nucleon tensor charge, gT, is an important quantity in the search for beyond the Standard Model tensor interactions in neutron and nuclear β-decays as well as the contribution of the quark electric dipole moment (EDM) to the neutron EDM. We present results from the QCDSF/UKQCD/CSSM collaboration for the tensor charge, gT, using lattice QCD methods and the Feynman-Hellmann theorem. We use a flavour symmetry breaking method to systematically approach the physical quark mass using ensembles that span three lattice spacings. 

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