TY - JOUR AB - The rise of exascale supercomputers has fueled competition among GPU vendors, driving lattice QCD developers to write code that supports multiple APIs. Moreover, new developments in algorithms and physics research require frequent updates to existing software. These challenges have to be balanced against constantly changing personnel. At the same time, there is a wide range of applications for HISQ fermions in QCD studies. This situation encourages the development of software featuring a HISQ action that is flexible, high-performing, open source, easy to use, and easy to adapt. In this technical paper, we explain the design strategy, provide implementation details, list available algorithms and modules, and show key performance indicators for SIMULATeQCD, a simple multi-GPU lattice code for large-scale QCD calculations, mainly developed and used by the HotQCD collaboration. The code is publicly available on GitHub. AU - Mazur, Lukas AU - Bollweg, Dennis AU - Clarke, David A. AU - Altenkort, Luis AU - Kaczmarek, Olaf AU - Larsen, Rasmus AU - Shu, Hai-Tao AU - Goswami, Jishnu AU - Scior, Philipp AU - Sandmeyer, Hauke AU - Neumann, Marius AU - Dick, Henrik AU - Ali, Sajid AU - Kim, Jangho AU - Schmidt, Christian AU - Petreczky, Peter AU - Mukherjee, Swagato ID - 46120 JF - Computer Physics Communications TI - SIMULATeQCD: A simple multi-GPU lattice code for QCD calculations ER - TY - JOUR AU - Altenkort, Luis AU - Eller, Alexander M. AU - Francis, Anthony AU - Kaczmarek, Olaf AU - Mazur, Lukas AU - Moore, Guy D. AU - Shu, Hai-Tao ID - 46119 IS - 1 JF - Physical Review D SN - 2470-0010 TI - Viscosity of pure-glue QCD from the lattice VL - 108 ER - TY - JOUR AB - While FPGA accelerator boards and their respective high-level design tools are maturing, there is still a lack of multi-FPGA applications, libraries, and not least, benchmarks and reference implementations towards sustained HPC usage of these devices. As in the early days of GPUs in HPC, for workloads that can reasonably be decoupled into loosely coupled working sets, multi-accelerator support can be achieved by using standard communication interfaces like MPI on the host side. However, for performance and productivity, some applications can profit from a tighter coupling of the accelerators. FPGAs offer unique opportunities here when extending the dataflow characteristics to their communication interfaces. In this work, we extend the HPCC FPGA benchmark suite by multi-FPGA support and three missing benchmarks that particularly characterize or stress inter-device communication: b_eff, PTRANS, and LINPACK. With all benchmarks implemented for current boards with Intel and Xilinx FPGAs, we established a baseline for multi-FPGA performance. Additionally, for the communication-centric benchmarks, we explored the potential of direct FPGA-to-FPGA communication with a circuit-switched inter-FPGA network that is currently only available for one of the boards. The evaluation with parallel execution on up to 26 FPGA boards makes use of one of the largest academic FPGA installations. AU - Meyer, Marius AU - Kenter, Tobias AU - Plessl, Christian ID - 38041 JF - ACM Transactions on Reconfigurable Technology and Systems KW - General Computer Science SN - 1936-7406 TI - Multi-FPGA Designs and Scaling of HPC Challenge Benchmarks via MPI and Circuit-Switched Inter-FPGA Networks ER - TY - CHAP AU - Hansmeier, Tim AU - Kenter, Tobias AU - Meyer, Marius AU - Riebler, Heinrich AU - Platzner, Marco AU - Plessl, Christian ED - Haake, Claus-Jochen ED - Meyer auf der Heide, Friedhelm ED - Platzner, Marco ED - Wachsmuth, Henning ED - Wehrheim, Heike ID - 45893 T2 - On-The-Fly Computing -- Individualized IT-services in dynamic markets TI - Compute Centers I: Heterogeneous Execution Environments VL - 412 ER - TY - CONF AU - Opdenhövel, Jan-Oliver AU - Plessl, Christian AU - Kenter, Tobias ID - 46190 T2 - Proceedings of the 13th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies TI - Mutation Tree Reconstruction of Tumor Cells on FPGAs Using a Bit-Level Matrix Representation ER - TY - CONF AU - Faj, Jennifer AU - Kenter, Tobias AU - Faghih-Naini, Sara AU - Plessl, Christian AU - Aizinger, Vadym ID - 46188 T2 - Proceedings of the Platform for Advanced Scientific Computing Conference TI - Scalable Multi-FPGA Design of a Discontinuous Galerkin Shallow-Water Model on Unstructured Meshes ER - TY - CONF AU - Prouveur, Charles AU - Haefele, Matthieu AU - Kenter, Tobias AU - Voss, Nils ID - 46189 T2 - Proceedings of the Platform for Advanced Scientific Computing Conference TI - FPGA Acceleration for HPC Supercapacitor Simulations ER - TY - CONF AB - The computation of electron repulsion integrals (ERIs) over Gaussian-type orbitals (GTOs) is a challenging problem in quantum-mechanics-based atomistic simulations. In practical simulations, several trillions of ERIs may have to be computed for every time step. In this work, we investigate FPGAs as accelerators for the ERI computation. We use template parameters, here within the Intel oneAPI tool flow, to create customized designs for 256 different ERI quartet classes, based on their orbitals. To maximize data reuse, all intermediates are buffered in FPGA on-chip memory with customized layout. The pre-calculation of intermediates also helps to overcome data dependencies caused by multi-dimensional recurrence relations. The involved loop structures are partially or even fully unrolled for high throughput of FPGA kernels. Furthermore, a lossy compression algorithm utilizing arbitrary bitwidth integers is integrated in the FPGA kernels. To our best knowledge, this is the first work on ERI computation on FPGAs that supports more than just the single most basic quartet class. Also, the integration of ERI computation and compression it a novelty that is not even covered by CPU or GPU libraries so far. Our evaluation shows that using 16-bit integer for the ERI compression, the fastest FPGA kernels exceed the performance of 10 GERIS ($10 \times 10^9$ ERIs per second) on one Intel Stratix 10 GX 2800 FPGA, with maximum absolute errors around $10^{-7}$ - $10^{-5}$ Hartree. The measured throughput can be accurately explained by a performance model. The FPGA kernels deployed on 2 FPGAs outperform similar computations using the widely used libint reference on a two-socket server with 40 Xeon Gold 6148 CPU cores of the same process technology by factors up to 6.0x and on a new two-socket server with 128 EPYC 7713 CPU cores by up to 1.9x. AU - Wu, Xin AU - Kenter, Tobias AU - Schade, Robert AU - Kühne, Thomas AU - Plessl, Christian ID - 43228 T2 - 2023 IEEE 31st Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM) TI - Computing and Compressing Electron Repulsion Integrals on FPGAs ER - TY - JOUR AB - The non-orthogonal local submatrix method applied to electronic structure–based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32-mixed floating-point arithmetic when using 4400 NVIDIA A100 GPUs of the Perlmutter system. This is enabled by a modification of the original method that pushes the sustained fraction of the peak performance to about 80%. Example calculations are performed for SARS-CoV-2 spike proteins with up to 83 million atoms. AU - Schade, Robert AU - Kenter, Tobias AU - Elgabarty, Hossam AU - Lass, Michael AU - Kühne, Thomas AU - Plessl, Christian ID - 45361 JF - The International Journal of High Performance Computing Applications KW - Hardware and Architecture KW - Theoretical Computer Science KW - Software SN - 1094-3420 TI - Breaking the exascale barrier for the electronic structure problem in ab-initio molecular dynamics ER - TY - GEN AB - Viscous hydrodynamics serves as a successful mesoscopic description of the Quark-Gluon Plasma produced in relativistic heavy-ion collisions. In order to investigate, how such an effective description emerges from the underlying microscopic dynamics we calculate the hydrodynamic and non-hydrodynamic modes of linear response in the sound channel from a first-principle calculation in kinetic theory. We do this with a new approach wherein we discretize the collision kernel to directly calculate eigenvalues and eigenmodes of the evolution operator. This allows us to study the Green's functions at any point in the complex frequency space. Our study focuses on scalar theory with quartic interaction and we find that the analytic structure of Green's functions in the complex plane is far more complicated than just poles or cuts which is a first step towards an equivalent study in QCD kinetic theory. AU - Ochsenfeld, Stephan AU - Schlichting, Sören ID - 50172 T2 - arXiv:2308.04491 TI - Hydrodynamic and Non-hydrodynamic Excitations in Kinetic Theory -- A Numerical Analysis in Scalar Field Theory ER - TY - GEN AB - Memory Gym presents a suite of 2D partially observable environments, namely Mortar Mayhem, Mystery Path, and Searing Spotlights, designed to benchmark memory capabilities in decision-making agents. These environments, originally with finite tasks, are expanded into innovative, endless formats, mirroring the escalating challenges of cumulative memory games such as ``I packed my bag''. This progression in task design shifts the focus from merely assessing sample efficiency to also probing the levels of memory effectiveness in dynamic, prolonged scenarios. To address the gap in available memory-based Deep Reinforcement Learning baselines, we introduce an implementation that integrates Transformer-XL (TrXL) with Proximal Policy Optimization. This approach utilizes TrXL as a form of episodic memory, employing a sliding window technique. Our comparative study between the Gated Recurrent Unit (GRU) and TrXL reveals varied performances across different settings. TrXL, on the finite environments, demonstrates superior sample efficiency in Mystery Path and outperforms in Mortar Mayhem. However, GRU is more efficient on Searing Spotlights. Most notably, in all endless tasks, GRU makes a remarkable resurgence, consistently outperforming TrXL by significant margins. Website and Source Code: https://github.com/MarcoMeter/endless-memory-gym/ AU - Pleines, Marco AU - Pallasch, Matthias AU - Zimmer, Frank AU - Preuss, Mike ID - 50221 T2 - arXiv:2309.17207 TI - Memory Gym: Towards Endless Tasks to Benchmark Memory Capabilities of Agents ER - TY - CHAP AU - Alt, Christoph AU - Kenter, Tobias AU - Faghih-Naini, Sara AU - Faj, Jennifer AU - Opdenhövel, Jan-Oliver AU - Plessl, Christian AU - Aizinger, Vadym AU - Hönig, Jan AU - Köstler, Harald ID - 46191 SN - 0302-9743 T2 - Lecture Notes in Computer Science TI - Shallow Water DG Simulations on FPGAs: Design and Comparison of a Novel Code Generation Pipeline ER - TY - GEN AB - This preprint makes the claim of having computed the $9^{th}$ Dedekind Number. This was done by building an efficient FPGA Accelerator for the core operation of the process, and parallelizing it on the Noctua 2 Supercluster at Paderborn University. The resulting value is 286386577668298411128469151667598498812366. This value can be verified in two steps. We have made the data file containing the 490M results available, each of which can be verified separately on CPU, and the whole file sums to our proposed value. AU - Van Hirtum, Lennart AU - De Causmaecker, Patrick AU - Goemaere, Jens AU - Kenter, Tobias AU - Riebler, Heinrich AU - Lass, Michael AU - Plessl, Christian ID - 43439 T2 - arXiv:2304.03039 TI - A computation of D(9) using FPGA Supercomputing ER - TY - GEN AB - We investigate the early time development of the anisotropic transverse flow and spatial eccentricities of a fireball with various particle-based transport approaches using a fixed initial condition. In numerical simulations ranging from the quasi-collisionless case to the hydrodynamic regime, we find that the onset of $v_n$ and of related measures of anisotropic flow can be described with a simple power-law ansatz, with an exponent that depends on the amount of rescatterings in the system. In the few-rescatterings regime we perform semi-analytical calculations, based on a systematic expansion in powers of time and the cross section, which can reproduce the numerical findings. AU - Borghini, Nicolas AU - Borrell, Marc AU - Roch, Hendrik ID - 32177 T2 - arXiv:2201.13294 TI - Early time behavior of spatial and momentum anisotropies in kinetic theory across different Knudsen numbers ER - TY - GEN AB - We test the ability of the "escape mechanism" to create the anisotropic flow observed in high-energy nuclear collisions. We compare the flow harmonics $v_n$ in the few-rescatterings regime from two types of transport simulations, with $2\to 2$ and $2\to 0$ collision kernels respectively, and from analytical calculations neglecting the gain term of the Boltzmann equation. We find that the even flow harmonics are similar in the three approaches, while the odd harmonics differ significantly. AU - Bachmann, Benedikt AU - Borghini, Nicolas AU - Feld, Nina AU - Roch, Hendrik ID - 32178 T2 - arXiv:2203.13306 TI - Even anisotropic-flow harmonics are from Venus, odd ones are from Mars ER - TY - JOUR AU - Hou, W AU - Yao, Y AU - Li, Y AU - Peng, B AU - Shi, K AU - Zhou, Z AU - Pan, J AU - Liu, M AU - Hu, J ID - 32183 IS - 1 JF - Frontiers of materials science SN - 2095-025x TI - Linearly shifting ferromagnetic resonance response of La0.7Sr0.3MnO3 thin film for body temperature sensors VL - 16 ER - TY - JOUR AU - Wojciechowski, M ID - 32234 JF - Data Brief SN - 2352-3409 TI - Dataset for random uniform distributions of 2D circles and 3D spheres. VL - 43 ER - TY - THES AU - Lass, Michael ID - 32414 TI - Bringing Massive Parallelism and Hardware Acceleration to Linear Scaling Density Functional Theory Through Targeted Approximations ER - TY - GEN AB - The Julia programming language has evolved into a modern alternative to fill existing gaps in scientific computing and data science applications. Julia leverages a unified and coordinated single-language and ecosystem paradigm and has a proven track record of achieving high performance without sacrificing user productivity. These aspects make Julia a viable alternative to high-performance computing's (HPC's) existing and increasingly costly many-body workflow composition strategy in which traditional HPC languages (e.g., Fortran, C, C++) are used for simulations, and higher-level languages (e.g., Python, R, MATLAB) are used for data analysis and interactive computing. Julia's rapid growth in language capabilities, package ecosystem, and community make it a promising universal language for HPC. This paper presents the views of a multidisciplinary group of researchers from academia, government, and industry that advocate for an HPC software development paradigm that emphasizes developer productivity, workflow portability, and low barriers for entry. We believe that the Julia programming language, its ecosystem, and its community provide modern and powerful capabilities that enable this group's objectives. Crucially, we believe that Julia can provide a feasible and less costly approach to programming scientific applications and workflows that target HPC facilities. In this work, we examine the current practice and role of Julia as a common, end-to-end programming model to address major challenges in scientific reproducibility, data-driven AI/machine learning, co-design and workflows, scalability and performance portability in heterogeneous computing, network communication, data management, and community education. As a result, the diversification of current investments to fulfill the needs of the upcoming decade is crucial as more supercomputing centers prepare for the exascale era. AU - Churavy, Valentin AU - Godoy, William F AU - Bauer, Carsten AU - Ranocha, Hendrik AU - Schlottke-Lakemper, Michael AU - Räss, Ludovic AU - Blaschke, Johannes AU - Giordano, Mosè AU - Schnetter, Erik AU - Omlin, Samuel AU - Vetter, Jeffrey S AU - Edelman, Alan ID - 36879 TI - Bridging HPC Communities through the Julia Programming Language ER - TY - JOUR AB - AbstractTailored nanoscale quantum light sources, matching the specific needs of use cases, are crucial building blocks for photonic quantum technologies. Several different approaches to realize solid-state quantum emitters with high performance have been pursued and different concepts for energy tuning have been established. However, the properties of the emitted photons are always defined by the individual quantum emitter and can therefore not be controlled with full flexibility. Here we introduce an all-optical nonlinear method to tailor and control the single photon emission. We demonstrate a laser-controlled down-conversion process from an excited state of a semiconductor quantum three-level system. Based on this concept, we realize energy tuning and polarization control of the single photon emission with a control-laser field. Our results mark an important step towards tailored single photon emission from a photonic quantum system based on quantum optical principles. AU - Jonas, B. AU - Heinze, Dirk Florian AU - Schöll, E. AU - Kallert, P. AU - Langer, T. AU - Krehs, S. AU - Widhalm, A. AU - Jöns, Klaus AU - Reuter, Dirk AU - Schumacher, Stefan AU - Zrenner, Artur ID - 40523 IS - 1 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - Nonlinear down-conversion in a single quantum dot VL - 13 ER - TY - JOUR AU - Altenkort, Luis AU - Eller, Alexander M. AU - Kaczmarek, O. AU - Mazur, Lukas AU - Moore, Guy D. AU - Shu, Hai-Tao ID - 46121 IS - 9 JF - Physical Review D SN - 2470-0010 TI - Lattice QCD noise reduction for bosonic correlators through blocking VL - 105 ER - TY - GEN AB - Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing. AU - Gavini, Vikram AU - Baroni, Stefano AU - Blum, Volker AU - Bowler, David R. AU - Buccheri, Alexander AU - Chelikowsky, James R. AU - Das, Sambit AU - Dawson, William AU - Delugas, Pietro AU - Dogan, Mehmet AU - Draxl, Claudia AU - Galli, Giulia AU - Genovese, Luigi AU - Giannozzi, Paolo AU - Giantomassi, Matteo AU - Gonze, Xavier AU - Govoni, Marco AU - Gulans, Andris AU - Gygi, François AU - Herbert, John M. AU - Kokott, Sebastian AU - Kühne, Thomas AU - Liou, Kai-Hsin AU - Miyazaki, Tsuyoshi AU - Motamarri, Phani AU - Nakata, Ayako AU - Pask, John E. AU - Plessl, Christian AU - Ratcliff, Laura E. AU - Richard, Ryan M. AU - Rossi, Mariana AU - Schade, Robert AU - Scheffler, Matthias AU - Schütt, Ole AU - Suryanarayana, Phanish AU - Torrent, Marc AU - Truflandier, Lionel AU - Windus, Theresa L. AU - Xu, Qimen AU - Yu, Victor W. -Z. AU - Perez, Danny ID - 33493 T2 - arXiv:2209.12747 TI - Roadmap on Electronic Structure Codes in the Exascale Era ER - TY - CONF AU - Karp, Martin AU - Podobas, Artur AU - Kenter, Tobias AU - Jansson, Niclas AU - Plessl, Christian AU - Schlatter, Philipp AU - Markidis, Stefano ID - 46193 T2 - International Conference on High Performance Computing in Asia-Pacific Region TI - A High-Fidelity Flow Solver for Unstructured Meshes on Field-Programmable Gate Arrays: Design, Evaluation, and Future Challenges ER - TY - GEN AB - The CP2K program package, which can be considered as the swiss army knife of atomistic simulations, is presented with a special emphasis on ab-initio molecular dynamics using the second-generation Car-Parrinello method. After outlining current and near-term development efforts with regards to massively parallel low-scaling post-Hartree-Fock and eigenvalue solvers, novel approaches on how we plan to take full advantage of future low-precision hardware architectures are introduced. Our focus here is on combining our submatrix method with the approximate computing paradigm to address the immanent exascale era. AU - Kühne, Thomas AU - Plessl, Christian AU - Schade, Robert AU - Schütt, Ole ID - 32404 T2 - arXiv:2205.14741 TI - CP2K on the road to exascale ER - TY - JOUR AB - A parallel hybrid quantum-classical algorithm for the solution of the quantum-chemical ground-state energy problem on gate-based quantum computers is presented. This approach is based on the reduced density-matrix functional theory (RDMFT) formulation of the electronic structure problem. For that purpose, the density-matrix functional of the full system is decomposed into an indirectly coupled sum of density-matrix functionals for all its subsystems using the adaptive cluster approximation to RDMFT. The approximations involved in the decomposition and the adaptive cluster approximation itself can be systematically converged to the exact result. The solutions for the density-matrix functionals of the effective subsystems involves a constrained minimization over many-particle states that are approximated by parametrized trial states on the quantum computer similarly to the variational quantum eigensolver. The independence of the density-matrix functionals of the effective subsystems introduces a new level of parallelization and allows for the computational treatment of much larger molecules on a quantum computer with a given qubit count. In addition, for the proposed algorithm techniques are presented to reduce the qubit count, the number of quantum programs, as well as its depth. The evaluation of a density-matrix functional as the essential part of our approach is demonstrated for Hubbard-like systems on IBM quantum computers based on superconducting transmon qubits. AU - Schade, Robert AU - Bauer, Carsten AU - Tamoev, Konstantin AU - Mazur, Lukas AU - Plessl, Christian AU - Kühne, Thomas ID - 33226 JF - Phys. Rev. Research TI - Parallel quantum chemistry on noisy intermediate-scale quantum computers VL - 4 ER - TY - GEN AB - Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing. AU - Gavini, Vikram AU - Baroni, Stefano AU - Blum, Volker AU - Bowler, David R. AU - Buccheri, Alexander AU - Chelikowsky, James R. AU - Das, Sambit AU - Dawson, William AU - Delugas, Pietro AU - Dogan, Mehmet AU - Draxl, Claudia AU - Galli, Giulia AU - Genovese, Luigi AU - Giannozzi, Paolo AU - Giantomassi, Matteo AU - Gonze, Xavier AU - Govoni, Marco AU - Gulans, Andris AU - Gygi, François AU - Herbert, John M. AU - Kokott, Sebastian AU - Kühne, Thomas AU - Liou, Kai-Hsin AU - Miyazaki, Tsuyoshi AU - Motamarri, Phani AU - Nakata, Ayako AU - Pask, John E. AU - Plessl, Christian AU - Ratcliff, Laura E. AU - Richard, Ryan M. AU - Rossi, Mariana AU - Schade, Robert AU - Scheffler, Matthias AU - Schütt, Ole AU - Suryanarayana, Phanish AU - Torrent, Marc AU - Truflandier, Lionel AU - Windus, Theresa L. AU - Xu, Qimen AU - Yu, Victor W. -Z. AU - Perez, Danny ID - 46275 T2 - arXiv:2209.12747 TI - Roadmap on Electronic Structure Codes in the Exascale Era ER - TY - JOUR AU - Schade, Robert AU - Kenter, Tobias AU - Elgabarty, Hossam AU - Lass, Michael AU - Schütt, Ole AU - Lazzaro, Alfio AU - Pabst, Hans AU - Mohr, Stephan AU - Hutter, Jürg AU - Kühne, Thomas AU - Plessl, Christian ID - 33684 JF - Parallel Computing KW - Artificial Intelligence KW - Computer Graphics and Computer-Aided Design KW - Computer Networks and Communications KW - Hardware and Architecture KW - Theoretical Computer Science KW - Software SN - 0167-8191 TI - Towards electronic structure-based ab-initio molecular dynamics simulations with hundreds of millions of atoms VL - 111 ER - TY - JOUR AU - Meyer, Marius AU - Kenter, Tobias AU - Plessl, Christian ID - 27364 JF - Journal of Parallel and Distributed Computing SN - 0743-7315 TI - In-depth FPGA Accelerator Performance Evaluation with Single Node Benchmarks from the HPC Challenge Benchmark Suite for Intel and Xilinx FPGAs using OpenCL ER - TY - JOUR AB - Recent advances in numerical methods significantly pushed forward the understanding of electrons coupled to quantized lattice vibrations. At this stage, it becomes increasingly important to also account for the effects of physically inevitable environments. In particular, we study the transport properties of the Hubbard-Holstein Hamiltonian that models a large class of materials characterized by strong electron-phonon coupling, in contact with a dissipative environment. Even in the one-dimensional and isolated case, simulating the quantum dynamics of such a system with high accuracy is very challenging due to the infinite dimensionality of the phononic Hilbert spaces. For this reason, the effects of dissipation on the conductance properties of such systems have not been investigated systematically so far. We combine the non-Markovian hierarchy of pure states method and the Markovian quantum jumps method with the newly introduced projected purified density-matrix renormalization group, creating powerful tensor-network methods for dissipative quantum many-body systems. Investigating their numerical properties, we find a significant speedup up to a factor $\sim 30$ compared to conventional tensor-network techniques. We apply these methods to study dissipative quenches, aiming for an in-depth understanding of the formation, stability, and quasi-particle properties of bipolarons. Surprisingly, our results show that in the metallic phase dissipation localizes the bipolarons, which is reminiscent of an indirect quantum Zeno effect. However, the bipolaronic binding energy remains mainly unaffected, even in the presence of strong dissipation, exhibiting remarkable bipolaron stability. These findings shed light on the problem of designing real materials exhibiting phonon-mediated high-$T_\mathrm{C}$ superconductivity. AU - Moroder, Mattia AU - Grundner, Martin AU - Damanet, François AU - Schollwöck, Ulrich AU - Mardazad, Sam AU - Flannigan, Stuart AU - Köhler, Thomas AU - Paeckel, Sebastian ID - 50146 JF - Physical Review B 107, 214310 (2023) TI - Stable bipolarons in open quantum systems ER - TY - JOUR AB - We develop a general decomposition of an ensemble of initial density profiles in terms of an average state and a basis of modes that represent the event-by-event fluctuations of the initial state. The basis is determined such that the probability distributions of the amplitudes of different modes are uncorrelated. Based on this decomposition, we quantify the different types and probabilities of event-by-event fluctuations in Glauber and Saturation models and investigate how the various modes affect different characteristics of the initial state. We perform simulations of the dynamical evolution with KoMPoST and MUSIC to investigate the impact of the modes on final-state observables and their correlations. AU - Borghini, Nicolas AU - Borrell, Marc AU - Feld, Nina AU - Roch, Hendrik AU - Schlichting, Sören AU - Werthmann, Clemens ID - 50148 JF - Phys. Rev. C 107 (2023) 034905 TI - Statistical analysis of initial state and final state response in heavy-ion collisions ER - TY - JOUR AB - Abstract RNA editing processes are strikingly different in animals and plants. Up to thousands of specific cytidines are converted into uridines in plant chloroplasts and mitochondria whereas up to millions of adenosines are converted into inosines in animal nucleo-cytosolic RNAs. It is unknown whether these two different RNA editing machineries are mutually incompatible. RNA-binding pentatricopeptide repeat (PPR) proteins are the key factors of plant organelle cytidine-to-uridine RNA editing. The complete absence of PPR mediated editing of cytosolic RNAs might be due to a yet unknown barrier that prevents its activity in the cytosol. Here, we transferred two plant mitochondrial PPR-type editing factors into human cell lines to explore whether they could operate in the nucleo-cytosolic environment. PPR56 and PPR65 not only faithfully edited their native, co-transcribed targets but also different sets of off-targets in the human background transcriptome. More than 900 of such off-targets with editing efficiencies up to 91%, largely explained by known PPR-RNA binding properties, were identified for PPR56. Engineering two crucial amino acid positions in its PPR array led to predictable shifts in target recognition. We conclude that plant PPR editing factors can operate in the entirely different genetic environment of the human nucleo-cytosol and can be intentionally re-engineered towards new targets. AU - Lesch, Elena AU - Schilling, Maximilian T AU - Brenner, Sarah AU - Yang, Yingying AU - Gruss, Oliver J AU - Knoop, Volker AU - Schallenberg-Rüdinger, Mareike ID - 50149 IS - 17 JF - Nucleic Acids Research KW - Genetics SN - 0305-1048 TI - Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells VL - 50 ER - TY - JOUR AB - N-body methods are one of the essential algorithmic building blocks of high-performance and parallel computing. Previous research has shown promising performance for implementing n-body simulations with pairwise force calculations on FPGAs. However, to avoid challenges with accumulation and memory access patterns, the presented designs calculate each pair of forces twice, along with both force sums of the involved particles. Also, they require large problem instances with hundreds of thousands of particles to reach their respective peak performance, limiting the applicability for strong scaling scenarios. This work addresses both issues by presenting a novel FPGA design that uses each calculated force twice and overlaps data transfers and computations in a way that allows to reach peak performance even for small problem instances, outperforming previous single precision results even in double precision, and scaling linearly over multiple interconnected FPGAs. For a comparison across architectures, we provide an equally optimized CPU reference, which for large problems actually achieves higher peak performance per device, however, given the strong scaling advantages of the FPGA design, in parallel setups with few thousand particles per device, the FPGA platform achieves highest performance and power efficiency. AU - Menzel, Johannes AU - Plessl, Christian AU - Kenter, Tobias ID - 28099 IS - 1 JF - ACM Transactions on Reconfigurable Technology and Systems SN - 1936-7406 TI - The Strong Scaling Advantage of FPGAs in HPC for N-body Simulations VL - 15 ER - TY - CONF AU - Meyer, Marius ID - 27365 T2 - Proceedings of the 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies TI - Towards Performance Characterization of FPGAs in Context of HPC using OpenCL Benchmarks ER - TY - CONF AU - Nickchen, Tobias AU - Heindorf, Stefan AU - Engels, Gregor ID - 20886 T2 - Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision TI - Generating Physically Sound Training Data for Image Recognition of Additively Manufactured Parts ER - TY - JOUR AB - Abstract The defining feature of active particles is that they constantly propel themselves by locally converting chemical energy into directed motion. This active self-propulsion prevents them from equilibrating with their thermal environment (e.g. an aqueous solution), thus keeping them permanently out of equilibrium. Nevertheless, the spatial dynamics of active particles might share certain equilibrium features, in particular in the steady state. We here focus on the time-reversal symmetry of individual spatial trajectories as a distinct equilibrium characteristic. We investigate to what extent the steady-state trajectories of a trapped active particle obey or break this time-reversal symmetry. Within the framework of active Ornstein–Uhlenbeck particles we find that the steady-state trajectories in a harmonic potential fulfill path-wise time-reversal symmetry exactly, while this symmetry is typically broken in anharmonic potentials. AU - Dabelow, Lennart AU - Bo, Stefano AU - Eichhorn, Ralf ID - 32243 IS - 3 JF - Journal of Statistical Mechanics: Theory and Experiment KW - Statistics KW - Probability and Uncertainty KW - Statistics and Probability KW - Statistical and Nonlinear Physics SN - 1742-5468 TI - How irreversible are steady-state trajectories of a trapped active particle? VL - 2021 ER - TY - GEN AB - We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine learning potentials. We achieve this breakthrough by combining innovations in linear-scaling AIMD, efficient and approximate sparse linear algebra, low and mixed-precision floating-point computation on GPUs, and a compensation scheme for the errors introduced by numerical approximations. The core of our work is the non-orthogonalized local submatrix method (NOLSM), which scales very favorably to massively parallel computing systems and translates large sparse matrix operations into highly parallel, dense matrix operations that are ideally suited to hardware accelerators. We demonstrate that the NOLSM method, which is at the center point of each AIMD step, is able to achieve a sustained performance of 324 PFLOP/s in mixed FP16/FP32 precision corresponding to an efficiency of 67.7% when running on 1536 NVIDIA A100 GPUs. AU - Schade, Robert AU - Kenter, Tobias AU - Elgabarty, Hossam AU - Lass, Michael AU - Schütt, Ole AU - Lazzaro, Alfio AU - Pabst, Hans AU - Mohr, Stephan AU - Hutter, Jürg AU - Kühne, Thomas D. AU - Plessl, Christian ID - 32244 T2 - arXiv:2104.08245 TI - Towards Electronic Structure-Based Ab-Initio Molecular Dynamics Simulations with Hundreds of Millions of Atoms ER - TY - GEN AB - Optical travelling wave antennas offer unique opportunities to control and selectively guide light into a specific direction which renders them as excellent candidates for optical communication and sensing. These applications require state of the art engineering to reach optimized functionalities such as high directivity and radiation efficiency, low side lobe level, broadband and tunable capabilities, and compact design. In this work we report on the numerical optimization of the directivity of optical travelling wave antennas made from low-loss dielectric materials using full-wave numerical simulations in conjunction with a particle swarm optimization algorithm. The antennas are composed of a reflector and a director deposited on a glass substrate and an emitter placed in the feed gap between them serves as an internal source of excitation. In particular, we analysed antennas with rectangular- and horn-shaped directors made of either Hafnium dioxide or Silicon. The optimized antennas produce highly directional emission due to the presence of two dominant guided TE modes in the director in addition to leaky modes. These guided modes dominate the far-field emission pattern and govern the direction of the main lobe emission which predominately originates from the end facet of the director. Our work also provides a comprehensive analysis of the modes, radiation patterns, parametric influences, and bandwidths of the antennas that highlights their robust nature. AU - Farheen, Henna AU - Leuteritz, Till AU - Linden, Stefan AU - Myroshnychenko, Viktor AU - Förstner, Jens ID - 32245 T2 - arXiv:2106.02468 TI - Optimization of optical waveguide antennas for directive emission of light ER - TY - GEN AB - The interaction between quantum light and matter is being intensively studied for systems that are enclosed in high-$Q$ cavities which strongly enhance the light-matter coupling. However, for many applications, cavities with lower $Q$-factors are preferred due to the increased spectral width of the cavity mode. Here, we investigate the interaction between quantum light and matter represented by a $\Lambda$-type three-level system in lossy cavities, assuming that cavity losses are the dominant loss mechanism. We demonstrate that cavity losses lead to non-trivial steady states of the electronic occupations that can be controlled by the loss rate and the initial statistics of the quantum fields. The mechanism of formation of such steady states can be understood on the basis of the equations of motion. Analytical expressions for steady states and their numerical simulations are presented and discussed. AU - Rose, H. AU - Tikhonova, O. V. AU - Meier, T. AU - Sharapova, P. ID - 32236 T2 - arXiv:2109.00842 TI - Steady states of $Λ$-type three-level systems excited by quantum light in lossy cavities ER - TY - JOUR AU - Kaczmarek, Olaf AU - Mazur, Lukas AU - Sharma, Sayantan ID - 46122 IS - 9 JF - Physical Review D SN - 2470-0010 TI - Eigenvalue spectra of QCD and the fate of UA(1) breaking towards the chiral limit VL - 104 ER - TY - JOUR AU - Altenkort, Luis AU - Eller, Alexander M. AU - Kaczmarek, O. AU - Mazur, Lukas AU - Moore, Guy D. AU - Shu, H.-T. ID - 46124 IS - 1 JF - Physical Review D SN - 2470-0010 TI - Heavy quark momentum diffusion from the lattice using gradient flow VL - 103 ER - TY - JOUR AU - Altenkort, Luis AU - Eller, Alexander M. AU - Kaczmarek, O. AU - Mazur, Lukas AU - Moore, Guy D. AU - Shu, H.-T. ID - 46123 IS - 11 JF - Physical Review D SN - 2470-0010 TI - Sphaleron rate from Euclidean lattice correlators: An exploration VL - 103 ER - TY - CONF AU - Kenter, Tobias AU - Shambhu, Adesh AU - Faghih-Naini, Sara AU - Aizinger, Vadym ID - 46194 T2 - Proceedings of the Platform for Advanced Scientific Computing Conference TI - Algorithm-hardware co-design of a discontinuous Galerkin shallow-water model for a dataflow architecture on FPGA ER - TY - CONF AU - Karp, Martin AU - Podobas, Artur AU - Jansson, Niclas AU - Kenter, Tobias AU - Plessl, Christian AU - Schlatter, Philipp AU - Markidis, Stefano ID - 46195 T2 - 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) TI - High-Performance Spectral Element Methods on Field-Programmable Gate Arrays : Implementation, Evaluation, and Future Projection ER - TY - CHAP AB - Solving partial differential equations on unstructured grids is a cornerstone of engineering and scientific computing. Nowadays, heterogeneous parallel platforms with CPUs, GPUs, and FPGAs enable energy-efficient and computationally demanding simulations. We developed the HighPerMeshes C++-embedded Domain-Specific Language (DSL) for bridging the abstraction gap between the mathematical and algorithmic formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different parallel programming and runtime models on the other hand. Thus, the HighPerMeshes DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HighPerMeshes DSL, and demonstrate its usage with three examples, a Poisson and monodomain problem, respectively, solved by the continuous finite element method, and the discontinuous Galerkin method for Maxwell’s equation. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters, is presented. Finally, the achievable performance and scalability are demonstrated for a typical example problem on a multi-core CPU cluster. AU - Alhaddad, Samer AU - Förstner, Jens AU - Groth, Stefan AU - Grünewald, Daniel AU - Grynko, Yevgen AU - Hannig, Frank AU - Kenter, Tobias AU - Pfreundt, Franz-Josef AU - Plessl, Christian AU - Schotte, Merlind AU - Steinke, Thomas AU - Teich, Jürgen AU - Weiser, Martin AU - Wende, Florian ID - 21587 KW - tet_topic_hpc SN - 0302-9743 T2 - Euro-Par 2020: Parallel Processing Workshops TI - HighPerMeshes – A Domain-Specific Language for Numerical Algorithms on Unstructured Grids ER - TY - CHAP AU - Ramaswami, Arjun AU - Kenter, Tobias AU - Kühne, Thomas AU - Plessl, Christian ID - 29936 SN - 0302-9743 T2 - Applied Reconfigurable Computing. Architectures, Tools, and Applications TI - Evaluating the Design Space for Offloading 3D FFT Calculations to an FPGA for High-Performance Computing ER - TY - JOUR AU - Alhaddad, Samer AU - Förstner, Jens AU - Groth, Stefan AU - Grünewald, Daniel AU - Grynko, Yevgen AU - Hannig, Frank AU - Kenter, Tobias AU - Pfreundt, Franz‐Josef AU - Plessl, Christian AU - Schotte, Merlind AU - Steinke, Thomas AU - Teich, Jürgen AU - Weiser, Martin AU - Wende, Florian ID - 24788 JF - Concurrency and Computation: Practice and Experience KW - tet_topic_hpc SN - 1532-0626 TI - The HighPerMeshes framework for numerical algorithms on unstructured grids ER - TY - JOUR AB -

The effect of traces of ethanol in supercritical carbon dioxide on the mixture's thermodynamic properties is studied by molecular simulations and Taylor dispersion measurements.

AU - Chatwell, René Spencer AU - Guevara-Carrion, Gabriela AU - Gaponenko, Yuri AU - Shevtsova, Valentina AU - Vrabec, Jadran ID - 32240 IS - 4 JF - Physical Chemistry Chemical Physics KW - Physical and Theoretical Chemistry KW - General Physics and Astronomy SN - 1463-9076 TI - Diffusion of the carbon dioxide–ethanol mixture in the extended critical region VL - 23 ER - TY - CONF AU - Karp, Martin AU - Podobas, Artur AU - Jansson, Niclas AU - Kenter, Tobias AU - Plessl, Christian AU - Schlatter, Philipp AU - Markidis, Stefano ID - 29937 T2 - 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) TI - High-Performance Spectral Element Methods on Field-Programmable Gate Arrays : Implementation, Evaluation, and Future Projection ER - TY - CHAP AU - Nickchen, Tobias AU - Engels, Gregor AU - Lohn, Johannes ID - 18789 SN - 9783030543334 T2 - Industrializing Additive Manufacturing TI - Opportunities of 3D Machine Learning for Manufacturability Analysis and Component Recognition in the Additive Manufacturing Process Chain ER - TY - JOUR AB -

State-of-the-art methods in materials science such as artificial intelligence and data-driven techniques advance the investigation of photovoltaic materials.

AU - Mirhosseini, Hossein AU - Kormath Madam Raghupathy, Ramya AU - Sahoo, Sudhir K. AU - Wiebeler, Hendrik AU - Chugh, Manjusha AU - Kühne, Thomas D. ID - 32246 IS - 46 JF - Physical Chemistry Chemical Physics KW - Physical and Theoretical Chemistry KW - General Physics and Astronomy SN - 1463-9076 TI - In silico investigation of Cu(In,Ga)Se2-based solar cells VL - 22 ER -