@article{46121, author = {{Altenkort, Luis and Eller, Alexander M. and Kaczmarek, O. and Mazur, Lukas and Moore, Guy D. and Shu, Hai-Tao}}, issn = {{2470-0010}}, journal = {{Physical Review D}}, number = {{9}}, publisher = {{American Physical Society (APS)}}, title = {{{Lattice QCD noise reduction for bosonic correlators through blocking}}}, doi = {{10.1103/physrevd.105.094505}}, volume = {{105}}, year = {{2022}}, } @unpublished{33493, abstract = {{Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical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.}}, author = {{Gavini, Vikram and Baroni, Stefano and Blum, Volker and Bowler, David R. and Buccheri, Alexander and Chelikowsky, James R. and Das, Sambit and Dawson, William and Delugas, Pietro and Dogan, Mehmet and Draxl, Claudia and Galli, Giulia and Genovese, Luigi and Giannozzi, Paolo and Giantomassi, Matteo and Gonze, Xavier and Govoni, Marco and Gulans, Andris and Gygi, François and Herbert, John M. and Kokott, Sebastian and Kühne, Thomas and Liou, Kai-Hsin and Miyazaki, Tsuyoshi and Motamarri, Phani and Nakata, Ayako and Pask, John E. and Plessl, Christian and Ratcliff, Laura E. and Richard, Ryan M. and Rossi, Mariana and Schade, Robert and Scheffler, Matthias and Schütt, Ole and Suryanarayana, Phanish and Torrent, Marc and Truflandier, Lionel and Windus, Theresa L. and Xu, Qimen and Yu, Victor W. -Z. and Perez, Danny}}, booktitle = {{arXiv:2209.12747}}, title = {{{Roadmap on Electronic Structure Codes in the Exascale Era}}}, year = {{2022}}, } @inproceedings{46193, author = {{Karp, Martin and Podobas, Artur and Kenter, Tobias and Jansson, Niclas and Plessl, Christian and Schlatter, Philipp and Markidis, Stefano}}, booktitle = {{International Conference on High Performance Computing in Asia-Pacific Region}}, publisher = {{ACM}}, title = {{{A High-Fidelity Flow Solver for Unstructured Meshes on Field-Programmable Gate Arrays: Design, Evaluation, and Future Challenges}}}, doi = {{10.1145/3492805.3492808}}, year = {{2022}}, } @unpublished{32404, abstract = {{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.}}, author = {{Kühne, Thomas and Plessl, Christian and Schade, Robert and Schütt, Ole}}, booktitle = {{arXiv:2205.14741}}, title = {{{CP2K on the road to exascale}}}, year = {{2022}}, } @article{33226, abstract = {{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.}}, author = {{Schade, Robert and Bauer, Carsten and Tamoev, Konstantin and Mazur, Lukas and Plessl, Christian and Kühne, Thomas}}, journal = {{Phys. Rev. Research}}, pages = {{033160}}, publisher = {{American Physical Society}}, title = {{{Parallel quantum chemistry on noisy intermediate-scale quantum computers}}}, doi = {{10.1103/PhysRevResearch.4.033160}}, volume = {{4}}, year = {{2022}}, } @unpublished{46275, abstract = {{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.}}, author = {{Gavini, Vikram and Baroni, Stefano and Blum, Volker and Bowler, David R. and Buccheri, Alexander and Chelikowsky, James R. and Das, Sambit and Dawson, William and Delugas, Pietro and Dogan, Mehmet and Draxl, Claudia and Galli, Giulia and Genovese, Luigi and Giannozzi, Paolo and Giantomassi, Matteo and Gonze, Xavier and Govoni, Marco and Gulans, Andris and Gygi, François and Herbert, John M. and Kokott, Sebastian and Kühne, Thomas and Liou, Kai-Hsin and Miyazaki, Tsuyoshi and Motamarri, Phani and Nakata, Ayako and Pask, John E. and Plessl, Christian and Ratcliff, Laura E. and Richard, Ryan M. and Rossi, Mariana and Schade, Robert and Scheffler, Matthias and Schütt, Ole and Suryanarayana, Phanish and Torrent, Marc and Truflandier, Lionel and Windus, Theresa L. and Xu, Qimen and Yu, Victor W. -Z. and Perez, Danny}}, booktitle = {{arXiv:2209.12747}}, title = {{{Roadmap on Electronic Structure Codes in the Exascale Era}}}, year = {{2022}}, } @article{33684, author = {{Schade, Robert and Kenter, Tobias and Elgabarty, Hossam and Lass, Michael and Schütt, Ole and Lazzaro, Alfio and Pabst, Hans and Mohr, Stephan and Hutter, Jürg and Kühne, Thomas and Plessl, Christian}}, issn = {{0167-8191}}, journal = {{Parallel Computing}}, keywords = {{Artificial Intelligence, Computer Graphics and Computer-Aided Design, Computer Networks and Communications, Hardware and Architecture, Theoretical Computer Science, Software}}, publisher = {{Elsevier BV}}, title = {{{Towards electronic structure-based ab-initio molecular dynamics simulations with hundreds of millions of atoms}}}, doi = {{10.1016/j.parco.2022.102920}}, volume = {{111}}, year = {{2022}}, } @article{27364, author = {{Meyer, Marius and Kenter, Tobias and Plessl, Christian}}, issn = {{0743-7315}}, journal = {{Journal of Parallel and Distributed Computing}}, title = {{{In-depth FPGA Accelerator Performance Evaluation with Single Node Benchmarks from the HPC Challenge Benchmark Suite for Intel and Xilinx FPGAs using OpenCL}}}, doi = {{10.1016/j.jpdc.2021.10.007}}, year = {{2022}}, } @article{50146, abstract = {{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.}}, author = {{Moroder, Mattia and Grundner, Martin and Damanet, François and Schollwöck, Ulrich and Mardazad, Sam and Flannigan, Stuart and Köhler, Thomas and Paeckel, Sebastian}}, journal = {{Physical Review B 107, 214310 (2023)}}, title = {{{Stable bipolarons in open quantum systems}}}, doi = {{10.1103/PhysRevB.107.214310}}, year = {{2022}}, } @article{50148, abstract = {{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.}}, author = {{Borghini, Nicolas and Borrell, Marc and Feld, Nina and Roch, Hendrik and Schlichting, Sören and Werthmann, Clemens}}, journal = {{Phys. Rev. C 107 (2023) 034905}}, title = {{{Statistical analysis of initial state and final state response in heavy-ion collisions}}}, doi = {{10.1103/PhysRevC.107.034905}}, year = {{2022}}, } @article{50149, abstract = {{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.}}, author = {{Lesch, Elena and Schilling, Maximilian T and Brenner, Sarah and Yang, Yingying and Gruss, Oliver J and Knoop, Volker and Schallenberg-Rüdinger, Mareike}}, issn = {{0305-1048}}, journal = {{Nucleic Acids Research}}, keywords = {{Genetics}}, number = {{17}}, pages = {{9966--9983}}, publisher = {{Oxford University Press (OUP)}}, title = {{{Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells}}}, doi = {{10.1093/nar/gkac752}}, volume = {{50}}, year = {{2022}}, } @article{28099, abstract = {{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.}}, author = {{Menzel, Johannes and Plessl, Christian and Kenter, Tobias}}, issn = {{1936-7406}}, journal = {{ACM Transactions on Reconfigurable Technology and Systems}}, number = {{1}}, pages = {{1--30}}, title = {{{The Strong Scaling Advantage of FPGAs in HPC for N-body Simulations}}}, doi = {{10.1145/3491235}}, volume = {{15}}, year = {{2021}}, } @inproceedings{27365, author = {{Meyer, Marius}}, booktitle = {{Proceedings of the 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies}}, title = {{{Towards Performance Characterization of FPGAs in Context of HPC using OpenCL Benchmarks}}}, doi = {{10.1145/3468044.3468058}}, year = {{2021}}, } @inproceedings{20886, author = {{Nickchen, Tobias and Heindorf, Stefan and Engels, Gregor}}, booktitle = {{Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision}}, location = {{Hawaii}}, pages = {{1994--2002}}, title = {{{Generating Physically Sound Training Data for Image Recognition of Additively Manufactured Parts}}}, year = {{2021}}, } @article{32243, abstract = {{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.}}, author = {{Dabelow, Lennart and Bo, Stefano and Eichhorn, Ralf}}, issn = {{1742-5468}}, journal = {{Journal of Statistical Mechanics: Theory and Experiment}}, keywords = {{Statistics, Probability and Uncertainty, Statistics and Probability, Statistical and Nonlinear Physics}}, number = {{3}}, publisher = {{IOP Publishing}}, title = {{{How irreversible are steady-state trajectories of a trapped active particle?}}}, doi = {{10.1088/1742-5468/abe6fd}}, volume = {{2021}}, year = {{2021}}, } @unpublished{32244, abstract = {{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.}}, author = {{Schade, Robert and Kenter, Tobias and Elgabarty, Hossam and Lass, Michael and Schütt, Ole and Lazzaro, Alfio and Pabst, Hans and Mohr, Stephan and Hutter, Jürg and Kühne, Thomas D. and Plessl, Christian}}, booktitle = {{arXiv:2104.08245}}, title = {{{Towards Electronic Structure-Based Ab-Initio Molecular Dynamics Simulations with Hundreds of Millions of Atoms}}}, year = {{2021}}, } @unpublished{32245, abstract = {{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.}}, author = {{Farheen, Henna and Leuteritz, Till and Linden, Stefan and Myroshnychenko, Viktor and Förstner, Jens}}, booktitle = {{arXiv:2106.02468}}, title = {{{Optimization of optical waveguide antennas for directive emission of light}}}, year = {{2021}}, } @unpublished{32236, abstract = {{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.}}, author = {{Rose, H. and Tikhonova, O. V. and Meier, T. and Sharapova, P. }}, booktitle = {{arXiv:2109.00842}}, title = {{{Steady states of $Λ$-type three-level systems excited by quantum light in lossy cavities}}}, year = {{2021}}, } @article{46122, author = {{Kaczmarek, Olaf and Mazur, Lukas and Sharma, Sayantan}}, issn = {{2470-0010}}, journal = {{Physical Review D}}, number = {{9}}, publisher = {{American Physical Society (APS)}}, title = {{{Eigenvalue spectra of QCD and the fate of UA(1) breaking towards the chiral limit}}}, doi = {{10.1103/physrevd.104.094518}}, volume = {{104}}, year = {{2021}}, } @article{46124, author = {{Altenkort, Luis and Eller, Alexander M. and Kaczmarek, O. and Mazur, Lukas and Moore, Guy D. and Shu, H.-T.}}, issn = {{2470-0010}}, journal = {{Physical Review D}}, number = {{1}}, publisher = {{American Physical Society (APS)}}, title = {{{Heavy quark momentum diffusion from the lattice using gradient flow}}}, doi = {{10.1103/physrevd.103.014511}}, volume = {{103}}, year = {{2021}}, }