AutoPas in ls1 mardyn: Massively parallel particle simulations with node-level auto-tuning
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Hans-Joachim Bungartz | Philipp Neumann | Jadran Vrabec | Steffen Seckler | Matthias Heinen | Fabio Alexander Gratl | H. Bungartz | J. Vrabec | Philipp Neumann | Steffen Seckler | M. Heinen | F. Gratl
[1] Ivo F. Sbalzarini,et al. OpenFPM: A scalable open framework for particle and particle-mesh codes on parallel computers , 2018, Comput. Phys. Commun..
[2] Grigori Fursin. Collective Tuning Initiative: automating and accelerating development and optimization of computing systems , 2009 .
[3] Hans-Joachim Bungartz,et al. Load Balancing for Molecular Dynamics Simulations on Heterogeneous Architectures , 2016, 2016 IEEE 23rd International Conference on High Performance Computing (HiPC).
[4] Ananta Tiwari,et al. Online Adaptive Code Generation and Tuning , 2011, 2011 IEEE International Parallel & Distributed Processing Symposium.
[5] Steve Plimpton,et al. Fast parallel algorithms for short-range molecular dynamics , 1993 .
[6] John A. Nelder,et al. A Simplex Method for Function Minimization , 1965, Comput. J..
[7] P. Hopkins. A new class of accurate, mesh-free hydrodynamic simulation methods , 2014, 1409.7395.
[8] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[9] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[10] Carsten Kutzner,et al. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS , 2015, EASC.
[11] Pablo G. Debenedetti,et al. On the use of the Verlet neighbor list in molecular dynamics , 1990 .
[12] L. Verlet. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .
[13] Peng Wang,et al. Implementing molecular dynamics on hybrid high performance computers - short range forces , 2011, Comput. Phys. Commun..
[14] 王东东,et al. Computer Methods in Applied Mechanics and Engineering , 2004 .
[15] Junichiro Makino,et al. Implementation and performance of FDPS: a framework for developing parallel particle simulation codes , 2016, 1601.03138.
[16] Bruce Hendrickson,et al. Dynamic load balancing in computational mechanics , 2000 .
[17] Stefan Leye,et al. Flexible experimentation in the modeling and simulation framework JAMES II - implications for computational systems biology , 2010, Briefings Bioinform..
[18] I-Hsin Chung,et al. Active Harmony: Towards Automated Performance Tuning , 2002, ACM/IEEE SC 2002 Conference (SC'02).
[19] C. Holm,et al. ESPResSo 4.0 – an extensible software package for simulating soft matter systems , 2018, The European Physical Journal Special Topics.
[20] Roland Ewald,et al. Automatic Algorithm Selection for Complex Simulation Problems , 2011, Vieweg+Teubner Verlag.
[21] Erwin Laure,et al. Solving Software Challenges for Exascale , 2014, Lecture Notes in Computer Science.
[22] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[23] V. Springel. The Cosmological simulation code GADGET-2 , 2005, astro-ph/0505010.
[24] Michael M. Resch,et al. TweTriS: Twenty trillion-atom simulation , 2019, Int. J. High Perform. Comput. Appl..
[25] Pedro Gonnet. Pairwise verlet lists: Combining cell lists and verlet lists to improve memory locality and parallelism , 2012, J. Comput. Chem..
[26] Steven J. Plimpton,et al. Optimizing legacy molecular dynamics software with directive-based offload , 2015, Comput. Phys. Commun..
[27] Stephen M. Longshaw,et al. DualSPHysics: Open-source parallel CFD solver based on Smoothed Particle Hydrodynamics (SPH) , 2015, Comput. Phys. Commun..
[28] Junichiro Makino,et al. A Fast Parallel Treecode with GRAPE , 2004 .
[29] Stefan Becker,et al. ls1 mardyn: The massively parallel molecular dynamics code for large systems , 2014, Journal of chemical theory and computation.
[30] Robert E. Rudd,et al. COARSE-GRAINED MOLECULAR DYNAMICS AND THE ATOMIC LIMIT OF FINITE ELEMENTS , 1998 .
[31] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[32] O'Connell,et al. Molecular dynamics-continuum hybrid computations: A tool for studying complex fluid flows. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[33] Andrey Semin,et al. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency , 2016, SC16: International Conference for High Performance Computing, Networking, Storage and Analysis.
[34] P. Murdin. MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY , 2005 .
[35] Hans-Joachim Bungartz,et al. MaMiCo: Software design for parallel molecular-continuum flow simulations , 2016, Comput. Phys. Commun..
[36] Hans-Joachim Bungartz,et al. AutoPas: Auto-Tuning for Particle Simulations , 2019, 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).