Zobrazeno 1 - 10
of 12
pro vyhledávání: '"Ivo Kabadshow"'
Publikováno v:
SCITEPRESS-Science and Technology Publications 218-225 (2022). doi:10.5220/0011144400003274
12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications, Lisbon, Portugal, 2022-07-14-2022-07-16
12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications, Lisbon, Portugal, 2022-07-14-2022-07-16
Molecular dynamics simulations (MDS), no matter in which form, have always spent a lot of effort on the time-consuming part of direct particle-to-particle interactions (O(N 2 )). Even if the interaction radius of each particle is limited, it remains
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7f9fd7a0b0f028e2f1cf350980d69d4a
https://hdl.handle.net/2128/32457
https://hdl.handle.net/2128/32457
Autor:
Andreas Beckmann, Carsten Kutzner, Helmut Grubmüller, Bartosz Kohnke, Gert Lube, Holger Dachsel, Ivo Kabadshow
Publikováno v:
The international journal of high performance computing applications 35(1), 97-117 (2021). doi:10.1177/1094342020964857
Solving an N-body problem, electrostatic or gravitational, is a crucial task and the main computational bottleneck in many scientific applications. Its direct solution is an ubiquitous showcase example for the compute power of graphics processing uni
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1ef234dcc255322339ffa2b8990e6b9c
https://juser.fz-juelich.de/record/889151
https://juser.fz-juelich.de/record/889151
Publikováno v:
ACM New York, NY, USA 1-10 (2020). doi:10.1145/3394277.3401858
Proceedings of the Platform for Advanced Scientific Computing Conference-ACM New York, NY, USA, 2020.-ISBN 9781450379939-doi:10.1145/3394277.3401858
Proceedings of the Platform for Advanced Scientific Computing Conference-ACM New York, NY, USA, 2020.-ISBN 9781450379939-doi:10.1145/3394277.3401858PASC '20: Platform for Advanced Scientific Computing Conference, Geneva, Switzerland, 2020-06-29-2020-07-01
PASC
Proceedings of the Platform for Advanced Scientific Computing Conference-ACM New York, NY, USA, 2020.-ISBN 9781450379939-doi:10.1145/3394277.3401858
Proceedings of the Platform for Advanced Scientific Computing Conference-ACM New York, NY, USA, 2020.-ISBN 9781450379939-doi:10.1145/3394277.3401858PASC '20: Platform for Advanced Scientific Computing Conference, Geneva, Switzerland, 2020-06-29-2020-07-01
PASC
Today's processors become fatter, not faster. However, the exploitation of these massively parallel compute resources remains a challenge for many traditional HPC applications regarding scalability, portability and programmability. To tackle this cha
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::820fc899839068104e6e4d55da8e49a3
https://hdl.handle.net/2128/26687
https://hdl.handle.net/2128/26687
Autor:
Bartosz Kohnke, Gerrit Groenhof, Andreas Beckmann, Holger Dachsel, Plamen Dobrev, Thomas Ullmann, Helmut Grubmüller, David Haensel, Carsten Kutzner, Ivo Kabadshow, Berk Hess, Laura Morgenstern
Publikováno v:
Software for Exascale Computing-SPPEXA 2016-2019 ISBN: 9783030479558
Software for Exascale Computing
Software for Exascale Computing-SPPEXA 2016-2019
Lecture Notes in Computational Science and Engineering
Cham : Springer International Publishing, Lecture Notes in Computational Science and Engineering 517-543 (2020).
Software for Exascale Computing
Software for Exascale Computing-SPPEXA 2016-2019
Lecture Notes in Computational Science and Engineering
Cham : Springer International Publishing, Lecture Notes in Computational Science and Engineering 517-543 (2020).
Atomistic simulations of large biomolecular systems with chemical variability such as constant pH dynamic protonation offer multiple challenges in high performance computing. One of them is the correct treatment of the involved electrostatics in an e
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::74f85db29d86cc358028b596ef7a01f9
https://doi.org/10.1007/978-3-030-47956-5_17
https://doi.org/10.1007/978-3-030-47956-5_17
Publikováno v:
Lecture Notes in Computer Science ISBN: 9783030504359
ICCS (7)
428-441 (2020). doi:10.1007/978-3-030-50436-6_31
Computational Science – ICCS 2020
Computational Science – ICCS 2020International Conference on Computational Science 2020, ICCS 2020, Amsterdam, The Netherlands, 2020-06-03-2020-06-05
ICCS (7)
428-441 (2020). doi:10.1007/978-3-030-50436-6_31
Computational Science – ICCS 2020
Computational Science – ICCS 2020International Conference on Computational Science 2020, ICCS 2020, Amsterdam, The Netherlands, 2020-06-03-2020-06-05
Following the trend towards Exascale, today’s supercomputers consist of increasingly complex and heterogeneous compute nodes. To exploit the performance of these systems, research software in HPC needs to keep up with the rapid development of hardw
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::365b04187c44163f5398c1593265e894
https://doi.org/10.1007/978-3-030-50436-6_31
https://doi.org/10.1007/978-3-030-50436-6_31
Autor:
Ivo Kabadshow, Holger Dachsel, Carsten Kutzner, Berk Hess, R. Thomas Ullmann, Helmut Grubmüller, Andreas Beckmann, Bartosz Kohnke, David Haensel
Publikováno v:
Biophysical Journal
A Flexible, GPU - Powered Fast Multipole Method for Realistic Biomolecular Simulations in Gromacs
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ca1e7ca666976b6ced2a68fa3cc6f110
https://hdl.handle.net/11858/00-001M-0000-002D-785C-511858/00-001M-0000-002D-785E-1
https://hdl.handle.net/11858/00-001M-0000-002D-785C-511858/00-001M-0000-002D-785E-1
Publikováno v:
Lecture Notes in Computational Science and Engineering ISBN: 9783319405261
Software for Exascale Computing
Software for Exascale Computing
The simulation of long-range electrostatic interactions in huge particle ensembles is a vital issue in current scientific research. The Fast Multipole Method (FMM) is able to compute those Coulomb interactions with extraordinary speed and controlled
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::03e33682dde58f428ea2478ef4b47e1b
https://doi.org/10.1007/978-3-319-40528-5_22
https://doi.org/10.1007/978-3-319-40528-5_22
Gromex: Electrostatics with Chemical Variability for Realistic Molecular Simulations on the Exascale
Autor:
Holger Dachsel, Berk Hess, R. Thomas Ullmann, Helmut Grubmüller, Ivo Kabadshow, Carsten Kutzner, David Haensel, Bartosz Kohnke, Andreas Beckmann
Publikováno v:
Biophysical Journal
Molecular electrostatics, notably in proteins and other macromolecules, is complicated by the presence of titratable sites which occur in different forms whose charge distribution differs, e.g., due to protonation or reduction in response to changes
Autor:
Andreas Beckmann, Ivo Kabadshow
Publikováno v:
Lecture Notes in Computational Science and Engineering ISBN: 9783319229966
This article provides an in-depth analysis and high-level C++ optimization strategies for the most time-consuming kernels of a Fast Multipole Method (FMM). The two main kernels of a Coulomb FMM are formulated to support different hardware features, s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7a5116a26c00a4f0c977006b0cef1590
https://doi.org/10.1007/978-3-319-22997-3_2
https://doi.org/10.1007/978-3-319-22997-3_2
Autor:
Franz Gähler, Matthias Bolten, Godehard Sutmann, Daniel Potts, Frederik Heber, Rene Halver, Olaf Lenz, Michael Pippig, Julian Iseringhausen, Michael Hofmann, Florian Fahrenberger, Christian Holm, Holger Dachsel, Axel Arnold, Ivo Kabadshow
Publikováno v:
Physical review / E 88(6), 063308 (2013). doi:10.1103/PhysRevE.88.063308
Based on a parallel scalable library for Coulomb interactions in particle systems, a comparison between the fast multipole method (FMM), multigrid-based methods, fast Fourier transform (FFT)-based methods, and a Maxwell solver is provided for the cas
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dbb5e44f5442fca58e0869223b1d4001
https://pub.uni-bielefeld.de/record/2650803
https://pub.uni-bielefeld.de/record/2650803