Publikationen SGS: Bibliographie 2018 BibTeX
@inproceedings {INPROC-2018-52,
author = {Nehzat Emamy and Pascal Litty and Thomas Klotz and Miriam Mehl and Oliver R{\"o}hrle},
title = {{POD-DEIM model order reduction of the Monodomain Reaction-Diffusion Sub-Model of the Neuro-Muscular System}},
booktitle = {IUTAM Symposium on Model Order Reduction of Coupled Systems; Stuttgart, Germany, May 22-25, 2018: MORCOS 2018},
editor = {J. Fehr and B. Haasdonk},
publisher = {Springer},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--14},
type = {Konferenz-Beitrag},
month = {Mai},
year = {2018},
isbn = {879-3-030-21012-0},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {We apply POD-DEIM model order reduction to a 0D/1D model used to simulate the
propagation of action potentials through the myocardium or along skeletal
muscle fibers. This corresponding system of ODEs (reaction) and PDEs
(diffusion) is called the monodomain equation. 0D sets of ODEs describing the
ionic currents flowing across the cell membrane are coupled along muscle fibers
through a \$1\$D diffusion process for the transmembrane potential. Due to the
strong coupling of the transmembrane potential and other state variables
describing the behavior of the membrane, a total reduction strategy including
all degrees of freedom turns out to be more efficient than a reduction of only
the transmembrane potential. The total reduction approach is four orders of
magnitude more accurate than partial reduction and shows a faster convergence
in the number of POD modes with respect to the mesh refinement. A speedup of
\$2.7\$ is achieved for a 1D mesh with \$320\$ nodes. Considering the DEIM
approximation in combination with the total reduction, the nonlinear functions
corresponding to the ionic state variables are also approximated in addition to
the nonlinear ionic current in the monodomain equation. We observe that the
same number of DEIM interpolation points as the number of POD modes is the
optimal choice regarding stability, accuracy and runtime for the current
POD-DEIM approach.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-52&engl=0}
}
@inproceedings {INPROC-2018-51,
author = {Nehzat Emamy and Pascal Litty and Thomas Klotz and Miriam Mehl and Oliver R{\"o}hrle},
title = {{POD-DEIM model order reduction for the Monodomain reaction-dissusion equation in neuro-muscular system}},
booktitle = {Proceedings of 6th European Conference on Computational Mechanics (Solids, Structures and Coupled Problems) (ECCM 6) and the 7th European Conference on Computational Fluid Dynamics (ECFD 7); Glasgow, UK, June 11-15, 2018},
editor = {Roger Owen and Ren{\'e} de Borst and Jason Reese and Chris Pearce},
publisher = {International Center for Numerical Methods in Engineerin (CIMNE)},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {2514--2524},
type = {Konferenz-Beitrag},
month = {Juni},
year = {2018},
isbn = {978-84-947311-6-7},
language = {Englisch},
cr-category = {A General Literature,
G Mathematics of Computing,
E Data},
ee = {ftp://ftp.informatik.uni-stuttgart.de/pub/library/ncstrl.ustuttgart_fi/INPROC-2018-51/INPROC-2018-51.pdf},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {We apply the POD-DEIM model order reduction to the propagation of the
transmembrane potential along \$1\$D muscle fibers. This propagation is
represented using the monodomain partial differential equation. The monodomain
equation, which is a reaction-diffusion equation, is coupled through its
reaction term with a set of ordinary differential equations, which provide the
ionic current across the cell membrane. Due to the strong coupling of the
transmembrane potential and ionic state variables, we reduce them all together
proposing a total reduction strategy. We compare the current strategy with the
conventional strategy of reducing the transmembrane potential. Considering the
current approach, the discrete system matrix is slightly modified to adjust for
the size. However, size of the precomputed reduced system matrix remains the
same, which means the same computational cost. The current approach appears to
be four orders of magnitude more accurate considering the equivalent number of
modes on the same grid in comparison to the conventional approach. Moreover, it
shows a faster convergence in the number of POD modes with respect to the grid
refinement. Using the DEIM approximation of nonlinear functions in combination
with the total reduction, the nonlinear functions corresponding to the ionic
state variables are also approximated besides the nonlinear ionic current in
the monodomain equation. For the current POD-DEIM approach, it appears that the
same number of DEIM interpolation points as the number of POD modes is the
optimal choice regarding stability, accuracy and runtime.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-51&engl=0}
}
@inproceedings {INPROC-2018-50,
author = {Steffen Hirschmann and Michael Lahnert and Carolin Schober and Malte Brunn and Miriam Mehl and Dirk Pfl{\"u}ger},
title = {{Load-Balancing and Spatial Adaptivity for Coarse-Grained Molecular Dynamics Applications}},
booktitle = {High Performance Computing in Science and Engineering '18},
editor = {Wolfgang E. Nagel and Dietmar H. Kr{\"o}ner and Michael M. Resch},
publisher = {Springer International Publishing},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--510},
type = {Konferenz-Beitrag},
month = {Oktober},
year = {2018},
isbn = {978-3-030-13324-5},
doi = {10.1007/978-3-030-13325-2},
language = {Englisch},
cr-category = {G.1.0 Numerical Analysis General},
ee = {ftp://ftp.informatik.uni-stuttgart.de/pub/library/ncstrl.ustuttgart_fi/INPROC-2018-50/INPROC-2018-50.pdf},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {We present our approach for a scalable implementation of coupled soft matter
simulations for inhomogeneous applications based on the simulation package
ESPResSo and an extended version of the adaptive grid framework p4est. Our main
contribution in this paper is the development and implementation of a joint
partitioning of two or more distinct octree-based grids based on the concept of
a finest common tree. This concept guarantees that, on all grids, the same
process is responsible for each point in space and, thus, avoids communication
of data in overlapping volumes handled in different partitions. We achieve up
to 85 \% parallel efficiency in a weak scaling setting. Our proposed algorithms
take only a small fraction of the overall runtime of grid adaption.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-50&engl=0}
}
@inproceedings {INPROC-2018-09,
author = {Julian Valentin and Dirk Pfl{\"u}ger},
title = {{Fundamental Splines on Sparse Grids and Their Application to Gradient-Based Optimization}},
booktitle = {Sparse Grids and Applications - Miami 2016},
editor = {Jochen Garcke and Dirk Pfl{\"u}ger and Clayton G. Webster and Guannan Zhang},
publisher = {Springer},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
series = {Lecture Notes in Computational Science and Engineering},
volume = {123},
pages = {229--251},
type = {Konferenz-Beitrag},
month = {Januar},
year = {2018},
doi = {10.1007/978-3-319-75426-0_10},
keywords = {sparse grids; optimization; B-splines},
language = {Englisch},
cr-category = {G.1.6 Numerical Analysis Optimization},
ee = {https://dx.doi.org/10.1007/978-3-319-75426-0_10},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-09&engl=0}
}
@inproceedings {INPROC-2018-08,
author = {David Pfander and Gregor Dai{\ss} and Dirk Pfl{\"u}ger and Dominic Marcello and Hartmut Kaiser},
title = {{Accelerating Octo-Tiger: Stellar Mergers on Intel Knights Landing with HPX}},
booktitle = {Proceedings of the 6th International Workshop on OpenCL},
publisher = {ACM},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--9},
type = {Konferenz-Beitrag},
month = {Mai},
year = {2018},
language = {Englisch},
cr-category = {D.1 Programming Techniques,
D.3.4 Programming Languages Processors,
G.4 Mathematical Software},
contact = {submitted},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {The optimization of performance of complex simulation codes with high
computational demands, such as Octo-Tiger, is an ongoing challenge. Octo-Tiger
is an astrophysics code simulating the evolution of star systems based on the
fast multipole method on adaptive octrees. It was implemented using high-level
C++ libraries, specifically HPX and Vc, which allows its use on different
hardware platforms. Recently, we have demonstrated excellent scalability in a
distributed setting. In this paper, we study Octo-Tiger{\^a}€™s node-level
performance on an Intel Knights Landing platform. We focus on the fast
multipole method, as it is Octo-Tiger{\^a}€™s computationally most demanding
component. By using HPX and a futurization approach, we can efficiently
traverse the adaptive octrees in parallel. On the core-level, threads process
sub-grids using multiple 743-element stencils. In numerical experiments,
simulating the time evolution of a rotating star on an Intel Xeon Phi 7250
Knights Landing processor, Octo-Tiger shows good parallel efficiency and
achieves up to 408 GFLOPS. This results in a speedup of 2x compared to a
24-core Skylake-SP platform, using the same high-level abstractions.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-08&engl=0}
}
@inproceedings {INPROC-2018-07,
author = {David Pfander and Malte Brunn and Dirk Pfl{\"u}ger},
title = {{AutoTuneTMP: Auto-Tuning in C++ With Runtime Template Metaprogramming}},
booktitle = {2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
publisher = {IEEE},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--10},
type = {Konferenz-Beitrag},
month = {Mai},
year = {2018},
keywords = {auto-tuning; template metaprogramming; just-in-time compilation; performance engineering},
language = {Englisch},
cr-category = {D.3.4 Programming Languages Processors},
contact = {submitted},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-07&engl=0}
}
@article {ART-2018-08,
author = {Chris P. Bradley and Nehzat Emamy and Thomas Ertl and Dominik G{\"o}ddeke and Andreas Hessenthaler and Thomas Klotz and Aaron Kr{\"a}mer and Michael Krone and Benjamin Maier and Miriam Mehl and Tobias Rau and Oliver R{\"o}hrle},
title = {{Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems}},
journal = {Frontiers in Physiology},
publisher = {frontiers},
volume = {9},
pages = {816--816},
type = {Artikel in Zeitschrift},
month = {Juli},
year = {2018},
doi = {10.3389/fphys.2018.00816},
language = {Englisch},
cr-category = {G.0 Mathematics of Computing General},
ee = {https://www.frontiersin.org/article/10.3389/fphys.2018.00816},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2018-08&engl=0}
}
@article {ART-2018-03,
author = {Stefanie Stalter and Leonid Yelash and Nehzat Emamy and Antonia Statt and Martin Hanke and Luk{\'a}\&\#269 and Maria Ov{\'a}-Medvid’ov{\'a} and Peter Virnau},
title = {{Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats}},
journal = {Computer Physics Communications},
publisher = {Elsevier},
volume = {224},
pages = {198--208},
type = {Artikel in Zeitschrift},
month = {M{\"a}rz},
year = {2018},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {Heterogeneous multiscale methods (HMM) combine molecular accuracy of
particle-based simulations with the computational efficiency of continuum
descriptions to model flow in soft matter liquids. In these schemes, molecular
simulations typically pose a computational bottleneck, which we investigate in
detail in this study. We find that it is preferable to simulate many small
systems as opposed to a few large systems, and that a choice of a simple
isokinetic thermostat is typically sufficient while thermostats such as
Lowe{\^a}€“Andersen allow for simulations at elevated viscosity. We discuss
suitable choices for time steps and finite-size effects which arise in the
limit of very small simulation boxes. We also argue that if colloidal systems
are considered as opposed to atomistic systems, the gap between microscopic and
macroscopic simulations regarding time and length scales is significantly
smaller. We propose a novel reduced-order technique for the coupling to the
macroscopic solver, which allows us to approximate a non-linear stress{\^a}€“strain
relation efficiently and thus further reduce computational effort of
microscopic simulations.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2018-03&engl=0}
}
@article {ART-2018-02,
author = {Julian Valentin and Michael Sprenger and Dirk Pfl{\"u}ger and Oliver R{\"o}hrle},
title = {{Gradient-Based Optimization with B-Splines on Sparse Grids for Solving Forward-Dynamics Simulations of Three-Dimensional, Continuum-Mechanical Musculoskeletal System Models}},
journal = {International Journal for Numerical Methods in Biomedical Engineering},
publisher = {Wiley},
pages = {1--16},
type = {Artikel in Zeitschrift},
month = {Januar},
year = {2018},
doi = {10.1002/cnm.2965},
language = {Englisch},
cr-category = {G.1.1 Numerical Analysis Interpolation,
G.1.6 Numerical Analysis Optimization},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2018-02&engl=0}
}
