@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-2016-57,
author = {Michael Lahnert and Takayuki Aoki and Carsten Burstedde and Miriam Mehl},
title = {{Minimally-Invasive Integration of P4est in Espresso for Adaptive Lattice-Boltzmann}},
booktitle = {The 30th Computational Fluid Dynamics Symposium ; Tokyo, Japan, December 12--14, 2016.},
publisher = {Japan Society of Fluid Mechanics},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--7},
type = {Konferenz-Beitrag},
month = {Dezember},
year = {2016},
language = {Deutsch},
cr-category = {I.6 Simulation and Modeling},
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-2016-57&engl=0}
}
@inproceedings {INPROC-2016-20,
author = {Michael Lahnert and Carsten Burstedde and Christian Holm and Miriam Mehl and Georg Rempfer and Florian Weik},
title = {{Towards Lattice-Boltzmann on Dynamically Adaptive Grids -- Minimally-Invasive Grid Exchange in ESPResSo}},
booktitle = {ECCOMAS Congress 2016, VII European Congress on Computational Methods in Applied Sciences and Engineering},
editor = {M. Papadrakakis and V. Papadopoulos and G. Stefanou and V. Plevris},
publisher = {ECCOMAS},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--25},
type = {Konferenz-Beitrag},
month = {Juni},
year = {2016},
language = {Englisch},
cr-category = {G.1.8 Partial Differential Equations},
ee = {https://www.eccomas2016.org/proceedings/pdf/4659.pdf},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {We present the minimally-invasive exchange of the regular Cartesian grid in the
lattice-Boltzmann solver of ESPResSo by a dynamically-adaptive octree grid.
Octree grids are favoured by computer scientists over other grid types as they
are very memory-efficient. In addition, they represent a natural generalisation
of regular Cartesian grids, such that most discretisation details of a regular
grid solver can be maintained. Optimised codes, however, require a special
tree-oriented grid traversal, which typically conflicts with existing
simulation codes using various iterators, some for only parts of the grid,
e.g., boundaries. ESPResSo is a large software package developed for
soft-matter simulations involving fluid flow, electrostatic, and electrokinetic
effects, and molecular dynamics. The currently used regular Cartesian grid
hinders the simulation of realistic domain sizes and significant time periods,
a problem that can be solved using grid adaptivity. In a first step, we focus
on the lattice-Boltzmann flow solver in ESPResSo. p4est is a grid framework,
that already provides dynamically adaptive quadtree and octree grids together
with high-level interfaces for flexible grid traversals with direct neighbour
access in all grid components. In this paper, we first describe extensions of
p4est that were necessary to fulfill certain application requirements. The
second part of our work consists of the minimally-invasive changes in ESPResSo
preserving the expertise accumulated in the software's implementation over
years. Our numerical results demonstrate physical correctness of the
implementation, good parallel scalability and low overhead of the dynamical
grid adaptivity. These are prerequisites to actually profit from grid
adaptivity in terms of being able to simulate larger domains over longer time
periods with limited computational resources. Thus, the current status forms a
solid basis for further steps such as the development of refinement criteria,
the setup of more realistic application scenarios, and a GPU implementation.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2016-20&engl=0}
}
@article {ART-2019-06,
author = {Miriam Mehl and Michael Lahnert},
title = {{Adaptive grid implementation for parallel continuum mechanics methods in particle simulations}},
journal = {The European Physical Journal Special Topics},
editor = {Christian Holm and Thomas Ertl and Siegfried Schmauder and Johannes K{\"a}stner and Joachim Gross},
publisher = {Springer Berlin Heidelberg},
volume = {227},
number = {14},
pages = {1757--1778},
type = {Artikel in Zeitschrift},
month = {M{\"a}rz},
year = {2019},
doi = {10.1140/epjst/e2019-800161-5},
language = {Deutsch},
cr-category = {G.0 Mathematics of Computing General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {In this tutorial review paper, we present our minimally invasive approach for
integrating dynamically adaptive tree-structured grids into existing simulation
software that has been developed for regular Cartesian grids. We introduce
different physical models that we target and that span a wide range of typical
simulation characteristics -- from grid-based Lattice-Boltzmann, finite volume
and finite difference discretized models to particle-based molecular dynamics
models. We derive the respective typical data access requirements and
extensions of the algorithms to adaptively refined grids along with possible
grid adaptivity criteria. In addition, after introducing basics of
tree-structured adaptively refined grids, we present the adaptive grid
framework p4est and our enhancement of p4est in order to provide a grid and
partitioning infrastructure that can easily be used in existing simulation
codes. Finally, we explain how such a grid infrastructure can be integrated
into regular grid codes in general in three major steps and how we integrated
p4est in the soft matter simulation package ESPResSo in particular. A summary
of results fro m previously published performance and scalability studies
together with new results for more realistic coupled simulation scenarios shows
the efficiency and validity of the resulting new version of ESPResSo.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2019-06&engl=0}
}
@inbook {INBOOK-2017-06,
author = {Steffen Hirschmann and Malte Brunn and Michael Lahnert and Colin W. Glass and Miriam Mehl and Dirk Pfl{\"u}ger},
title = {{Load balancing with p4est for Short-Range Molecular Dynamics with ESPResSo}},
series = {Advances in Parallel Computing},
publisher = {IOS Press},
volume = {32},
pages = {455--464},
type = {Beitrag in Buch},
month = {September},
year = {2017},
doi = {10.3233/978-1-61499-843-3-455},
language = {Englisch},
cr-category = {G.0 Mathematics of Computing General},
ee = {ftp://ftp.informatik.uni-stuttgart.de/pub/library/ncstrl.ustuttgart_fi/INBOOK-2017-06/INBOOK-2017-06.pdf},
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=INBOOK-2017-06&engl=0}
}