32,710 research outputs found
Reproducibility, accuracy and performance of the Feltor code and library on parallel computer architectures
Feltor is a modular and free scientific software package. It allows
developing platform independent code that runs on a variety of parallel
computer architectures ranging from laptop CPUs to multi-GPU distributed memory
systems. Feltor consists of both a numerical library and a collection of
application codes built on top of the library. Its main target are two- and
three-dimensional drift- and gyro-fluid simulations with discontinuous Galerkin
methods as the main numerical discretization technique. We observe that
numerical simulations of a recently developed gyro-fluid model produce
non-deterministic results in parallel computations. First, we show how we
restore accuracy and bitwise reproducibility algorithmically and
programmatically. In particular, we adopt an implementation of the exactly
rounded dot product based on long accumulators, which avoids accuracy losses
especially in parallel applications. However, reproducibility and accuracy
alone fail to indicate correct simulation behaviour. In fact, in the physical
model slightly different initial conditions lead to vastly different end
states. This behaviour translates to its numerical representation. Pointwise
convergence, even in principle, becomes impossible for long simulation times.
In a second part, we explore important performance tuning considerations. We
identify latency and memory bandwidth as the main performance indicators of our
routines. Based on these, we propose a parallel performance model that predicts
the execution time of algorithms implemented in Feltor and test our model on a
selection of parallel hardware architectures. We are able to predict the
execution time with a relative error of less than 25% for problem sizes between
0.1 and 1000 MB. Finally, we find that the product of latency and bandwidth
gives a minimum array size per compute node to achieve a scaling efficiency
above 50% (both strong and weak)
Data-driven modelling of biological multi-scale processes
Biological processes involve a variety of spatial and temporal scales. A
holistic understanding of many biological processes therefore requires
multi-scale models which capture the relevant properties on all these scales.
In this manuscript we review mathematical modelling approaches used to describe
the individual spatial scales and how they are integrated into holistic models.
We discuss the relation between spatial and temporal scales and the implication
of that on multi-scale modelling. Based upon this overview over
state-of-the-art modelling approaches, we formulate key challenges in
mathematical and computational modelling of biological multi-scale and
multi-physics processes. In particular, we considered the availability of
analysis tools for multi-scale models and model-based multi-scale data
integration. We provide a compact review of methods for model-based data
integration and model-based hypothesis testing. Furthermore, novel approaches
and recent trends are discussed, including computation time reduction using
reduced order and surrogate models, which contribute to the solution of
inference problems. We conclude the manuscript by providing a few ideas for the
development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and
Multiscale Dynamics (American Scientific Publishers
Curriculum Guidelines for Undergraduate Programs in Data Science
The Park City Math Institute (PCMI) 2016 Summer Undergraduate Faculty Program
met for the purpose of composing guidelines for undergraduate programs in Data
Science. The group consisted of 25 undergraduate faculty from a variety of
institutions in the U.S., primarily from the disciplines of mathematics,
statistics and computer science. These guidelines are meant to provide some
structure for institutions planning for or revising a major in Data Science
The ALPS project: open source software for strongly correlated systems
We present the ALPS (Algorithms and Libraries for Physics Simulations)
project, an international open source software project to develop libraries and
application programs for the simulation of strongly correlated quantum lattice
models such as quantum magnets, lattice bosons, and strongly correlated fermion
systems. Development is centered on common XML and binary data formats, on
libraries to simplify and speed up code development, and on full-featured
simulation programs. The programs enable non-experts to start carrying out
numerical simulations by providing basic implementations of the important
algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC)
using non-local updates, extended ensemble simulations, exact and full
diagonalization (ED), as well as the density matrix renormalization group
(DMRG). The software is available from our web server at
http://alps.comp-phys.org.Comment: For full software and introductory turorials see
http://alps.comp-phys.or
Development of a device to simulate tooth mobility
Objectives: The testing of new materials under simulation of oral conditions is essential in medicine. For simulation of fracture strength different simulation devices are used for test set-up. The results of these in vitro tests differ because there is no standardization of tooth mobility in simulation devices. The aim of this study is to develop a simulation device that depicts the tooth mobility curve as accurately as possible and creates reproducible and scalable mobility curves. Materials and methods: With the aid of published literature and with the help of dentists, average forms of tooth classes were generated. Based on these tooth data, different abutment tooth shapes and different simulation devices were designed with a CAD system and were generated with a Rapid Prototyping system. Then, for all simulation devices the displacement curves were created with a universal testing machine and compared with the tooth mobility curve. With this new information, an improved adapted simulation device was constructed. Results: A simulations device that is able to simulate the mobility curve of natural teeth with high accuracy and where mobility is reproducible and scalable was developed
Chaste: an open source C++ library for computational physiology and biology
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials
Brownian dynamics simulations of planar mixed flows of polymer solutions at finite concentrations
Periodic boundary conditions for planar mixed flows are implemented in the
context of a multi-chain Brownian dynamics simulation algorithm. The effect of
shear rate , and extension rate , on the size of
polymer chains, \left, and on the polymer contribution to
viscosity, , is examined for solutions of FENE dumbbells at finite
concentrations, with excluded volume interactions between the beads taken into
account. The influence of the mixedness parameter, , and flow strength,
, on \left and , is also examined, where
corresponds to pure shear flow, and
corresponds to pure extensional flow. It is shown that there exists a critical
value, , such that the flow is shear dominated for , and extension dominated for .Comment: 18 pages, 12 figures, to appear in Chemical Engineering Scienc
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