160 lines
3.3 KiB
TeX
160 lines
3.3 KiB
TeX
\section{Intro}
|
||
|
||
\begin{frame}{NAStJA: An MPI Stencil Code Solver}
|
||
\begin{figure}
|
||
\includegraphics[width=\textwidth]{nastja.png}
|
||
\end{figure}
|
||
|
||
\begin{itemize}
|
||
\item CiS uses NAStJA under the hood
|
||
\item NAStJA is a massively parallel stencil code solver \\
|
||
$\implies$ CiS extensions should be stencils
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\begin{frame}{ECM Viscoelasticity:\\A Factor in Cell Behavior}
|
||
\begin{figure}
|
||
\includegraphics[width=0.6\textwidth]{ecm-cells.png}
|
||
\end{figure}
|
||
|
||
\begin{itemize}
|
||
\item Collagen networks in the ECM mechanically restrict cells
|
||
\item Collagen networks are \emph{viscoelastic}
|
||
\item ECM viscoelasticity influences cell behavior
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\section{ECM Model}
|
||
|
||
\begin{frame}{Modeling ECM Mechanics in CiS}
|
||
How can we model ECM mechanics in CiS?
|
||
|
||
\vfill{}
|
||
|
||
Two main requirements:
|
||
|
||
\begin{itemize}
|
||
\item Model exhibits viscoelastic properties
|
||
\item Model can be implemented as a stencil in NAStJA
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\begin{frame}{ECM Models in Literature}
|
||
\begin{figure}
|
||
\includegraphics[width=0.8\textwidth]{models.png}
|
||
\end{figure}
|
||
|
||
\begin{itemize}
|
||
\item A host of different ECM models exist
|
||
\item Various foci, e.g. mechanics, growth factors
|
||
\item Various approaches, e.g. FEM, Molecular Dynamics
|
||
\item But: So far no approach is suitable as a stencil
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\begin{frame}{My Approach}
|
||
Two main requirements:
|
||
|
||
\begin{itemize}
|
||
\item Model exhibits viscoelastic properties
|
||
\item Model can be implemented as a stencil in NAStJA
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\vfill
|
||
|
||
\section{Methods}
|
||
|
||
\begin{frame}{Lattice Boltzmann Method}
|
||
\begin{figure}
|
||
\includegraphics[width=\textwidth]{lbm.png}
|
||
\end{figure}
|
||
|
||
\begin{itemize}
|
||
\item Discretized particle velocities per lattice site
|
||
\item Update Step: Streaming + Collision
|
||
\item Usually used for hydrodynamics
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\begin{frame}{Elastic Lattice Model}
|
||
\begin{figure}
|
||
\includegraphics[width=0.4\textwidth]{elm.png}
|
||
\end{figure}
|
||
|
||
\begin{itemize}
|
||
\item A square lattice based discrete particle method
|
||
\item Each lattice site represents a particle
|
||
\item Particles are connected to neighbors by springs
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\section{Implementation}
|
||
|
||
\begin{frame}{Implementation}
|
||
\begin{itemize}
|
||
\item Starting point: NAStJA + CiS
|
||
\item Benchmark different implementations against each other
|
||
\begin{itemize}
|
||
\item CPU
|
||
\item Vectorized
|
||
\item GPU
|
||
\end{itemize}
|
||
\item Optimize for
|
||
\begin{itemize}
|
||
\item Scaling behavior
|
||
\item Wall clock time
|
||
\item etc.
|
||
\end{itemize}
|
||
\end{itemize}
|
||
\end{frame}
|
||
|
||
\begin{comment}
|
||
\section{Intro}
|
||
\subsection{Subsection 1.1}
|
||
\frame{
|
||
\frametitle{Example slide A}
|
||
\begin{itemize}
|
||
\item PCM, Citation: \cite{dh76,kl07} %\language
|
||
\pause
|
||
\item Bullet point 2
|
||
\item \dots
|
||
\end{itemize}
|
||
}
|
||
\subsection{Subsection 1.2}
|
||
\frame{
|
||
\frametitle{Example slide B}
|
||
\begin{block}{Block 1}
|
||
\begin{itemize}
|
||
\item Test: <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||
\pause
|
||
\item Bullet point 2
|
||
\item \dots
|
||
\end{itemize}
|
||
\end{block}
|
||
}
|
||
\section{Section 2}
|
||
\frame{
|
||
\frametitle{Example slide C}
|
||
\begin{exampleblock}{Example 1}
|
||
\begin{itemize}
|
||
\item Bullet point 1
|
||
\pause
|
||
\item Bullet point 2
|
||
\item \dots
|
||
\end{itemize}
|
||
\end{exampleblock}
|
||
}
|
||
\frame{
|
||
\frametitle{Example slide D}
|
||
\begin{alertblock}{Alert 1}
|
||
\begin{itemize}
|
||
\item Bullet point 1
|
||
\pause
|
||
\item Bullet point 2
|
||
\item \dots
|
||
\end{itemize}
|
||
\end{alertblock}
|
||
}
|
||
\end{comment}
|