new

diff --git a/BookGPU/Chapters/chapter5/ch5.tex b/BookGPU/Chapters/chapter5/ch5.tex
index f7eabb40b73e179a4441664b461099c2f8e06610..51a1f4dd7d3b8f8ae9dd9a051ca85a286302e81d 100644 (file)
--- a/BookGPU/Chapters/chapter5/ch5.tex
+++ b/BookGPU/Chapters/chapter5/ch5.tex
@@ -3,7 +3,7 @@
 %\chapterauthor{Allan S. Nielsen}{Technical University of Denmark}
 %\chapterauthor{Bernd Dammann}{Technical University of Denmark}
 
 %\chapterauthor{Allan S. Nielsen}{Technical University of Denmark}
 %\chapterauthor{Bernd Dammann}{Technical University of Denmark}
 

-\chapter[Software components for heterogeneous manycore architectures]{Development of software components for heterogeneous manycore architectures}\label{ch5}
+\chapter[Development of software components for heterogeneous many-core architectures]{Development of software components for heterogeneous many-core architectures}\label{ch5}

 
 %Subjects:
 %\begin{itemize}
 
 %Subjects:
 %\begin{itemize}

diff --git a/BookGPU/Chapters/chapter7/biblio7.bib b/BookGPU/Chapters/chapter7/biblio7.bib
index 22678b24160b072865512a0e47a8f4b6ea9367c4..decfed8d865d055e59550e351444abd31cf7a7bf 100644 (file)
--- a/BookGPU/Chapters/chapter7/biblio7.bib
+++ b/BookGPU/Chapters/chapter7/biblio7.bib
@@ -375,6 +375,12 @@ keywords = "Informatiquealgorithmique",
 keywords = "Exaflop"
 }
 
 keywords = "Exaflop"
 }
 

+@MISC{ch7:Kirby03de-aliasingon,
+    author = {Kirby, R.M. and Karniadakis, G.E.},
+    title = {De-aliasing on non-uniform grids: algorithms and applications },
+    year = {2003}
+}
+

 @misc{ ch7:lessismore,
   author = "Feldman, M.",
   title = "{Less is More: Exploiting Single Precision Math in HPC}",
 @misc{ ch7:lessismore,
   author = "Feldman, M.",
   title = "{Less is More: Exploiting Single Precision Math in HPC}",

diff --git a/BookGPU/Chapters/chapter7/ch7.tex b/BookGPU/Chapters/chapter7/ch7.tex
index 03703d476d30c9391eb9fc5e89b6aedc5836488a..d1918d4462846cec6afe78a361be2f537386a470 100644 (file)
--- a/BookGPU/Chapters/chapter7/ch7.tex
+++ b/BookGPU/Chapters/chapter7/ch7.tex
@@ -13,10 +13,10 @@
 \caption{Snapshot of steady state wave field generated by a Series 60 ship hull.}
 \end{figure}
 
 \caption{Snapshot of steady state wave field generated by a Series 60 ship hull.}
 \end{figure}
 

-\newpage
-In this chapter, we use our library for heterogenous and massively parallel GPU implementations. The library is written in Compute Unified Device Architecture (CUDA) C/C++ and a fully nonlinear and dispersive free surface water wave model \cite{ch7:EngsigKarupEtAl2011} is implemented. We describe how flexible-order finite difference\index{finite difference} (stencil) approximations to the partial differential equations of the model can be prototyped using library components provided in an in-house library. In this library hardware-specific implementation details are hidden via template-based components, as described in Chapter \ref{ch5}. We provide details of the modeling basis and important unique numerical properties which have been made tuneable to create a powerful and robust tool that can be tailored for specific purposes in engineering analysis. The model is based on unified potential flow theory and can be applied in scientific applications related to maritime engineering. It can be applied for cost-efficient estimation of broad banded wave propagation, transformation of irregular multidirectional waves over variable depth, kinematics and structural wave loads over large areas and scales.

 
 

-A main motivation of this work is to deliver exceptional performance to minimize calculation times, using modern parallel hardware technologies in combination with a proper choice of discretization methods and data-local algorithms with optimal complexity. This enable work and memory requirements to grow (scale) linearly with problem size on a suitable hardware system. For the wave model this is achieved by explicit time integration and iterative solution of a large nonsymmetric and sparse linear $\sigma$-transformed Laplace problem. For the latter, we use an iterative Preconditioned Defect Correction (PDC) method, accelerated using a geometric multigrid preconditioning strategy. We use modern programming paradigms in the form of Message Passing Interface (MPI) and CUDA for development of a novel massively parallel wave modelling tool, executable on modern heterogenous many-core hardware.
+In this chapter, we use our library for heterogenous and massively parallel GPU implementations. The library is written in Compute Unified Device Architecture (CUDA) C/C++ and a fully nonlinear and dispersive free surface water wave model \cite{ch7:EngsigKarupEtAl2011} is implemented. We describe how flexible-order finite difference\index{finite difference} (stencil) approximations to the partial differential equations of the model can be prototyped using library components provided in an in-house library. In this library hardware-specific implementation details are hidden via template-based components, as described in Chapter \ref{ch5}. We provide details of the modeling basis and important unique numerical properties which have been made tunable to create a powerful and robust tool that can be tailored for specific purposes in engineering analysis. The model is based on unified potential flow theory and can be applied in scientific applications related to maritime engineering. It can be applied for cost-efficient estimation of broad banded wave propagation, transformation of irregular multidirectional waves over variable depth, kinematics and structural wave loads over large areas and scales.
+
+A main motivation of this work is to deliver exceptional performance to minimize calculation times, using modern parallel hardware technologies in combination with a proper choice of discretization methods and data-local algorithms with optimal complexity. This enable work and memory requirements to grow (scale) linearly with problem size on a suitable hardware system. For the wave model this is achieved by explicit time integration and iterative solution of a large nonsymmetric and sparse linear $\sigma$-transformed Laplace problem. For the latter, we use an iterative Preconditioned Defect Correction (PDC) method, accelerated using a geometric multigrid preconditioning strategy. We use modern programming paradigms in the form of Message Passing Interface (MPI) and CUDA for development of a novel massively parallel wave modeling tool, executable on modern heterogenous many-core hardware.

 
 One purpose of the developed numerical model is to ultimately perform hydrodynamic calculations in the time domain for practical analysis and simulation, e.g., to enable computationally intensive interactive real-time simulations. Realistic interactive simulations are, with present technology and available computational resources, a tremendous challenge in this setting. Yet, our aim is to take a first step in this direction and compute first-order accurate hydrodynamics for near-realistic simulations of unsteady ship-wave dynamics in a large ship simulator, used for training purposes in seakeeping operations. For this type of application, a mandatory ingredient for real-time and interactive simulation is a truly high-performance parallel implementation to ensure data processing in time for interactive visualization and responses. Details of the model properties, implementation, and promising novel combinations of techniques and algorithms for acceleration of performance are presented. Numerical experiments and benchmarks are provided to demonstrate the accuracy and efficiency of the model across recent generations of many-core CUDA-enabled hardware.
 
 
 One purpose of the developed numerical model is to ultimately perform hydrodynamic calculations in the time domain for practical analysis and simulation, e.g., to enable computationally intensive interactive real-time simulations. Realistic interactive simulations are, with present technology and available computational resources, a tremendous challenge in this setting. Yet, our aim is to take a first step in this direction and compute first-order accurate hydrodynamics for near-realistic simulations of unsteady ship-wave dynamics in a large ship simulator, used for training purposes in seakeeping operations. For this type of application, a mandatory ingredient for real-time and interactive simulation is a truly high-performance parallel implementation to ensure data processing in time for interactive visualization and responses. Details of the model properties, implementation, and promising novel combinations of techniques and algorithms for acceleration of performance are presented. Numerical experiments and benchmarks are provided to demonstrate the accuracy and efficiency of the model across recent generations of many-core CUDA-enabled hardware.
 


@@ -36,25 +36,25 @@ A key problem is that improvements in performance require porting legacy codes\f
 %
 %However, increasing amounts of applications are utilizing accelerators to parts of their code to gain speedups albeit with less dramatic improvements of performance as one can potentially find by adapting most, if not all of the application to modern hardware.
 
 %
 %However, increasing amounts of applications are utilizing accelerators to parts of their code to gain speedups albeit with less dramatic improvements of performance as one can potentially find by adapting most, if not all of the application to modern hardware.
 

-In this work, we explore some of these trends by developing, by bottom-up-design, a water wave model which can be utilized in maritime engineering and with the intended use on affordable office desktops as well as on more expensive modern compute clusters for engineering analysis purposes.  
+In this work, we explore some of these trends by developing, by bottom-up-design, a water-wave model which can be utilized in maritime engineering and with the intended use on affordable office desktops as well as on more expensive modern compute clusters for engineering analysis purposes.  

 
 \section{On modeling paradigms for highly nonlinear and dispersive water waves}
 \label{ch7:sec:modernwavemodellingparadigms}
 
 We see the development of new or improved hardware technologies as a key driver for exploring new and revisiting existing approaches that can contribute to next-generation modeling techniques.
 
 
 \section{On modeling paradigms for highly nonlinear and dispersive water waves}
 \label{ch7:sec:modernwavemodellingparadigms}
 
 We see the development of new or improved hardware technologies as a key driver for exploring new and revisiting existing approaches that can contribute to next-generation modeling techniques.
 

-For instance, the dominant wave modeling paradigm today for numerical simulation in coastal engineering tools is the use of Boussinesq-type \index{Boussinesq models} formulations for approximate solution of unified potential flow\index{potential flow} equations over varying bathymetry \cite{ch7:MS98}. The use of Boussinesq-type models in engineering tools was pioneered in 1978 by Abott et. al. \cite{ch7:AbottEtAl1978,ch7:AbottEtAl1984} based on the original Boussinesq equations due to Peregrine \cite{ch7:Peregrine1967} for calculations of waves in a harbor area. New formulations for highly nonlinear and dispersive water waves, useful for description of wave propagation in the important application range from deep to shallow areas, have been the subject of intense research for more than two decades. Such higher order formulations can be derived by first introducing an infinite Mclaurin series solution to the Laplace equation as described in \cite{ch7:AMS99}. This technique was later generalized to arbitrary expansion levels \cite{ch7:MBL02}. By analytical truncation of such series solutions, a polynomial variation in the vertical is assumed and provides the basis for efficient higher order Boussinesq-type formulations \cite{ch7:MBS03,ch7:Bingham2009467} for fully nonlinear and dispersive water waves. It is attractive, since it is then possible to eliminate the vertical coordinate in the analytical formulation of the Laplace problem. The resulting approximate model contains higher order derivatives to describe dispersion and these require careful treatment in numerical models. Thus, this truncation procedure inherently limits the practical application range, however, it can be significantly improved via Pad\'e approximations together with the introduction of free parameters for extending the finite application range by mathematical optimization to enhance accuracy in dispersion, kinematics and shoaling characteristics.
+For instance, the dominant wave modeling paradigm today for numerical simulation in coastal engineering tools is the use of Boussinesq-type \index{Boussinesq models} formulations for approximate solution of unified potential flow\index{potential flow} equations over varying bathymetry \cite{ch7:MS98}. The use of Boussinesq-type models in engineering tools was pioneered in 1978 by Abott et. al. \cite{ch7:AbottEtAl1978,ch7:AbottEtAl1984} based on the original Boussinesq equations due to Peregrine \cite{ch7:Peregrine1967} for calculations of waves in a harbor area. New formulations for highly nonlinear and dispersive water waves, useful for description of wave propagation in the important application range from deep to shallow areas, have been the subject of intense research for more than two decades. Such higher order formulations can be derived by first introducing an infinite Mclaurin series solution to the Laplace equation as described in \cite{ch7:AMS99}. This technique was later generalized to arbitrary expansion levels \cite{ch7:MBL02}. By analytical truncation of such series solutions, a polynomial variation in the vertical is assumed and provides the basis for efficient higher order Boussinesq-type formulations \cite{ch7:MBS03,ch7:Bingham2009467} for fully nonlinear and dispersive water waves. It is attractive, since it is then possible to eliminate the vertical coordinate in the analytical formulation of the Laplace problem. The resulting approximate model contains higher order derivatives to describe dispersion and these require careful treatment in numerical models. Thus, this truncation procedure inherently limits the practical application range; however, it can be significantly improved via Pad\'e approximations together with the introduction of free parameters for extending the finite application range by mathematical optimization to enhance accuracy in dispersion, kinematics, and shoaling characteristics.

 
 Main challenges of Boussinesq-type models are accurate and large-scale simulation of waves propagating towards near-shore from deep to shallow waters through surf zones, while accounting for high-order dispersive and nonlinear effects \cite{ch7:Cavaleri2007603}. Within the last two decades, much research has focused on extending the application range through improved formulations in terms of dispersion, shoaling, kinematic and nonlinear properties. The ultimate high-order Boussinesq-type model due to \cite{ch7:MBS03} was at the time considered a breakthrough in this direction, and since then promising new formulations have been proposed. For example, the methodology behind Boussinesq-type formulations can be extended via a multilayer approach \cite{ch7:LynettEtAl2004a,ch7:LynettEtAl2004b,ch7:ChazelEtAl2010} that makes it possible to achieve a similar range of application and levels of accuracy, but without higher derivatives in the formulation that can cause numerical difficulties.
 
 Boussinesq-type formulations for free surface waves are conventionally evaluated against the unified potential flow theory to evaluate limits to application range and accuracy limits. The use of unified potential theory as a basis for numerical models has traditionally been perceived as too expensive \cite{ch7:Lin2008} to solve in comparison with the typically more efficient Boussinesq-type models. This may be true in a strict comparison between the models, especially with respect to applications towards the more restricted shallow regions. However, this is in spite of the fact that a numerical unified potential flow model can be used for a larger range of practical scientific applications. A unified potential flow model has at most second-order derivatives in the formulation. In a numerical setting it has good opportunities for balancing accuracy and work effort by appropriate tuning of discrete parameters. This comes without a need for changing the underlying wave model to extend application range towards deep waters. Thus, the main problem related to the practical use of a unified model in maritime applications is arguably an issue of numerical efficiency.
 
 
 Main challenges of Boussinesq-type models are accurate and large-scale simulation of waves propagating towards near-shore from deep to shallow waters through surf zones, while accounting for high-order dispersive and nonlinear effects \cite{ch7:Cavaleri2007603}. Within the last two decades, much research has focused on extending the application range through improved formulations in terms of dispersion, shoaling, kinematic and nonlinear properties. The ultimate high-order Boussinesq-type model due to \cite{ch7:MBS03} was at the time considered a breakthrough in this direction, and since then promising new formulations have been proposed. For example, the methodology behind Boussinesq-type formulations can be extended via a multilayer approach \cite{ch7:LynettEtAl2004a,ch7:LynettEtAl2004b,ch7:ChazelEtAl2010} that makes it possible to achieve a similar range of application and levels of accuracy, but without higher derivatives in the formulation that can cause numerical difficulties.
 
 Boussinesq-type formulations for free surface waves are conventionally evaluated against the unified potential flow theory to evaluate limits to application range and accuracy limits. The use of unified potential theory as a basis for numerical models has traditionally been perceived as too expensive \cite{ch7:Lin2008} to solve in comparison with the typically more efficient Boussinesq-type models. This may be true in a strict comparison between the models, especially with respect to applications towards the more restricted shallow regions. However, this is in spite of the fact that a numerical unified potential flow model can be used for a larger range of practical scientific applications. A unified potential flow model has at most second-order derivatives in the formulation. In a numerical setting it has good opportunities for balancing accuracy and work effort by appropriate tuning of discrete parameters. This comes without a need for changing the underlying wave model to extend application range towards deep waters. Thus, the main problem related to the practical use of a unified model in maritime applications is arguably an issue of numerical efficiency.
 

-To address this issue, we have recently proposed a new approach in a proof-of-concept that combines modern many-core hardware with appropriate numerical and parallel strategies to facilitate efficient, accurate and scalable solution of water wave problems~\cite{ch7:EngsigKarupEtAl2011}. The use of potential theory for unsteady water wave computations can be traced at least back to 1975 \cite{ch7:HausslingVanEseltine1975}, and the fully nonlinear potential equations have been solved using various numerical methods since then, e.g., see reviews \cite{ch7:Yeung1982,ch7:TsaiYue1996,ch7:DiasBridges2006,ch7:Lin2008}. In the context of the finite-difference method, an efficient and scalable second-order geometric multigrid approach was first proposed by Li and Fleming in 1997 \cite{ch7:LiFleming1997}. Since then, the numerical strategy has been significantly improved in several works \cite{ch7:BinghamZhang2007,ch7:EBL08} that have led to more efficient and robust discretization techniques, with the objective of developing a general purpose strategy, that can be used for a broad range of practical maritime applications. Recently, a comparison with a High-Order Spectral (HOS) model \cite{ch7:DucrozetEtAl2011} was also reported to assess  accuracy and relative differences in efficiency on single-core hardware against a superior spectral modeling basis for a numerical wave tank setup in a structured domain with a flat sea bed.
+To address this issue, we have recently proposed a new approach in a proof-of-concept that combines modern many-core hardware with appropriate numerical and parallel strategies to facilitate efficient, accurate, and scalable solution of water wave problems~\cite{ch7:EngsigKarupEtAl2011}. The use of potential theory for unsteady water wave computations can be traced at least back to 1975 \cite{ch7:HausslingVanEseltine1975}, and the fully nonlinear potential equations have been solved using various numerical methods since then, e.g., see reviews \cite{ch7:Yeung1982,ch7:TsaiYue1996,ch7:DiasBridges2006,ch7:Lin2008}. In the context of the finite-difference method, an efficient and scalable second-order geometric multigrid approach was first proposed by Li and Fleming in 1997 \cite{ch7:LiFleming1997}. Since then, the numerical strategy has been significantly improved in several works \cite{ch7:BinghamZhang2007,ch7:EBL08} that have led to more efficient and robust discretization techniques, with the objective of developing a general purpose strategy, that can be used for a broad range of practical maritime applications. Recently, a comparison with a High-Order Spectral (HOS) model \cite{ch7:DucrozetEtAl2011} was also reported to assess  accuracy and relative differences in efficiency on single-core hardware against a superior spectral modeling basis for a numerical wave tank setup in a structured domain with a flat sea bed.

 
 \section{Governing equations}
 \label{ch7:goveq}
 
 
 \section{Governing equations}
 \label{ch7:goveq}
 

-We describe how, by physical principles via mathematical procedures and assumptions, it is possible to formulate a fully nonlinear and dispersive water wave model, describing incompressible, irrotational and inviscid fluid\index{fluid} flow above an uneven seabed.
+We describe how, by physical principles via mathematical procedures and assumptions, it is possible to formulate a fully nonlinear and dispersive water wave model, describing incompressible, irrotational, and inviscid fluid\index{fluid} flow above an uneven seabed.

 
 Conservation of mass\index{mass conservation} for an infinitely small control volume can be stated as
 \begin{align}
 
 Conservation of mass\index{mass conservation} for an infinitely small control volume can be stated as
 \begin{align}


@@ -76,7 +76,7 @@ where $p$ is pressure and ${\bf F}$ is the net force vector acting on the fluid
 
 The material derivative for a comoving coordinate system used in Lagrangian formulations
 \begin{align}
 
 The material derivative for a comoving coordinate system used in Lagrangian formulations
 \begin{align}

-\frac{D}{Dt}\equiv \frac{\partial }{\partial t} + ({\bf u}\cdot \nabla),
+\frac{D}{Dt}\equiv \frac{\partial }{\partial t} + ({\bf u}\cdot \nabla)

 \end{align}
 is defined as the sum of a time derivative and a convective term measured in a static (Eularian) coordinate system and accounts for the time rate of change following the motion. Thus, for the velocity vector ${\bf u}$, the total acceleration is defined as
 \begin{align}
 \end{align}
 is defined as the sum of a time derivative and a convective term measured in a static (Eularian) coordinate system and accounts for the time rate of change following the motion. Thus, for the velocity vector ${\bf u}$, the total acceleration is defined as
 \begin{align}


@@ -85,7 +85,7 @@ is defined as the sum of a time derivative and a convective term measured in a s
 \end{align}
 where the curl of the velocity field ${\boldsymbol \omega}\equiv\nabla\times {\bf u}$ is referred to as the vorticity vector field accounting for rotation of fluid particles. If we assume that the flow is irrotational
 \begin{align}
 \end{align}
 where the curl of the velocity field ${\boldsymbol \omega}\equiv\nabla\times {\bf u}$ is referred to as the vorticity vector field accounting for rotation of fluid particles. If we assume that the flow is irrotational
 \begin{align}

-\nabla\times {\bf u} = 0,
+\nabla\times {\bf u} = 0

 \end{align}
 and make use of the following relationship known from vector calculus
 \begin{align}
 \end{align}
 and make use of the following relationship known from vector calculus
 \begin{align}


@@ -196,9 +196,9 @@ Incident wave and absorbing boundary conditions are imposed via an embedded pena
 \label{ch7:sec:nummodel}
 
 The unified potential flow model is attractive as a basis due to the underlying analytical properties.
 \label{ch7:sec:nummodel}
 
 The unified potential flow model is attractive as a basis due to the underlying analytical properties.

-From a numerical point of view, an efficient and scalable discretization strategy should be based on using a data-local method, e.g., a flexible-order finite difference method for discretely approximating the governing equations and imposing boundary conditions via fictitious ghost points techniques as described in \cite{ch7:BinghamZhang2007,ch7:EBL08}. Such an approach has several attractive features from a scientific computing perspective. For example, finite difference methods are among the simplest and most efficient methods due to the use of structured grids and data structures. This results in low implementation and computational complexity which maps efficiently to modern computer architectures. Formal accuracy and tuneable numerics are achieved by employing flexible-order finite difference\index{finite difference} (local stencil)\index{stencil} approximations. 
+From a numerical point of view, an efficient and scalable discretization strategy should be based on using a data-local method, e.g., a flexible-order finite difference method for discretely approximating the governing equations and imposing boundary conditions via fictitious ghost points techniques as described in \cite{ch7:BinghamZhang2007,ch7:EBL08}. Such an approach has several attractive features from a scientific computing perspective. For example, finite difference methods are among the simplest and most efficient methods due to the use of structured grids and data structures. This results in low implementation and computational complexity which maps efficiently to modern computer architectures. Formal accuracy and tunable numerics are achieved by employing flexible-order finite difference\index{finite difference} (local stencil)\index{stencil} approximations. 

 
 

-We present scalability and performance tests based on the same two test environments outlined in Chapter \ref{ch5}, Section \ref{ch5:sec:testenvironments}, plus a third test environment based on the most recent hardware generation:
+We present scalability and performance tests based on the same two test environments outlined in Chapter \ref{ch5}, Section \ref{ch5:sec:testenvironments}, plus a fourth test environment based on the most recent hardware generation:

 \begin{description}
 \item[Test environment 4.] Desktop with dual-socket Sandy Bridge Intel Xeon E5-2670 (2.60 GHz) processors, 64GB RAM, 2x Nvidia Tesla K20 GPUs.
 \end{description}
 \begin{description}
 \item[Test environment 4.] Desktop with dual-socket Sandy Bridge Intel Xeon E5-2670 (2.60 GHz) processors, 64GB RAM, 2x Nvidia Tesla K20 GPUs.
 \end{description}


@@ -314,7 +314,7 @@ and are all imaginary confirming the hyperbolic (energy-conserving) nature of th
 \begin{align}
 \max|\lambda(\mathcal{J}_h)| = \lim_{kh\to\infty}|\lambda(\mathcal{J}_h)|\leq C(N_z)\sqrt{\frac{g}{h}}.
 \end{align}
 \begin{align}
 \max|\lambda(\mathcal{J}_h)| = \lim_{kh\to\infty}|\lambda(\mathcal{J}_h)|\leq C(N_z)\sqrt{\frac{g}{h}}.
 \end{align}

-Similar results were reported for the first time in the context of high-order Boussinesq-type equations in \cite{ch7:ENG06,ch7:EHBM06} and recently it has been shown \cite{ch7:EE13} that widely used implicitly-implicit Boussinesq-type equations can be re-formulated to have bounded eigenspectra using high-order discretisation methods. This is an important practical property of the discrete scheme as it is favorable to numerical stability. It implies that the linear model is not severely limited by the spatial resolution in the horizontal for a specific choice of the number  of collocation nodes ($N_z$) in the vertical. This suggests that the model is quite robust due to insensitivity in the choice of time step, with the implication that local grid adaptivity can be used for improving spatial accuracy. Interestingly, for the unified potential flow model we find that this also holds for nonlinear simulations. Large time steps can be chosen when using dense grids and high-order numerics without severely degrading overall numerical stability and efficiency. This is confirmed in numerical experiments and demonstrated in Figure \ref{ch7:numexp}. However, for very steep nonlinear waves and very densely clustered nonuniform grids, stability is found to be compromised without filtering. A proper filtering strategy, e.g., based on a super collocation technique \cite{ch7Kirby03de-aliasingon}, can be used to remedy stability problems without destroying accuracy. 
+Similar results were reported for the first time in the context of high-order Boussinesq-type equations in \cite{ch7:ENG06,ch7:EHBM06} and recently it has been shown \cite{ch7:EE13} that widely used implicitly-implicit Boussinesq-type equations can be re-formulated to have bounded eigenspectra using high-order discretisation methods. This is an important practical property of the discrete scheme as it is favorable to numerical stability. It implies that the linear model is not severely limited by the spatial resolution in the horizontal for a specific choice of the number  of collocation nodes ($N_z$) in the vertical. This suggests that the model is quite robust due to insensitivity in the choice of time step, with the implication that local grid adaptivity can be used for improving spatial accuracy. Interestingly, for the unified potential flow model we find that this also holds for nonlinear simulations. Large time steps can be chosen when using dense grids and high-order numerics without severely degrading overall numerical stability and efficiency. This is confirmed in numerical experiments and demonstrated in Figure \ref{ch7:numexp}. However, for very steep nonlinear waves and very densely clustered nonuniform grids, stability is found to be compromised without filtering. A proper filtering strategy, e.g., based on a super collocation technique \cite{ch7:Kirby03de-aliasingon}, can be used to remedy stability problems without destroying accuracy. 

 %
 \begin{figure}[!htb]
 \centering
 %
 \begin{figure}[!htb]
 \centering


@@ -334,7 +334,7 @@ Similar results were reported for the first time in the context of high-order Bo
 % MainLaplace2D_ex035_nonlinearLaplace.m
 \includegraphics[width=0.45\textwidth]{Chapters/chapter7/figures/SFwaves_snapshots_clustered-eps-converted-to.pdf}
 }
 % MainLaplace2D_ex035_nonlinearLaplace.m
 \includegraphics[width=0.45\textwidth]{Chapters/chapter7/figures/SFwaves_snapshots_clustered-eps-converted-to.pdf}
 }

-\caption[Numerical experiments to assess stability properties of numerical wave model.]{Numerical experiments to assess stability properties of numerical wave model. In three cases, computed snapshots are taken of the wave elevation over one wave period of time. In (a) the grid distribution of nodes in a one-parameter mapping for the grid is illustrated. Results from changes in wave elevation are illustrated for (b) a mildly nonlinear standing wave on a highly clustered grid, (c) regular stream function wave of medium steepness in shallow water $(kh,H/L)=(0.5,0.0292)$ on a uniform grid ($N_x=80$), and (d) a nonuniform grid with a minimal grid spacing 20 times smaller(!). In every case the step size remains fixed at $\Delta t = T/160$ s corresponding to a Courant number $C_r=c\tfrac{\Delta t}{\Delta x}=0.5$ for the uniform grid. A sixth order scheme and explicit EKR4 time-stepping are used in each test case.}
+\caption[Numerical experiments to assess stability properties of numerical wave model.]{Numerical experiments to assess stability properties of numerical wave model. In three cases, computed snapshots are taken of the wave elevation over one wave period of time. In (a) the grid distribution of nodes in a one-parameter mapping for the grid is illustrated. Results from changes in wave elevation are illustrated for (b) a mildly nonlinear standing wave on a highly clustered grid, (c) a regular stream function wave of medium steepness in shallow water $(kh,H/L)=(0.5,0.0292)$ on a uniform grid ($N_x=80$), and (d) a nonuniform grid with a minimal grid spacing 20 times smaller(!). In every case the step size remains fixed at $\Delta t = T/160$ s corresponding to a Courant number $C_r=c\tfrac{\Delta t}{\Delta x}=0.5$ for the uniform grid. A sixth order scheme and explicit EKR4 time-stepping are used in each test case.}

 \label{ch7:numexp}
 \end{figure}
 %\newpage
 \label{ch7:numexp}
 \end{figure}
 %\newpage


@@ -365,7 +365,7 @@ The first term is similar to a first-order accurate Forward Euler\index{forward
 \partial_t g = \mathcal{N}(g) + \frac{1-\Gamma(x)}{\tau} (g_e(t,x)-g(t,x)), \quad {\bf x}\in\Omega_\Gamma,
 \end{align}
 %
 \partial_t g = \mathcal{N}(g) + \frac{1-\Gamma(x)}{\tau} (g_e(t,x)-g(t,x)), \quad {\bf x}\in\Omega_\Gamma,
 \end{align}
 %

-where $\mathcal{N}$ represents a general nonlinear operator for the right-hand side. The immediate advantage is that a time-stepping scheme can easily be interchanged in a model implementation. The added term is a source term resulting in forcing inside relaxation zones when $g_e(t,x)\neq g(t,x)$ and $\Gamma(x)\neq1$ and otherwise has no effect. The strength of the forcing is influenced by the arbitrary parameter $\tau\in\mathbb{R}_+$ which can be defined to match the time scale of the dynamics. We have found that  $\tau\approx\Delta t$ works well, however, it is possible that a more optimal choice exist. Note that a too small $\tau$ may degrade the numerical stability of the model.
+where $\mathcal{N}$ represents a general nonlinear operator for the right-hand side. The immediate advantage is that a time-stepping scheme can easily be interchanged in a model implementation. The added term is a source term resulting in forcing inside relaxation zones when $g_e(t,x)\neq g(t,x)$ and $\Gamma(x)\neq1$ and otherwise has no effect. The strength of the forcing is influenced by the arbitrary parameter $\tau\in\mathbb{R}_+$ which can be defined to match the time scale of the dynamics. We have found that  $\tau\approx\Delta t$ works well; however, it is possible that a more optimal choice exist. Note that a too small $\tau$ may degrade the numerical stability of the model.

 
 A simple validation of the zones is shown in Figure \ref{ch7:figstandwave} where waves are generated at the left wall and propagate to the right wall, where reflection occurs leading to formation of standing waves due to the resulting interaction with the incident waves inside the numerical wave tank.
 
 
 A simple validation of the zones is shown in Figure \ref{ch7:figstandwave} where waves are generated at the left wall and propagate to the right wall, where reflection occurs leading to formation of standing waves due to the resulting interaction with the incident waves inside the numerical wave tank.
 

diff --git a/BookGPU/frontmatter/preface.tex b/BookGPU/frontmatter/preface.tex
index 9fbc466327565846a04a0b1bd5b7a4e24d9fe92e..178e0cc3d9475f83ab3e103d5fe1ce3beda7e7d7 100644 (file)
--- a/BookGPU/frontmatter/preface.tex
+++ b/BookGPU/frontmatter/preface.tex
@@ -37,4 +37,4 @@ illustrates three other applications that are not included in the previous
 parts.
 
 Some codes presented in this book are available online on my webpage:
 parts.
 
 Some codes presented in this book are available online on my webpage:

-http://members.femto-st.fr/raphael-couturier/gpu-book/ 
+http://members.femto-st.fr/raphael-couturier/en/gpu-book/