X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/book_gpu.git/blobdiff_plain/ab6faec96e0c06da1a3dc2eb8eeb3cdfc1a4528f..637049bfdd22c413d65ad0548d2d18a70a1fa6be:/BookGPU/Chapters/chapter14/ch14.tex?ds=inline

diff --git a/BookGPU/Chapters/chapter14/ch14.tex b/BookGPU/Chapters/chapter14/ch14.tex
index 916717d..9759ba7 100755
--- a/BookGPU/Chapters/chapter14/ch14.tex
+++ b/BookGPU/Chapters/chapter14/ch14.tex
@@ -217,7 +217,7 @@ for (is = 0; is < nsites; is++) {
 \begin{figure}[!t]
 \centering
 \includegraphics[width=12cm]{Chapters/chapter14/figures/decomphalo}
-\caption{Left: the lattice is decomposed between MPI tasks. For
+\caption[The lattice is decomposed between MPI tasks.]{Left: the lattice is decomposed between MPI tasks. For
   clarity we show a 2D decomposition of a 3D lattice, but in practice
   we decompose in all 3 dimensions. Halo cells are added to each
   sub-domain (as shown on the upper right for a single slice) which store
@@ -437,7 +437,7 @@ a simulation in terms of accounting budgets, or electricity.
 \begin{figure}[!t]
 \centering
 \includegraphics[width=10cm]{Chapters/chapter14/figures/two_graphs_ud}
-\caption{The weak (top) and strong (bottom) scaling of \textit{Ludwig}.  Closed
+\caption[The weak (top) and strong (bottom) scaling of \textit{Ludwig}.]{The weak (top) and strong (bottom) scaling of \textit{Ludwig}.  Closed
   shapes denote results using the CPU version run on the Cray
   XE6 (using two 16-core AMD Interlagos CPUs per node), while open
   shapes denote results using the GPU version on the Cray XK6 (using a
@@ -498,7 +498,7 @@ scaling for the larger systems.
 \centering
 %\includegraphics[width=10cm]{Chapters/chapter14/figures/bbl}
 \includegraphics[width=10cm]{Chapters/chapter14/figures/colloid_new}
-\caption{
+\caption[A two-dimensional schematic picture of spherical particles on the lattice.]{
 A two-dimensional schematic picture of spherical particles on the lattice.
 Left: a particle is allowed
 to move continuously across the lattice, and the position of the
@@ -619,7 +619,7 @@ stage everywhere instead of moving the look-up table to the GPU and
 introducing the associated logic.
 Ultimately, the GPU might favour other boundary methods which treat solid and
 fluid on a somewhat more equal basis, for example, the immersed boundary
-method \cite{ch14:immersed,ch14:immersed-lb} or smoothed profile method
+method \cite{ch14:immersed1,ch14:immersed2,ch14:immersed-lb} or smoothed profile method
 \cite{ch14:spm}.
 However, the approach adopted here  allows us to exploit
 the GPU for the intensive fluid simulation whilst maintaining the complex
@@ -958,8 +958,8 @@ by UK EPSRC under grant EV/J007404/1.
 % set second argument of \begin to the number of references
 % (used to reserve space for the reference number labels box)
 
-
-\begin{thebibliography}{1}
+\putbib[Chapters/chapter14/biblio14]
+%\begin{thebibliography}{1}
 
 %\bibitem{IEEEhowto:kopka}
 %H.~Kopka and P.~W. Daly, \emph{A Guide to \LaTeX}, 3rd~ed.\hskip 1em plus
@@ -967,22 +967,22 @@ by UK EPSRC under grant EV/J007404/1.
 
 
 
-\bibitem{succi-book}
-S. Succi, \textit{The lattice Boltzmann equation and beyond},
-Oxford University Press, Oxford, 2001.
+%% \bibitem{succi-book}
+%% S. Succi, \textit{The lattice Boltzmann equation and beyond},
+%% Oxford University Press, Oxford, 2001.
 
 %\bibitem{mpi-standard}
 %Message Passing Interface Forum, http://www.mpi-forum.org 
 
-\bibitem{desplat}
-Desplat, J.-C., I. Pagonabarraga, and P. Bladon,
-\textit{LUDWIG: A parallel lattice-Boltzmann code for complex fluids}.
-Comput. Phys. Comms., \textbf{134}, 273, 2001.
+%% \bibitem{desplat}
+%% Desplat, J.-C., I. Pagonabarraga, and P. Bladon,
+%% \textit{LUDWIG: A parallel lattice-Boltzmann code for complex fluids}.
+%% Comput. Phys. Comms., \textbf{134}, 273, 2001.
 
-\bibitem{aidun2010}
-C.K. Aidun and J.R. Clausen,
-\textit{Lattice Boltzmann method for complex flows},
-Ann. Rev. Fluid Mech., \textbf{42} 439--472 (2010).
+%% \bibitem{aidun2010}
+%% C.K. Aidun and J.R. Clausen,
+%% \textit{Lattice Boltzmann method for complex flows},
+%% Ann. Rev. Fluid Mech., \textbf{42} 439--472 (2010).
 
 %\bibitem{bray1994}
 %A.J. Bray,
@@ -1001,10 +1001,10 @@ Ann. Rev. Fluid Mech., \textbf{42} 439--472 (2010).
 %fluid systems},
 %Phys. Rev. E, \textbf{54}, 5041--5052 (1996).
 
-\bibitem{stratford2008}
-K. Stratford and I. Pagonabarraga,
-Parallel domain decomposition for lattice Boltzmann with moving particles,
-\textit{Comput. Math. with Applications} \textbf{55}, 1585 (2008).
+%% \bibitem{stratford2008}
+%% K. Stratford and I. Pagonabarraga,
+%% Parallel domain decomposition for lattice Boltzmann with moving particles,
+%% \textit{Comput. Math. with Applications} \textbf{55}, 1585 (2008).
 
 %\bibitem{xe6}
 %Cray XE6 Product Brochure, available from
@@ -1017,146 +1017,146 @@ Parallel domain decomposition for lattice Boltzmann with moving particles,
 %http://www.cray.com/Products/XK6/XK6.aspx (2011)
 
 
-\bibitem{wei2004}
-X. Wei, W. Li, K. M\"uller, and A.E. Kaufman,
-\textit{The lattice Boltzmann method for simulating gaseous phenomena},
-IEEE Transactions on Visualization and Computer Graphics,
-\textbf{10}, 164--176 (2004).
+%% \bibitem{wei2004}
+%% X. Wei, W. Li, K. M\"uller, and A.E. Kaufman,
+%% \textit{The lattice Boltzmann method for simulating gaseous phenomena},
+%% IEEE Transactions on Visualization and Computer Graphics,
+%% \textbf{10}, 164--176 (2004).
 %% Apparently first LB via GPU; a serious contribution using single fluid
 %%d3q19 single relaxation time.
 
-\bibitem{zhu2006}
-H. Zhu, X. Liu, Y. Liu, and E. Wu,
-\textit{Simulation of miscible binary mixtures based on lattice Boltzmann method},
-Comp. Anim. Virtual Worlds, \textbf{17}, 403--410 (2006).
+%% \bibitem{zhu2006}
+%% H. Zhu, X. Liu, Y. Liu, and E. Wu,
+%% \textit{Simulation of miscible binary mixtures based on lattice Boltzmann method},
+%% Comp. Anim. Virtual Worlds, \textbf{17}, 403--410 (2006).
 %% Single relaxation (MRT mentioned) time d3q19 apparently sound although
 %%not a lot of detail. Pre-cuda so graphics code.
 
-\bibitem{zhao2007}
-Y. Zhao,
-\textit{Lattice Boltzmann based PDE solver on the GPU},
-Visual Comput., doi 10.1007/s00371-0070191-y (2007).
-
-\bibitem{toelke2010}
-J. T\"olke,
-Implementation of a lattice Boltzmann kernel using the compute unified
-device architecture developed by nVIDIA,
-Comput. Visual Sci. 13 29--39 (2010).
-
-\bibitem{fan2004}
-Z. Fan, F. Qiu, A. Kaufman, and S. Yoakum-Stover,
-\textit{GPU cluster for high performance computing},
-Proceedings of ACM/IEEE Supercomputing Conference, pp. 47--59,
-IEEE Computer Society Press, Pittsburgh, PA (2004).
-
-\bibitem{myre2011}
-J. Myre, S.D.C. Walsh, D. Lilja, and M.O. Saar,
-\textit{Performance analysis of single-phase, multiphase, and multicomponent
-lattice Boltzmann fluid flow simulations on GPU clusters},
-Concurrency Computat.: Pract. Exper., \textbf{23}, 332--350 (2011).
-
-\bibitem{obrecht2011}
-C. Obrecht, F. Kuznik, B. Tourancheau, and J.-J. Roux,
-\textit{Multi-GPU implementation of the lattice Boltzmann method},
-Comput. Math. with Applications,
-doi:10.1016/j.camwa.2011.02.020 (2011).
-
-\bibitem{bernaschi2010}
-M. Bernaschi, M. Fatica, S. Melchionna, S. Succi, and E. Kaxiras,
-\textit{A flexible high-performance lattice Boltzmann GPU code for the
-simulations of fluid flow in complex geometries},
-Concurrency Computat.: Pract. Exper., \textbf{22}, 1--14 (2010).
-
-\bibitem{xian2011}
-W. Xian and A. Takayuki,
-\textit{Multi-GPU performance of incompressible flow computation by
-lattice Boltzmann method on GPU cluster},
-Parallel Comput., doi:10.1016/j.parco.2011.02.007 (2011). 
-
-\bibitem{feichtinger2011}
-C. Feichtinger, J. Habich, H. K\"ostler, G. Hager, U. R\"ude, and
-G. Wellein,
-A flexible patch-based lattice Boltzmann parallelization approach
-for heterogeneous GPU-CPU clusters,
-\textit{Parallel Computing} \textbf{37} 536--549 (2011).
-
-\bibitem{wellein2006}
-G. Wellein, T. Zeiser, G Hager, and S. Donath,
-On the single processor performance of simple lattice Boltzmann kernels,
-\textit{Computers and Fluids}, \textbf{35}, 910--919 (2006).
-
-\bibitem{pohl2003}
-T. Pohl, M. Kowarschik, J. Wilke, K. Igelberger, and U. R\"ude,
-Optimization and profiling of the cache performance of parallel
-lattice Boltzmann code,
-\textit{Parallel Process Lett.} \textit{13} 549--560 (2003).
-
-\bibitem{mattila2007}
-K. Mattila, J. Hyv\"aluoma, T. Rossi, M. Aspn\"as and J. Westerholm,
-An efficient swap algorithm for the lattice Boltzmann method,
-\textit{Comput. Phys. Comms.} \textit{176} 200-210 (2007).
-
-\bibitem{wittmann2012}
-M. Wittmann, T. Zeiser, G. Hager, and G. Wellein,
-Comparison of different propagation steps for lattice Boltzmann methods,
-\textit{Comput. Math with Appl.} doi:10.1016/j.camwa.2012.05.002 (2012).
-
-\bibitem{walshsaar2012}
-S.D.C. Walsh and M.O. Saar,
-Developing extensible lattice Boltzmann simulators for general-purpose
-graphics-processing units,
-\textit{Comm. Comput. Phys.}, \textbf{13} 867--879 (2013).
-
-
-\bibitem{williams2011}
-S. Williams, L. Oliker, J. Carter, and J Shalf,
-Extracting ultra-scale lattice Boltzmann performance via
-hierarchical and distributed auto-tuning,
-\textit{Proc. SC2011}.
-
-
-\bibitem{ch14:stratford-jsp2005}
-K. Stratford, R. Adhikari, I. Pagonabarraga, and J.-C. Desplat,
-\textit{Lattice Boltzmann for Binary Fluids with Suspended Colloids},
-J. Stat. Phys. \textbf{121}, 163 (2005).
-
-\bibitem{ladd1994}
-A.J.C. Ladd,
-Numerical simulations of particle suspensions via a discretized
-Boltzmann equation. Part 1. Theoretical foundation,
-\textit{J. Fluid Mech.} \textbf{271} 285--309 (1994);
-Part II. Numerical results,
-\textit{ibid.} \textbf{271} 311--339 (1994).
+%% \bibitem{zhao2007}
+%% Y. Zhao,
+%% \textit{Lattice Boltzmann based PDE solver on the GPU},
+%% Visual Comput., doi 10.1007/s00371-0070191-y (2007).
+
+%% \bibitem{toelke2010}
+%% J. T\"olke,
+%% Implementation of a lattice Boltzmann kernel using the compute unified
+%% device architecture developed by nVIDIA,
+%% Comput. Visual Sci. 13 29--39 (2010).
+
+%% \bibitem{fan2004}
+%% Z. Fan, F. Qiu, A. Kaufman, and S. Yoakum-Stover,
+%% \textit{GPU cluster for high performance computing},
+%% Proceedings of ACM/IEEE Supercomputing Conference, pp. 47--59,
+%% IEEE Computer Society Press, Pittsburgh, PA (2004).
+
+%% \bibitem{myre2011}
+%% J. Myre, S.D.C. Walsh, D. Lilja, and M.O. Saar,
+%% \textit{Performance analysis of single-phase, multiphase, and multicomponent
+%% lattice Boltzmann fluid flow simulations on GPU clusters},
+%% Concurrency Computat.: Pract. Exper., \textbf{23}, 332--350 (2011).
+
+%% \bibitem{obrecht2011}
+%% C. Obrecht, F. Kuznik, B. Tourancheau, and J.-J. Roux,
+%% \textit{Multi-GPU implementation of the lattice Boltzmann method},
+%% Comput. Math. with Applications,
+%% doi:10.1016/j.camwa.2011.02.020 (2011).
+
+%% \bibitem{bernaschi2010}
+%% M. Bernaschi, M. Fatica, S. Melchionna, S. Succi, and E. Kaxiras,
+%% \textit{A flexible high-performance lattice Boltzmann GPU code for the
+%% simulations of fluid flow in complex geometries},
+%% Concurrency Computat.: Pract. Exper., \textbf{22}, 1--14 (2010).
+
+%% \bibitem{xian2011}
+%% W. Xian and A. Takayuki,
+%% \textit{Multi-GPU performance of incompressible flow computation by
+%% lattice Boltzmann method on GPU cluster},
+%% Parallel Comput., doi:10.1016/j.parco.2011.02.007 (2011). 
+
+%% \bibitem{feichtinger2011}
+%% C. Feichtinger, J. Habich, H. K\"ostler, G. Hager, U. R\"ude, and
+%% G. Wellein,
+%% A flexible patch-based lattice Boltzmann parallelization approach
+%% for heterogeneous GPU-CPU clusters,
+%% \textit{Parallel Computing} \textbf{37} 536--549 (2011).
+
+%% \bibitem{wellein2006}
+%% G. Wellein, T. Zeiser, G Hager, and S. Donath,
+%% On the single processor performance of simple lattice Boltzmann kernels,
+%% \textit{Computers and Fluids}, \textbf{35}, 910--919 (2006).
+
+%% \bibitem{pohl2003}
+%% T. Pohl, M. Kowarschik, J. Wilke, K. Igelberger, and U. R\"ude,
+%% Optimization and profiling of the cache performance of parallel
+%% lattice Boltzmann code,
+%% \textit{Parallel Process Lett.} \textit{13} 549--560 (2003).
+
+%% \bibitem{mattila2007}
+%% K. Mattila, J. Hyv\"aluoma, T. Rossi, M. Aspn\"as and J. Westerholm,
+%% An efficient swap algorithm for the lattice Boltzmann method,
+%% \textit{Comput. Phys. Comms.} \textit{176} 200-210 (2007).
+
+%% \bibitem{wittmann2012}
+%% M. Wittmann, T. Zeiser, G. Hager, and G. Wellein,
+%% Comparison of different propagation steps for lattice Boltzmann methods,
+%% \textit{Comput. Math with Appl.} doi:10.1016/j.camwa.2012.05.002 (2012).
+
+%% \bibitem{walshsaar2012}
+%% S.D.C. Walsh and M.O. Saar,
+%% Developing extensible lattice Boltzmann simulators for general-purpose
+%% graphics-processing units,
+%% \textit{Comm. Comput. Phys.}, \textbf{13} 867--879 (2013).
+
+
+%% \bibitem{williams2011}
+%% S. Williams, L. Oliker, J. Carter, and J Shalf,
+%% Extracting ultra-scale lattice Boltzmann performance via
+%% hierarchical and distributed auto-tuning,
+%% \textit{Proc. SC2011}.
+
+
+%% \bibitem{ch14:stratford-jsp2005}
+%% K. Stratford, R. Adhikari, I. Pagonabarraga, and J.-C. Desplat,
+%% \textit{Lattice Boltzmann for Binary Fluids with Suspended Colloids},
+%% J. Stat. Phys. \textbf{121}, 163 (2005).
+
+%% \bibitem{ladd1994}
+%% A.J.C. Ladd,
+%% Numerical simulations of particle suspensions via a discretized
+%% Boltzmann equation. Part 1. Theoretical foundation,
+%% \textit{J. Fluid Mech.} \textbf{271} 285--309 (1994);
+%% Part II. Numerical results,
+%% \textit{ibid.} \textbf{271} 311--339 (1994).
  
 
-\bibitem{nguyen2002}
-N.-Q. Nguyen and A.J.C. Ladd,
-Lubrication corrections for lattice Boltzmann simulations of particle
-suspensions,
-\textit{Phys. Rev. E} \textbf{66} 046708 (2002).
-
-\bibitem{ch14:immersed}
-C.S. Peskin,
-Flow patterns around heart valves; a numerical method,
-\textit{J. Comp. Phys.}, \textbf{10}, 252--271 (1972);
-C.S. Peskin,
-The immersed boundary method,
-\textit{Acta Nummerica} \textbf{11} 479--517 (2002).
-
-\bibitem{ch14:immersed-lb}
-Z.-G. Feng and E.E. Michaelides,
-The immersed boundary-lattice Boltzmann method for solving
-fluid-particles interaction problem,
-\textit{J. Comp. Phys.}, \textbf{195} 602--628 (2004).
-
-\bibitem{ch14:spm}
-Y. Nakayama and R. Yammamoto,
-Simulation method to resolve hydrodynamic interactions in colloidal
-dispersions,
-\textit{Phys. Rev. E}, \textbf{71} 036707 (2005).
-
-
-\end{thebibliography}
+%% \bibitem{nguyen2002}
+%% N.-Q. Nguyen and A.J.C. Ladd,
+%% Lubrication corrections for lattice Boltzmann simulations of particle
+%% suspensions,
+%% \textit{Phys. Rev. E} \textbf{66} 046708 (2002).
+
+%% \bibitem{ch14:immersed}
+%% C.S. Peskin,
+%% Flow patterns around heart valves; a numerical method,
+%% \textit{J. Comp. Phys.}, \textbf{10}, 252--271 (1972);
+%% C.S. Peskin,
+%% The immersed boundary method,
+%% \textit{Acta Nummerica} \textbf{11} 479--517 (2002).
+
+%% \bibitem{ch14:immersed-lb}
+%% Z.-G. Feng and E.E. Michaelides,
+%% The immersed boundary-lattice Boltzmann method for solving
+%% fluid-particles interaction problem,
+%% \textit{J. Comp. Phys.}, \textbf{195} 602--628 (2004).
+
+%% \bibitem{ch14:spm}
+%% Y. Nakayama and R. Yammamoto,
+%% Simulation method to resolve hydrodynamic interactions in colloidal
+%% dispersions,
+%% \textit{Phys. Rev. E}, \textbf{71} 036707 (2005).
+
+
+%\end{thebibliography}
 
 
 
