source: palm/trunk/TUTORIAL/SOURCE/parallelization.tex @ 970

Last change on this file since 970 was 945, checked in by maronga, 12 years ago

added/updated several tutorial files

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1% $Id: parallelization.tex 945 2012-07-17 15:43:01Z maronga $
2\input{header_tmp.tex}
3%\input{../header_lectures.tex}
4
5\usepackage[utf8]{inputenc}
6\usepackage{ngerman}
7\usepackage{pgf}
8\usetheme{Dresden}
9\usepackage{subfigure}
10\usepackage{units}
11\usepackage{multimedia}
12\usepackage{hyperref}
13\newcommand{\event}[1]{\newcommand{\eventname}{#1}}
14\usepackage{xmpmulti}
15\usepackage{tikz}
16\usetikzlibrary{shapes,arrows,positioning}
17\usetikzlibrary{decorations.markings}             %neues paket
18\usetikzlibrary{decorations.pathreplacing}        %neues paket
19\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
20\usepackage{amsmath}
21\usepackage{amssymb}
22\usepackage{multicol}
23\usepackage{pdfcomment}
24\usepackage{graphicx}
25\usepackage{listings}
26\lstset{showspaces=false,language=fortran,basicstyle=
27        \ttfamily,showstringspaces=false,captionpos=b}
28
29\institute{Institut fÌr Meteorologie und Klimatologie, Leibniz UniversitÀt Hannover}
30\date{last update: \today}
31\event{PALM Seminar}
32\setbeamertemplate{navigation symbols}{}
33
34\setbeamertemplate{footline}
35  {
36    \begin{beamercolorbox}[rightskip=-0.1cm]&
37     {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}}
38    \end{beamercolorbox}
39    \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,
40      leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}
41      {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}
42    \end{beamercolorbox}
43    \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}
44    \end{beamercolorbox}
45  }
46%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}}
47
48\title[Parallelization]{Parallelization}
49\author{Siegfried Raasch}
50
51\begin{document}
52
53% Folie 1
54\begin{frame}
55   \titlepage
56\end{frame}
57
58\section{Parallelization}
59\subsection{Parallelization}
60
61% Folie 2
62\begin{frame}
63   \frametitle{Basics of Parallelization}
64   \tikzstyle{yellow} = [rectangle,  fill=yellow!20, text width=0.6\textwidth, font=\scriptsize]
65   \scriptsize
66   \textbf{Parallelization:}
67   \begin{itemize}
68      \item<2-> All processor elements (PE, core) are carrying out the same program (SIMD).
69      \item<3-> Each PE of a parallel computer operates on a different set of data.
70   \end{itemize}
71
72   \ \\
73   \onslide<4->\textbf{Realization:}
74   \begin{columns}[T]
75      \begin{column}{0.45\textwidth}
76         \onslide<5->each PE solves the equations for a different subdomain of the total domain
77         \begin{center}
78            \includegraphics[width=0.5\textwidth]{parallelization_figures/subdomain.png}
79         \end{center}
80         \onslide<7->each PE only knows the variable values from its subdomain, communication / data exchange between PEs is necessary\\
81         \onslide<9->\textbf{message passing model (MPI)}
82      \end{column}
83      \begin{column}{0.45\textwidth}
84         \onslide<6->program loops are parallelized, i.e. each processor solves for a subset of the total index range
85         \begin{center}
86            \begin{tikzpicture}[auto, node distance=0]
87               \node [yellow] (1) {%
88               \texttt{!\$OMP DO}\\
89               \texttt{\quad \quad DO  i = 1, 100}\\
90               \quad \quad \quad $\vdots$\\
91               \texttt{\quad \quad ENDDO}};
92            \end{tikzpicture}
93         \end{center}
94         \onslide<8-> parallelization can easily be done by the compiler, if all PEs have access to all variables (shared memory)\\
95         \onslide<10-> \textbf{shared memory model (OpenMP)}
96      \end{column}
97   \end{columns}
98\end{frame}
99
100% Folie 3
101\begin{frame}
102   \frametitle{Basic Architectures of Massively Parallel Computers}
103   \tikzstyle{info} = [rectangle, text width=0.25\textwidth, font=\scriptsize]
104   
105   
106   \begin{center}
107      \begin{tikzpicture}
108
109         \node (center) at (0,1) {};
110         \onslide<2-> \node (Network) at (-3.5,1) [ellipse,fill=green!20] {Network};
111         \node (dis_mem) at (-3.5,-1) [text width=0.28\textwidth] {\footnotesize \textbf{distributed} memory\\(Cray-T3E)};
112         \onslide<3-> \node (add_mem) at (3.5,1) [rectangle, draw] {adressable memory};
113         \node (sha_mem) at (3.5,-1) [text width=0.35\textwidth] {\footnotesize \textbf{shared} memory\\(SGI-Altix, multicore PCs)};
114         \onslide<7-> \node (MPI) at (-3.5,-3) [ellipse,fill=yellow!90] {MPI};
115         \onslide<8-> \node (OpenMP) at (3.5,-3) [ellipse,fill=yellow!90] {OpenMP};         
116         \onslide<6-> \node (clustered_systems) at (0,-3) [draw, text width=0.15\textwidth] {clustered systems};
117         \node (cs_info) at (0,-4.2) [text width=0.4\textwidth] {\footnotesize (IBM-Regatta, Linux-Cluster,
118NEC-SX, SGI-ICE, Cray-XT4)};
119
120% Adressable memory node (big)
121
122         \onslide<3-> \node (p1) at (2,-0.05) [draw,circle, scale=0.9] {\scriptsize p};
123         \node (p2) at (2.6,-0.05) [draw,circle, scale=0.9] {\scriptsize p};
124         \node (p3) at (3.2,-0.05) [draw,circle, scale=0.9] {\scriptsize p};
125         \node (p4) at (3.8,-0.05) [draw,circle, scale=0.9] {\scriptsize p};
126         \node (p5) at (4.4,-0.05) [draw,circle, scale=0.9] {\scriptsize p};
127         \node (p6) at (5,-0.05) [draw,circle, scale=0.9] {\scriptsize p};
128         
129         \draw[-] (3.5,0.7) -- (3.5,0.4);
130         \draw[-] (2,0.4) -- (5,0.4);
131         \draw[-] (2,0.4) -- (p1);
132         \draw[-] (2.6,0.4) -- (p2);
133         \draw[-] (3.2,0.4) -- (p3);         
134         \draw[-] (3.8,0.4) -- (p4);
135         \draw[-] (4.4,0.4) -- (p5);         
136         \draw[-] (5,0.4) -- (p6);
137         
138% Adressable memory node (small)   
139         \onslide<4->
140         \draw[->, thick] (1.5,0.2) -- (0.4,0.2) ;   
141         \node at (0,0.2) [scale=0.2] {%
142         \begin{tikzpicture}
143           
144            \node (add_mem_small) at (3.5,0.9) [ultra thick, rectangle, draw, minimum width=3cm] {};
145            \node (p1_small) at (2,-0.05) [ultra thick, draw,circle, scale=0.9] {};
146            \node (p2_small) at (2.6,-0.05) [ultra thick, draw,circle, scale=0.9] {};
147            \node (p3_small) at (3.2,-0.05) [ultra thick, draw,circle, scale=0.9] {};
148            \node (p4_small) at (3.8,-0.05) [ultra thick, draw,circle, scale=0.9] {};
149            \node (p5_small) at (4.4,-0.05) [ultra thick, draw,circle, scale=0.9] {};
150            \node (p6_small) at (5,-0.05) [ultra thick, draw,circle, scale=0.9] {};
151         
152            \draw[-, ultra thick] (add_mem_small.south) -- (3.5,0.4);
153            \draw[-, ultra thick] (2,0.4) -- (5,0.4);
154            \draw[-, ultra thick] (2,0.4) -- (p1_small);
155            \draw[-, ultra thick] (2.6,0.4) -- (p2_small);
156            \draw[-, ultra thick] (3.2,0.4) -- (p3_small);         
157            \draw[-, ultra thick] (3.8,0.4) -- (p4_small);
158            \draw[-, ultra thick] (4.4,0.4) -- (p5_small);         
159            \draw[-, ultra thick] (5,0.4) -- (p6_small);
160           
161           
162         \end{tikzpicture}
163         } ;
164         
165         \onslide<5->
166         \node (add_info) at (0,-0.1) [scale=0.9] {\scriptsize node};
167
168% Black Arrows
169         \onslide<6-> \draw[->, thick] (-2.5,-1.5) -- (-0.8,-2.2) ;
170         \draw[->, thick] (2.5,-1.5) -- (0.8,-2.2) ;
171
172% MPI Arrows
173         \onslide<7-> \draw[->, ultra thick, color=yellow] (-3.5,-2.7) -- (-3.5,-1.5) ;
174         \draw[->, ultra thick, color=yellow] (-2.9,-3) -- (-1.0,-3.0) ;
175         \draw[->, ultra thick, color=yellow] (-3.0,-2.8) -- (1.5,-1.0) ;
176
177% OpenMP Arrows         
178         \onslide<8-> \draw[->, ultra thick, color=yellow] (3.5,-2.6) -- (3.5,-1.5) ;
179         \draw[->, ultra thick, color=yellow] (2.5,-2.8) -- (-2.5,0.7) ;
180         
181% Network decorations
182         \onslide<2-> \node (pr1) at (-4.6,0.7) [draw,circle,scale=0.5] {};
183         \node (mem1) at (-4.6,0.45) [draw,rectangle,scale=0.5] {};
184         \draw[-] (-4.5,0.9) -- (pr1);
185         \draw[-] (mem1) -- (pr1);
186         \draw[-] ([xshift=0.02cm]pr1.east) -- ([xshift=0.3cm, yshift=-0.2cm]pr1.east);
187         \draw[-] ([xshift=0.02cm]mem1.east) -- ([xshift=0.3cm, yshift=-0.2cm]mem1.east); 
188         \node at (-3.7,0.45) {\tiny processor};   
189         \node at (-3.3,0.25) {\tiny adressable memory};   
190         
191         \node (pr2) at (-4.6,1.3) [draw,circle,scale=0.5] {};
192         \node (mem2) at (-4.6,1.55) [draw,rectangle,scale=0.5] {};
193         \draw[-] (-4.5,1.1) -- (pr2);
194         \draw[-] (mem2) -- (pr2);
195         \node (pr3) at (-3.9,1.5) [draw,circle,scale=0.5] {};
196         \node (mem3) at (-3.9,1.75) [draw,rectangle,scale=0.5] {};
197         \draw[-] (-3.8,1.3) -- (pr3);
198         \draw[-] (mem3) -- (pr3);       
199         \node (pr4) at (-4.9,0.95) [draw,circle,scale=0.5] {};
200         \node (mem4) at (-4.9,0.7) [draw,rectangle,scale=0.5] {};
201         \draw[-] (-4.55,1.0) -- (pr4);
202         \draw[-] (mem4) -- (pr4);   
203         \node (pr5) at (-3.0,1.5) [draw,circle,scale=0.5] {};
204         \node (mem5) at (-3.0,1.75) [draw,rectangle,scale=0.5] {};
205         \draw[-] (-3.08,1.3) -- (pr5);
206         \draw[-] (mem5) -- (pr5);   
207         \node (pr6) at (-2.2,1.1) [draw,circle,scale=0.5] {};
208         \node (mem6) at (-2.2,1.35) [draw,rectangle,scale=0.5] {};
209         \draw[-] (-2.45,1.0) -- (pr6);
210         \draw[-] (mem6) -- (pr6);   
211                           
212      \end{tikzpicture}
213   \end{center}
214
215\end{frame}
216
217% Folie 4
218\begin{frame}
219   \frametitle{PALM Parallelization Model}
220   \scriptsize
221   \onslide<2-> \textbf{General demands for a parallelized program:}
222   \begin{itemize}
223      \item<3-> Load balancing
224      \item<4-> Small communication overhead
225      \item<5-> Scalability (up to large numbers of processors)
226   \end{itemize}
227   \vspace{2mm}
228   \onslide<6-> \textbf{The basic parallelization method used for PALM is a 2D-domain decomposition along $x$ and $y$:}\\
229   \begin{columns}[T]
230      \begin{column}{0.3\textwidth}
231         \onslide<7-> \includegraphics[width=1.0\textwidth]{parallelization_figures/subdomain.png}
232      \end{column}
233      \begin{column}{0.6\textwidth}
234         \ \\
235         \onslide<8-> contiguous data in memory (FORTRAN):\\
236         \ \\
237         \ \\
238         \textcolor{blue}{columns of i}\\
239         \textcolor{red}{no contiguous data at all}\\
240         \onslide<9-> \textcolor{blue}{columns of k}\\
241         \textcolor{red}{planes of k,j (all data contiguous)}
242      \end{column}
243   \end{columns}   
244   \vspace{2mm}
245   \begin{itemize}
246      \item<10-> Alternatively, a 1D-decomposition along $x$ or $y$ may be used in case of slow networks, but this generally doesn't scale for processor numbers $>$ 256.
247      \item<11-> Message passing is realized using MPI.
248      \item<12-> OpenMP parallelization as well as mixed usage of OpenMP and
249MPI is also possible. (OpenMP tests and optimization is under way)
250   \end{itemize}
251\end{frame}
252
253% Folie 5
254\begin{frame}
255   \frametitle{Implications of Decomposition}
256   \scriptsize
257   \begin{columns}[T]
258      \begin{column}{0.5\textwidth}
259         \begin{itemize}
260            \item<2-> Central finite differences cause \textcolor{red}{local data dependencies}\\
261            \ \\
262            solution:  introduction of \textcolor{red}{ghost points}
263            \vspace{5mm}
264           
265            \begin{flushright}
266               \onslide<3-> $\left. \dfrac{\partial \psi}{\partial x} \right|_i = \dfrac{\psi_{i+1} - \psi_{i-1}}{2 \Delta x}$
267            \end{flushright}
268            \vspace{10mm}
269            \item<4-> FFT and linear equation solver cause \textcolor{red}{non-local data dependencies}\\
270            \ \\
271            solution: transposition of 3D-arrays
272         \end{itemize}
273      \end{column}
274      \begin{column}{0.6\textwidth}
275      \begin{center}
276         \vspace{-5mm}
277         \onslide<3-> \includegraphics[width=0.7\textwidth]{parallelization_figures/ghost_points.png}
278         \vspace{4mm}
279         \onslide<5-> \includegraphics[width=0.8\textwidth]{parallelization_figures/fft.png} \end{center}
280         \vspace{-4mm}
281         \textbf{Example: transpositions for solving the poisson equation}
282      \end{column}
283   \end{columns}   
284\end{frame} 
285
286% Folie 6
287\begin{frame}
288   \frametitle{How to Use the Parallelized Version of PALM}   
289   \scriptsize
290   \begin{columns}[T]
291      \begin{column}{1.12\textwidth}
292         \begin{itemize} 
293            \item<1-> The parallel version of PALM is switched on by \texttt{mrun}-option ''\texttt{-K parallel}''. Additionally, the number of required processors and the number of tasks per node (number of PEs to be used on one node) have to be provided:\\
294                 \quad \texttt{mrun ... -K parallel -X64 -T8 ...}
295                 \item<2-> From an accounting point of view, it is always most efficient to use all PEs of a node (\texttt{-T8}) (in case of a ''non-shared'' usage of nodes).
296                 \item<3-> If a normal unix-kernel operating system (not a micro-kernel) is running on each CPU, then there migth be a speed-up of the code, if 1-2 PEs less than the total number of PEs on the node are used.
297                 \item<4-> On machines with a comparably slow network, a 1D-decomposition (along $x$) should be used, because then only two transpositions have to be carried out by the pressure solver. A 1D-decomposition is automatically used for NEC-machines (e.g.  \texttt{-h necriam}). The virtual processor grid to be used can be set manually by d3par-parameters \texttt{npex} and \texttt{npey}.
298            \item<6-> Using the Open-MP parallelization does not yield any advantage over using a pure domain decomposition with MPI (contrary to expectations, it mostly slows down the computational speed), but this may change on cluster systems for very large number of processors ($>$10000?).\\       
299         \end{itemize}
300         \begin{center}
301         \vspace{-7mm}
302         \onslide<5-> \includegraphics[width=0.13\textwidth]{parallelization_figures/folie_6.png}
303         \end{center}
304      \end{column}
305   \end{columns} 
306\end{frame}
307
308% Folie 7
309\begin{frame}
310   \frametitle{MPI Communication}   
311   \scriptsize
312   \begin{columns}[T]
313      \begin{column}{1.12\textwidth}
314         \begin{itemize}
315            \item<1-> MPI (message passing interface) is a portable interface for communication between PEs (FORTRAN or C library).
316            \vspace{2mm}
317            \item<2-> To make MPI available on HLRN‘s SGI-ICE, the module \texttt{mpt} must be loaded by setting the \texttt{\%modules} option  in .mrun.config appropriately:
318
319                 \quad \texttt{\%modules   ...:mpt:...} 
320            \vspace{2mm}
321                 \item<2-> The path to the MPI-library may have to be given in the compiler call, by setting an appropriate option in the configuration file .mrun.config:
322
323                 \quad \texttt{\%lopts  -axW:-cpp:-r8:-nbs:-Vaxlib:\textcolor{blue}{-L:<replace by mpi library path>:-lmpi}}
324            \vspace{2mm}
325                 \item<3-> All MPI calls must be within\\
326                 \quad \texttt{CALL MPI\_INIT( ierror )}\\
327                 \quad $\vdots$\\
328            \quad \texttt{CALL MPI\_FINALIZE( ierror )}\\
329         \end{itemize}
330         
331      \end{column}
332   \end{columns} 
333\end{frame}
334
335% Folie 8
336\begin{frame}
337   \frametitle{Communication Within PALM}   
338   \small
339   \begin{itemize}
340      \item<1-> MPI calls within PALM are available when using the \texttt{mrun}-option ''\texttt{-K parallel}''.
341      \item<2-> Communication is needed for
342      \begin{itemize}
343         \footnotesize
344         \item<2-> exchange of ghost points
345         \item<3-> transpositions (FFT-poisson-solver)
346         \item<4-> calculating global sums (e.g. for calculating horizontal averages)
347      \end{itemize}
348      \item<5-> Additional MPI calls are required to define the so-called virtual processor grid and to define special data types needed for more comfortable exchange of data.
349   \end{itemize}
350\end{frame}
351
352% Folie 9
353\begin{frame}
354   \frametitle{Virtual Processor Grid Used in PALM}   
355   \footnotesize
356   The processor grid and special data types are defined in file \texttt{init\_pegrid.f90}
357   \begin{itemize}
358      \item<2-> PALM uses a two-dimensional virtual processor grid (in case of a 1D-decomposition, it has only one element along $y$). It is defined by a so called communicator (here: \texttt{comm2d}):\\
359      \scriptsize
360      \quad \texttt{ndim = 2}\\
361           \quad \texttt{pdims(1) = npex    ! \# of processors along x}\\
362           \quad \texttt{pdims(2) = npey    ! \# of processors along y}\\
363           \quad \texttt{cyclic(1) = .TRUE.}\\
364           \quad \texttt{cyclic(2) = .TRUE.}\\
365
366           \quad \texttt{CALL MPI\underline{\ }CART\underline{\ }CREATE( MPI\underline{\ }COMM\underline{\ }WORLD, ndim, pdims, cyclic,  \&}\\
367           \quad \texttt{\hspace{10.5em} reorder, \textcolor{blue}{comm2d}, ierr )} 
368      \item<3-> The processor number (id) with respect to this processor grid, \texttt{myid}, is given by:\\
369      \scriptsize
370      \quad \texttt{CALL MPI\underline{\ }COMM\underline{\ }RANK( comm2d, \textcolor{blue}{myid}, ierr )}     
371      \item<4-> The ids of the neighbouring PEs are determined by:\\
372      \scriptsize
373      \quad \texttt{CALL MPI\underline{\ }CARD\underline{\ }SHIFT( comm2d, 0, 1, \textcolor{blue}{pleft}\textcolor{blue}{pright}, ierr )}\\
374      \quad \texttt{CALL MPI\underline{\ }CARD\underline{\ }SHIFT( comm2d, 1, 1, \textcolor{blue}{psouth}, \textcolor{blue}{pnorth}, ierr )}
375   \end{itemize}
376\end{frame}
377
378% Folie 10
379\begin{frame}
380   \frametitle{Exchange of ghost points}   
381   \scriptsize
382         \begin{itemize}
383            \item<1-> Ghost points are stored in additional array elements added at the horizontal boundaries of the subdomains, e.g.\\
384            \tiny
385            \quad \texttt{u(:,:,nxl\textcolor{blue}{-ngl}), u(:,:,nxr\textcolor{blue}{+ngl})    ! left and right boundary}\\
386            \quad \texttt{u(:,nys\textcolor{blue}{-ngl},:), u(:,nyn\textcolor{blue}{+ngl},:)    ! south and north boundary}\\
387            \hspace{3mm}
388            \item<2-> \scriptsize The exchange of ghost points is done in file \texttt{exchange\underline{\ }horiz.f90}\\
389            \textbf{\underline{Simplified} example:} synchroneous exchange of ghost points along $x$ ($yz$-planes, send left, receive right plane):\\
390            \tiny
391            \quad \texttt{CALL MPI\underline{\ }SENDRECV( ar(nzb,nys-\textcolor{blue}{ngl},nxl),   ngp\underline{\ }yz, MPI\underline{\ }REAL, pleft,  0,}\\
392            \quad \texttt{\hspace{9.5em}ar(nzb,nys-\textcolor{blue}{ngl},nxr+1), ngp\underline{\ }yz, MPI\underline{\ }REAL, pright, 0,}\\
393            \quad \texttt{\hspace{9.5em}comm2d, status, ierr )}\\
394            \hspace{3mm}
395            \item<3-> \scriptsize In the real code special MPI data types (vectors) are defined for exchange of $yz$/$xz$-planes for performance reasons and because array elements to be exchanged are not consecutively stored in memory for $xz$-planes:\\
396            \tiny
397            \quad \texttt{ngp\underline{\ }yz(0) = (nzt - nzb + 2) * (nyn - nys + 1 + 2 * \textcolor{blue}{ngl} )}\\
398            \quad \texttt{CALL MPI\underline{\ }TYPE\underline{\ }VECTOR( \textcolor{blue}{ngl}, ngp\underline{\ }yz(0), ngp\underline{\ }yz(0), MPI\underline{\ }REAL, type\underline{\ }yz(0), ierr )}\\ 
399            \quad \texttt{CALL MPI\underline{\ }TYPE\underline{\ }COMMIT( type\underline{\ }xz(0), ierr )   ! see file init\underline{\ }pegrid.f90}\\
400            \ \\
401            \quad \texttt{CALL MPI\underline{\ }SENDRECV( ar(nzb,nys-ngl,nxl), type\underline{\ }yz(grid\underline{\ }level), MPI\underline{\ }REAL, pleft, 0, ...}\\
402         \end{itemize}       
403\end{frame}
404
405% Folie 11
406\begin{frame}
407   \frametitle{Transpositions}   
408   \footnotesize
409    \begin{columns}[T]
410      \begin{column}{1.05\textwidth}
411         \begin{itemize}
412            \item<1-> Transpositions can be found in file \texttt{transpose.f90} (several subroutines for 1D- or 2D-decompositions; they are called mainly from the FFT pressure solver, see \texttt{poisfft.f90}.\\
413            \ \\
414            \item<2-> The following example is for a transposition from $x$ to $y$, i.e. for the input array all data elements along $x$ reside on the same PE, while after the transposition, all elements along $y$ are on the same PE:\\
415            \ \\
416            \scriptsize
417            \texttt{!}\\
418            \texttt{!--   in SUBROUTINE transpose\underline{\ }xy:}\\
419           \texttt{CALL MPI\underline{\ }ALLTOALL( f\underline{\ }inv(nys\underline{\ }x,nzb\underline{\ }x,0), sendrecvcount\underline{\ }xy, MPI\underline{\ }REAL, \&}\\
420           \texttt{\hspace{9.5em}work(1), \hspace{6.5em}sendrecvcount\underline{\ }xy, MPI\underline{\ }REAL, \&}\\
421           \texttt{\hspace{9.5em}comm1dy, ierr )}\\
422           \ \\
423           \item<3-> The data resorting before and after the calls of MPI\_ALLTOALL is highly optimized to account for the different processor architectures.
424         \end{itemize}
425      \end{column}
426   \end{columns} 
427\end{frame}
428
429% Folie 12
430\begin{frame}
431   \frametitle{Parallel I/O} 
432   \scriptsize
433   \begin{columns}[T]
434      \begin{column}{1.1\textwidth}
435         \begin{itemize}
436            \item<1-> PALM writes and reads some of the input/output files in parallel, i.e. each processor writes/reads his own file. \textbf{Each file then has a different name!}\\
437            \ \\
438            \textbf{Example:} binary files for restart are written into a subdirectory of the PALM working directory:\\
439            \quad \texttt{BINOUT/\_0000}\\
440                 \quad \texttt{BINOUT/\_0001}\\
441                 \quad $\vdots$
442                 \item<2-> These files can be handled (copied) by \texttt{mrun} using the file attribute \texttt{pe} in the configuration file:\\
443                 \texttt{BINOUT  out:loc:pe restart \~{}/palm/current\underline{\ }version/JOBS/\$fname/RESTART  \underline{\ }d3d}\\
444                 \ \\
445                 \onslide<3->In this case, filenames are interpreted as directory names.
446                 An \texttt{mrun} call using option\\
447                 ''\texttt{-d example\underline{\ }cbl -r restart}'' will copy the local \textbf{\underline{directory}} \texttt{BINOUT} to the \textbf{\underline{directory}} \texttt{.../RESTART/example\underline{\ }cbl\underline{\ }d3d}  .
448         \end{itemize}
449         \onslide<4-> \textbf{General comment:}
450         \begin{itemize}
451            \item Parallel I/O on a large number of files ($>$1000) currently may cause severe file system problems (e.g. on Lustre file systems). A workaround for this problem will\\ be available soon.
452         \end{itemize}
453      \end{column}
454   \end{columns} 
455\end{frame}
456
457
458
459% Folie 13
460\begin{frame}
461   \frametitle{PALM Parallel I/O for 2D/3D Data} 
462   \footnotesize
463   \begin{itemize}
464      \item<1-> 2D- and 3D-data output is also written in parallel by the processors (2D: by default, 3D: generally).
465      \item<2-> Because the graphics software (\texttt{ncview}, \texttt{ncl}, \texttt{ferret}, etc.) expect the data to be in one file, these output files have to be merged to one single file after PALM has finished.\\
466      \ \\
467      This is done within the job by calling the utility program \texttt{combine\underline{\ }plot\underline{\ }fields.x} after PALM has successfully finished.
468      \item<3-> \texttt{combine\underline{\ }plot\underline{\ }fields.x} is automatically executed by \texttt{mrun}.
469      \item<4-> The executable \texttt{combine\underline{\ }plot\underline{\ }fields.x} is created during the installation process by the command\\
470      \ \\
471      \quad \texttt{mbuild -u -h <host identifier>}
472   \end{itemize}
473\end{frame}
474
475% Folie 14
476\begin{frame}
477   \frametitle{Performance Examples (I)} 
478   \begin{itemize}
479      \item Simulation using 1536 * 768 * 242 grid points  ($\sim$ 60 GByte)
480   \end{itemize}
481   \includegraphics[scale=0.28]{parallelization_figures/perf_left.png} 
482   \includegraphics[scale=0.28]{parallelization_figures/perf_right.png}
483   \includegraphics[scale=0.28]{parallelization_figures/legende.png}  \\
484   \scriptsize
485      \begin{columns}[T]
486         \begin{column}{0.18\textwidth}
487         \end{column}
488         \begin{column}{0.4\textwidth}
489            IBM-Regatta, HLRN, Hannover\\
490            (1D domain decomposition)
491         \end{column}
492         \begin{column}{0.4\textwidth}
493            Sun Fire X4600, Tokyo Institute of Technology\\
494(2D domain decomposition)
495         \end{column} 
496         \begin{column}{0.2\textwidth}
497         \end{column}           
498         
499      \end{columns}
500
501\end{frame}
502
503% Folie 15
504\begin{frame}
505   \frametitle{Performance Examples (II)} 
506   \begin{itemize}
507      \item Simulation with $2048^3$ grid points  ($\sim$ 2 TByte memory)
508   \end{itemize}
509      \begin{columns}[T]
510         \begin{column}{0.5\textwidth}
511            \includegraphics[scale=0.25]{parallelization_figures/perf_3.png} \\
512            \scriptsize
513            \quad SGI-ICE2, HLRN-II, Hannover\\
514            \quad (2D-domain decomposition)
515         \end{column}
516         \begin{column}{0.5\textwidth}
517            \vspace{35mm}
518            \onslide<2-> currently largest simulation feasible on that system:\\
519            \ \\
520            $4096^3$ grid points
521         \end{column} 
522      \end{columns}
523\end{frame}
524
525\end{document}
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