source: palm/trunk/TUTORIAL/SOURCE/program_control.tex @ 1598

Last change on this file since 1598 was 1515, checked in by boeske, 10 years ago

several updates in the tutorial

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1% $Id: program_control.tex 1515 2015-01-02 11:35:51Z raasch $
2\input{header_tmp.tex}
3%\input{header_LECTURE.tex}
4
5\usepackage[utf8]{inputenc}
6\usepackage{ngerman}
7\usepackage{pgf}
8\usepackage{subfigure}
9\usepackage{units}
10\usepackage{multimedia}
11\usepackage{hyperref}
12\newcommand{\event}[1]{\newcommand{\eventname}{#1}}
13\usepackage{xmpmulti}
14\usepackage{tikz}
15\usetikzlibrary{shapes,arrows,positioning,decorations.pathreplacing}
16\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
17\def\Tinytwo{\fontsize{3pt}{3pt}\selectfont}
18
19%---------- neue Pakete
20\usepackage{amsmath}
21\usepackage{amssymb}
22\usepackage{multicol}
23\usepackage{pdfcomment}
24\usepackage{listings}
25\lstset{showspaces=false,language=fortran,basicstyle=
26        \ttfamily,showstringspaces=false, captionpos=b,aboveskip=0pt,belowskip=0pt}
27
28\institute{Institute of Meteorology and Climatology, Leibniz UniversitÀt Hannover}
29\selectlanguage{english}
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  }%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.eps}}
46
47\title[Program Control by Physical Parameters]{Program Control by Physical Parameters}
48\author{PALM group}
49
50% Notes:
51% jede subsection bekommt einen punkt im menu (vertikal ausgerichtet.
52% jeder frame in einer subsection bekommt einen punkt (horizontal ausgerichtet)
53\begin{document}
54% Folie 1
55\begin{frame}
56\titlepage
57\end{frame}
58
59\section{Program Control by Physical Parameters}
60\subsection{Program Control by Physical Parameters}
61
62% Folie 2
63\begin{frame}
64   \frametitle{Steering of PALM and Interpreting the Output}
65   \begin{itemize}
66      \item<1->{This section section describes how to steer the model and how to interpret the model output (\textbf{it does not explain, how to start and control model runs}).}
67      \item<2->{It gives a general overview of the input and output files and explaines the contents of the most important files in some detail.}
68   \end{itemize}
69\end{frame}
70
71% Folie 3
72\begin{frame}
73   \frametitle{PALM Input/Output Overview (I)}
74   \tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small]   
75   \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny]
76   \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny]
77   \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny]
78   \tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny]
79   \tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny]
80   \tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny]
81   \tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny]
82   \tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny]
83
84   \tikzstyle{line} = [draw, -latex']
85   
86   \begin{tikzpicture} [auto]
87    \node[start] (palm) {\textbf{PALM}};
88
89    \uncover<2->{\node[yellow1] (parameterfile) [above left=1.5cm of palm] {parameter file \\ for steering};}
90    \uncover<6->{\node[red] (restartdata1) [above right=1.8cm of palm] {restart data};}
91    \uncover<5->{\node[red] (restartdata2) [below=4.5cm of restartdata1] {restart data};}
92
93    \uncover<4->{
94    \node[orange1] (timeseries) [below left=4.4cm of palm] {time series};
95    \node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged};
96    \node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged};
97
98    \path<4->[line] (palm) -- (timeseries);
99    \path<4->[line] (palm) -- (2dsectionstime);
100    \path<4->[line] (palm) -- (3ddatatime);
101   
102    \node[orange1] (1dmean) [above=0.2cm of timeseries] {1D mean \\ profiles};
103    \node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections};
104    \node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data};}
105
106    \path<4->[line] (palm) -- (1dmean);
107    \path<4->[line] (palm) -- (2dsections);
108    \path<4->[line] (palm) -- (3ddata);
109
110    \uncover<3->{\node[yellow2] (headerfile) [above=0.5cm of 2dsections]{header file};}
111    \uncover<3->{\node[yellow1] (runcontrol) [right=0.5cm of headerfile]{run control output\\ (parameter settings + \\ timestep informations)};}
112    \uncover<3->{\node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements};}
113
114    \node (program) [right=2.8cm of palm] {program};
115    \uncover<2->{\node (steeringdata) [right=0.45cm of restartdata1] {steering data};}
116    \uncover<3->{\node (run) [right=2.7cm of runcontrol] {run informations};}
117    \uncover<4->{\node (analysis) [right=3.8cm of 3ddata] {analysis data};}
118
119    \uncover<7->{
120    \node[yellow3] (yellow) [below=0.5 of timeseries] {};
121    \node (ascii) [right=0.1cm of yellow] {ASCII};
122    \node[orange3] (orange) [right=0.4cm of ascii] {};
123    \node (netcdf) [right=0.1cm of orange] {netCDF};
124    \node[red2] (red) [right=0.4cm of netcdf] {};
125    \node (binary) [right=0.1cm of red] {binary};}
126
127    \path<2->[line] (parameterfile) -- (palm);
128    \path<3->[line] (palm) -- (cpumeasure);
129    \path<3->[line] (palm) -- (headerfile);
130    \path<3->[line] (palm) -- (runcontrol);
131    \path<5->[line] (palm) -- (restartdata2);
132    \path<6->[line] (restartdata1) -- (palm);
133    \path<6->[line,dashed] (restartdata2) -- (restartdata1);   
134   \end{tikzpicture}
135\end{frame}
136
137% Folie 4
138\begin{frame}
139   \frametitle{PALM Input/Output Overview (II)}
140   \tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small]   
141   \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny]
142   \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny]
143   \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny]
144   \tikzstyle{yellow4} = [rectangle, draw, fill=yellow!100, text width=1.8cm, font=\Tiny]
145   \tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny]
146   \tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny]
147   \tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny]
148   \tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny]
149   \tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny]
150
151   \tikzstyle{line} = [draw, -]
152   
153   \begin{tikzpicture} [auto]
154    \node[start] (palm) {\textbf{PALM}};
155
156    \node[yellow1] (parameterfile) [above left=1cm of palm] {parameter file \\ for steering};
157    \node[red] (restartdata1) [above right=1.3cm of palm] {restart data};
158    \node[red] (restartdata2) [below=2.5cm of restartdata1] {restart data};
159
160    \node[yellow1] (runcontrol) [below=0.4cm of palm]{run control output\\ (parameter settings + \\ timestep informations)};
161    \node[yellow2] (headerfile) [left=0.5cm of runcontrol]{header file};
162    \node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements};
163
164    \node[orange1] (1dmean) [below=0.3cm of cpumeasure] {1D mean \\ profiles};
165    \node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections};
166    \node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data};
167
168    \node[orange1] (timeseries) [below=0.2cm of 1dmean] {time series};
169    \node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged};
170    \node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged};
171
172    \node (program) [right=2.8cm of palm] {program};
173    \node (steeringdata) [right=0.8cm of restartdata1] {steering data};
174    \node (run) [right=2.5cm of runcontrol] {run informations};
175    \node (analysis) [right=3.6cm of 3ddata] {analysis data};
176   
177    \node[yellow3] (yellow) [below=0.3 of timeseries] {};
178    \node (ascii) [right=0.1cm of yellow] {ASCII};
179    \node[orange3] (orange) [right=0.4cm of ascii] {};
180    \node (netcdf) [right=0.1cm of orange] {netCDF};
181    \node[red2] (red) [right=0.4cm of netcdf] {};
182    \node (binary) [right=0.1cm of red] {binary};
183
184    %--------- neue Ordner
185    \uncover<2->{
186    \node[yellow4] (currentversion) [above=0.6cm of parameterfile] {current\_version/};
187    \node[yellow4] (jobs) [right=0.3cm of currentversion] {JOBS/};
188    \node[yellow4] (runidentifier) [right=0.4cm of jobs] {\textless run\_identifier \textgreater/};
189    \node[yellow4] (input) [above right=1cm of runidentifier] {INPUT/};
190    \node[yellow4] (monitoring) [below=0.1cm of input] {MONITORING/};
191    \node[yellow4] (output) [below=0.1cm of monitoring] {OUTPUT/};
192    \node[yellow4] (restart) [below=0.1cm of output] {RESTART\_DATA/};}
193
194    \uncover<3->{\node[yellow4] (input2) [below=0.1cm of parameterfile] {INPUT/};}
195    \uncover<4->{\node[yellow4] (monitoring2) [above=0.6cm of headerfile] {MONITORING/};}
196    \uncover<6->{\node[yellow4] (restart2) [below=0.1cm of restartdata1] {RESTART\_DATA/};}
197    \uncover<7->{\node[yellow4] (tmpdata) [below=0.1cm of restart2] {/tmp\_data\_catalog/};}
198    \uncover<5->{\node[yellow4] (output2) [below=0.5cm of restartdata2] {OUTPUT/};}
199
200    \path[line]<2-> (currentversion) -- (jobs);
201    \path[line]<2-> (jobs) -- (runidentifier);
202    \path[line]<2-> (runidentifier.east) -- (input.west);
203    \path[line]<2-> (runidentifier.east) -- (monitoring.west);
204    \path[line]<2-> (runidentifier.east) -- (output.west);
205    \path[line]<2-> (runidentifier.east) -- (restart.west);
206
207    \draw<4->[decorate,decoration={brace,raise=6pt,amplitude=9pt},thick]
208       (-4.5,-0.95)--(-1,-0.95) ;
209    \draw<5->[decorate,decoration={brace,mirror,raise=5pt,amplitude=6pt},thick]
210       (0.45,-3)--(0.45,-1.9) ;   
211   \end{tikzpicture}
212\end{frame}
213
214% Folie 5
215\begin{frame}
216   \frametitle{The Parameter File}
217   \tikzstyle{box} = [rectangle, draw, text width=0.9\textwidth, font=\tiny]
218   \tikzstyle{line} = [draw, thick, -latex']
219   \footnotesize
220   \begin{itemize}
221      \item<1->{Physical and numerical features of a PALM run (e.g. initial and boundary conditions, numerical methods)
222            are controlled by a so called \textbf{parameter file} which uses FORTRAN-NAMELIST syntax.} 
223      \item<2->{General structure of a FORTRAN-NAMELIST file}
224   \end{itemize}   
225   \begin{tikzpicture}[auto] 
226   \uncover<3->{   
227      \node[box](firstbox){ \begin{tabbing}       
228         \quad \&abcd \quad \=no\_of\_eggs = 100, litres\_of\_milk = 50.0, \= \\
229                 \>kilos\_of\_butter = 20.0, \> /  \end{tabbing}}
230   \node[font=\tiny] (leading_blank) at (-5,0.8) {\textbf{leading blank}};
231   \node[font=\tiny] (namelist) at (-2,0.8) {\textbf{NAMELIST group}};
232   \node[font=\tiny] (terminating) at (3,0.8) {\textbf{terminating character}};
233   \path[line] (-5,0.7) -- (-4.8,0); 
234   \path[line] (-2,0.7) -- (-4,0);
235   \path[line] (3,0.7) -- (0.2,-0.3);}
236   \end{tikzpicture}
237   \begin{itemize}
238      \item<4->{This file can be read from a FORTRAN program in the following way:} 
239   \end{itemize}
240   \begin{tikzpicture}[auto, node distance=0]
241   \uncover<4->{     
242      \node[box](secondbox){ \begin{tabbing} 
243         INTEGER :: \=no\_of\_eggs = 30 \\
244         REAL :: \> litres\_of\_milk = 0.0, kilos\_of\_butter, kilos\_of\_cream = 33.0 \\
245         \\
246         NAMELIST /abcd/ \quad no\_of\_eggs, litres\_of\_milk, kilos\_of\_butter, kilos\_of\_cream \\
247         \\
248         OPEN ( 1, FILE='Filename' ) \\
249         \\
250         READ ( 1, abcd ) \end{tabbing}};}       
251   \end{tikzpicture}
252   \normalsize 
253\end{frame}
254
255% Folie 6
256\begin{frame}
257   \frametitle{An Example of PALM - NAMELIST Input}
258   \tikzstyle{box} = [rectangle, draw, text width=\textwidth, font=\tiny]
259   \begin{tikzpicture}[auto, node distance=0]     
260      \node[box](box){ \begin{tabbing} 
261         \&inipar \=nx = 39, ny = 39, nz = 40, \\
262                  \>dx = 50.0, dy = 50.0, dz = 50.0, \\
263                  \\
264                  \>initializing\_actions = 'set\_constant\_profiles', \\ 
265                  \>ug\_surface = 0.0, vg\_surface = 0.0, \\
266                  \\
267                  \>pt\_vertical\_gradient  \qquad = 0.0, 1.0, \\
268                  \>pt\_vertical\_gradient\_level = 0.0, 800.0, \\
269                  \\
270                  \>surface\_heatflux = 0.1, bc\_pt\_b ='neumann', / \\
271                  \\
272                  \\
273         \&d3par  \>end\_time = 3600.0, \\
274                  \\
275                  \>dt\_dopr = 900.0, averaging\_interval\_pr = 600.0, \\
276                  \>data\_output\_pr = 'pt', 'u', 'v', / \\ \end{tabbing}};       
277   \end{tikzpicture}
278   \footnotesize
279   \vspace{-3mm}
280   \begin{itemize}
281      \item<2->{There are two NAMELIST groups ({\tt \&inipar} and {\tt \&d3par}).} 
282      \item<3->{Assignments to parameters in {\tt\&inipar} are ignored within restart runs \\
283            (exception: {\tt initializing\_actions} = {\tt'read\_restart\_data'} is obligatory for restart runs).}
284      \item<4->{Values of {\tt \&d3par} parameters can be changed for restart runs.}
285   \end{itemize}
286\end{frame}
287
288% Folie 7
289\begin{frame}[fragile]
290   \tikzstyle{green} = [rectangle, draw, fill=green!30, text width=2.1\textwidth, font=\Tinytwo]
291   \frametitle{The Run Control File}
292   \scriptsize
293   \begin{itemize}
294      \item<1->{For initial runs, the parameter settings and many additional informations about the run (header informations) are printed at the beginning of this file.}
295      \item<2->{The parameter settings are followed by values of specific model variables for certain timesteps (one line for each timestep, the output intervall can be
296            controlled by run parameter {\tt dt\_run\_control}).}
297   \end{itemize}
298   \onslide<3->{\textbf{Contents of this timestep output should be carefully checked after each run, because it allows a first control, if the model had run correctly, or if any
299      errors have occurred!}}
300   \par\bigskip
301   \begin{tikzpicture}[scale=0.51, every node/.style={scale=0.51}]
302      \node [green]{\begin{lstlisting} 
303 ******************************      ------------------------------------------
304 * PALM 3.10  Rev: 1443       *      atmosphere - 3D - run without 1D - prerun
305 ******************************      ------------------------------------------
306
307 Date:                 30-07-14      Run:       example_cbl         
308 Time:                 14:41:23      Run-No.:   00
309 Run on host:           lccrayh
310 Number of PEs:               8      Processor grid (x,y): (  2,  4) calculated
311 ------------------------------------------------------------------------------
312.
313.
314.
315Run-control output:
316------------------
317
318RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
319---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
320  0      0 00:00:00.00  20.0000A  -0.2192D -0.2169D -0.1214  0.000  1.38   0.000E+00    800.  0.106E-02  0.000E+00  0.000E+00  0.000E+00   11  32   5    5  37  29    4  26   0    0.000    0.000       0
321  0      1 00:00:20.00  20.0000A  -0.2192  -0.2169  -0.1214  0.001  0.69  -0.124E+03    100.  0.105E-02  0.948E-03  0.491E-05  0.355E-15   11  32   5    5  37  29    4  26   0    0.000    0.000       0
322  0      2 00:00:40.00  20.0000D  -0.2151  -0.2176  -0.1209  0.001  0.69  -0.125E+03    100.  0.104E-02  0.940E-03  0.802E-05  0.359E-15   11  32   5    5  37  29    4  26   0    0.000    0.000       0
323.
324.
325
326\end{lstlisting}
327      };
328   \end{tikzpicture}
329\end{frame}
330
331% Folie 8
332\begin{frame}[fragile]
333   \tikzstyle{green} = [rectangle, draw, fill=green!30, text width=0.9\textwidth, font=\Tiny]
334   \frametitle{The Header File}
335   \scriptsize
336   \begin{itemize}
337      \item{The header file contains nearly the same informations as the header of the run control file of the initial run.} 
338      \item<2->{It is generated for \textbf{every} run (initial run as well as restart runs).}
339      \item<3->{It is created at the beginning \textbf{and} at the end of a run (overwrites the file created at beginning).}
340      \item<4->{Only at the end, cpu time information is included!}
341   \end{itemize}
342   \begin{center}
343   \begin{tikzpicture}[scale=1, every node/.style={scale=1}]
344      \node [green]{\begin{lstlisting}
345.
346.
347.
348 Run time and time step information:
349 ----------------------------------
350
351 Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
352 Start time:              0.000 s
353 End time:             3600.000 s
354
355 Time reached:         3601.930 s
356 CPU-time used:           4.391 s     per timestep:                     0.017 s
357                                      per second of simulated time:     0.001 s
358
359
360 Computational grid and domain size:
361 ----------------------------------
362
363 Grid length:      dx =     50.000 m    dy =     50.000 m    dz =     50.000 m
364.
365.
366.
367\end{lstlisting}
368      };
369   \end{tikzpicture}
370   \end{center}
371   \normalsize
372\end{frame}
373
374% Folie 9
375\begin{frame}[fragile]
376   \tikzstyle{green} = [rectangle, draw, fill=green!30, text width=1.4\textwidth, font=\Tiny]
377   \frametitle{CPU Measurements File}
378   \begin{columns}[c]
379   \column{0.42\textwidth}
380      \scriptsize
381      \begin{itemize}
382         \item{Contains informations about the CPU requirements of single parts of the program.}
383         \item<2->{It should be inspected regularly in order to find out, if the code is still well optimized (e.g. load balance).} 
384         \item<3->{Prognostic-equations and pressure solver ({\tt pres}) should be the main consumer.}
385         \item<4->{For larger grids ($1024^3$ points), {\tt pres} may need up to 50\% of the total time or more.}
386         \item<5->{Time needed for communication (sum of {\tt exchange\_horiz}({\tt \_2d}) and {\tt mpi\_alltoall}) should not exceed about 10-15\% of the total time.}
387      \end{itemize}
388      \normalsize
389   \column{0.58\textwidth}
390      \vspace{-5mm}
391   \begin{tikzpicture}[scale=0.75, every node/.style={scale=0.75}]
392      \node [green]{\begin{lstlisting}
393PALM 3.10  Rev: 1443  run: example_cbl.00  host: lccrayh  30-07-14 14:41:23
394-----------
395
396CPU measures for     8 PEs (    2(x) *     4(y) tasks *    1 threads):
397
398gridpoints (x/y/z):                        40 *    40 *    40
399nr of timesteps:                          253
400cpu time per grid point and timestep:       0.27546 * 10**-6 s
401----------------------------------------------------------------------
402
403place:                        mean        counts      min       max       rms
404                           sec.      %                sec.      sec.      sec.
405------------------------------------------------------------------------------
406total                     4.460   100.00       1     4.460     4.460     0.001
407all progn.equations       2.943    65.98     759     2.905     2.982     0.028
408pres                      0.611    13.70     760     0.611     0.611     0.000
409diffusivities             0.338     7.59     759     0.338     0.339     0.001
410exchange-horiz-progn      0.146     3.28     759     0.108     0.185     0.028
411calculate_timestep        0.118     2.64     253     0.070     0.125     0.018
412flow_statistics           0.103     2.31     254     0.102     0.104     0.001
413prandtl_fluxes            0.062     1.40     759     0.062     0.063     0.000
414initialisation            0.062     1.39       1     0.061     0.061     0.001
415data_output_2d            0.028     0.62      10     0.021     0.028     0.002
416sum_up_3d_data            0.004     0.10     146     0.004     0.005     0.000
417disturb_field             0.004     0.08      10     0.003     0.007     0.001
418run_control               0.003     0.07     254     0.000     0.000     0.008
419last actions              0.003     0.07       1     0.003     0.003     0.000
420data_output_tseries       0.003     0.06     253     0.000     0.000     0.007
421data_output_profiles      0.001     0.02       4     0.000     0.000     0.002
422swap_timelevel            0.000     0.01     759     0.000     0.000     0.000
423user_actions              0.000     0.01     759     0.000     0.000     0.000
424average_3d_data           0.000     0.00       2     0.000     0.000     0.000
425
426special measures:
427-------------------------------------------------------------------------------
428timesteps                 4.391    98.45     253     4.391     4.391     0.000
429poisfft                   0.441     9.90     760     0.440     0.443     0.001
430exchange_horiz            0.233     5.22    6866     0.193     0.275     0.029
431fft_y                     0.122     2.73     760     0.121     0.122     0.000
432fft_x                     0.121     2.71     760     0.121     0.121     0.000
433transpo invers            0.084     1.89     760     0.084     0.085     0.000
434transpo forward           0.077     1.72     760     0.075     0.078     0.001
435mpi_alltoall              0.063     1.42    4560     0.060     0.065     0.002
436divergence                0.043     0.97    1520     0.043     0.044     0.000
437tridia                    0.036     0.81     760     0.036     0.036     0.000
438exchange_horiz_2d         0.021     0.47    3795     0.019     0.022     0.001
439\end{lstlisting}
440      };
441   \end{tikzpicture}
442   \end{columns}
443\end{frame}
444
445% Folie 10
446\begin{frame}
447   \frametitle{Other Files}
448   \small
449   \begin{itemize}
450      \item<1->{Data output files (1D profiles and timeseries, 2D cross sections, 3D volume data) are by default in \textbf{netCDF} format which is suitable to be processed by
451            public domain graphics software like \textbf{ncview}, \textbf{ferret}, \textbf{ncl} (used by PALM group), \textbf{IDL}, etc. \\
452            \par\bigskip
453            For a first look, {\tt ncview} is a convenient tool.}
454      \item<2->{{\tt ncdump} can be used to display the netCDF file contents in ASCII format ({\tt ncdump -c} displays only header informations).}
455      \item<3->{The simple viewer for netCDF-data - {\tt ncview} - as well as ncl graphic software is available on the notebooks and on the IMUK-cluster.}
456   \end{itemize}
457\end{frame}
458
459% Folie 11
460\begin{frame}
461   \frametitle{Steering by Unix Environment Variables}
462   \scriptsize
463   Most features of PALM are controlled by the parameter file but a few are exclusively controlled by unix environment variables. The most important one is  {\tt write\_binary}. \\
464   \par\bigskip
465   Setting \\
466   \par\medskip
467   {\centering \texttt{ write\_binary = true} \\
468   \par\medskip
469   within the shell causes PALM to write binary data for restart runs at the end of a run.}
470   \par\bigskip
471   \uncover<2->{Setting of these environment variables is automatically done by  {\tt mrun}. It generates a local file (named {\tt ENVPAR}) in FORTRAN-NAMELIST-format, which is then
472   read by PALM. This file includes the following variables:} \\
473   \par\bigskip
474   \tiny
475   \uncover<3->{
476   \begin{tabular}{|p{3cm}|p{4cm}|p{3cm}|} \hline
477      \textbf{Variable}                 & \textbf{Meaning} & \textbf{Value set by {\tt mrun}-option} \\
478      \hline
479      {\tt host}                        & host identifier that mrun is using for the host on which the job is running & {\tt -h}    \\
480      {\tt maximum\_cpu\_time\_allowed} & cpu time allowed for the job                                                & {\tt -t}    \\
481      {\tt run\_identifier}             & identification string for the run    & {\tt -d}    \\
482      {\tt tasks\_per\_node}            & number of MPI tasks to be started on each node     & {\tt -T}     \\
483      {\tt write\_binary}               & switch for writing binary data to be used for restart runs     & {\tt -r} (+setting in configuration file {\tt .mrun.config)}  \\
484      \hline
485   \end{tabular}}
486   \normalsize
487\end{frame}
488
489% Folie 12
490\begin{frame}
491   \frametitle{PALM / netCDF Documentation}
492   \begin{itemize}
493      \item<1->{A detailed description of how to use PALM and a complete list of steering parameters and their meaning can be found on the PALM-server: \\
494            \par\bigskip
495            \textbf{http://palm.muk.uni-hannover.de/wiki/doc/toc}}
496      \par\bigskip
497      \item<2->{General information about the netCDF data format can be found under \\
498            \par\bigskip
499            \textbf{http://www.unidata.ucar.edu/software/netcdf/}}
500   \end{itemize}
501\end{frame}
502
503\end{document}
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