source: palm/trunk/TUTORIAL/SOURCE/ncl.tex @ 1080

Last change on this file since 1080 was 1080, checked in by maronga, 9 years ago

several updates in the tutorial

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1%$Id: ncl.tex 1080 2012-12-13 13:39:39Z 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{calc}                             %neues paket
18\usetikzlibrary{decorations.markings}             %neues paket
19\usetikzlibrary{decorations.pathreplacing}        %neues paket
20\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
21\usepackage{amsmath}
22\usepackage{amssymb}
23\usepackage{multicol}
24\usepackage{pdfcomment}
25\usepackage{graphicx}
26\usepackage{listings}
27\lstset{showspaces=false,language=fortran,basicstyle=
28        \ttfamily,showstringspaces=false,captionpos=b}
29
30\institute{Institut fÌr Meteorologie und Klimatologie, Leibniz UniversitÀt Hannover}
31\date{last update: \today}
32\event{PALM Seminar}
33\setbeamertemplate{navigation symbols}{}
34
35\setbeamertemplate{footline}
36  {
37    \begin{beamercolorbox}[rightskip=-0.1cm]&
38     {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}}
39    \end{beamercolorbox}
40    \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,
41      leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}
42      {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}
43    \end{beamercolorbox}
44    \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}
45    \end{beamercolorbox}
46  }
47%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}}
48
49\title[Introduction to NCL]{Introduction to NCL}
50\author{Siegfried Raasch}
51
52\begin{document}
53
54% Folie 1
55\begin{frame}
56\titlepage
57\end{frame}
58
59\section{Introduction to NCL}
60\subsection{Introduction to NCL}
61
62% Folie 2
63\begin{frame}
64   \frametitle{Visualization of PALM Output Data}
65   \small
66   \begin{itemize}     
67           \item<1-> There are several ways how you can visualize netCDF data
68           \item<1-> If you are lacking experience in the visualization of netCDF data or if you have not yet found your favourite way how to visualize netCDF data, here is one recommendation:
69      \item<2-> NCL – The \textbf{N}CAR \textbf{C}ommand \textbf{L}anguage
70      \item<2-> Developed by the Computational \& Information Systems Laboratory at the NCAR (continuously updated)
71      \item<2-> Detailed information is available under http://www.ncl.ucar.edu
72      \item<3-> With the information revealed in this talk you will be able to visualize the output of this week's simulations
73   \end{itemize}   
74\end{frame}
75
76% Folie 3
77\begin{frame}
78   \frametitle{What is NCL and Which are its Advantages? (I)}
79   \small
80   \begin{itemize}     
81           \item<1-> Interpreted language designed specifically for scientific data processing and visualization, free available
82           \item<2-> Portable: it is running on many different operating systems including Solaris, AIX, IRIX, Linux, MacOSX, DecAlpha, Cygwin/Windows
83      \item<3-> It's a powerful tool for file input and output, visualization and data analysis (but please \textbf{avoid the excessive usage of loops}, as NCL is an interpreted language) $\rightarrow$ integrated processing environment
84   \end{itemize} 
85   \centering
86   \onslide<3-> \includegraphics[scale=0.28]{ncl_figures/ncl.png}
87   
88\end{frame}
89
90% Folie 4
91\begin{frame}
92   \frametitle{What is NCL and Which are its Advantages? (II)}
93   \small
94   \begin{itemize}     
95           \item<1-> Supports calling C and FORTRAN extended routines
96           \item<1-> Over 600 functions and procedures for visualization and data analysis are provided with NCL
97           \item<2-> Interactive mode: \texttt{\$ ncl}\\
98      \texttt{ncl 0>}
99      \item<3-> each line is interpreted as it is entered
100      \item<1-> Batch mode: \texttt{\$ ncl ncl\underline{ }script.ncl}\\
101      interpreter of complete scripts, variables within the NCL script can\\
102      be steered by providing additional parameters with the ncl call\\
103      \texttt{\$ ncl ncl\underline{ }script.ncl parameter1=value}
104      \texttt{'parameter2=\dq string\dq ' ...}
105   \end{itemize} 
106
107\end{frame}
108
109% Folie 5
110\begin{frame}
111   \frametitle{What is NCL and Which are its Advantages? (III)}
112
113   \begin{itemize}     
114           \item<1-> Complete Programming Language
115           \begin{itemize}   
116              \footnotesize
117              \item<1-> data types
118              \item<1-> variables
119              \item<1-> operators
120              \item<1-> expressions
121              \item<1-> loops
122              \item<1-> functions/procedures/graphics
123      \end{itemize} 
124           \item<2-> Features
125           \begin{itemize}   
126              \footnotesize
127              \item<2-> query / manipulate meta data
128              \item<2-> import data in a variety of formats
129              \item<2-> array syntax / operations
130              \item<2-> can use user FORTRAN/C codes and commercial libraries
131              \item<2-> most functions/procedures ignore missing data
132      \end{itemize} 
133   \end{itemize} 
134
135\end{frame}
136
137% Folie 6
138\begin{frame}
139   \frametitle{How to Install NCL (Under Linux) (I)?}
140   \small
141   \begin{itemize}     
142           \item<1-> Detailed information is available under\\
143      \underline{http://www.ncl.ucar.edu/Download/index.shtml}
144           \item<1-> Request an Earth System Grid account
145      \underline{http://www.earthsystemgrid.org/}
146           \item<2-> Download the appropriate binaries e.g. \texttt{A.tar.gz} for your system e.g. to \texttt{\$HOME}
147      \item<2-> \texttt{\% gunzip \$HOME/A.tar.gz}
148      \item<2-> \texttt{\% mkdir -p /usr/local}\\
149      \quad \texttt{\% cd /usr/local}\\
150      \quad \texttt{\% tar -xvf \$HOME/A.tar}
151   \end{itemize} 
152
153\end{frame}
154
155% Folie 7
156\begin{frame}
157   \frametitle{How to Install NCL (Under Linux) (II)?}
158   \footnotesize 
159   \begin{itemize}     
160           \item<1-> Set the \texttt{NCARG\underline{ }ROOT} environment variable and your search path to where NCL/NCARG resides\\
161           csh: \texttt{setenv NCARG\underline{ }ROOT /usr/local/}\\
162           \hspace{1.6em} \texttt{setenv PATH /usr/local/bin:\$PATH}\\
163           bash/ksh: \texttt{export NCARG\underline{ }ROOT=/usr/local/}\\
164           \hspace{4.1em} \texttt{export PATH=/usr/local/bin:\$PATH}\\
165           \vspace{3mm}
166      \item<2-> Set the DISPLAY environment variable to indicate where to display graphics as for any X11 Windows application that you run\\
167      e.g. ksh: \texttt{export DISPLAY=localhost:13.0}, or use \texttt{ssh -X} to tunnel X-communication.\\
168      \vspace{3mm}
169      \item<3-> Test your NCL installation\\
170      \quad \texttt{\% ng4ex gsun01}\\
171      NCL script gsun01n.ncl is copied to your working directory and run through NCL. An X11 window should pop up.
172   \end{itemize} 
173
174\end{frame}
175
176% Folie 8
177\begin{frame}
178   \frametitle{NCL Scripts Delivered with PALM (I)}
179   \footnotesize 
180   \begin{itemize}     
181           \item<1-> Together with the PALM installation you have also received four NCL scripts, a configuration file and a manual; they can be found in the directory\\
182           \texttt{\$HOME/palm/current\underline{ }version/trunk/SCRIPTS/NCL/}
183      \item<2-> All standard netCDF data output of PALM can be visualized by one of the scripts:
184      \begin{itemize}
185         \scriptsize
186         \item[-]<2-> \texttt{cross\underline{ }sections.ncl} (2D/3D data, e.g. contour or vector plots)
187         \item[-]<2-> \texttt{profiles.ncl} (profile data)
188         \item[-]<2-> \texttt{timeseries.ncl} (time series data)
189         \item[-]<2-> \texttt{spectra.ncl} (spectra data)
190      \end{itemize} 
191      \item<3-> To run these NCL scripts you can use the shell script \texttt{palmplot} which can be found in the directory\\
192      \texttt{\$HOME/palm/current\underline{ }version/trunk/SCRIPTS}
193      \item<4-> The output of the plots can be changed with several parameters; these parameters can be either written in the prompt (when calling the shell script \texttt{palmplot}) or modified within the configuration file \texttt{.ncl.config}
194   \end{itemize} 
195
196\end{frame}
197
198% Folie 9
199\begin{frame}
200   \frametitle{NCL Scripts Delivered with PALM (II)}
201
202   Using \texttt{.ncl.config}
203   \small
204   \begin{itemize}     
205           \item[-]<1-> Please create a personal configuration file by copying the default configuration file \texttt{.ncl.config.default} to the PALM working directory \texttt{\$HOME/palm/current\underline{ }version} and naming it \texttt{.ncl.config}
206           \item[-]<2-> \texttt{.ncl.config} is used by NCL directly, thus the parameters have to be written according to the rules of the scripting language NCL
207           \item[-]<3-> The configuration file contains all steering parameters with a short description and can be modified to personal needs
208   \end{itemize} 
209
210\end{frame}
211
212% Folie 10
213\begin{frame}
214   \frametitle{NCL Scripts Delivered with PALM (III)}
215
216   Using \texttt{palmplot} (I)
217   \footnotesize
218   \begin{itemize}     
219           \item[-]<1-> The shell script is used as follows:\\
220      \texttt{palmplot <plot\underline{ }identifier>}
221      \item[-]<1-> \texttt{<plot\underline{ }identifier>} has to be \texttt{xy}, \texttt{xz}, \texttt{yz}, \texttt{pr}, \texttt{sp} or \texttt{ts} depending on the data to be plotted
222   \end{itemize}     
223   \vspace{3mm}
224   \onslide<2->\begin{tabular}{ccc}
225      \textbf{plot\underline{ }identifier} & \textbf{data used} & \textbf{ncl script}\\
226           xy & instantaneous or time-averaged xy or 3D data & cross\underline{ }sections.ncl\\
227           xz & instantaneous or time-averaged xz or 3D data & cross\underline{ }sections.ncl\\
228           yz & instantaneous or time-averaged yz or 3D data & cross\underline{ }sections.ncl\\
229           pr & profile or 3D data & profiles.ncl\\
230           sp & spectra data & spectra.ncl\\
231           ts & time series data & timeseries.ncl\\ 
232   \end{tabular}
233
234\end{frame}
235
236% Folie 11
237\begin{frame}
238   \frametitle{NCL Scripts Delivered with PALM (IV)}
239
240   Using \texttt{palmplot} (II)
241   \footnotesize
242   \begin{itemize}     
243           \item[-]<1-> To change the output of the plot you can also use:\\
244      \scriptsize \texttt{palmplot \textbf{plot\underline{ }identifier} parameter=value parameter=string ...} 
245      \footnotesize \\
246      \vspace{2mm}
247      \item[-]<2-> A list of all available parameters can be found in the configuration file \texttt{.ncl.config} or in the documentation:\\
248      \uncover<3->{\texttt{http://palm.muk.uni-hannover.de/wiki/doc/app/nclparlist}}\\
249      \vspace{2mm}
250      \item[-]<4-> Parameters specified in the prompt override parameters given in the configuration file\\
251      \vspace{2mm}
252      \item[-]<5-> String parameters which can contain lists (\texttt{var}, \texttt{c\underline{ }var}, \texttt{vec1}, \texttt{vec2}, \texttt{plotvec}) have to be set in single quotes and the list itself has to be separated by blanks, e.g. \texttt{var='pt u w'}\\
253      \vspace{2mm}
254      \item[-]<1-> A short introduction for using the shell script is given by typing\\
255      \texttt{palmplot ?}
256   \end{itemize}     
257
258\end{frame}
259
260% Folie 12
261\begin{frame}
262   \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (I)}
263   \small
264   \begin{itemize}     
265           \item<1-> Starting the example run with the command\\
266           \vspace{2mm}
267      \texttt{mrun -d example\underline{ }cbl ... -r 'd3\# pr\# ts\# xy\# xz\#'}\\
268      \vspace{2mm}
269      results in the following output files in\\
270      \vspace{2mm}
271      \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}:\\
272      \texttt{example\underline{ }cbl\underline{ }pr.nc}, \texttt{example\underline{ }cbl\underline{ }xy.nc}, \texttt{example\underline{ }cbl\underline{ }xz.nc},\\
273      \texttt{example\underline{ }cbl\underline{ }ts.nc}
274      \item<2-> Example: Visualization of the time series data\\
275      \vspace{2mm}
276      Goal: Output as eps-file \texttt{timeseries.eps} (by default the plot would be output to an X11 window)
277   \end{itemize}     
278
279\end{frame}
280
281% Folie 13
282\begin{frame}
283   \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (II)}
284   \small
285   \begin{itemize}     
286           \item<1-> In order to reach the goal you can either ...
287      \item<1-> ... Change to the directory\\
288      \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}\\
289      and use the shell script with the command\\
290      \vspace{2mm}
291      \texttt{palmplot ts file\underline{ }1=example\underline{ }cbl\underline{ }ts.nc format\underline{ }out=eps file\underline{ }out=timeseries}\\
292      \vspace{2mm}
293      Thus, the script \texttt{timeseries.ncl} is called and some of the parameters in the configuration file \texttt{.ncl.config} are directly set by specifying the related parameters in the command line,\\
294      \vspace{2mm}
295      \onslide<2-> e.g. \texttt{file\underline{ }1 = <netCDF file>} \textbf{(Note: the input file has always to be specified!)}, \texttt{file\underline{ }out = <output file>}
296   \end{itemize}     
297
298\end{frame}
299
300% Folie 14
301\begin{frame}
302   \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (III)}
303   \footnotesize
304   ... or you can modify the configuration file \texttt{.ncl.config}, e.g.\\
305   \vspace{2mm}
306   \texttt{if(.not. isvar(\dq file\underline{ }1\dq))then}\\
307   \quad \quad \texttt{file\underline{ }1 = \dq File in\dq}\\
308   \texttt{end if}\\
309   \vspace{2mm}
310   \onslide<2-> has to be changed to\\
311   \vspace{2mm}
312\texttt{if(.not. isvar(\dq file\underline{ }1\dq))then}\\
313   \quad \quad \texttt{file\underline{ }1 = \dq \$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }ts.nc\dq}\\
314   \texttt{end if}
315
316\end{frame}
317
318% Folie 15
319\begin{frame}
320   \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (IV)}
321   \footnotesize
322   \begin{itemize}
323      \item<1-> Both ways will lead to the creation of a new file called \texttt{timeseries.eps} in the directory\\
324      \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}
325   \end{itemize}
326   \centering
327   \onslide<2->\includegraphics[scale=0.4]{ncl_figures/vis1.png}
328   
329\end{frame}
330
331% Folie 16
332\begin{frame}
333   \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (V)}
334   \footnotesize
335   \begin{itemize}
336      \item<1-> If you only want to get the plot of the time series of one variable, e.g. the maximum of the velocity component u, you can add the command line parameter \texttt{var='umax'} or modify the configuration file respectively, e.g.\\
337      \vspace{2mm}
338      \texttt{if(.not. isvar(\dq var\dq ))then}\\
339      \quad \quad \texttt{var = \dq ,umax,\dq }\\       
340      \texttt{end if}
341   \end{itemize}
342   \centering
343   \onslide<2->\includegraphics[scale=0.7]{ncl_figures/vis2.png}
344   
345\end{frame}
346
347% Folie 17
348\begin{frame}[t]
349   \tikzstyle{plain} = [rectangle, text width=0.27\textwidth, font=\small]
350   \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (VI)}
351   \footnotesize
352   Plot profiles with the command\\
353   \quad \texttt{palmplot pr file\underline{ }1=example\underline{ }cbl\underline{ }pr.nc}\\
354   \vspace{3mm}
355   Profiles of same dimension are plotted\\
356   together, e.g. total, resolved and\\
357   subgridscale temperature flux (default)\\
358   \vspace{3mm}
359   (This composition is written to the\\
360   NetCDF header by the \texttt{d3par}\\
361   parameter \texttt{cross\underline{ }profiles})\\
362   \vspace{3mm}
363   If you add the parameter var=all to\\
364   the command, all profiles will be plotted\\
365   separately
366   \begin{tikzpicture}[remember picture, overlay]
367      \node at (current page.north west){%
368      \begin{tikzpicture}[overlay]
369         \node[plain,anchor=west] at (72mm,-51.5mm) {\includegraphics[scale=0.32]{ncl_figures/vis3.png}};
370      \end{tikzpicture}
371      };
372   \end{tikzpicture}
373   
374\end{frame}
375
376% Folie 18
377\begin{frame}
378   \frametitle{More Comments}
379   \small
380   \begin{itemize}     
381           \item<1-> The other NCL scripts delivered with PALM can be used in a similar way, however the parameters that can be specified differ from script to script
382           \item<2-> There are plenty of parameters for each script. Please have a look to the NCL documentation (\texttt{http://palm.muk.uni-hannover.de/wiki/doc/app/nclparlist}) for detailed information
383      \item<1-> If one of the program aborts and there is no comment, check the configuration file - the scripts should not abort with the default values. Be sure to use the right data type (e.g.: integer = 2; float = 2.0; double = 2.0d; string = \dq name\dq ) 
384   \end{itemize}   
385\end{frame}
386
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393
394\end{document}
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