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source: palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex @ 1597

Last change on this file since 1597 was 1526, checked in by keck, 10 years ago

several updates in the tutorial
  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 41.9 KB
Line 
1% $Id: runs_with_mrun.tex 1526 2015-01-22 12:47:21Z gronemeier $
2\input{header_tmp.tex}
3%\input{../header_lectures.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}
16\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
17\usepackage{amsmath}
18\usepackage{amssymb}
19\usepackage{multicol}
20\usepackage{pdfcomment}
21\usepackage{graphicx}
22\usepackage{listings}
23\lstset{showspaces=false,language=fortran,basicstyle=
24        \ttfamily,showstringspaces=false,captionpos=b,aboveskip=0pt,belowskip=0pt}
25
26\institute{Institute of Meteorology and Climatology, Leibniz UniversitÀt Hannover}
27\selectlanguage{english}
28\date{last update: \today}
29\event{PALM Seminar}
30\setbeamertemplate{navigation symbols}{}
31
32\setbeamertemplate{footline}
33  {
34    \begin{beamercolorbox}[rightskip=-0.1cm]&
35     {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}}
36    \end{beamercolorbox}
37    \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,
38      leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}
39      {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}
40    \end{beamercolorbox}
41    \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}
42    \end{beamercolorbox}
43  }
44
45%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}}
46
47\title[Carrying out runs using mrun]{Carrying out runs using \texttt{mrun}}
48\author{PALM group}
49
50\begin{document}
51
52% Folie 1
53\begin{frame}
54\titlepage
55\end{frame}
56
57\section{Carrying out runs using mrun}
58\subsection{Carrying out runs using mrun}
59
60% Folie 2
61\begin{frame}
62   \frametitle{What is \texttt{mrun}?}
63   \footnotesize
64   \begin{itemize}
65      \item<1-> \texttt{mrun} (\textbf{m}odel \textbf{run}) is a shell script (using
66      \texttt{bash}/\texttt{ksh}-syntax) which can be used to compile and run programs, including
67      the handling of input/output files.
68      \vspace{3mm}
69      \item<2-> The \texttt{mrun}-command has a number of options to control the
70      program execution\\
71         \vspace{3mm}
72         \quad \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\
73         \vspace{3mm}
74         All options including a short description can be displayed by entering\\
75         \vspace{3mm}
76         \quad \texttt{mrun ?}
77      \vspace{4mm}
78      \item<3-> The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} 
79   \end{itemize}
80\end{frame}
81
82% Folie 3
83\begin{frame}
84   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\tiny]
85   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, font=\tiny]
86   \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\tiny]
87   \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\tiny]
88   \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\tiny]
89   \tikzstyle{line} = [draw, -]
90   \tikzstyle{alert} = [rectangle, draw, text width=0.77\textwidth, font=\scriptsize]
91 
92   \scriptsize
93   \frametitle{Carrying Out Runs Using \texttt{mrun}}
94   \textbf{Carrying out a program run typically needs two steps:}\\
95   \vspace{1mm}
96   \quad 1. compilation\\
97   \qquad \texttt{f95  ...  file1.f90 file2.f90 ...}\\
98   \vspace{1mm}
99   \onslide<2->\quad 2. execution\\
100   \qquad \texttt{a.out}\\
101   \vspace{3mm}
102   \onslide<3->\textbf{Besides, a program needs input data and creates output data:}\\
103   
104   \onslide<4->\begin{tikzpicture}[auto, node distance=0]
105      \node [green] (first) {\textbf{a.out/} };
106      \node [dummy, right=0.1cm of first] (second) {};
107     
108      \node [yellow, above=0.4cm of second] (third) {\textbf{parameter for steering}};
109      \node [yellow, below=0.4cm of third] (fourth) {\textbf{control output}};
110      \node [yellow, below=0.3cm of fourth] (fifth) {\textbf{output for analysis}};
111     
112      \node [info, above=-0.1cm of third] (sixth) {input file};
113      \node [info, above=-0.1cm of fourth] (seventh) {output file 1};
114      \node [info, above=-0.1cm of fifth] (eight) {output file 2};
115
116      \draw [->] (third.west) -- (first.north);
117      \draw [->] (first.east) -- (fourth.west);
118      \draw [->] (first.south) -- (fifth.west);
119     
120      \uncover<5->{\node [white, right=0.25cm of third] (ninth) {
121         \texttt{OPEN (11, FILE='PARIN', FORM='FORMATTED')}};}
122      \uncover<5->{\node [white, right=0.25cm of fourth] (tenth) {
123         \texttt{OPEN (15, FILE='RUN\underline{ }CONTROL', FORM='FORMATTED')}};}
124      \uncover<5->{\node [white, right=0.25cm of fifth] (eleventh) {
125         \texttt{OPEN (40, FILE=‘DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF', FORM='FORMATTED')}};}
126   \end{tikzpicture}
127   
128   \vspace{3mm}
129   \scriptsize
130   \onslide<6->\textcolor{red}{\textbf{Problems:} The user has to copy or rename output files, if
131   he/she wants to run the program more than once and if he concurrently wants to keep
132   the files from the former run(s). If he/she is using different input parameter files for steering, these files also have
133   to be copied into the working directory before the program is executed.}\\
134   \vspace{1mm}
135   \begin{tikzpicture}[auto, node distance=0]
136      \uncover<7->{\node [alert] (alert) {\textcolor{red}{\textbf{It is therefore very desirable to automate these tasks!}}};}
137   \end{tikzpicture}
138\end{frame}
139
140% Folie 4
141\begin{frame}
142   \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize]
143   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize]
144   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.10\textwidth, font=\scriptsize]
145   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny]
146   \scriptsize
147   \frametitle{\texttt{mrun}: Principal Mode of Operation (I)}
148   \texttt{mrun} \textbf{runs a program (in our case the PALM model) by carrying out the following principle tasks in a sequential order:}\\
149   \begin{enumerate}
150      \tiny
151      \item<2-> Create a temporary working directory and change into this directory:\\
152      \vspace{1.5mm}
153      \scriptsize \quad \texttt{mkdir <tmpdir>/<username>.<randomnumber>}\\
154      \quad \texttt{cd <tmpdir>/<username>.<randomnumber>}\\
155      \tiny \ \\
156      The path of \texttt{<tmpdir>} is given in the configuration file
157      \texttt{.mrun.config} by the environment variable \texttt{tmp\underline{ }user\underline{ }catalog}, e.g.:\\
158      \vspace{1.5mm}
159           \scriptsize \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /tmp \hspace{30mm} <hi>  parallel}\\
160           \tiny \ \\
161           \onslide<3-> On Cray-XC30: \\
162      \vspace{1.5mm}
163           \scriptsize \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /gfs1/work/<username>
164           \hspace{5mm} lcsgih parallel}
165      \vspace{1mm}
166           \begin{center}
167              \begin{tikzpicture}[auto, node distance=0]
168            \uncover<4->{\node [green] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
169         \end{tikzpicture}
170           \end{center}
171           \vspace{2mm}
172           \item<5-> \fontsize{7}{1} Copy the input files from a directory of the user into this working directory:\\
173           \vspace{1mm}
174           \onslide<6-> \tiny \quad \texttt{cp <user\underline{ }input\underline{ }file1>
175           /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file1>}\\
176      \quad \texttt{cp <user\underline{ }input\underline{ }file2>
177      /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file2>}\\
178      \vspace{2mm}
179      \scriptsize
180      \begin{center}
181              \begin{tikzpicture}[auto, node distance=0]
182             
183            \uncover<8->{\node [green] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
184       
185            \uncover<7->{\node [yellowsmall, above=0.1cm of green] (yellow2) {JOBS/};}
186            \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\underline{ }version/};}
187            \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
188            \uncover<7->{\node [yellowsmall, right=0.2cm of yellow3] (yellow4) {INPUT/};}
189           
190            \draw<7-> [-] (yellow1.east) -- (yellow2.west);
191            \draw<7-> [-] (yellow2.east) -- (yellow3.west);
192            \draw<7-> [-] (yellow3.east) -- (yellow4.west);
193           
194            \node [dummy, right=0.06cm of yellow4] (dummy1) {};
195            \node [dummy, below=0.38cm of dummy1] (dummy2) {};
196           
197            \draw<9-> [-] (yellow4.east) -- (dummy1.center);
198            \draw<9-> [-] (dummy1.center) -- (dummy2.center);
199            \draw<9-> [->] (dummy2.center) -- (green.east);
200           
201         \end{tikzpicture}
202           \end{center}
203     
204        \end{enumerate}
205
206\end{frame}
207
208% Folie 5
209\begin{frame}
210   \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm]
211   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm]
212   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
213   
214   \frametitle{\texttt{mrun}: Principal Mode of Operation (II)}
215
216        \begin{enumerate}
217      \setcounter{enumi}{2}
218           \item<1-> Copy the pre-compiled routines to the temporary working directory:\\
219     
220      \begin{center}
221              \begin{tikzpicture}[auto, node distance=0]
222                 \uncover<2->{\node [yellow] (yellow) {current\underline{ }version/};}
223                 \uncover<1->{\node [dummy, right=0.0cm of yellow] (dummy1) {};}
224                 \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\underline{ }DEPOSITORY\underline{ }\textit{parallel}/};}
225                 \uncover<1->{\node [dummy, right=0.2cm of green1] (dummy2) {};}
226            \uncover<3->{\node [green, below=0.5cm of dummy1] (green2) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
227             \uncover<1->{\node [dummy, below=0.5cm of dummy2] (dummy3) {};}
228             \uncover<4->{\node [dummy, right=0.0cm of dummy3] (text) {Makefile\\
229                 *.f90\\
230                 *.o\\
231                 ...\\ \ \\};}
232             
233             \draw<2-> [-] (yellow.east) -- (green1.west);
234             \draw<4-> [-] (green1.east) -- (dummy2.center);
235             \draw<4-> [-] (dummy2.center) -- (dummy3.center);
236             \draw<4-> [->] (dummy3.center) -- (green2.east);
237              \end{tikzpicture}
238           \end{center}
239           
240           \item<5-> Compile the main program and use pre-compiled object files:\\
241     \quad \texttt{f95 palm.f90 *.o ...   ( make Makefile)}
242      \item<6-> Execute the program:\\
243     \quad \texttt{a.out}
244   \end{enumerate}
245\end{frame}
246
247% Folie 6
248\begin{frame}
249   \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm]
250   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\scriptsize, minimum height=0.6cm]
251   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
252   
253   \frametitle{\texttt{mrun}: Principal Mode of Operation (III)}
254   \footnotesize 
255        \begin{enumerate}
256      \setcounter{enumi}{5}
257           \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\
258       \vspace{1mm}
259       \tiny \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\
260      \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\
261      \footnotesize 
262      \begin{center}
263         \begin{tikzpicture}[auto, node distance=0]
264            \uncover<2->{\node [yellow] (yellow1) {MONITORING/ };}
265
266            \uncover<2->{\node [dummy, right=0.2cm of yellow1] (dummy2) {};}
267            \uncover<2->{\node [dummy, above=0.2cm of dummy2] (dummy1) {};}
268            \uncover<2->{\node [dummy, below=0.2cm of dummy2] (dummy3) {};}
269           
270            \uncover<2->{\node [yellow, left=0.2cm of dummy3] (yellow2) {OUTPUT/};}
271            \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
272            \uncover<2->{\node [yellow, left=0.2cm of yellow3] (yellow4) {JOBS/};}
273            \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};}
274                                             
275                 \uncover<2-3>{\node [green, left=4.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
276                 
277            \draw<2-3> [-] (green.east) -- (dummy1.center);
278            \draw<2-3> [-] (dummy2.center) -- (dummy1.center);
279            \draw<2-3> [-] (dummy3.center) -- (dummy1.center);
280           
281            \draw<2-3> [->] (dummy2.center) -- (yellow1.east);
282            \draw<2-3> [->] (dummy3.center) -- (yellow2.east);
283           
284            \draw<2-> [-] (yellow2.west) -- (yellow3.east);
285            \draw<2-> [-] (yellow3.west) -- (yellow4.east);
286            \draw<2-> [-] (yellow4.west) -- (yellow5.east);
287               
288        \end{tikzpicture}
289     \end{center}
290           
291           \item<3-> Delete the temporary working directory\\
292      \quad \texttt{rm -rf /<tmpdir>/<username>.<randomnumber>}\\
293      \vspace{2mm}
294      \onslide<5->\textcolor{red}{Question: How does \texttt{mrun} know which files have to be copied and where from or where to they have to be copied?}
295
296   \end{enumerate}
297\end{frame}
298
299% Folie 7
300\begin{frame}
301   \tikzstyle{small} = [rectangle, text width=0.08\textwidth, font=\scriptsize]
302   \tikzstyle{large} = [rectangle, text width=0.45\textwidth, font=\scriptsize]
303   \tikzstyle{box} = [rectangle, draw, text width=0.2\textwidth, font=\scriptsize]
304   \tikzstyle{boxbig} = [rectangle, draw, text width=0.4\textwidth, font=\scriptsize]
305   \tikzstyle{dummy} = [rectangle, text width=0.0\textwidth, font=\scriptsize, minimum height=0.5cm]
306   
307   \frametitle{Steering File Copy by the Configuration File (I)}
308   \scriptsize
309   \textbf{Copying of files is controlled by so called} \textit{file connection statements}. \textbf{They connect local files in the temporary working directory with permanent files residing in the directory of the user.}\\
310   \vspace{3mm}
311   Principle example of a file connection statement (for the PALM parameter file):
312   \vspace{-3mm}
313   \begin{center}
314           \begin{tikzpicture}[auto, node distance=0]
315         \uncover<1->{\node [small] (part1) {\texttt{PARIN}};}
316         \uncover<1->{\node [dummy, left=-0.2cm of part1] (dummy1) {};}
317         \uncover<1->{\node [dummy, below=1.25cm of dummy1] (dummy3) {};}
318         \uncover<1->{\node [small, right=0.0cm of part1] (part2) {\quad \texttt{in}};}
319         \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
320         \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
321              \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
322              \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
323              \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
324                   
325         \uncover<2->{\node [boxbig, below=1.25cm of dummy2] (box1) {local filename in the working directory (must correspond to the filename in the \texttt{OPEN} statement of the program)};}
326              \draw<2-> [->] (dummy3.north) -- (dummy1.south);
327             
328              \uncover<3->{\node [box, below=0.7cm of part2] (box2) {file attributes};}
329              \draw<3-> [->] (box2.north) -- (part2.south);
330             
331              \uncover<4->{\node [box, below=0.2cm of part3] (box3) {activating string};}
332              \draw<4-> [->] (box3.north) -- (part3.south);
333                     
334              \uncover<5->{\node [box, below=0.2cm of part4] (box4) {directory in which the permanent user file resides};}
335              \draw<5-> [->] (box4.north) -- (part4.south);
336             
337         \uncover<6->{\node [box, below=0.2cm of part5] (box5) {suffix of the permanent filename};}
338              \draw<6-> [->] (box5.north) -- (part5.south);
339             
340         \uncover<7->{\node [box, below=1.0cm of part6] (box6) {additional suffix for netCDF files};}
341              \draw<7-> [->] (box6.north) -- (part6.south);   
342           \end{tikzpicture}
343        \end{center}
344   
345\end{frame}
346
347
348% Folie 8
349\begin{frame}
350   \tikzstyle{small} = [rectangle, text width=0.08\textwidth, font=\scriptsize]
351   \tikzstyle{large} = [rectangle, text width=0.45\textwidth, font=\scriptsize]
352   \tikzstyle{box} = [rectangle, draw, text width=0.2\textwidth, font=\scriptsize]
353   \tikzstyle{boxbig} = [rectangle, draw, text width=0.4\textwidth, font=\scriptsize]
354   \tikzstyle{dummy} = [rectangle, text width=0.0\textwidth, font=\scriptsize, minimum height=0.5cm]
355   
356   \frametitle{Steering File Copy by the Configuration File (II)}
357   \scriptsize
358   \begin{center}
359           \begin{tikzpicture}[auto, node distance=0]
360         \uncover<1->{\node [small] (part1) {\texttt{PARIN}};}
361         \uncover<1->{\node [dummy, left=-0.2cm of part1] (dummy1) {};}
362         \uncover<1->{\node [dummy, below=1.25cm of dummy1] (dummy3) {};}
363         \uncover<1->{\node [small, right=0.0cm of part1] (part2) {\quad \texttt{in}};}
364         \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
365         \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
366              \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
367              \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
368              \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
369                   
370         \uncover<1->{\node [boxbig, below=1.25cm of dummy2] (box1) {local filename in the working directory (must correspond to the filename in the \texttt{OPEN} statement of the program)};}
371              \draw<1-> [->] (dummy3.north) -- (dummy1.south);
372             
373              \uncover<1->{\node [box, below=0.7cm of part2] (box2) {file attributes};}
374              \draw<1-> [->] (box2.north) -- (part2.south);
375             
376              \uncover<1->{\node [box, below=0.2cm of part3] (box3) {activating string};}
377              \draw<1-> [->] (box3.north) -- (part3.south);
378                     
379              \uncover<1->{\node [box, below=0.2cm of part4] (box4) {directory in which the permanent user file resides};}
380              \draw<1-> [->] (box4.north) -- (part4.south);
381             
382         \uncover<1->{\node [box, below=0.2cm of part5] (box5) {suffix of the permanent filename};}
383              \draw<1-> [->] (box5.north) -- (part5.south);
384             
385         \uncover<1->{\node [box, below=1.0cm of part6] (box6) {additional suffix for netCDF files};}
386              \draw<1-> [->] (box6.north) -- (part6.south);   
387           \end{tikzpicture}
388        \end{center}
389   \vspace{3mm}
390   \onslide<2->The full name of the permanent file results from the directory name, the suffix and the value of \texttt{mrun}-Option \texttt{-d}, which defines the so-called \textbf{base name} of all files handled by \texttt{mrun}:\\
391   \footnotesize \quad \texttt{mrun -d \textcolor{blue}{example\underline{ }cbl} ...}\\
392   \vspace{1mm}
393   \scriptsize gives the filename\\
394   \vspace{1mm}
395   \footnotesize \quad \texttt{\~{}/palm/current\underline{ }version/JOB/INPUT/\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d}\\
396   \quad \texttt{( ... /\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d\textcolor{red}{.nc} )}
397   
398\end{frame}
399
400
401% Folie 9
402\begin{frame}
403   \frametitle{Steering File Copy by the Configuration File (III)}
404   \tiny
405   \onslide<1-> The \textbf{base name} can additionally be a part of the directory name
406   by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\
407   \vspace{1mm}
408   \scriptsize\quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
409   \vspace{4mm}
410   \onslide<2-> \tiny Using the call\\
411   \vspace{1mm}
412   \scriptsize \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\
413   \vspace{1mm}
414   \tiny the input file will be expected under\\
415   \vspace{1mm}
416   \scriptsize \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\
417   \vspace{4mm}
418   \onslide<3-> \tiny In this way, all files handled by the \texttt{mrun}-call are stored in
419   the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as
420   part of their names, so they can be easily identified as \grqq belonging\grqq\, to the model
421   run initiated by that \texttt{mrun} call.\\
422   \ \\
423   \onslide<4-> Instead of always writing the full path name (i.e.
424   \texttt{\~{}/palm/current\underline{ }version/JOBS}), an environment variable can be declared for
425   this at the beginning of the configuration file and be used in the file
426   connection statements:\\
427   \vspace{1mm}
428   \scriptsize \quad \texttt{\%base\underline{ }data  \~{}/palm/current\underline{ }version/JOBS}\\
429   \quad \texttt{PARIN in d3\#  \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
430   \ \\
431   \onslide<5-> \tiny This easily allows to change the directories for all input/output files
432   by just changing the value of \texttt{base\underline{ }data}.
433   
434\end{frame}
435
436% Folie 10
437\begin{frame}
438   \frametitle{Steering File Copy by the Configuration File (IV)}
439   \tiny
440   \onslide<1-> File connection statements which shall be carried out,
441   have to be activated by giving their activation string in the
442   \texttt{mrun}-option \texttt{-r}:\\
443   \vspace{1mm}
444   \scriptsize \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\
445   \ \\
446   \onslide<2-> \tiny The permanent file\\
447   \vspace{1mm}
448   \scriptsize \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} \\
449   \vspace{2mm}
450   \tiny will only be copied to the local file PARIN by using the call:\\
451   \vspace{1mm}
452   \scriptsize \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\
453   \ \\
454   \onslide<3-> \tiny \textbf{Example for an output file:}\\
455   The file connection statement\\
456   \vspace{1mm}
457   \scriptsize \quad \texttt{DATA\underline{ }1D\underline{ }PR\_NETCDF out:loc pr\# } \\
458   ~~~~~~\texttt{\~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}s\\
459   \vspace{2mm}
460   \onslide<4-> \tiny will copy (after program execution) the local file \\
461   \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file \\
462   \vspace{1mm}
463   \scriptsize \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc}\\
464   \vspace{1mm}
465   \tiny if \texttt{mrun} is called with the options\\
466   \vspace{1mm}
467   \scriptsize \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...}
468   
469\end{frame}
470
471% Folie 11
472\begin{frame}
473   \frametitle{Steering File Copy by the Configuration File (V)}
474   \scriptsize 
475   \onslide<1-> \texttt{mrun} never replaces/overwrites existing files!\\
476   \ \\
477   \tiny Instead, new, so-called file cycles are created.\\
478   If an output file, e.g.\\
479   \vspace{1mm}
480   \scriptsize \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc}\\
481   \ \\
482   \ \\
483   \tiny has been created from a first call of \texttt{mrun} and if the same \texttt{mrun} 
484   call is submitted again, the second call will not replace the file
485   \texttt{example\underline{ }cbl\underline{ }rc}, but will create a new file with name:\\
486   \vspace{1mm}
487   \scriptsize \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc.1}\\
488   \ \\
489   \ \\
490   \onslide<2-> \tiny In case of netCDF-files, the file cycle number is inserted before
491   the netCDF-suffix .nc, e.g.\\
492   \vspace{1mm}
493   \scriptsize \quad \texttt{example\underline{ }cbl\underline{ }pr.1.nc}\\
494   \ \\
495   \ \\
496   \onslide<3-> \tiny The implemented file cycle mechanism does not allow to use
497   any other dots "'."'  in the path or filename:\\
498   \vspace{1mm}
499   \scriptsize \quad \texttt{\~{}/palm/version\underline{ }3.6/JOBS/example.sbl/MONITORING/example.sbl\underline{ }rc}\\
500\end{frame}
501
502% Folie 12
503\begin{frame}[fragile]
504   \frametitle{\normalsize File Connection Statements From the Default \texttt{.mrun.config} file}
505   \begin{columns}
506      \column{1.1\textwidth}
507      \tiny
508      \begin{lstlisting}
509#----------------------------------------------------------------------------
510# List of input-files
511#----------------------------------------------------------------------------
512PARIN                    in:job        d3#      $base_data/$fname/INPUT    _p3d
513PARIN                    in:job        d3f      $base_data/$fname/INPUT    _p3df
514TOPOGRAPHY_DATA          in:locopt     d3#:d3f  $base_data/$fname/INPUT    _topo
515NUDGING_DATA             in:locopt     d3#:d3f  $base_data/$fname/INPUT    _nudge
516LSF_DATA                 in:locopt     d3#:d3f  $base_data/$fname/INPUT    _lsf
517BININ                    in:loc:flpe   d3f      $base_data/$fname/RESTART  _d3d
518PARTICLE_RESTART_DATA_IN in:loc:flpe   prtf     $base_data/$fname/RESTART  _rprt
519DATA_1D_PR_NETCDF        in:locopt     prf      $base_data/$fname/OUTPUT   _pr     nc
520DATA_1D_SP_NETCDF        in:locopt     spf      $base_data/$fname/OUTPUT   _sp     nc
521DATA_1D_TS_NETCDF        in:locopt     tsf      $base_data/$fname/OUTPUT   _ts     nc
522DATA_1D_PTS_NETCDF       in:locopt     ptsf     $base_data/$fname/OUTPUT   _pts    nc
523DATA_2D_XY_NETCDF        in:locopt     xyf      $base_data/$fname/OUTPUT   _xy     nc
524DATA_2D_XY_AV_NETCDF     in:locopt     xyf      $base_data/$fname/OUTPUT   _xy_av  nc
525DATA_2D_XZ_NETCDF        in:locopt     xzf      $base_data/$fname/OUTPUT   _xz     nc
526DATA_2D_YZ_NETCDF        in:locopt     yzf      $base_data/$fname/OUTPUT   _yz     nc
527DATA_3D_NETCDF           in:locopt     3df      $base_data/$fname/OUTPUT   _3d     nc
528DATA_PRT_NETCDF          in:locopt:pe  prtf     $base_data/$fname/OUTPUT   _prt
529#
530#----------------------------------------------------------------------------
531# List of output-files
532#----------------------------------------------------------------------------
533BINOUT                    out:loc:flpe restart   $base_data/$fname/RESTART  _d3d
534PARTICLE_RESTART_DATA_OUT out:loc:flpe prt#:prtf $base_data/$fname/RESTART  _rprt
535#
536RUN_CONTROL       out:loc:tr   d3#     $base_data/$fname/MONITORING  _rc
537RUN_CONTROL       out:loc:tra  d3f     $base_data/$fname/MONITORING  _rc
538HEADER            out:loc:tr   d3#     $base_data/$fname/MONITORING  _header
539HEADER            out:loc:tra  d3f     $base_data/$fname/MONITORING  _header
540CPU_MEASURES      out:loc:tr   d3#     $base_data/$fname/MONITORING  _cpu
541CPU_MEASURES      out:loc:tra  d3f     $base_data/$fname/MONITORING  _cpu
542      \end{lstlisting}
543   \end{columns}
544
545
546\end{frame}
547
548% Folie 13
549\begin{frame}[fragile]
550   \frametitle{Additional Features of \texttt{mrun} (I)}
551   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.975\textwidth, font=\Tiny]
552   \begin{itemize}
553      \footnotesize
554      \item<1-> Generating batch jobs on local \textbf{and} remote host.
555      \item<2-> Setting of unix environment variables for job and model control (e.g. for determining compiler options, etc.).
556      \item<3-> Values have to be set in the \texttt{mrun} configuration file \texttt{.mrun.config}:
557   \end{itemize}
558   \onslide<4->
559   \begin{center}
560      \begin{tikzpicture}
561        \node [yellow]{\begin{lstlisting}
562%tmp_user_catalog    /gfs1/work/<replace by your HLRN-III username>     lccrayh parallel
563%tmp_data_catalog    /gfs1/work/<replace by your HLRN-III username>     lccrayh parallel
564%compiler_name       ftn                                                lccrayh parallel
565%compiler_name_ser   ftn                                                lccrayh parallel
566%cpp_options         -e:Z:-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:...
567%mopts               -j:4                                               lccrayh parallel
568%fopts               -em:-O3:-hnoomp:-hfp3:-hdynamic                    lccrayh parallel
569%lopts               -em:-O3:-hnoomp:-hfp3:-hdynamic:-dynamic           lccrayh parallel
570%remote_username     <replace by your HLRN-III username>                lccrayh parallel
571%memory              2300                                               lccrayh parallel
572%modules             fftw:cray-hdf5-parallel:cray-netcdf-hdf5parallel   lccrayh parallel
573\end{lstlisting}};
574      \end{tikzpicture}
575   \end{center}
576\end{frame}
577
578% Folie 14
579\begin{frame}[fragile]
580   \frametitle{Additional Features of \texttt{mrun} (II)}
581   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.9\textwidth, font=\Tiny]
582
583   \begin{itemize}
584      \footnotesize
585      \item<1-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands).
586      These commands can also be defined in the \texttt{mrun} configuration file:
587      \onslide<2->
588      \begin{center}
589         \begin{tikzpicture}
590            \node [yellow]{\begin{lstlisting}
591IC:echo ``PALM will soon start to execute in \$PWD'' > /home/h/niksiraa/mrun_messages
592EC:ls -al
593OC:tar -cf DEBUG.tar DEBUG_*
594\end{lstlisting}};
595         \end{tikzpicture}
596      \end{center}
597      \item<3-> Automatic generation of restart jobs.
598   \end{itemize}
599
600
601\end{frame}
602
603% Folie 15
604\begin{frame}[fragile]
605   \frametitle{PALM \textit{Interactive} Example Run Using \texttt{mrun}: Tracing the Run by the User}
606   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
607   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
608   \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.55\textwidth, font=\tiny, minimum height=0.6cm]
609   \tikzstyle{notes} = [rectangle, text width=0.26\textwidth, font=\tiny, minimum height=0.6cm]
610   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny, minimum height=0.6cm]
611      \tikzstyle{green_term} = [rectangle, draw, fill=green!30, text width=0.83\textwidth, font=\Tiny,scale=0.6]
612   \vspace{-1.0cm}
613   \begin{center}
614           \begin{tikzpicture}[auto, node distance=0]
615         \uncover<1->{\node [yellow] (box1) {\textbf{start run on local machine:}\\
616                                            \texttt{mrun -d example\underline{ }cbl -h lcmuknb ...}};}
617         \uncover<1->{\node [dummy, right=1.4cm of box1] (dummy1) {};}
618         \uncover<2->{\node [notes, above=-0.3cm of dummy1] (notes1) {temporary working directory is created, all required files are copied there};}
619         \uncover<3->{\node [green, right=1.4cm of dummy1] (box2) {\textbf{follow run messages on terminal}};}
620         \uncover<4->{\node [green, below=0.5cm of box2] (box3) {
621         \textbf{as soon as message}
622         
623         \texttt{*** execution starts in directory\\ \quad \dq <tmpdir>\dq\, }\\
624         \ \\
625         \textbf{you can change to this directory (in a new terminal) and watch the progess of timesteps}
626
627         \texttt{cd <tmpdir>}\\
628         \texttt{tail -f RUN\underline{ }CONTROL}\\
629         \ \\
630         However, this might be difficult in case of short run times, because the run may have finished before you have entered the commands!
631         };}
632         \coordinate[below=0.3cm of box3] (A);
633         \uncover<1->{\node [dummy, left=0.3cm of box3] (dummy2) {};}
634         \uncover<6->{\node [notes, below=0.0cm of A, text width=0.35\textwidth] (notes2) {results are copied from temporary working directory to the user‘s permanent directory};}
635         \uncover<7->{\node [yellow_big, left=2.5cm of A] (box4) {
636         \textbf{check, if the output files have sucessfully been transferred to the permanent directory:}\\
637         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING}\\
638         \texttt{ls -al}\\
639         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT}\\
640         \texttt{ls -al}
641};}
642         \draw<2-> [->,color=blue] (box1.east) -- (box2.west);   
643         \draw<4-> [->,color=blue] (box2.south) -- (box3.north); 
644         \draw<6-> [-,color=blue] (box3.south) -- (A); 
645         \draw<6-> [->,color=blue] (A) -- (box4.east); 
646         \onslide<5->\node [green_term, left=1.2cm of box3] (terminal) {\begin{lstlisting} 
647  *** running on: laptop laptop
648
649      ... reading environment parameters from ENVPAR      --- finished
650      ... reading NAMELIST parameters from PARIN      --- finished
651      ... creating virtual PE grids + MPI derived data types      --- finished
652      ... checking parameters      --- finished
653      ... allocating arrays      --- finished
654      ... initializing with constant profiles      --- finished
655      ... initializing statistics, boundary conditions, etc.      --- finished
656      ... creating initial disturbances      --- finished
657      ... calling pressure solver      --- finished
658      --- leaving init_3d_model
659      --- start with time-stepping
660
661      [XXXXXXXXXXXXXXXXXXXXXXXXXXXX________________________________]  53.3 left
662\end{lstlisting}
663         };
664         \uncover<5->{\node [notes, above=0.0cm of terminal, text width=0.55\textwidth] (notes_terminal) {Starting from version 3.10 (r 1402), some progress messages and a progress bar for estimating the time required to finish the simulation is output on the terminal};}
665         %\draw<5-> [->,color=blue] (box3.west) -- (terminal.east);
666         \onslide<1-> 
667           \end{tikzpicture}
668        \end{center}
669\end{frame}
670
671% Folie 16
672\begin{frame}
673   \frametitle{PALM \textit{Batch} Example Run (on HLRN, remote) Using \texttt{mrun}: Tracing the Run by the User}
674\tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, font=\Tiny]
675\tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.4\textwidth, font=\Tiny]
676\tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.4\textwidth, font=\Tiny]
677\tikzstyle{dummy} = [text width=0.2\textwidth, font=\Tiny]
678\tikzstyle{alert} = [rectangle, draw, text width=0.5\textwidth, font=\scriptsize]
679\tikzstyle{line} = [draw, -latex']
680\begin{itemize}
681   \item \small Reminder: Running batch jobs requires a directory \texttt{~/job\underline{ }queue} for the job protocol files on the local \underline{and} remote host.
682\end{itemize}
683\begin{tikzpicture}[auto, node distance=0]
684    \node [yellow] (first) {
685       \textbf{start job on local machine:}\\
686       \texttt{mrun -d example\underline{ }cbl -h lccrayh ...}
687    };
688\uncover<2->{
689    \node [dummy, right=0.5cm of first] (dummy) {
690       transfer of job by \texttt{scp} \\
691       \ \\
692       \ \\
693       submit of job by executing the \texttt{msub} command via \texttt{ssh}
694    };
695}
696\uncover<3->{
697    \node [green, right=3.5cm of first] (second) {
698       \textbf{follow job execution on remote host, by} \\
699       \texttt{showq} (better: \texttt{showq | grep hzkurs})
700    };
701}
702\uncover<4->{
703    \node [green, below=0.2cm of second] (third) {
704       \textbf{if job is running, you may follow its progress by watching the job protocol (does not work on HLRN-III system!):} \\ 
705       \texttt{cd \~{}/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
706    };
707}
708\uncover<5->{
709    \node [green, below=0.2cm of third] (fourth) {
710       \textbf{when job is running, change to directory \texttt{<tmp\underline{ }usr\underline{ }catalog>} and try to find there the latest directory \texttt{<HLRN-username>.<randomnumber>} \\ change to this directory and execute}\\
711       \texttt{tail -f RUN\underline{ }CONTROL}
712    };
713}
714\uncover<6->{
715    \node [green, below=0.2cm of fourth] (fifth) {
716       \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\
717       \texttt{cd \~{}/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}
718    };
719}
720\uncover<7->{
721    \node [dummy, left=0.001mm of fifth] (dummy) {
722       transfer results by \texttt{scp} \\
723       \ \\
724       \ \\
725    };
726}
727\uncover<8->{
728    \node [yellow2, left=2.5cm of fifth] (sixth) {
729       \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\
730       \texttt{cd \~{}/job\_queue \\ ls -al \\ cd \~{}/palm/current\_version/JOBS/example \\ ls -al *}
731    };
732}
733\uncover<9->{
734     \node [alert, below=0.5cm of first.south east] (alert) {
735        \textcolor{red}{Attention: Commands for submitting jobs and the behaviour of job protocol files are depending on the queueing system! Manual adjustments may be required in the \textbf{mrun} and \textbf{subjob} script!}
736     };
737}
738    \path<2-> [line] (first) -- (second);
739    \path<4-> [line] (second) -- (third);
740    \path<5-> [line] (third) -- (fourth);
741    \path<6-> [line] (fourth) -- (fifth);
742    \path<7-> [line] (fifth) -- (sixth);
743\end{tikzpicture}
744\end{frame}
745
746
747
748% Folie 17
749\begin{frame}
750   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
751   \tikzstyle{green_small} = [rectangle, draw, fill=green!20, text width=0.12\textwidth, font=\scriptsize, minimum height=0.6cm]
752   \tikzstyle{yellow_small} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\scriptsize, minimum height=0.6cm]
753   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm]
754   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
755   \tikzstyle{notes} = [rectangle, text width=0.15\textwidth, font=\scriptsize, minimum height=0.6cm]
756   
757   \frametitle{PALM Runs Using \texttt{mrun}: Further Details}
758   \begin{itemize}
759      \footnotesize
760      \item<2-> For every (initial) run, \texttt{mrun} creates a source directory which contains copies of
761      \begin{itemize}
762         \footnotesize
763         \item<4-> those source code files to be translated (always the main program, \texttt{palm.f90}, plus user interface files)
764         \item<4-> the Makefile
765         \item<5-> the configuration file
766         \item<6-> the mrun script
767      \end{itemize}
768   \end{itemize}
769   
770   \vspace{-0.8cm}
771   \begin{center}
772           \begin{tikzpicture}[auto, node distance=0]
773           
774         \uncover<3->{\node [yellow_small] (box1) {\$HOME/};}
775         \uncover<3->{\node [yellow_small, right=0.2cm of box1] (box2) {palm/};}
776         \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\underline{ }version/};}
777         \uncover<3->{\node [green_small, right=0.4cm of box3] (box4) {trunk/};}
778         
779         \uncover<1->{\node [dummy, right=1.0cm of box4] (dummy1) {};}
780         
781         \uncover<3->{\node [green_small, above=-0.2cm of dummy1] (box5) {SCRIPTS};}
782         \uncover<3->{\node [green_small, below=-0.2cm of dummy1] (box6) {SOURCE};}
783         
784         \uncover<6->{\node [notes, right=0.1cm of box5] (notes1) {\texttt{mrun}};}
785         \uncover<4->{\node [notes, right=0.1cm of box6] (notes2) {\texttt{Makefile \\ palm.f90}};}
786         \uncover<5->{\node [notes, below=0.1cm of box3] (notes3) {\texttt{.mrun.config}};}
787         
788         \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\underline{ }FOR\underline{ }RUN\underline{ }$<$run\underline{ }identifier$>$};}
789         
790         \uncover<1->{\node [dummy, left=1.5cm of box7] (dummy2) {};}
791         \uncover<1->{\node [dummy, right=2.0cm of box5] (dummy3) {};}
792         \uncover<1->{\node [dummy, right=1.8cm of box6] (dummy4) {};}
793         \uncover<1->{\node [dummy, below=0.2cm of dummy4] (dummy5) {};}
794         \draw<3-> [-] (box1.east) -- (box2.west); 
795         \draw<3-> [-] (box2.east) -- (box3.west); 
796         \draw<3-> [-] (box3.east) -- (box4.west); 
797         \draw<3-> [-] (box4.east) -- (box5.west); 
798         \draw<3-> [-] (box4.east) -- (box6.west);     
799         \draw<3-> [-] (box3.east) -- (box7.west);   
800         \draw<6-> [-] ([xshift=-0.8cm]notes1.east) -- (dummy3.center);   
801         \draw<4-> [-] ([xshift=-0.4cm]notes2.east) -- (dummy4.center);
802         \draw<4-> [-] (dummy4.center) -- ([yshift=0.1cm]dummy5.center);
803         \draw<4-> [->] ([yshift=0.1cm]dummy5.center) -- ([yshift=0.1cm]box7.east);
804         \draw<6-> [-] (dummy3.center) -- ([xshift=0.2cm, yshift=-0.1cm]dummy5.center);
805         \draw<6-> [->] ([xshift=0.2cm, yshift=-0.1cm]dummy5.center) -- ([yshift=-0.1cm]box7.east);
806         \draw<5-> [-] ([yshift=0.3cm]dummy2.center) -- (dummy2.center);   
807         \draw<5-> [->] (dummy2.center) -- (box7.west);   
808           \end{tikzpicture}
809        \end{center}
810   
811   \begin{itemize}
812      \footnotesize
813      \item<7-> These files are used in the run/job. They are also used by restart jobs, which guarantees, that all jobs in a job chain are using the same information. Please never modify these directories, unless you exactly know, what you are doing.
814   \end{itemize}
815\end{frame}
816
817
818% Folie 17
819\begin{frame}
820 \footnotesize \texttt{mrun}
821   \frametitle{PALM Runs Using \texttt{mrun}: most important \texttt{mrun} options}
822   \begin{itemize}
823      \footnotesize
824      \item<2-> \texttt{-d example\_cbl}
825      \begin{itemize}
826         \item[] \tiny run identifier, basefile/directory name of all data files of this run
827      \end{itemize}
828      \item<3-> \texttt{-h} host identifier
829      \begin{itemize}
830         \item[] \tiny host on which the run shall be performed (reminder: this is not the UNIX hostname):\\ \texttt{lcmuknb, lcmuk, lccrayh...}
831      \end{itemize}
832      \item<4-> \texttt{-K parallel}
833      \begin{itemize}
834         \item[] \tiny run in parallel on several processor cores
835      \end{itemize}
836      \item<5-> \texttt{-X 4}
837      \begin{itemize}
838         \item[] \tiny number of processors to be used
839      \end{itemize}
840      \item<6-> \texttt{-T 4}
841      \begin{itemize}
842         \item[] \tiny number of tasks to be started on one node of the computer
843      \end{itemize}
844      \item<7-> \texttt{-t 100}
845      \begin{itemize}
846         \item[] \tiny CPU time allowed to be used for the batch jobs
847      \end{itemize}
848      \item<8-> \texttt{-b}
849      \begin{itemize}
850         \item[] \tiny run in batch mode
851      \end{itemize}
852      \item<9-> \texttt{-q mpp1q}
853      \begin{itemize}
854         \item[] \tiny batch job queue
855      \end{itemize}
856      \item<10-> \texttt{-r \dq ...\dq}
857      \begin{itemize}
858         \item[] \tiny activation strings
859      \end{itemize}
860   \end{itemize}   
861\end{frame}
862\end{document}
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