source: palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex @ 964

Last change on this file since 964 was 964, checked in by raasch, 9 years ago

old profil-parameters (cross_xtext, cross_normalized_x, etc. ) and respective code removed
(check_open, check_parameters, close_file, data_output_profiles, data_output_spectra, header, modules, parin)

reformatting (netcdf)

append feature removed from unit 14 (check_open)

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1% $Id: runs_with_mrun.tex 964 2012-07-26 09:14:24Z raasch $
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\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
18\usepackage{amsmath}
19\usepackage{amssymb}
20\usepackage{multicol}
21\usepackage{pdfcomment}
22\usepackage{graphicx}
23\usepackage{listings}
24\lstset{showspaces=false,language=fortran,basicstyle=
25        \ttfamily,showstringspaces=false,captionpos=b}
26
27\institute{Institut fÌr Meteorologie und Klimatologie, Leibniz UniversitÀt Hannover}
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{Siegfried Raasch}
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   \begin{itemize}
64      \item<1-> \texttt{mrun} (\textbf{m}odel \textbf{run}) is a shell script (using
65      \texttt{ksh}-syntax) which can be used to compile and run programs, including
66      the handling of input/output files.
67      \vspace{4mm}
68      \item<2-> The \texttt{mrun}-command has a number of options to control the
69      program execution\\
70         \quad \footnotesize \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\
71         \normalsize All options including a short description can be displayed by entering\\
72         \quad \footnotesize \texttt{mrun ?}
73      \vspace{4mm}
74      \item<3-> \normalsize The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} 
75   \end{itemize}
76\end{frame}
77
78% Folie 3
79\begin{frame}
80   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\tiny]
81   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, font=\tiny]
82   \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\tiny]
83   \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\tiny]
84   \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\tiny]
85   \tikzstyle{line} = [draw, -]
86   \tikzstyle{alert} = [rectangle, draw, text width=0.77\textwidth, font=\scriptsize]
87 
88   \scriptsize
89   \frametitle{Carrying Out Runs Using \texttt{mrun}}
90   \textbf{Carrying out a program run typically needs two steps:}\\
91   \vspace{1mm}
92   \quad 1. compilation\\
93   \qquad \texttt{f90  ...  file1.f90 file2.f90 ...}\\
94   \vspace{1mm}
95   \onslide<2->\quad 2. execution\\
96   \qquad \texttt{a.out}\\
97   \vspace{3mm}
98   \onslide<3->\textbf{Besides, a program needs input data and creates output data:}\\
99   
100   \onslide<4->\begin{tikzpicture}[auto, node distance=0]
101      \node [green] (first) {\textbf{a.out/} };
102      \node [dummy, right=0.1cm of first] (second) {};
103     
104      \node [yellow, above=0.4cm of second] (third) {\textbf{parameter for steering}};
105      \node [yellow, below=0.4cm of third] (fourth) {\textbf{control output}};
106      \node [yellow, below=0.3cm of fourth] (fifth) {\textbf{output for analysis}};
107     
108      \node [info, above=-0.1cm of third] (sixth) {input file};
109      \node [info, above=-0.1cm of fourth] (seventh) {output file 1};
110      \node [info, above=-0.1cm of fifth] (eight) {output file 2};
111
112      \draw [->] (third.west) -- (first.north);
113      \draw [->] (first.east) -- (fourth.west);
114      \draw [->] (first.south) -- (fifth.west);
115     
116      \uncover<5->{\node [white, right=0.25cm of third] (ninth) {
117         \texttt{OPEN (11, FILE='PARIN', FORM='FORMATTED')}};}
118      \uncover<5->{\node [white, right=0.25cm of fourth] (tenth) {
119         \texttt{OPEN (15, FILE='RUN\underline{ }CONTROL', FORM='FORMATTED')}};}
120      \uncover<5->{\node [white, right=0.25cm of fifth] (eleventh) {
121         \texttt{OPEN (40, FILE=‘DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF', FORM='FORMATTED')}};}
122   \end{tikzpicture}
123   
124   \vspace{3mm}
125   \scriptsize
126   \onslide<6->\textcolor{red}{\textbf{Problems:} The user has to copy or rename output files, if
127   he/she wants to run the program more than once and if he concurrently wants to keep
128   the files from the former run(s).\\
129   If he/she is using different input parameter files for steering, these files also have
130   to be copied into the working directory before the program is executed.}\\
131   \vspace{1mm}
132   \begin{tikzpicture}[auto, node distance=0]
133      \uncover<7->{\node [alert] (alert) {\textcolor{red}{\textbf{It is therefore very desirable to automate these tasks!}}};}
134   \end{tikzpicture}
135\end{frame}
136
137% Folie 4
138\begin{frame}
139   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize]
140   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize]
141   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.10\textwidth, font=\scriptsize]
142   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny]
143   
144   \frametitle{\texttt{mrun}: Principal Mode of Operation (I)}
145   \scriptsize \texttt{mrun} \textbf{runs a program (in our case the PALM model) by carrying out the following principle tasks in a sequential order:}\\
146   \vspace{1mm}
147   \begin{enumerate}
148      \item<2-> Create a temporary working directory and change into this directory:\\
149      \quad \texttt{mkdir <tempdir>/<username>.<randomnumber>}\\
150      \quad \texttt{cd <tempdir>/<username>.<randomnumber>}\\
151      \ \\
152      The path of \texttt{<tempdir>} is given in the configuration file
153      \texttt{.mrun.config} by the environment variable \texttt{tmp\underline{ }user\underline{ }catalog}, e.g.:\\
154           \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /tmp \hspace{30mm} <hi>  parallel}\\
155           \ \\
156           \onslide<3-> On SGI-ICE: \\
157           \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /gfs2/work/<username>
158           \hspace{5mm} lcsgih parallel}
159           \begin{center}
160              \begin{tikzpicture}[auto, node distance=0]
161            \uncover<4->{\node [green] (green) {/tmp/$<$username$>$.$<$randomnumber$>$};}
162         \end{tikzpicture}
163           \end{center}
164           \vspace{2mm}
165           \item<5-> Copy the input files from a directory of the user into this working directory:\\
166           \vspace{1mm}
167           \onslide<6-> \tiny \quad \texttt{cp <user\underline{ }input\underline{ }file1>
168           /tmp/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file1>}\\
169      \quad \texttt{cp <user\underline{ }input\underline{ }file2>
170      /tmp/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file2>}\\
171      \vspace{2mm}
172      \scriptsize
173      \begin{center}
174              \begin{tikzpicture}[auto, node distance=0]
175             
176            \uncover<8->{\node [green] (green) {/tmp/$<$username$>$.$<$randomnumber$>$};}
177       
178            \uncover<7->{\node [yellowsmall, above=0.1cm of green] (yellow2) {JOBS/};}
179            \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\underline{ }version/};}
180            \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
181            \uncover<7->{\node [yellowsmall, right=0.2cm of yellow3] (yellow4) {INPUT/};}
182           
183            \draw<7-> [-] (yellow1.east) -- (yellow2.west);
184            \draw<7-> [-] (yellow2.east) -- (yellow3.west);
185            \draw<7-> [-] (yellow3.east) -- (yellow4.west);
186           
187            \node [dummy, right=0.1cm of yellow4] (dummy1) {};
188            \node [dummy, right=2.055cm of green] (dummy2) {};
189           
190            \draw<9-> [-] (yellow4.east) -- (dummy1.center);
191            \draw<9-> [-] (dummy1.center) -- (dummy2.center);
192            \draw<9-> [->] (dummy2.center) -- (green.east);
193           
194         \end{tikzpicture}
195           \end{center}
196     
197        \end{enumerate}
198
199\end{frame}
200
201% Folie 5
202\begin{frame}
203   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
204   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm]
205   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
206   
207   \frametitle{\texttt{mrun}: Principal Mode of Operation (II)}
208
209        \begin{enumerate}
210      \setcounter{enumi}{2}
211           \item<1-> Copy the pre-compiled routines to the temporary working directory:\\
212     
213      \begin{center}
214              \begin{tikzpicture}[auto, node distance=0]
215                 \uncover<2->{\node [yellow] (yellow) {current\underline{ }version/};}
216                 \uncover<1->{\node [dummy, right=0.0cm of yellow] (dummy1) {};}
217                 \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\underline{ }DEPOSITORY\underline{ }\textit{parallel}/};}
218                 \uncover<1->{\node [dummy, right=0.2cm of green1] (dummy2) {};}
219            \uncover<3->{\node [green, below=0.5cm of dummy1] (green2) {/tmp/$<$username$>$.$<$randomnumber$>$};}
220             \uncover<1->{\node [dummy, below=0.5cm of dummy2] (dummy3) {};}
221             \uncover<4->{\node [dummy, right=0.0cm of dummy3] (text) {Makefile\\
222                 *.f90\\
223                 *.o\\
224                 ...\\ \ \\};}
225             
226             \draw<2-> [-] (yellow.east) -- (green1.west);
227             \draw<4-> [-] (green1.east) -- (dummy2.center);
228             \draw<4-> [-] (dummy2.center) -- (dummy3.center);
229             \draw<4-> [->] (dummy3.center) -- (green2.east);
230              \end{tikzpicture}
231           \end{center}
232           
233           \item<5-> Compile the main program and use pre-compiled object files:\\
234     \quad \texttt{f90 palm.f90 *.o ...   ( make Makefile)}
235      \item<6-> Execute the program:\\
236     \quad \texttt{a.out}
237   \end{enumerate}
238\end{frame}
239
240% Folie 6
241\begin{frame}
242   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
243   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm]
244   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
245   
246   \frametitle{\texttt{mrun}: Principal Mode of Operation (III)}
247   \footnotesize 
248        \begin{enumerate}
249      \setcounter{enumi}{5}
250           \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\
251       \tiny \quad \texttt{cp /tmp/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\
252      \quad \texttt{cp /tmp/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\
253      \footnotesize 
254      \begin{center}
255              \begin{tikzpicture}[auto, node distance=0]
256            \uncover<2->{\node [yellow] (yellow1) {MONITORING/};}
257
258            \uncover<2->{\node [dummy, right=0.2cm of yellow1] (dummy2) {};}
259            \uncover<2->{\node [dummy, above=0.2cm of dummy2] (dummy1) {};}
260            \uncover<2->{\node [dummy, below=0.2cm of dummy2] (dummy3) {};}
261           
262            \uncover<2->{\node [yellow, left=0.2cm of dummy3] (yellow2) {OUTPUT/};}
263            \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
264            \uncover<2->{\node [yellow, left=0.2cm of yellow3] (yellow4) {JOBS/};}
265            \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};}
266                                             
267                 \uncover<2-3>{\node [green, left=5.0cm of dummy1] (green) {/tmp/$<$username$>$.$<$randomnumber$>$};}
268                 
269            \draw<2-3> [-] (green.east) -- (dummy1.center);
270            \draw<2-3> [-] (dummy2.center) -- (dummy1.center);
271            \draw<2-3> [-] (dummy3.center) -- (dummy1.center);
272           
273            \draw<2-3> [->] (dummy2.center) -- (yellow1.east);
274            \draw<2-3> [->] (dummy3.center) -- (yellow2.east);
275           
276            \draw<2-> [-] (yellow2.west) -- (yellow3.east);
277            \draw<2-> [-] (yellow3.west) -- (yellow4.east);
278            \draw<2-> [-] (yellow4.west) -- (yellow5.east);
279               
280              \end{tikzpicture}
281           \end{center}
282           
283           \item<3-> Delete the temporary working directory\\
284      \quad \texttt{rm -rf /tmp/<username>.<randomnumber>}\\
285      \vspace{2mm}
286      \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?}
287
288   \end{enumerate}
289\end{frame}
290
291% Folie 7
292\begin{frame}
293   \tikzstyle{small} = [rectangle, text width=0.08\textwidth, font=\scriptsize]
294   \tikzstyle{large} = [rectangle, text width=0.45\textwidth, font=\scriptsize]
295   \tikzstyle{box} = [rectangle, draw, text width=0.2\textwidth, font=\scriptsize]
296   \tikzstyle{boxbig} = [rectangle, draw, text width=0.4\textwidth, font=\scriptsize]
297   \tikzstyle{dummy} = [rectangle, text width=0.0\textwidth, font=\scriptsize, minimum height=0.5cm]
298   
299   \frametitle{Steering File Copy by the Configuration File (I)}
300   \scriptsize
301   \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.}\\
302   \vspace{1mm}
303   Principle example of a file connection statement (for the PALM parameter file):
304   \vspace{-3mm}
305   \begin{center}
306           \begin{tikzpicture}[auto, node distance=0]
307         \uncover<1->{\node [small] (part1) {\texttt{PARIN}};}
308         \uncover<1->{\node [dummy, left=-0.2cm of part1] (dummy1) {};}
309         \uncover<1->{\node [dummy, below=1.25cm of dummy1] (dummy3) {};}
310         \uncover<1->{\node [small, right=0.0cm of part1] (part2) {\quad \texttt{in}};}
311         \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
312         \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
313              \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
314              \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
315              \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
316                   
317         \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)};}
318              \draw<2-> [->] (dummy3.north) -- (dummy1.south);
319             
320              \uncover<3->{\node [box, below=0.7cm of part2] (box2) {file attributes};}
321              \draw<3-> [->] (box2.north) -- (part2.south);
322             
323              \uncover<4->{\node [box, below=0.2cm of part3] (box3) {activating string};}
324              \draw<4-> [->] (box3.north) -- (part3.south);
325                     
326              \uncover<5->{\node [box, below=0.2cm of part4] (box4) {directory in which the permanent user file resides};}
327              \draw<5-> [->] (box4.north) -- (part4.south);
328             
329         \uncover<6->{\node [box, below=0.2cm of part5] (box5) {suffix of the permanent filename};}
330              \draw<6-> [->] (box5.north) -- (part5.south);
331             
332         \uncover<7->{\node [box, below=1.0cm of part6] (box6) {additional suffix for netCDF files};}
333              \draw<7-> [->] (box6.north) -- (part6.south);   
334           \end{tikzpicture}
335        \end{center}
336   
337   \onslide<8->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}:\\
338   \quad \texttt{mrun -d \textcolor{blue}{example\underline{ }cbl} ...}\\
339   gives the filename\\
340   \quad \texttt{\~{}/palm/current\underline{ }version/JOB/INPUT/\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d}\\
341   \quad \texttt{( ... /\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d\textcolor{red}{.nc} )}
342   
343\end{frame}
344
345% Folie 8
346\begin{frame}
347   \frametitle{Steering File Copy by the Configuration File (II)}
348   \scriptsize
349   \onslide<1-> The \textbf{base name} can additionally be a part of the directory name
350   by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\
351   \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
352   \ \\
353   \onslide<2-> Using the call\\
354   \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\
355   the input file will be expected under\\
356   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\
357   \ \\
358   \onslide<3-> In this way, all files handled by the \texttt{mrun}-call are stored in
359   the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as
360   part of their names, so they can be easily identified as \grqq belonging\grqq\, to the model
361   run initiated by that \texttt{mrun} call.\\
362   \ \\
363   \onslide<4-> Instead of always writing the full path name (i.e.
364   \texttt{\~{}/palm/current\underline{ }version/JOBS}), an environment variable can be declared for
365   this at the beginning of the configuration file and be used in the file
366   connection statements:\\
367   \quad \texttt{\%base\underline{ }data  \~{}/palm/current\underline{ }version/JOBS}\\
368   \quad \texttt{PARIN in d3\#  \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
369   \ \\
370   \onslide<5-> This easily allows to change the directories for all input/output files
371   by just changing the value of \texttt{base\underline{ }data}.
372   
373\end{frame}
374
375% Folie 9
376\begin{frame}
377   \frametitle{Steering File Copy by the Configuration File (III)}
378   \scriptsize
379   \onslide<1-> File connection statements which shall be carried out,
380   have to be activated by giving their activation string in the
381   \texttt{mrun}-option \texttt{-r}:\\
382   \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\
383   \ \\
384   \onslide<2-> The permanent file
385   \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} 
386   will only be copied to the local file PARIN by using the call:\\
387   \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\
388   \ \\
389   \onslide<3-> \textbf{Example for an output file:}\\
390   The file connection statement\\
391   \quad \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF out:loc pr\# 
392   \~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}\\
393   \onslide<4-> will copy (after program execution) the local file
394   \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file
395   \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc} if
396   \texttt{mrun} is called with the options\\
397   \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...}
398   
399\end{frame}
400
401% Folie 10
402\begin{frame}
403   \frametitle{Steering File Copy by the Configuration File (IV)}
404   \scriptsize
405   \onslide<1-> \texttt{mrun} never replaces/overwrites existing files!\\
406   \ \\
407   Instead, new, so-called file cycles are created.\\
408   If an output file, e.g.\\
409   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc}\\
410   \ \\
411   has been created from a first call of \texttt{mrun} and if the same \texttt{mrun} 
412   call is submitted again, the second call will not replace the file
413   \texttt{example\underline{ }cbl\underline{ }rc}, but will create a new file with name:\\
414   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc.1}\\
415   \ \\
416   \onslide<2->In case of netCDF-files, the file cycle number is inserted before
417   the netCDF-suffix .nc, e.g.\\
418   \quad \texttt{example\underline{ }cbl\underline{ }pr.1.nc}\\
419   \ \\
420   \onslide<3->The implemented file cycle mechanism does not allow to use
421   any other dots "'."'  in the path or filename:\\
422   \quad \texttt{\~{}/palm/version\underline{ }3.6/JOBS/example.sbl/MONITORING/example.sbl\underline{ }rc}
423\end{frame}
424
425% Folie 11
426\begin{frame}[fragile]
427   \frametitle{\normalsize File Connection Statements From the Default \texttt{.mrun.config} file}
428   \begin{columns}
429      \column{1.1\textwidth}
430      \tiny
431      \begin{lstlisting}
432#----------------------------------------------------------------------------
433# List of input-files
434#----------------------------------------------------------------------------
435PARIN                    in:job        d3#      $base_data/$fname/INPUT    _p3d
436PARIN                    in:job        d3f      $base_data/$fname/INPUT    _p3df
437TOPOGRAPHY_DATA          in:locopt     d3#:d3f  $base_data/$fname/INPUT    _topo
438BININ                    in:loc:flpe   d3f      $base_data/$fname/RESTART  _d3d
439PARTICLE_RESTART_DATA_IN in:loc:flpe   prtf     $base_data/$fname/RESTART  _rprt
440DATA_1D_PR_NETCDF        in:locopt     prf      $base_data/$fname/OUTPUT   _pr     nc
441DATA_1D_SP_NETCDF        in:locopt     spf      $base_data/$fname/OUTPUT   _sp     nc
442DATA_1D_TS_NETCDF        in:locopt     tsf      $base_data/$fname/OUTPUT   _ts     nc
443DATA_1D_PTS_NETCDF       in:locopt     ptsf     $base_data/$fname/OUTPUT   _pts    nc
444DATA_2D_XY_NETCDF        in:locopt     xyf      $base_data/$fname/OUTPUT   _xy     nc
445DATA_2D_XY_AV_NETCDF     in:locopt     xyf      $base_data/$fname/OUTPUT   _xy_av  nc
446DATA_2D_XZ_NETCDF        in:locopt     xzf      $base_data/$fname/OUTPUT   _xz     nc
447DATA_2D_YZ_NETCDF        in:locopt     yzf      $base_data/$fname/OUTPUT   _yz     nc
448DATA_3D_NETCDF           in:locopt     3df      $base_data/$fname/OUTPUT   _3d     nc
449DATA_PRT_NETCDF          in:locopt:pe  prtf     $base_data/$fname/OUTPUT   _prt
450#
451#----------------------------------------------------------------------------
452# List of output-files
453#----------------------------------------------------------------------------
454BINOUT                    out:loc:flpe restart   $base_data/$fname/RESTART  _d3d
455PARTICLE_RESTART_DATA_OUT out:loc:flpe prt#:prtf $base_data/$fname/RESTART  _rprt
456#
457RUN_CONTROL       out:loc:tr   d3#     $base_data/$fname/MONITORING  _rc
458RUN_CONTROL       out:loc:tra  d3f     $base_data/$fname/MONITORING  _rc
459HEADER            out:loc:tr   d3#     $base_data/$fname/MONITORING  _header
460HEADER            out:loc:tra  d3f     $base_data/$fname/MONITORING  _header
461CPU_MEASURES      out:loc:tr   d3#     $base_data/$fname/MONITORING  _cpu
462CPU_MEASURES      out:loc:tra  d3f     $base_data/$fname/MONITORING  _cpu
463#
464DATA_1D_PR_NETCDF    out:loc:tr   pr#:prf   $base_data/$fname/OUTPUT  _pr     nc
465DATA_1D_SP_NETCDF    out:loc:tr   sp#:spf   $base_data/$fname/OUTPUT  _sp     nc
466DATA_1D_TS_NETCDF    out:loc:tr   ts#:tsf   $base_data/$fname/OUTPUT  _ts     nc
467DATA_1D_PTS_NETCDF   out:loc:tr   pts#:ptsf $base_data/$fname/OUTPUT  _pts    nc
468DATA_2D_XY_NETCDF    out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy     nc
469DATA_2D_XY_AV_NETCDF out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy_av  nc
470DATA_2D_XZ_NETCDF    out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz     nc
471DATA_2D_XZ_AV_NETCDF out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz_av  nc
472DATA_2D_YZ_NETCDF    out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz     nc
473DATA_2D_YZ_AV_NETCDF out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz_av  nc
474DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d     nc
475DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av  nc
476DATA_MASK_01_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01     nc
477DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01_av  nc
478DATA_MASK_02_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02     nc
479DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02_av  nc
480DATA_MASK_03_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03     nc
481DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03_av  nc
482DATA_MASK_04_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04     nc
483DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04_av  nc
484DATA_MASK_05_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05     nc
485DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05_av  nc
486DATA_MASK_06_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06     nc
487DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06_av  nc
488DATA_MASK_07_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07     nc
489DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07_av  nc
490DATA_MASK_08_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08     nc
491DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08_av  nc
492DATA_MASK_09_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09     nc
493DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09_av  nc
494DATA_MASK_10_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10     nc
495DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10_av  nc
496DATA_MASK_11_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11     nc
497DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11_av  nc
498DATA_MASK_12_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12     nc
499DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12_av  nc
500DATA_MASK_13_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13     nc
501DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13_av  nc
502DATA_MASK_14_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14     nc
503DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14_av  nc
504DATA_MASK_15_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15     nc
505DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15_av  nc
506DATA_MASK_16_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16     nc
507DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16_av  nc
508DATA_MASK_17_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17     nc
509DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17_av  nc
510DATA_MASK_18_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18     nc
511DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18_av  nc
512DATA_MASK_19_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19     nc
513DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19_av  nc
514DATA_MASK_20_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20     nc
515DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20_av  nc
516DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
517DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr
518#
519DVRP_LOG          out:loc:tr   dv#       $base_data/$fname/MONITORING  _dvrp_log
520DVRP_LOG          out:loc:tra  dvf       $base_data/$fname/MONITORING  _dvrp_log
521PARTICLE_INFO     out:loc:tr   pt#       $base_data/$fname/MONITORING  _prt_info
522PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
523PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
524
525      \end{lstlisting}
526   \end{columns}
527\end{frame}
528
529% Folie 12
530\begin{frame}
531   \frametitle{Additional Features of \texttt{mrun}}
532   \begin{itemize}
533      \footnotesize
534      \item<1-> Generating batch jobs on local \textbf{and} remote host.
535      \item<2-> Setting of unix environment variables for job and model control (e.g. for determining compiler options, etc.).
536      \item<3-> Values have to be set in the \texttt{mrun} configuration file \texttt{.mrun.config}:
537   \end{itemize}
538   \onslide<4->\hspace{-1cm}\includegraphics[scale=0.3]{mrun_figures/add_feat1.png}
539   \begin{itemize}
540      \footnotesize
541      \item<5-> 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).
542      These commands can also be defined in the \texttt{mrun} configuration file:
543      \onslide<6-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png}
544      \item<7-> Automatic generation of restart jobs.
545   \end{itemize}
546\end{frame}
547
548% Folie 13
549\begin{frame}
550   \frametitle{PALM \textit{Interactive} Example Run Using \texttt{mrun}: Tracing the Run by the User}
551   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
552   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
553   \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.55\textwidth, font=\tiny, minimum height=0.6cm]
554   \tikzstyle{notes} = [rectangle, text width=0.26\textwidth, font=\tiny, minimum height=0.6cm]
555   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny, minimum height=0.6cm]
556   \vspace{-1.0cm}
557   \begin{center}
558           \begin{tikzpicture}[auto, node distance=0]
559         \uncover<1->{\node [yellow] (box1) {\textbf{start run on local machine:}\\
560                                            \texttt{mrun -d example\underline{ }cbl -h lcmuk ...}};}
561         \uncover<1->{\node [dummy, right=1.4cm of box1] (dummy1) {};}
562         \uncover<2->{\node [notes, above=-0.3cm of dummy1] (notes1) {temporary working directory is created, all required files are copied there};}
563         \uncover<3->{\node [green, right=1.4cm of dummy1] (box2) {\textbf{follow run messages on terminal}};}
564         \uncover<4->{\node [green, below=0.5cm of box2] (box3) {
565         \textbf{as soon as message}
566         
567         \texttt{*** execution starts in directory\\ \quad \dq <tempdir>\dq\, }\\
568         \ \\
569         \textbf{you can change to this directory (in a new terminal) and watch the progess of timesteps}
570
571         \texttt{cd <tempdir>}\\
572         \texttt{tail -f RUN\underline{ }CONTROL}\\
573         \ \\
574         However, this might be difficult in case of short run times, because the run may have finished before you have entered the commands!
575         };}
576         \coordinate[below=0.3cm of box3] (A);
577         \uncover<1->{\node [dummy, left=0.3cm of box3] (dummy2) {};}
578         \uncover<5->{\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};}
579         \uncover<6->{\node [yellow_big, left=2.5cm of A] (box4) {
580         \textbf{check, if the output files have sucessfully been transferred to the permanent directory:}\\
581         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING}\\
582         \texttt{ls -al}\\
583         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT}\\
584         \texttt{ls -al}
585};}
586         \draw<2-> [->,color=blue] (box1.east) -- (box2.west);   
587         \draw<4-> [->,color=blue] (box2.south) -- (box3.north); 
588         \draw<5-> [-,color=blue] (box3.south) -- (A); 
589         \draw<5-> [->,color=blue] (A) -- (box4.east);   
590           \end{tikzpicture}
591        \end{center}
592\end{frame}
593
594% Folie 14
595\begin{frame}
596   \frametitle{PALM \textit{Batch} Example Run (on HLRN, remote) Using \texttt{mrun}: Tracing the Run by the User}
597\tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, font=\Tiny]
598\tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.4\textwidth, font=\Tiny]
599\tikzstyle{dummy} = [text width=0.2\textwidth, font=\Tiny]
600\tikzstyle{alert} = [rectangle, draw, text width=0.5\textwidth, font=\scriptsize]
601\tikzstyle{line} = [draw, -latex']
602\begin{itemize}
603   \item Reminder: Running batch jobs requires a directory \texttt{~/job\underline{ }queue} for the job protocol files on the local \underline{and} remote host.
604\end{itemize}
605\begin{tikzpicture}[auto, node distance=0]
606    \node [yellow] (first) {
607       \textbf{start job on local machine:}\\
608       \texttt{mrun -d example\underline{ }cbl -h lcsgih ...}
609    };
610\uncover<2->{
611    \node [dummy, right=0.5cm of first] (dummy) {
612       transfer of job by \texttt{scp} \\
613       \ \\
614       \ \\
615       submit of job by executing the \texttt{msub} command via \texttt{ssh}
616    };
617}
618\uncover<3->{
619    \node [green, right=3.5cm of first] (second) {
620       \textbf{follow job execution on remote host, by} \\
621       \texttt{showq} (better: \texttt{showq | grep hzkurs})
622    };
623}
624\uncover<4->{
625    \node [green, below=0.2cm of second] (third) {
626       \textbf{if job is running, you may follow its progress by watching the job protocol:} \\ 
627       \texttt{cd \~/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
628    };
629}
630\uncover<5->{
631    \node [green, below=0.2cm of third] (fourth) {
632       \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}\\
633       \texttt{tail -f RUN\underline{ }CONTROL}
634    };
635}
636\uncover<6->{
637    \node [green, below=0.2cm of fourth] (fifth) {
638       \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\
639       \texttt{cd \~/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}
640    };
641}
642\uncover<7->{
643    \node [dummy, left=0.5cm of fifth] (dummy) {
644       transfer results by \texttt{scp} \\
645       \ \\
646       \ \\
647    };
648}
649\uncover<8->{
650    \node [yellow, left=3.5cm of fifth] (sixth) {
651       \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\
652       \texttt{cd \~/job\underline{ }queue \\ ls -al \\ cd ~/palm/current\underline{ }version/JOBS/example \\ ls -al *}
653    };
654}
655\uncover<9->{
656     \node [alert, below=0.5cm of first.south east] (alert) {
657        \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 mrun and subjob script!}
658     };
659}
660    \path<2-> [line] (first) -- (second);
661    \path<4-> [line] (second) -- (third);
662    \path<5-> [line] (third) -- (fourth);
663    \path<6-> [line] (fourth) -- (fifth);
664    \path<7-> [line] (fifth) -- (sixth);
665\end{tikzpicture}
666\end{frame}
667
668
669
670% Folie 15
671\begin{frame}
672   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
673   \tikzstyle{green_small} = [rectangle, draw, fill=green!20, text width=0.12\textwidth, font=\scriptsize, minimum height=0.6cm]
674   \tikzstyle{yellow_small} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\scriptsize, minimum height=0.6cm]
675   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm]
676   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
677   \tikzstyle{notes} = [rectangle, text width=0.15\textwidth, font=\scriptsize, minimum height=0.6cm]
678   
679   \frametitle{PALM Runs Using \texttt{mrun}: Further Details}
680   \begin{itemize}
681      \footnotesize
682      \item<2-> For every (initial) run, \texttt{mrun} creates a source directory which contains copies of
683      \begin{itemize}
684         \footnotesize
685         \item<4-> those source code files to be translated (always the main program, \texttt{palm.f90}, plus user interface files)
686         \item<4-> the Makefile
687         \item<5-> the configuration file
688         \item<6-> the mrun script
689      \end{itemize}
690   \end{itemize}
691   
692   \vspace{-0.8cm}
693   \begin{center}
694           \begin{tikzpicture}[auto, node distance=0]
695           
696         \uncover<3->{\node [yellow_small] (box1) {\$HOME/};}
697         \uncover<3->{\node [yellow_small, right=0.2cm of box1] (box2) {palm/};}
698         \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\underline{ }version/};}
699         \uncover<3->{\node [green_small, right=0.4cm of box3] (box4) {trunk/};}
700         
701         \uncover<1->{\node [dummy, right=1.0cm of box4] (dummy1) {};}
702         
703         \uncover<3->{\node [green_small, above=-0.2cm of dummy1] (box5) {SCRIPTS};}
704         \uncover<3->{\node [green_small, below=-0.2cm of dummy1] (box6) {SOURCE};}
705         
706         \uncover<6->{\node [notes, right=0.1cm of box5] (notes1) {\texttt{mrun}};}
707         \uncover<4->{\node [notes, right=0.1cm of box6] (notes2) {\texttt{Makefile \\ palm.f90}};}
708         \uncover<5->{\node [notes, below=0.1cm of box3] (notes3) {\texttt{.mrun.config}};}
709         
710         \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\underline{ }FOR\underline{ }RUN\underline{ }$<$run\underline{ }identifier$>$};}
711         
712         \uncover<1->{\node [dummy, left=1.5cm of box7] (dummy2) {};}
713         \uncover<1->{\node [dummy, right=2.0cm of box5] (dummy3) {};}
714         \uncover<1->{\node [dummy, right=1.8cm of box6] (dummy4) {};}
715         \uncover<1->{\node [dummy, below=0.2cm of dummy4] (dummy5) {};}
716         \draw<3-> [-] (box1.east) -- (box2.west); 
717         \draw<3-> [-] (box2.east) -- (box3.west); 
718         \draw<3-> [-] (box3.east) -- (box4.west); 
719         \draw<3-> [-] (box4.east) -- (box5.west); 
720         \draw<3-> [-] (box4.east) -- (box6.west);     
721         \draw<3-> [-] (box3.east) -- (box7.west);   
722         \draw<6-> [-] ([xshift=-0.8cm]notes1.east) -- (dummy3.center);   
723         \draw<4-> [-] ([xshift=-0.4cm]notes2.east) -- (dummy4.center);
724         \draw<4-> [-] (dummy4.center) -- ([yshift=0.1cm]dummy5.center);
725         \draw<4-> [->] ([yshift=0.1cm]dummy5.center) -- ([yshift=0.1cm]box7.east);
726         \draw<6-> [-] (dummy3.center) -- ([xshift=0.2cm, yshift=-0.1cm]dummy5.center);
727         \draw<6-> [->] ([xshift=0.2cm, yshift=-0.1cm]dummy5.center) -- ([yshift=-0.1cm]box7.east);
728         \draw<5-> [-] ([yshift=0.3cm]dummy2.center) -- (dummy2.center);   
729         \draw<5-> [->] (dummy2.center) -- (box7.west);   
730           \end{tikzpicture}
731        \end{center}
732   
733   \begin{itemize}
734      \footnotesize
735      \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.
736   \end{itemize}
737\end{frame}
738
739\end{document}
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