Changeset 1515 for palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex
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- Jan 2, 2015 11:35:51 AM (9 years ago)
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palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex
r973 r1515 6 6 \usepackage{ngerman} 7 7 \usepackage{pgf} 8 \usetheme{Dresden}9 8 \usepackage{subfigure} 10 9 \usepackage{units} … … 27 26 \ttfamily,showstringspaces=false,captionpos=b} 28 27 29 \institute{Institut fÃŒr Meteorologie und Klimatologie, Leibniz UniversitÀt Hannover} 28 \institute{Institute of Meteorology and Climatology, Leibniz UniversitÀt Hannover} 29 \selectlanguage{english} 30 30 \date{last update: \today} 31 31 \event{PALM Seminar} … … 47 47 48 48 \title[Carrying out restart runs with mrun]{Carrying out restart runs with \texttt{mrun}} 49 \author{ Siegfried Raasch}49 \author{PALM group} 50 50 51 51 \begin{document} … … 67 67 \begin{itemize} 68 68 \item<1-> A \textbf{ârestart runâ} is a model run, which starts with an initial condition given by the simulated flow at the end of a previous (restart or initial) run. 69 \item<2-> In order to carry out a restart run, a file has to be written at the end of the previous run, which contains the values of all flow variables at the necessary time steps (Runge-Kutta: $t$, leap-frog: $t$, $t-\Delta t$). This file has to be read at the beginning of the restart run.69 \item<2-> In order to carry out a restart run, a file has to be written at the end of the previous run, which contains the values of all flow variables at the last time step. This file has to be read at the beginning of the restart run. 70 70 \item<3-> Initial and respective restart runs form a so called \textbf{job chain}. 71 71 \end{itemize} … … 121 121 \quad \texttt{mrun -d test ... -r \dq d3f restart\dq}\\ 122 122 \vspace{1mm} 123 on the \textbf{local host}. Options of this command are nearly the same as of the initial run, but every sharp symbol(\grqq\#\grqq) in the activating strings is replaced by an \grqq f\grqq.123 on the \textbf{local host}. Options of this command are nearly the same as of the initial run, but every sharp character (\grqq\#\grqq) in the activating strings is replaced by an \grqq f\grqq. 124 124 \end{itemize} 125 125 \scriptsize … … 190 190 \vspace{-1mm} 191 191 \begin{itemize} 192 \item<1-> Typically, the binary restart files are very large, so that they cannot be stored in the user's home-directory because of limited filequotas. Also, hard disks where \texttt{/home} is stored are typically very slow, so that the copy process needs very long time.192 \item<1-> Typically, the binary restart files are very large, so that they cannot be stored in the user's home-directory because of limited disk quotas. Also, hard disks where \texttt{/home} is stored are typically very slow, so that the copy process needs very long time. 193 193 \vspace{1mm} 194 194 \item<2-> Using the file attribute \texttt{fl} (abbreviation for german \grqq Fortsetzungslauf\grqq) in the output file connection statement causes \texttt{mrun} to copy the local file to a special directory, which can be defined in the configuration file by the environment variable \texttt{tmp\underline{ }data\underline{ }catalog}. The permanent file described in the connection statement is also created, but it is \textbf{empty}. 195 195 \vspace{1mm} 196 \item<3-> At the end of the job, the second last cycle of the respective file with attribute \texttt{fl} is automatically deleted by \texttt{mrun} from the \texttt{tmp\underline{ }data\underline{ }catalog} in order to s pare disc space. This can be prevented by setting the\texttt{mrun}-option \grqq\texttt{-k}\grqq (keep data from previous run).196 \item<3-> At the end of the job, the second last cycle of the respective file with attribute \texttt{fl} is automatically deleted by \texttt{mrun} from the \texttt{tmp\underline{ }data\underline{ }catalog} in order to save disk space. This can be switched off with \texttt{mrun}-option \grqq\texttt{-k}\grqq (keep data from previous run). 197 197 \end{itemize} 198 198 \end{columns} … … 200 200 \onslide<4-> \textbf{Example:}\\ 201 201 \tiny \quad \texttt{\%base\underline{ }data\hspace{4.5em}\~{}/palm/current\underline{ }version/JOBS}\\ 202 \tiny \quad \texttt{\%tmp\underline{ }data\underline{ }catalog\hspace{1.0em}/gfs 2/work/niksiraa/palm\underline{ }restart\underline{ }data}\\202 \tiny \quad \texttt{\%tmp\underline{ }data\underline{ }catalog\hspace{1.0em}/gfs1/work/niksiraa/palm\underline{ }restart\underline{ }data}\\ 203 203 \vspace{1mm} 204 204 \tiny \quad \texttt{BINOUT\hspace{1.0em}out:loc:flpe\hspace{1.0em}restart\hspace{1.0em}\$base\underline{ }data/\$fname/RESTART\hspace{1.0em}\underline{ }d3d}\\ 205 205 \ \\ 206 206 \onslide<5-> \scriptsize \textbf{Files (directories) created when using \texttt{-d example\underline{ }cbl}:} \\ 207 \tiny \quad \texttt{/gfs 2/work/niksiraa/palm\underline{ }restart\underline{ }data/example\underline{ }cbl\underline{ }d3d}\\207 \tiny \quad \texttt{/gfs1/work/niksiraa/palm\underline{ }restart\underline{ }data/example\underline{ }cbl\underline{ }d3d}\\ 208 208 \tiny \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example/RESTART/example\underline{ }cbl\underline{ }d3d \# empty file (directory)}\\ 209 209 \vspace{2mm} 210 \onslide<6-> \scriptsize \textcolor{red}{Concerning input files, \texttt{mrun} always determines the current cycle number to be \underline{used from the contents of the directory definedby the file connection}\\ \underline{statement!}}210 \onslide<6-> \scriptsize \textcolor{red}{Concerning input files, \texttt{mrun} always determines the current cycle number to be \underline{used from the contents of the directory given by the file connection}\\ \underline{statement!}} 211 211 212 212 \end{frame} … … 214 214 215 215 % Folie 8 216 \begin{frame} 216 \begin{frame}[fragile] 217 217 \frametitle{Checking the Restart Job Execution} 218 \scriptsize 218 \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=1.2\textwidth, font=\Tiny,scale=0.8] 219 \scriptsize 220 \vspace{-40mm} 219 221 \begin{itemize} 220 222 \item essentially by looking at the messages in the job protocol file: 221 223 \end{itemize} 222 223 224 \centering 224 \includegraphics[width=0.93\textwidth]{restarts_with_mrun_figures/checking.png}225 225 \begin{tikzpicture}[remember picture, overlay] 226 \node[rectangle, draw,text width=0.29\textwidth, fill=white] at (-18mm,62mm) {\noindent \scriptsize In this example, restart time has been set 226 \node [yellow] (terminal) at (0mm,-30mm) {\begin{lstlisting} 227 *** execution starts in directory 228 "/gfs1/work/nikleboe/nikleboe.21239" 229 ---------------------------------------------------------------------------- 230 . 231 . 232 run will be terminated due to user settings of 233 restart_time / dt_restart 234 new restart time is: 3600. s 235 . 236 . 237 ---------------------------------------------------------------------------- 238 *** execution finished 239 . 240 . 241 ---------------------------------------------------------------------------- 242 *** all OUTPUT-files saved 243 244 245 *** initiating restart-run on "130.75.105.111" using command: 246 mrun -c.mrun.config -dexample_cbl -hlccrayh -Hlcmuk -m1500 -t3600 -qmpp1testq -R130.75.105.111 -Uboeske ... 247 248 ---------------------------------------------------------------------------- 249 *** ssh will be used to initiate restart-runs! 250 . 251 . 252 *** MRUN 2.1 Rev: 1358 $ 253 will be executed. Please wait ... 254 #------------------------------------------------------------------------# 255 | MRUN 2.1 Rev: 1358 $ Thu Jun 31 14:09:30 CEST 2014 | 256 | | 257 | called on: vaudaire | 258 . 259 . 260 | Files to be compiled: | 261 | palm.f90 user_example.f90 | 262 #------------------------------------------------------------------------# 263 . 264 . 265 ---------------------------------------------------------------------------- 266 *** restart-run initiated 267 268 269 --> all actions finished 270 271 Bye, bye nikleboe !! 272 \end{lstlisting} 273 }; 274 \node[rectangle, draw,text width=0.29\textwidth, fill=white] at (35mm,-5mm) {\noindent \scriptsize In this example, restart time has been set 227 275 228 276 manually by the user.}; … … 239 287 \column{1.07\textwidth} 240 288 \begin{itemize} 241 \item<1-> By default, PALM checks after every timestep, if enough time remains from the job cpu limit to carry out the next timestep:\\242 \vspace{1mm} 243 (\quad \ grqq\texttt{total job time}\grqq\, - \grqq\texttt{time already consumed}\grqq\,) \texttt{<=} \texttt{termination\underline{ }time\underline{ }needed}\\244 ( as given by \texttt{mrun}-option \texttt{-t} ...) \hspace{5mm} (as given by parameter in \texttt{\&d3par}-NAMELIST)\\289 \item<1-> By default, PALM checks after every timestep, if enough time remains from the job's cpu limit to carry out the next timestep:\\ 290 \vspace{1mm} 291 (\quad \textcolor{red}{\grqq\texttt{total job time}\grqq\,} - \grqq\texttt{time already consumed}\grqq\,) \texttt{<=} \textcolor{blue}{\texttt{termination\underline{ }time\underline{ }needed}}\\ 292 (\textcolor{red}{as given by \texttt{mrun}-option \texttt{-t} ...}) \hspace{5mm} (\textcolor{blue}{as given by parameter in \texttt{\&d3par}-NAMELIST})\\ 245 293 \vspace{3mm} 246 294 \item<2-> \texttt{termination\underline{ }time\underline{ }needed} has to include the cpu time needed before running PALM (e.g. for compilation, copying of input data, etc.; default value: 300 s)!\\ … … 249 297 \vspace{1mm} 250 298 \quad \quad \grqq\texttt{total job time}\grqq\, \texttt{<=} \texttt{termination\underline{ }time\underline{ }needed},\\ 251 \quad forces a restart after the firsttimestep!299 \quad forces a restart after every timestep! 252 300 \vspace{3mm} 253 301 \item<4-> \texttt{\&d3par}-parameters \texttt{restart\underline{ }time} and \texttt{dt\underline{ }restart} can be used to set restart time(s) manually.\\
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