Changeset 973 for palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex
- Timestamp:
- Aug 7, 2012 4:03:47 PM (12 years ago)
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palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex
r949 r973 93 93 94 94 95 % Folie 4 (Zu voll)?95 % Folie 4 96 96 \begin{frame} 97 97 \frametitle{Carrying Out Restart Runs With \texttt{mrun}} 98 98 \scriptsize 99 100 Concerning \texttt{mrun}, the first thing required to enable restart runs is to use the additional activating string \grqq \texttt{restart}\grqq\, in the \texttt{mrun}-call for the \underline{initial run}:\\ 101 \quad \texttt{mrun -d test ... -r ''d3\# restart''}\\ 102 This will have the following effects: 103 \vspace{2mm} 104 \begin{itemize} 105 \item<2-> At the end of the run, all necessary variables will bei written as binary data to the local file \texttt{BINOUT}. This is caused by an entry in the configuration file\\ 106 \quad \texttt{\%write\underline{ }binary true restart}\\ 107 which sets the environment variable \texttt{write\underline{ }binary}, which is in turn read by PALM from the local file \texttt{ENVPAR} created by \texttt{mrun}. 108 \item<3-> This binary file will be permanently stored in case that an appropriate file connection statement exists\\ 109 \begin{columns} 110 \column{1.05\textwidth} 111 \texttt{BINOUT out:loc:flpe restart \~{}/palm/current\underline{ }version/JOBS/\$fname/RESTART \underline{ }d3d} 112 \end{columns} 113 \item<4-> If, during the run, PALM detects that the simulation cannot be finished due to limited job time, it tells \texttt{mrun} (by creating a local file named \texttt{CONTINUE\underline{ }RUN}) that a restart job has to be started. \texttt{mrun} will then automatically start such a job by submitting the command\\ 114 \quad \texttt{mrun -d test ... -r ''d3f restart''}\\ 115 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. 116 \end{itemize} 117 \onslide<5->\textcolor{red}{\textbf{This effects the activation of file connections for the restart job!}} 99 \begin{columns}[T] 100 \begin{column}{1.0\textwidth} 101 Concerning \texttt{mrun}, the first thing required to enable restart runs is to use the additional activating string \grqq \texttt{restart}\grqq\, in the \texttt{mrun}-call for the \underline{initial run}:\\ 102 \vspace{1mm} 103 \quad \texttt{mrun -d test ... -r \dq d3\# restart\dq}\\ 104 \ \\ 105 This will have the following effects: 106 \vspace{1mm} 107 \tiny 108 \begin{itemize} 109 \item<2-> At the end of the run, all necessary variables will bei written as binary data to the local file \texttt{BINOUT}. This is caused by an entry in the configuration file\\ 110 \vspace{1mm} 111 \quad \texttt{\%write\underline{ }binary true restart}\\ 112 \vspace{1mm} 113 which sets the environment variable \texttt{write\underline{ }binary}, which is in turn read by PALM from the local file \texttt{ENVPAR} created by \texttt{mrun}. 114 \vspace{3mm} 115 \item<3-> This binary file will be permanently stored in case that an appropriate file connection statement exists\\ 116 \vspace{1mm} 117 \quad \texttt{BINOUT out:loc:flpe restart \~{}/palm/current\underline{ }version/JOBS/\$fname/RESTART \underline{ }d3d} 118 \vspace{3mm} 119 \item<4-> If, during the run, PALM detects that the simulation cannot be finished due to limited job time, it tells \texttt{mrun} (by creating a local file named \texttt{CONTINUE\underline{ }RUN}) that a restart job has to be started. \texttt{mrun} will then automatically start such a job by submitting the command\\ 120 \vspace{1mm} 121 \quad \texttt{mrun -d test ... -r \dq d3f restart\dq}\\ 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. 124 \end{itemize} 125 \scriptsize 126 \vspace{2mm} 127 \onslide<5->\textcolor{red}{\textbf{This effects the activation of file connections for the restart job!}} 128 \end{column} 129 \end{columns} 130 118 131 \end{frame} 119 132 … … 131 144 \begin{itemize} 132 145 \item<2-> For the restart job, the model receives a different parameter file than for the initial job (e.g. \texttt{example\underline{ }cbl\underline{ }p3d\textcolor{blue}{f}} instead of \texttt{example\underline{ }cbl\underline{ }p3d}).\\ 133 \vspace{ 2mm}146 \vspace{4mm} 134 147 The parameter file for the restart job is nearly the same as for the initial run, but it must contain the parameter setting\\ 148 \vspace{1mm} 135 149 \quad \texttt{initializing\underline{ }actions = 'read\underline{ }restart\underline{ }data'}\\ 150 \vspace{1mm} 136 151 in the \texttt{\&inipar}-NAMELIST-group. All other \texttt{\&inipar}-parameter-settings are ignored!\\ 137 \vspace{ 2mm}152 \vspace{4mm} 138 153 \texttt{\&d3par}-parameter values can freely be changed compared with the parameter file for the initial run.\\ 139 154 \vspace{4mm} 140 \item<3-> Input binary data file (\texttt{BININ}) is necessary (and available) only for restart jobs155 \item<3-> Input binary data file (\texttt{BININ}) is necessary (and available) only for\\ restart jobs 141 156 \end{itemize} 142 157 \end{frame} … … 167 182 168 183 169 % Folie 7 (Zu voll?)184 % Folie 7 170 185 \begin{frame} 171 186 \frametitle{Handling of Large Binary Data Files} … … 173 188 \begin{columns} 174 189 \column{1.1\textwidth} 190 \vspace{-1mm} 175 191 \begin{itemize} 176 192 \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 file quotas. Also, hard disks where \texttt{/home} is stored are typically very slow, so that the copy process needs very long time. 193 \vspace{1mm} 177 194 \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 \vspace{1mm} 178 196 \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 spare disc space. This can be prevented by setting the \texttt{mrun}-option \grqq\texttt{-k}\grqq (keep data from previous run). 179 197 \end{itemize} 180 198 \end{columns} 181 \ \\199 \vspace{2mm} 182 200 \onslide<4-> \textbf{Example:}\\ 183 201 \tiny \quad \texttt{\%base\underline{ }data\hspace{4.5em}\~{}/palm/current\underline{ }version/JOBS}\\ … … 189 207 \tiny \quad \texttt{/gfs2/work/niksiraa/palm\underline{ }restart\underline{ }data/example\underline{ }cbl\underline{ }d3d}\\ 190 208 \tiny \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example/RESTART/example\underline{ }cbl\underline{ }d3d \# empty file (directory)}\\ 191 \vspace{ 1mm}192 \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 defined by the file connection 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 defined by the file connection}\\ \underline{statement!}} 193 211 194 212 \end{frame} … … 222 240 \begin{itemize} 223 241 \item<1-> By default, PALM checks after every timestep, if enough time remains from the job cpu limit to carry out the next timestep:\\ 224 \quad \grqq\texttt{total job time}\grqq\, - \grqq\texttt{time already consumed}\grqq\, $\leftarrow$ \texttt{termination\underline{ }time\underline{ }needed}\\ 225 (as given by \texttt{mrun}-option \texttt{-t} ...) \hspace{5mm} (as given by parameter in \texttt{\&d3par}-NAMELIST) 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)\\ 245 \vspace{3mm} 226 246 \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)!\\ 227 247 \ \\ 228 248 \onslide<3-> \textbf{Warning:}\\ 229 \quad \quad \grqq\texttt{total job time}\grqq\, $\leftarrow$ \texttt{termination\underline{ }time\underline{ }needed},\\ 249 \vspace{1mm} 250 \quad \quad \grqq\texttt{total job time}\grqq\, \texttt{<=} \texttt{termination\underline{ }time\underline{ }needed},\\ 230 251 \quad forces a restart after the first timestep! 231 \item<4-> \texttt{\&d3par}-parameters \texttt{restart\underline{ }time} and \texttt{dt\underline{ }restart} can be used to set restart time(s) manually. 232 \item<5-> In case of manually setting the restart time, the default checking (see above) is still active and a restart will be automatically forced if the job reaches its cpu limit, even if the manually set restart time has not been reached! 252 \vspace{3mm} 253 \item<4-> \texttt{\&d3par}-parameters \texttt{restart\underline{ }time} and \texttt{dt\underline{ }restart} can be used to set restart time(s) manually.\\ 254 \vspace{3mm} 255 \item<5-> In case of manually setting the restart time, the default checking (see above) is still active and a restart will be automatically forced if the job reaches its cpu limit, even if the manually set restart time has not been reached!\\ 233 256 \end{itemize} 234 257 \end{columns} … … 243 266 \item<1-> After a job has finished (\texttt{end\underline{ }time} has been reached), the user can submit a restart job manually (provided that restart data have been saved) by entering:\\ 244 267 \vspace{2mm} 245 \quad \texttt{mrun ... -r ''d3f ...''...}\\268 \quad \texttt{mrun ... -r \dq d3f ...\dq\, ...}\\ 246 269 or\\ 247 \quad \texttt{mrun ... -r ''d3f restart ...''...}\\270 \quad \texttt{mrun ... -r \dq d3f restart ...\dq\, ...}\\ 248 271 \ \\ 249 272 \item<2-> Remember to increase the value of \texttt{end\underline{ }time} in the parameter file before submitting the job. 273 \vspace{2mm} 250 274 \item<3-> If a manually started restart job shall continue a run of a former job chain which is somewhere in the middle of this chain, all binary files with respective higher cycle numbers have to be deleted or removed from their respective directories. 251 275 \end{itemize}
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