Changeset 1649 for palm/trunk
- Timestamp:
- Sep 15, 2015 4:34:42 PM (9 years ago)
- Location:
- palm/trunk
- Files:
-
- 13 edited
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SCRIPTS/mbuild (modified) (1 diff)
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SCRIPTS/mrun (modified) (1 diff)
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TUTORIAL/SOURCE/exercise_cbl.tex (modified) (2 diffs)
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TUTORIAL/SOURCE/exercise_cumulus.tex (modified) (1 diff)
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TUTORIAL/SOURCE/exercise_topography.tex (modified) (1 diff)
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TUTORIAL/SOURCE/final_remarks.tex (modified) (3 diffs)
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TUTORIAL/SOURCE/fundamentals_of_les.tex (modified) (1 diff)
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TUTORIAL/SOURCE/installation.tex (modified) (2 diffs)
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TUTORIAL/SOURCE/mrun_steering_parameters.tex (modified) (1 diff)
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TUTORIAL/SOURCE/ncl.tex (modified) (2 diffs)
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TUTORIAL/SOURCE/numerics_bc.tex (modified) (1 diff)
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TUTORIAL/SOURCE/program_control.tex (modified) (4 diffs)
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TUTORIAL/SOURCE/user_defined_code.tex (modified) (2 diffs)
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palm/trunk/SCRIPTS/mbuild
r1623 r1649 1 #!/bin/ bash1 #!/bin/ksh 2 2 3 3 # mbuild - script for compiling the PALM code and its utility programs -
palm/trunk/SCRIPTS/mrun
r1623 r1649 1 #!/bin/ksh 1 #!/bin/ksh 2 2 3 3 # mrun - script for running PALM jobs -
palm/trunk/TUTORIAL/SOURCE/exercise_cbl.tex
r1534 r1649 165 165 \onslide<2-> You will find some more detailed information to solve this exercise in the PALM-online-documentation under:\\ 166 166 \ \\ 167 \small\url{http://palm.muk.uni-hannover.de/ wiki/doc/app/examples/cbl}\\167 \small\url{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/examples/cbl}\\ 168 168 \ \\ 169 169 \normalsize (Attention: This documentation is for atmospheric convection with free upper lid.) … … 172 172 \onslide<3-> \normalsize Please also visit\\ 173 173 \ \\ 174 \small\url{http://palm.muk.uni-hannover.de/ wiki/doc/app/netcdf}\\174 \small\url{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/netcdf}\\ 175 175 \ \\ 176 176 \normalsize where the complete PALM netCDF-data-output and the respective steering parameters are described. -
palm/trunk/TUTORIAL/SOURCE/exercise_cumulus.tex
r1544 r1649 214 214 \item<5-> Do not forget to adapt \texttt{user\_check\_data\_output\_pr} (for defining your user-profiles) and your parameter file (\texttt{userpar} namelist) for the output (with the parameter \texttt{data\_output\_pr\_user = 'your\_profile'})! 215 215 \item<6-> Check the online documentation of PALM for more detailed information on the implementation of user profiles:\\ 216 \texttt{\hphantom{aaa}http://palm.muk.uni-hannover.de/ wiki/doc/app/userint/output\#part\_1}\\216 \texttt{\hphantom{aaa}http://palm.muk.uni-hannover.de/trac/wiki/doc/app/userint/output\#part\_1}\\ 217 217 Further examples are also provided within the subroutines \texttt{user\_statistics} and \texttt{user\_check\_data\_output\_pr}. 218 218 -
palm/trunk/TUTORIAL/SOURCE/exercise_topography.tex
r1541 r1649 190 190 \scriptsize 191 191 Please see under \\ 192 \textbf{http://palm.muk.uni-hannover.de/ wiki/doc/app/netcdf} \\192 \textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/netcdf} \\ 193 193 \par\medskip 194 194 where the complete PALM netCDF-data-output and the respective steering parameters are described. 195 195 \par\medskip 196 196 For topography, see \\ 197 \textbf{http://palm.muk.uni-hannover.de/ wiki/doc/app/inipar\#topo}\\197 \textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/inipar\#topo}\\ 198 198 \par\medskip 199 199 and especially for raster topography, see also 200 \textbf{http://palm.muk.uni-hannover.de/ wiki/doc/app/iofiles\#TOPOGRAPHY\_DATA} \\200 \textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/iofiles\#TOPOGRAPHY\_DATA} \\ 201 201 \par\medskip 202 202 as well as the presentation ''Using topography (I)''. -
palm/trunk/TUTORIAL/SOURCE/final_remarks.tex
r1531 r1649 100 100 \vspace{-2mm} 101 101 \begin{itemize} 102 \item<2->{... about application for urban flows: \\ \par\medskip 102 \item<2->{... about the current model status (PALM 4.0) \\ \par\medskip 103 \tiny{\textbf{Maronga, B., Gryschka, M., Heinze, R., Hoffmann, F., Kanani-SÃŒhring, F., Keck, M., Ketelsen, K., Letzel, M. O., SÃŒhring, M., and Raasch, S., 2015}: The Parallelized Large-Eddy Simulation Model (PALM) 104 version 4.0 for atmospheric and oceanic flows: model formulation, recent developments, and future perspectives, Geosci. Model Dev., 8, 2515-2551, doi:10.5194/gmd-8-2515-2015. 105 \item<3->{... about application for urban flows: \\ \par\medskip 103 106 \tiny{\textbf{Letzel, M.O., M. Krane and S. Raasch, 2008}: High resolution urban large-eddy simulation studies 104 from street canyon to neighbourhood scale, Atmos. Env., 42, 8770-8784, doi:10.1016/j.atmosenv.2008.08.001. \\ 105 \textbf{Contact person}: Marius Keck keck@muk.uni-hannover.de}} 106 \item<3->{... about non-cyclic boundary conditions: \\ \par\medskip 107 from street canyon to neighbourhood scale, Atmos. Env., 42, 8770-8784, doi:10.1016/j.atmosenv.2008.08.001. 108 \item<4->{... about non-cyclic boundary conditions: \\ \par\medskip 107 109 \tiny{\textbf{Gryschka, M. and S. Raasch, 2005}: Roll Convection During a Cold Air Outbreak: A Large Eddy Simulation with Stationary Model Domain. 108 110 Geophys. Res. Lett., 32, L14805, doi:10.1029/2005GL022872. \\ \par\medskip 109 111 \textbf{Gryschka, M., C. DrÃŒe, D. Etling and S. Raasch. 2008}: On the influence of sea-ice inhomogeneities onto roll convection in 110 cold-air outbreaks, Geophys. Res. Lett., 35, L23804, doi:10.1029/2008GL035845.\\ 111 \textbf{Contact person}: Micha Gryschka gryschka@muk.uni-hannover.de}} 112 \item<4->{... about the Lagrangian particle model: \\ \par\medskip 112 cold-air outbreaks, Geophys. Res. Lett., 35, L23804, doi:10.1029/2008GL035845. 113 \item<5->{... about the Lagrangian particle model: \\ \par\medskip 113 114 \tiny{\textbf{Steinfeld, G., S. Raasch and T. Markkanen, 2008}: Footprints in homogeneously and heterogeneously driven boundary layers derived 114 115 from a Lagrangian stochastic particle model embedded into large-eddy simulation, Boundary-Layer Meteorol., 129, 225-248.\\ \par\medskip 115 \textbf{Riechelmann, T., Y. Noh and S. Raasch, 2012}: A new method for large-eddy simulations of clouds with Lagrangian droplets including the effects of turbulent collision., New J. Phys., 14, 065008.\\ 116 \textbf{Contact person}: Fabian Hoffmann hoffmann@muk.uni-hannover.de}} 117 \item<5->{... on our webpage: \\ 116 \textbf{Riechelmann, T., Y. Noh and S. Raasch, 2012}: A new method for large-eddy simulations of clouds with Lagrangian droplets including the effects of turbulent collision., New J. Phys., 14, 065008. 117 \item<6->{... on our webpage: \\ 118 118 \tiny{\textbf{http://palm.muk.uni-hannover.de}}} 119 \item< 6->{Current model status (PALM 4.0) will be published soon \\in \textit{Geoscientific Model Development}}119 \item<7->{Current model status (PALM 4.0) will be published soon \\in \textit{Geoscientific Model Development}} 120 120 \end{itemize} 121 121 \end{frame} … … 132 132 \item<4->{Read the online documentation.} 133 133 \item<5->{Discuss with colleagues (if you have).} 134 \item<6->{See the ticket system under \textbf{http://palm.muk.uni-hannover.de/ wiki/tickets} \\ if anyone reported a similar problem before.}135 \item<7->{Use the ticket system under \textbf{http://palm.muk.uni-hannover.de/ newticket} \\ and provide informations as detailed as possible134 \item<6->{See the ticket system under \textbf{http://palm.muk.uni-hannover.de/trac/wiki/tickets} \\ if anyone reported a similar problem before.} 135 \item<7->{Use the ticket system under \textbf{http://palm.muk.uni-hannover.de/trac/newticket} \\ and provide informations as detailed as possible 136 136 (revision number that you are using, job protocol with error message, parameter file, run control file, other relevant 137 137 output files, other relevant informations).} … … 146 146 \frametitle{PALM - Future Developments} 147 147 \begin{itemize} 148 \item<1->{ Hybrid MPI/OpenACC mode running on multiple GPUs}148 \item<1->{Immersed boundary layer method / viscous topography} 149 149 \vspace{5mm} 150 \item<2->{ Porting for Intel Xeon-Phi}150 \item<2->{Hybrid MPI/OpenACC mode running on multiple GPUs} 151 151 \vspace{5mm} 152 \item<3->{ Ready for deep convection using anelastic system of equations}152 \item<3->{Porting for Intel Xeon-Phi} 153 153 \vspace{5mm} 154 \item<4->{Nesting methods are under development} 154 \item<4->{Ready for deep convection using anelastic system of equations} 155 \vspace{5mm} 156 \item<5->{Nesting methods are under development} 155 157 \end{itemize} 156 158 \end{frame} -
palm/trunk/TUTORIAL/SOURCE/fundamentals_of_les.tex
r1526 r1649 163 163 \item<4->{\textbf{Problem:}} 164 164 \begin{itemize} 165 \item<4->{Limited computer resources (1996: $\sim$ $10^8$, today: $\sim$ $10^{1 1}$ gridpoints,165 \item<4->{Limited computer resources (1996: $\sim$ $10^8$, today: $\sim$ $10^{12}$ gridpoints, 166 166 but $\sim$ $10^{18}$ gridpoints needed, see prior slide).} 167 167 \item<4->{$\unit[1]{h}$ simulation of $10^9$ ($2048^3$) gridpoints on $512$ processors of the HLRN supercomputer needs $\unit[10]{h}$ CPU time.} -
palm/trunk/TUTORIAL/SOURCE/installation.tex
r1234 r1649 100 100 %\item<4->{We will start with installing PALM on a \textcolor{green}{local} computer and running it interactively.} 101 101 \item<4->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip 102 \url{http://palm.muk.uni-hannover.de/ wiki/doc/install}}102 \url{http://palm.muk.uni-hannover.de/trac/wiki/doc/install}} 103 103 \end{itemize} 104 104 \end{frame} … … 111 111 % \item<1->{The following slides describe the installation procedure for running PALM on a \textcolor{green}{local} computer and how to verify the installation.}\\ \par\medskip 112 112 % \item<2->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip 113 % \url{http://palm.muk.uni-hannover.de/ wiki/doc/install}}113 % \url{http://palm.muk.uni-hannover.de/trac/wiki/doc/install}} 114 114 % \end{itemize} 115 115 % \end{frame} -
palm/trunk/TUTORIAL/SOURCE/mrun_steering_parameters.tex
r1608 r1649 149 149 \begin{frame} 150 150 \frametitle{PALM - General Steering Parameters - Overview (II)} 151 \footnotesize A complete alphabetical list of all parameters can be found under: \url{http://palm.muk.uni-hannover.de/ wiki/doc/app/parlist}151 \footnotesize A complete alphabetical list of all parameters can be found under: \url{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/parlist} 152 152 153 153 \begin{itemize} -
palm/trunk/TUTORIAL/SOURCE/ncl.tex
r1532 r1649 280 280 configuration file \texttt{.ncl.config} or in the 281 281 documentation:\\ 282 \uncover<3->{\texttt{http://palm.muk.uni-hannover.de/ wiki/doc/app/nclparlist}}\\282 \uncover<3->{\texttt{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/nclparlist}}\\ 283 283 \vspace{2mm} 284 284 \item<4-> Parameters specified in the prompt override parameters given … … 439 439 look to the NCL documentation\\ 440 440 441 \quad \texttt{http://palm.muk.uni-hannover.de/ wiki/doc/app/nclparlist}\\441 \quad \texttt{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/nclparlist}\\ 442 442 443 443 for detailed information -
palm/trunk/TUTORIAL/SOURCE/numerics_bc.tex
r1515 r1649 685 685 \left. \frac{\partial \theta}{\partial z} \right\vert_{t=0}$$ 686 686 \item<3-> Pressure: Dirichlet $p=0$ 687 or Neumann $\dfrac{\partial p}{\partial z} = 0$687 ( Neumann $\dfrac{\partial p}{\partial z} = 0$ is better ) 688 688 \item<4-> SGS-TKE: Neumann $\dfrac{\partial e}{\partial z} = 0$ 689 689 \item<5-> A damping layer can be switched on in order to absorb -
palm/trunk/TUTORIAL/SOURCE/program_control.tex
r1515 r1649 301 301 \begin{tikzpicture}[scale=0.51, every node/.style={scale=0.51}] 302 302 \node [green]{\begin{lstlisting} 303 ****************************** 304 * PALM 3.10 Rev: 1443 *atmosphere - 3D - run without 1D - prerun305 ****************************** 306 307 Date: 30-07-14Run: example_cbl308 Time: 1 4:41:23Run-No.: 00309 Run on host: lccrayh310 Number of PEs: 8 Processor grid (x,y): ( 2, 4) calculated303 ****************************** -------------------------------------------- 304 * PALM 4.0 Rev: 1648 * atmosphere - 3D - run without 1D - prerun 305 ****************************** -------------------------------------------- 306 307 Date: 15-09-15 Run: example_cbl 308 Time: 17:34:44 Run-No.: 00 309 Run on host: lcmuk 310 Number of PEs: 4 Processor grid (x,y): ( 2, 2) calculated 311 311 ------------------------------------------------------------------------------ 312 312 . … … 391 391 \begin{tikzpicture}[scale=0.75, every node/.style={scale=0.75}] 392 392 \node [green]{\begin{lstlisting} 393 PALM 3.10 Rev: 1443 run: example_cbl.00 host: lccrayh 30-07-14 14:41:23393 PALM 4.0 Rev: 1648 run: example_cbl.00 host: lcmuk 15-09-15 17:34:44 394 394 ----------- 395 395 396 CPU measures for 8 PEs ( 2(x) * 4(y) tasks * 1 threads):396 CPU measures for 4 PEs ( 2(x) * 2(y) tasks * 1 threads): 397 397 398 398 gridpoints (x/y/z): 40 * 40 * 40 399 399 nr of timesteps: 253 400 cpu time per grid point and timestep: 0. 27546* 10**-6 s400 cpu time per grid point and timestep: 0.57070 * 10**-6 s 401 401 ---------------------------------------------------------------------- 402 402 … … 404 404 sec. % sec. sec. sec. 405 405 ------------------------------------------------------------------------------ 406 total 4.460 100.00 1 4.460 4.460 0.001 407 all progn.equations 2.943 65.98 759 2.905 2.982 0.028 408 pres 0.611 13.70 760 0.611 0.611 0.000 409 diffusivities 0.338 7.59 759 0.338 0.339 0.001 410 exchange-horiz-progn 0.146 3.28 759 0.108 0.185 0.028 411 calculate_timestep 0.118 2.64 253 0.070 0.125 0.018 412 flow_statistics 0.103 2.31 254 0.102 0.104 0.001 413 prandtl_fluxes 0.062 1.40 759 0.062 0.063 0.000 414 initialisation 0.062 1.39 1 0.061 0.061 0.001 415 data_output_2d 0.028 0.62 10 0.021 0.028 0.002 416 sum_up_3d_data 0.004 0.10 146 0.004 0.005 0.000 417 disturb_field 0.004 0.08 10 0.003 0.007 0.001 418 run_control 0.003 0.07 254 0.000 0.000 0.008 419 last actions 0.003 0.07 1 0.003 0.003 0.000 420 data_output_tseries 0.003 0.06 253 0.000 0.000 0.007 421 data_output_profiles 0.001 0.02 4 0.000 0.000 0.002 422 swap_timelevel 0.000 0.01 759 0.000 0.000 0.000 423 user_actions 0.000 0.01 759 0.000 0.000 0.000 406 total 9.241 100.00 1 9.241 9.241 0.000 407 all progn.equations 5.899 63.83 759 5.827 5.977 0.056 408 pres 1.508 16.32 760 1.506 1.508 0.002 409 diffusivities 0.632 6.84 759 0.624 0.642 0.006 410 exchange-horiz-progn 0.412 4.45 759 0.333 0.441 0.056 411 flow_statistics 0.270 2.92 254 0.269 0.271 0.001 412 calculate_timestep 0.205 2.21 253 0.150 0.223 0.031 413 prandtl_fluxes 0.150 1.63 759 0.148 0.153 0.002 414 sum_up_3d_data 0.016 0.17 146 0.016 0.016 0.000 415 initialisation 0.014 0.15 1 0.014 0.014 0.000 416 disturb_field 0.006 0.06 10 0.005 0.006 0.001 417 data_output_2d 0.004 0.04 10 0.003 0.004 0.000 418 data_output_tseries 0.003 0.04 253 0.000 0.000 0.006 419 run_control 0.003 0.03 254 0.000 0.000 0.005 420 swap_timelevel 0.001 0.01 759 0.001 0.001 0.000 421 last actions 0.001 0.01 1 0.000 0.001 0.000 424 422 average_3d_data 0.000 0.00 2 0.000 0.000 0.000 423 user_actions 0.000 0.00 759 0.000 0.000 0.000 424 data_output_profiles 0.000 0.00 4 0.000 0.000 0.000 425 425 426 426 special measures: 427 427 ------------------------------------------------------------------------------- 428 timesteps 4.391 98.45 253 4.391 4.3910.000429 poisfft 0. 441 9.90 760 0.440 0.443 0.001430 exchange_horiz 0. 233 5.22 6866 0.193 0.275 0.029431 fft_y 0.122 2.73 760 0.121 0.122 0.000 432 fft_ x 0.121 2.71 760 0.121 0.121 0.000433 transpo invers 0.084 1.89 760 0.084 0.085 0.000 434 transpo forward 0. 077 1.72 760 0.075 0.078 0.001435 mpi_alltoall 0. 063 1.42 4560 0.060 0.065 0.002436 divergence 0.043 0.97 1520 0.043 0.044 0.000 437 tridia 0.0 36 0.81 760 0.036 0.0360.000438 exchange_horiz_2d 0.0 21 0.47 3795 0.019 0.022 0.001428 timesteps 9.222 99.80 253 9.222 9.222 0.000 429 poisfft 0.871 9.42 760 0.868 0.873 0.002 430 exchange_horiz 0.588 6.37 6866 0.505 0.619 0.058 431 divergence 0.259 2.81 1520 0.258 0.261 0.001 432 fft_y 0.239 2.59 760 0.236 0.244 0.003 433 fft_x 0.238 2.58 760 0.236 0.243 0.002 434 transpo forward 0.195 2.12 760 0.187 0.202 0.006 435 mpi_alltoall 0.162 1.75 4560 0.148 0.169 0.008 436 transpo invers 0.113 1.22 760 0.109 0.114 0.002 437 tridia 0.083 0.90 760 0.082 0.084 0.000 438 exchange_horiz_2d 0.040 0.44 3795 0.034 0.046 0.005 439 439 \end{lstlisting} 440 440 }; … … 493 493 \item<1->{A detailed description of how to use PALM and a complete list of steering parameters and their meaning can be found on the PALM-server: \\ 494 494 \par\bigskip 495 \textbf{http://palm.muk.uni-hannover.de/ wiki/doc/toc}}495 \textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/toc}} 496 496 \par\bigskip 497 497 \item<2->{General information about the netCDF data format can be found under \\ -
palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex
r1531 r1649 516 516 \ \\ 517 517 See PALM online documentation under \\ 518 \textbf{http://palm.muk.uni-hannover.de/ wiki/doc/app/userint}\\518 \textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/userint}\\ 519 519 for detailed explanations. 520 520 … … 786 786 \item<6-> The online documentation gives very detailed instructions about how to modify the interface in order to output user-defined quantities under\\ 787 787 \vspace{1mm} 788 \textbf{http://palm.muk.uni-hannover.de/ wiki/doc/app/userint/output}788 \textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/app/userint/output} 789 789 \end{itemize} 790 790 \end{frame}
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