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program_control.tex @ 1828

Last change on this file since 1828 was 1649, checked in by knoop, 9 years ago
Latex lecture update for PALM seminar in Hong Kong
Property svn:keywords set to `Id`
File size: 24.3 KB

Rev	Line
[915]	1	% $Id: program_control.tex 1649 2015-09-15 16:34:42Z maronga $
	2	\input{header_tmp.tex}
[954]	3	%\input{header_LECTURE.tex}
[915]	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,decorations.pathreplacing}
	16	\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
[1515]	17	\def\Tinytwo{\fontsize{3pt}{3pt}\selectfont}
[915]	18
	19	%---------- neue Pakete
	20	\usepackage{amsmath}
	21	\usepackage{amssymb}
	22	\usepackage{multicol}
	23	\usepackage{pdfcomment}
[1515]	24	\usepackage{listings}
	25	\lstset{showspaces=false,language=fortran,basicstyle=
	26	\ttfamily,showstringspaces=false, captionpos=b,aboveskip=0pt,belowskip=0pt}
[915]	27
[1515]	28	\institute{Institute of Meteorology and Climatology, Leibniz UniversitÃ€t Hannover}
	29	\selectlanguage{english}
[915]	30	\date{last update: \today}
	31	\event{PALM Seminar}
	32	\setbeamertemplate{navigation symbols}{}
	33
	34	\setbeamertemplate{footline}
	35	{%
	36	\begin{beamercolorbox}[rightskip=-0.1cm]&
	37	{\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}}
	38	\end{beamercolorbox}
	39	\begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,%
	40	leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}%
	41	{\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}%
	42	\end{beamercolorbox}%
	43	% \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}%
	44	% \end{beamercolorbox}
	45	}%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.eps}}
	46
	47	\title[Program Control by Physical Parameters]{Program Control by Physical Parameters}
[1515]	48	\author{PALM group}
[915]	49
	50	% Notes:
	51	% jede subsection bekommt einen punkt im menu (vertikal ausgerichtet.
	52	% jeder frame in einer subsection bekommt einen punkt (horizontal ausgerichtet)
	53	\begin{document}
[945]	54	% Folie 1
[915]	55	\begin{frame}
	56	\titlepage
	57	\end{frame}
	58
[1515]	59	\section{Program Control by Physical Parameters}
	60	\subsection{Program Control by Physical Parameters}
	61
[945]	62	% Folie 2
[915]	63	\begin{frame}
	64	\frametitle{Steering of PALM and Interpreting the Output}
	65	\begin{itemize}
	66	\item<1->{This section section describes how to steer the model and how to interpret the model output (\textbf{it does not explain, how to start and control model runs}).}
	67	\item<2->{It gives a general overview of the input and output files and explaines the contents of the most important files in some detail.}
	68	\end{itemize}
	69	\end{frame}
	70
[945]	71	% Folie 3
[915]	72	\begin{frame}
	73	\frametitle{PALM Input/Output Overview (I)}
	74	\tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small]
	75	\tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny]
	76	\tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny]
	77	\tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny]
	78	\tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny]
	79	\tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny]
	80	\tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny]
	81	\tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny]
	82	\tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny]
	83
	84	\tikzstyle{line} = [draw, -latex']
	85
	86	\begin{tikzpicture} [auto]
	87	\node[start] (palm) {\textbf{PALM}};
	88
	89	\uncover<2->{\node[yellow1] (parameterfile) [above left=1.5cm of palm] {parameter file \\ for steering};}
	90	\uncover<6->{\node[red] (restartdata1) [above right=1.8cm of palm] {restart data};}
	91	\uncover<5->{\node[red] (restartdata2) [below=4.5cm of restartdata1] {restart data};}
	92
[945]	93	\uncover<4->{
	94	\node[orange1] (timeseries) [below left=4.4cm of palm] {time series};
	95	\node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged};
	96	\node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged};
[915]	97
[945]	98	\path<4->[line] (palm) -- (timeseries);
	99	\path<4->[line] (palm) -- (2dsectionstime);
	100	\path<4->[line] (palm) -- (3ddatatime);
	101
	102	\node[orange1] (1dmean) [above=0.2cm of timeseries] {1D mean \\ profiles};
[915]	103	\node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections};
[945]	104	\node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data};}
[915]	105
[945]	106	\path<4->[line] (palm) -- (1dmean);
	107	\path<4->[line] (palm) -- (2dsections);
	108	\path<4->[line] (palm) -- (3ddata);
[915]	109
[945]	110	\uncover<3->{\node[yellow2] (headerfile) [above=0.5cm of 2dsections]{header file};}
	111	\uncover<3->{\node[yellow1] (runcontrol) [right=0.5cm of headerfile]{run control output\\ (parameter settings + \\ timestep informations)};}
	112	\uncover<3->{\node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements};}
[915]	113
[945]	114	\node (program) [right=2.8cm of palm] {program};
	115	\uncover<2->{\node (steeringdata) [right=0.45cm of restartdata1] {steering data};}
	116	\uncover<3->{\node (run) [right=2.7cm of runcontrol] {run informations};}
	117	\uncover<4->{\node (analysis) [right=3.8cm of 3ddata] {analysis data};}
	118
[915]	119	\uncover<7->{
	120	\node[yellow3] (yellow) [below=0.5 of timeseries] {};
	121	\node (ascii) [right=0.1cm of yellow] {ASCII};
	122	\node[orange3] (orange) [right=0.4cm of ascii] {};
	123	\node (netcdf) [right=0.1cm of orange] {netCDF};
	124	\node[red2] (red) [right=0.4cm of netcdf] {};
	125	\node (binary) [right=0.1cm of red] {binary};}
	126
	127	\path<2->[line] (parameterfile) -- (palm);
	128	\path<3->[line] (palm) -- (cpumeasure);
	129	\path<3->[line] (palm) -- (headerfile);
	130	\path<3->[line] (palm) -- (runcontrol);
	131	\path<5->[line] (palm) -- (restartdata2);
	132	\path<6->[line] (restartdata1) -- (palm);
	133	\path<6->[line,dashed] (restartdata2) -- (restartdata1);
	134	\end{tikzpicture}
	135	\end{frame}
	136
[945]	137	% Folie 4
[915]	138	\begin{frame}
[945]	139	\frametitle{PALM Input/Output Overview (II)}
[915]	140	\tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small]
	141	\tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny]
	142	\tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny]
	143	\tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny]
	144	\tikzstyle{yellow4} = [rectangle, draw, fill=yellow!100, text width=1.8cm, font=\Tiny]
	145	\tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny]
	146	\tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny]
	147	\tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny]
	148	\tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny]
	149	\tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny]
	150
	151	\tikzstyle{line} = [draw, -]
	152
	153	\begin{tikzpicture} [auto]
	154	\node[start] (palm) {\textbf{PALM}};
	155
	156	\node[yellow1] (parameterfile) [above left=1cm of palm] {parameter file \\ for steering};
	157	\node[red] (restartdata1) [above right=1.3cm of palm] {restart data};
	158	\node[red] (restartdata2) [below=2.5cm of restartdata1] {restart data};
	159
	160	\node[yellow1] (runcontrol) [below=0.4cm of palm]{run control output\\ (parameter settings + \\ timestep informations)};
	161	\node[yellow2] (headerfile) [left=0.5cm of runcontrol]{header file};
	162	\node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements};
	163
	164	\node[orange1] (1dmean) [below=0.3cm of cpumeasure] {1D mean \\ profiles};
	165	\node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections};
	166	\node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data};
	167
	168	\node[orange1] (timeseries) [below=0.2cm of 1dmean] {time series};
	169	\node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged};
	170	\node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged};
	171
[945]	172	\node (program) [right=2.8cm of palm] {program};
	173	\node (steeringdata) [right=0.8cm of restartdata1] {steering data};
[915]	174	\node (run) [right=2.5cm of runcontrol] {run informations};
	175	\node (analysis) [right=3.6cm of 3ddata] {analysis data};
	176
	177	\node[yellow3] (yellow) [below=0.3 of timeseries] {};
	178	\node (ascii) [right=0.1cm of yellow] {ASCII};
	179	\node[orange3] (orange) [right=0.4cm of ascii] {};
	180	\node (netcdf) [right=0.1cm of orange] {netCDF};
	181	\node[red2] (red) [right=0.4cm of netcdf] {};
	182	\node (binary) [right=0.1cm of red] {binary};
	183
	184	%--------- neue Ordner
[945]	185	\uncover<2->{
[915]	186	\node[yellow4] (currentversion) [above=0.6cm of parameterfile] {current\_version/};
	187	\node[yellow4] (jobs) [right=0.3cm of currentversion] {JOBS/};
	188	\node[yellow4] (runidentifier) [right=0.4cm of jobs] {\textless run\_identifier \textgreater/};
	189	\node[yellow4] (input) [above right=1cm of runidentifier] {INPUT/};
	190	\node[yellow4] (monitoring) [below=0.1cm of input] {MONITORING/};
	191	\node[yellow4] (output) [below=0.1cm of monitoring] {OUTPUT/};
[945]	192	\node[yellow4] (restart) [below=0.1cm of output] {RESTART\_DATA/};}
[915]	193
[945]	194	\uncover<3->{\node[yellow4] (input2) [below=0.1cm of parameterfile] {INPUT/};}
	195	\uncover<4->{\node[yellow4] (monitoring2) [above=0.6cm of headerfile] {MONITORING/};}
	196	\uncover<6->{\node[yellow4] (restart2) [below=0.1cm of restartdata1] {RESTART\_DATA/};}
	197	\uncover<7->{\node[yellow4] (tmpdata) [below=0.1cm of restart2] {/tmp\_data\_catalog/};}
	198	\uncover<5->{\node[yellow4] (output2) [below=0.5cm of restartdata2] {OUTPUT/};}
[915]	199
[945]	200	\path[line]<2-> (currentversion) -- (jobs);
	201	\path[line]<2-> (jobs) -- (runidentifier);
	202	\path[line]<2-> (runidentifier.east) -- (input.west);
	203	\path[line]<2-> (runidentifier.east) -- (monitoring.west);
	204	\path[line]<2-> (runidentifier.east) -- (output.west);
	205	\path[line]<2-> (runidentifier.east) -- (restart.west);
[915]	206
[945]	207	\draw<4->[decorate,decoration={brace,raise=6pt,amplitude=9pt},thick]
[915]	208	(-4.5,-0.95)--(-1,-0.95) ;
[945]	209	\draw<5->[decorate,decoration={brace,mirror,raise=5pt,amplitude=6pt},thick]
	210	(0.45,-3)--(0.45,-1.9) ;
[915]	211	\end{tikzpicture}
	212	\end{frame}
	213
[945]	214	% Folie 5
[915]	215	\begin{frame}
	216	\frametitle{The Parameter File}
[945]	217	\tikzstyle{box} = [rectangle, draw, text width=0.9\textwidth, font=\tiny]
	218	\tikzstyle{line} = [draw, thick, -latex']
[915]	219	\footnotesize
	220	\begin{itemize}
[945]	221	\item<1->{Physical and numerical features of a PALM run (e.g. initial and boundary conditions, numerical methods)
[915]	222	are controlled by a so called \textbf{parameter file} which uses FORTRAN-NAMELIST syntax.}
[945]	223	\item<2->{General structure of a FORTRAN-NAMELIST file}
[915]	224	\end{itemize}
[945]	225	\begin{tikzpicture}[auto]
	226	\uncover<3->{
[915]	227	\node[box](firstbox){ \begin{tabbing}
[945]	228	\quad \&abcd \quad \=no\_of\_eggs = 100, litres\_of\_milk = 50.0, \= \\
	229	\>kilos\_of\_butter = 20.0, \> / \end{tabbing}};
	230	\node[font=\tiny] (leading_blank) at (-5,0.8) {\textbf{leading blank}};
	231	\node[font=\tiny] (namelist) at (-2,0.8) {\textbf{NAMELIST group}};
	232	\node[font=\tiny] (terminating) at (3,0.8) {\textbf{terminating character}};
	233	\path[line] (-5,0.7) -- (-4.8,0);
	234	\path[line] (-2,0.7) -- (-4,0);
	235	\path[line] (3,0.7) -- (0.2,-0.3);}
[915]	236	\end{tikzpicture}
	237	\begin{itemize}
[945]	238	\item<4->{This file can be read from a FORTRAN program in the following way:}
[915]	239	\end{itemize}
[945]	240	\begin{tikzpicture}[auto, node distance=0]
	241	\uncover<4->{
[915]	242	\node[box](secondbox){ \begin{tabbing}
	243	INTEGER :: \=no\_of\_eggs = 30 \\
	244	REAL :: \> litres\_of\_milk = 0.0, kilos\_of\_butter, kilos\_of\_cream = 33.0 \\
[945]	245	\\
[915]	246	NAMELIST /abcd/ \quad no\_of\_eggs, litres\_of\_milk, kilos\_of\_butter, kilos\_of\_cream \\
[945]	247	\\
[915]	248	OPEN ( 1, FILE='Filename' ) \\
[945]	249	\\
	250	READ ( 1, abcd ) \end{tabbing}};}
[915]	251	\end{tikzpicture}
	252	\normalsize
	253	\end{frame}
	254
[945]	255	% Folie 6
	256	\begin{frame}
	257	\frametitle{An Example of PALM - NAMELIST Input}
	258	\tikzstyle{box} = [rectangle, draw, text width=\textwidth, font=\tiny]
	259	\begin{tikzpicture}[auto, node distance=0]
	260	\node[box](box){ \begin{tabbing}
	261	\&inipar \=nx = 39, ny = 39, nz = 40, \\
	262	\>dx = 50.0, dy = 50.0, dz = 50.0, \\
	263	\\
	264	\>initializing\_actions = 'set\_constant\_profiles', \\
	265	\>ug\_surface = 0.0, vg\_surface = 0.0, \\
	266	\\
	267	\>pt\_vertical\_gradient \qquad = 0.0, 1.0, \\
	268	\>pt\_vertical\_gradient\_level = 0.0, 800.0, \\
	269	\\
	270	\>surface\_heatflux = 0.1, bc\_pt\_b ='neumann', / \\
	271	\\
	272	\\
	273	\&d3par \>end\_time = 3600.0, \\
	274	\\
	275	\>dt\_dopr = 900.0, averaging\_interval\_pr = 600.0, \\
	276	\>data\_output\_pr = 'pt', 'u', 'v', / \\ \end{tabbing}};
	277	\end{tikzpicture}
	278	\footnotesize
[1515]	279	\vspace{-3mm}
[945]	280	\begin{itemize}
	281	\item<2->{There are two NAMELIST groups ({\tt \&inipar} and {\tt \&d3par}).}
	282	\item<3->{Assignments to parameters in {\tt\&inipar} are ignored within restart runs \\
	283	(exception: {\tt initializing\_actions} = {\tt'read\_restart\_data'} is obligatory for restart runs).}
	284	\item<4->{Values of {\tt \&d3par} parameters can be changed for restart runs.}
	285	\end{itemize}
	286	\end{frame}
[915]	287
[945]	288	% Folie 7
[1515]	289	\begin{frame}[fragile]
	290	\tikzstyle{green} = [rectangle, draw, fill=green!30, text width=2.1\textwidth, font=\Tinytwo]
[915]	291	\frametitle{The Run Control File}
	292	\scriptsize
	293	\begin{itemize}
[945]	294	\item<1->{For initial runs, the parameter settings and many additional informations about the run (header informations) are printed at the beginning of this file.}
[915]	295	\item<2->{The parameter settings are followed by values of specific model variables for certain timesteps (one line for each timestep, the output intervall can be
	296	controlled by run parameter {\tt dt\_run\_control}).}
	297	\end{itemize}
[945]	298	\onslide<3->{\textbf{Contents of this timestep output should be carefully checked after each run, because it allows a first control, if the model had run correctly, or if any
	299	errors have occurred!}}
	300	\par\bigskip
[1515]	301	\begin{tikzpicture}[scale=0.51, every node/.style={scale=0.51}]
	302	\node [green]{\begin{lstlisting}
[1649]	303	****************************** --------------------------------------------
	304	* PALM 4.0 Rev: 1648 * atmosphere - 3D - run without 1D - prerun
	305	****************************** --------------------------------------------
[1515]	306
[1649]	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
[1515]	311	------------------------------------------------------------------------------
	312	.
	313	.
	314	.
	315	Run-control output:
	316	------------------
	317
	318	RUN ITER. HH:MM:SS.SS DT(E) UMAX VMAX WMAX U* W* THETA* Z_I ENERG. DISTENERG DIVOLD DIVNEW UMAX(KJI) VMAX(KJI) WMAX(KJI) ADVECX ADVECY MGCYC
	319	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
	320	0 0 00:00:00.00 20.0000A -0.2192D -0.2169D -0.1214 0.000 1.38 0.000E+00 800. 0.106E-02 0.000E+00 0.000E+00 0.000E+00 11 32 5 5 37 29 4 26 0 0.000 0.000 0
	321	0 1 00:00:20.00 20.0000A -0.2192 -0.2169 -0.1214 0.001 0.69 -0.124E+03 100. 0.105E-02 0.948E-03 0.491E-05 0.355E-15 11 32 5 5 37 29 4 26 0 0.000 0.000 0
	322	0 2 00:00:40.00 20.0000D -0.2151 -0.2176 -0.1209 0.001 0.69 -0.125E+03 100. 0.104E-02 0.940E-03 0.802E-05 0.359E-15 11 32 5 5 37 29 4 26 0 0.000 0.000 0
	323	.
	324	.
	325
	326	\end{lstlisting}
	327	};
	328	\end{tikzpicture}
[915]	329	\end{frame}
	330
[945]	331	% Folie 8
[1515]	332	\begin{frame}[fragile]
	333	\tikzstyle{green} = [rectangle, draw, fill=green!30, text width=0.9\textwidth, font=\Tiny]
[915]	334	\frametitle{The Header File}
	335	\scriptsize
	336	\begin{itemize}
	337	\item{The header file contains nearly the same informations as the header of the run control file of the initial run.}
	338	\item<2->{It is generated for \textbf{every} run (initial run as well as restart runs).}
	339	\item<3->{It is created at the beginning \textbf{and} at the end of a run (overwrites the file created at beginning).}
	340	\item<4->{Only at the end, cpu time information is included!}
	341	\end{itemize}
	342	\begin{center}
[1515]	343	\begin{tikzpicture}[scale=1, every node/.style={scale=1}]
	344	\node [green]{\begin{lstlisting}
	345	.
	346	.
	347	.
	348	Run time and time step information:
	349	----------------------------------
	350
	351	Timestep: variable maximum value: 20.000 s CFL-factor: 0.90
	352	Start time: 0.000 s
	353	End time: 3600.000 s
	354
	355	Time reached: 3601.930 s
	356	CPU-time used: 4.391 s per timestep: 0.017 s
	357	per second of simulated time: 0.001 s
	358
	359
	360	Computational grid and domain size:
	361	----------------------------------
	362
	363	Grid length: dx = 50.000 m dy = 50.000 m dz = 50.000 m
	364	.
	365	.
	366	.
	367	\end{lstlisting}
	368	};
	369	\end{tikzpicture}
[915]	370	\end{center}
	371	\normalsize
	372	\end{frame}
	373
[945]	374	% Folie 9
[1515]	375	\begin{frame}[fragile]
	376	\tikzstyle{green} = [rectangle, draw, fill=green!30, text width=1.4\textwidth, font=\Tiny]
[915]	377	\frametitle{CPU Measurements File}
	378	\begin{columns}[c]
	379	\column{0.42\textwidth}
	380	\scriptsize
	381	\begin{itemize}
	382	\item{Contains informations about the CPU requirements of single parts of the program.}
	383	\item<2->{It should be inspected regularly in order to find out, if the code is still well optimized (e.g. load balance).}
	384	\item<3->{Prognostic-equations and pressure solver ({\tt pres}) should be the main consumer.}
[1515]	385	\item<4->{For larger grids ($1024^3$ points), {\tt pres} may need up to 50\% of the total time or more.}
[915]	386	\item<5->{Time needed for communication (sum of {\tt exchange\_horiz}({\tt \_2d}) and {\tt mpi\_alltoall}) should not exceed about 10-15\% of the total time.}
	387	\end{itemize}
	388	\normalsize
	389	\column{0.58\textwidth}
[1515]	390	\vspace{-5mm}
	391	\begin{tikzpicture}[scale=0.75, every node/.style={scale=0.75}]
	392	\node [green]{\begin{lstlisting}
[1649]	393	PALM 4.0 Rev: 1648 run: example_cbl.00 host: lcmuk 15-09-15 17:34:44
[1515]	394	-----------
	395
[1649]	396	CPU measures for 4 PEs ( 2(x) * 2(y) tasks * 1 threads):
[1515]	397
	398	gridpoints (x/y/z): 40 * 40 * 40
	399	nr of timesteps: 253
[1649]	400	cpu time per grid point and timestep: 0.57070 * 10**-6 s
[1515]	401	----------------------------------------------------------------------
	402
	403	place: mean counts min max rms
	404	sec. % sec. sec. sec.
	405	------------------------------------------------------------------------------
[1649]	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
[1515]	422	average_3d_data 0.000 0.00 2 0.000 0.000 0.000
[1649]	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
[1515]	425
	426	special measures:
	427	-------------------------------------------------------------------------------
[1649]	428	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
[1515]	439	\end{lstlisting}
	440	};
	441	\end{tikzpicture}
[915]	442	\end{columns}
	443	\end{frame}
	444
[945]	445	% Folie 10
[915]	446	\begin{frame}
	447	\frametitle{Other Files}
[945]	448	\small
[915]	449	\begin{itemize}
	450	\item<1->{Data output files (1D profiles and timeseries, 2D cross sections, 3D volume data) are by default in \textbf{netCDF} format which is suitable to be processed by
[945]	451	public domain graphics software like \textbf{ncview}, \textbf{ferret}, \textbf{ncl} (used by PALM group), \textbf{IDL}, etc. \\
	452	\par\bigskip
[915]	453	For a first look, {\tt ncview} is a convenient tool.}
	454	\item<2->{{\tt ncdump} can be used to display the netCDF file contents in ASCII format ({\tt ncdump -c} displays only header informations).}
[1515]	455	\item<3->{The simple viewer for netCDF-data - {\tt ncview} - as well as ncl graphic software is available on the notebooks and on the IMUK-cluster.}
[915]	456	\end{itemize}
	457	\end{frame}
	458
[945]	459	% Folie 11
[915]	460	\begin{frame}
	461	\frametitle{Steering by Unix Environment Variables}
[945]	462	\scriptsize
[915]	463	Most features of PALM are controlled by the parameter file but a few are exclusively controlled by unix environment variables. The most important one is {\tt write\_binary}. \\
[945]	464	\par\bigskip
[915]	465	Setting \\
[945]	466	\par\medskip
	467	{\centering \texttt{ write\_binary = true} \\
	468	\par\medskip
	469	within the shell causes PALM to write binary data for restart runs at the end of a run.}
	470	\par\bigskip
	471	\uncover<2->{Setting of these environment variables is automatically done by {\tt mrun}. It generates a local file (named {\tt ENVPAR}) in FORTRAN-NAMELIST-format, which is then
	472	read by PALM. This file includes the following variables:} \\
	473	\par\bigskip
[915]	474	\tiny
[945]	475	\uncover<3->{
	476	\begin{tabular}{\|p{3cm}\|p{4cm}\|p{3cm}\|} \hline
[915]	477	\textbf{Variable} & \textbf{Meaning} & \textbf{Value set by {\tt mrun}-option} \\
	478	\hline
	479	{\tt host} & host identifier that mrun is using for the host on which the job is running & {\tt -h} \\
	480	{\tt maximum\_cpu\_time\_allowed} & cpu time allowed for the job & {\tt -t} \\
	481	{\tt run\_identifier} & identification string for the run & {\tt -d} \\
	482	{\tt tasks\_per\_node} & number of MPI tasks to be started on each node & {\tt -T} \\
[945]	483	{\tt write\_binary} & switch for writing binary data to be used for restart runs & {\tt -r} (+setting in configuration file {\tt .mrun.config)} \\
[915]	484	\hline
[945]	485	\end{tabular}}
[915]	486	\normalsize
	487	\end{frame}
	488
[945]	489	% Folie 12
[915]	490	\begin{frame}
	491	\frametitle{PALM / netCDF Documentation}
	492	\begin{itemize}
	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	\par\bigskip
[1649]	495	\textbf{http://palm.muk.uni-hannover.de/trac/wiki/doc/toc}}
[915]	496	\par\bigskip
	497	\item<2->{General information about the netCDF data format can be found under \\
	498	\par\bigskip
	499	\textbf{http://www.unidata.ucar.edu/software/netcdf/}}
	500	\end{itemize}
	501	\end{frame}
	502
[954]	503	\end{document}

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