source: palm/trunk/DOC/app/chapter_4.5.7.html @ 555

Last change on this file since 555 was 555, checked in by raasch, 12 years ago

New:
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Changed:


Documentation for surface_heatflux in case of prandtl_layer = .F. improved.

bugfix for wrong netcdf/3.6.3 module on lcsgi (mbuild, mrun)

Errors:


Bugfix in if statement (disturb_heatflux)

Bugfix: in 2201 statement: closing " was missing (interpret_config)

Bugfix: default setting of nzb_local for flat topography (init_grid)

Bugfix: wrong dimension used for ts_value_l (user_statistics)

disturb_heatflux, init_grid, interpret_config, user_statistics

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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
2<html><head>
3
4
5<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 4.5.7</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041029;14344622"> <meta name="CHANGED" content="20050119;9531085"> <meta name="KEYWORDS" content="parallel LES model"> <style>
6<!--
7@page { size: 21cm 29.7cm }
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9</style></head><body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.7
10Plots of
11isosurfaces, 2d cross sections and particles with dvrp</font></h4>
12<p style="line-height: 100%;"><span style="font-weight: bold;">Preliminary note:</span></p><p style="line-height: 100%;">Usage of the <span style="font-weight: bold;">dvrp</span>-software requires installation of additional software components (dvrp-library, streaming-server, browser-plugin) which are <span style="font-weight: bold;">not</span>
13part of the PALM distribution. Currently (May 2009), this software is
14only available on the the HLRN/IMUK system and partly on RIAM's NEC
15system. If you are interested in using <span style="font-weight: bold;">dvrp</span> on your system, please contact the PALM developers.</p><br><span style="font-weight: bold;">General remarks:</span><p style="line-height: 100%;">The <span style="font-weight: bold;">dvrp</span>
16software was originally developed by the RRZN
17(Stephan Olbrich, Carsten Chmielewski) and is meanwhile continuosly developed and improved under the name <span style="font-weight: bold;">dsvr</span> by the University of Düsseldorf (Prof. Stephan Olbrich, see webpage of the <a href="http://www.dsvr-software.de/">dsvr-software</a>). It allows to create 3d-animations with PALM,
18which can be displayed via a special plugin for internet browsers. With
19suitable graphic hardware (e.g. NVIDIA quattro FX cards) even stereoscopic views are
20possible.</p><p style="line-height: 100%;">
21In contrast to the other kinds of visualization output realized
22in PALM (1d-, 2d-, 3d-NetCDF output),
23where the data
24is output in a format suitable for many kinds of post-processing graphic software, the creation of animations via <span style="font-weight: bold;">dvrp</span>
25software is
26integrated in PALM, i.e. respective routines are directly called within
27the PALM code. The
28<span style="font-weight: bold;">dvrp</span>
29routines then output the
30graphic data
31(so-called plot-primitives, e.g. polygones of isosurfaces) in a special
32dvr format. Since the <span style="font-weight: bold;">dvrp</span>
33software is parallelized (i.e. each PE calculates the graphic data for
34its subdomain), the visualization of simulations with very
35large numbers of grid points is possible (which so far failed because
36of
37several problems: volume of the raw data, which rapidly may sum-up to
38several Terabytes; main memory size needed for graphic workstations, on
39which the visualization is to be carried out; the insufficient scalar
40(!)
41computing speed of commercial graphic software in case of such
42large numbers of grid points). </p>
43<p style="line-height: 100%;">The coupling of <span style="font-weight: bold;">dvrp</span> software and
44PALM
45as well as the visualization of the model results via <span style="font-weight: bold;">dvrp</span> has been
46the main focus of the BMBF project "Application of
47tele-immersion in long-distance networks" (2001-2002),
48which was a joint project of RRZN, ZIB and IMUK. This work was
49continued by RRZN in the DFG-funded project "<a href="http://www.rrzn.uni-hannover.de/evita.html">EVITA</a> - Untersuchung
50effizienter
51Methoden zur visuellen und haptischen tele-immersiven
52Exploration
53komplexer Volumen- und Strömungsdaten aus
54parallelisierten,
55dynamischen 3D-Simulationen" (2005-2007). </p>
56<p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold;">Using dvrp with PALM:</span></p><p style="line-height: 100%;">The calls of the <span style="font-weight: bold;">dvrp</span> routines are
57contained within a
58PALM software package (see chapter <a href="chapter_3.7.html">3.7</a>).
59To use this package, the additional option<tt style="font-family: monospace;"> </tt><font style="font-family: Courier New,Courier,monospace;" size="2">-p
60<span style="font-family: Helvetica,Arial,sans-serif;">“</span>dvrp_graphics<span style="font-family: Helvetica,Arial,sans-serif;">”</span></font><span style="font-family: monospace;">
61</span>has to be given in the <b>mrun</b> call. This
62automatically links the
63required libraries.
64Steering of the plot output is done via the package
65parameters (see chapter <a href="chapter_4.2.html">4.2</a>).
66In contrast to all other PALM output, <span style="font-weight: bold;">dvrp</span>
67graphic
68data are not output to local files but directly to a special remote
69computer which is defined via the package parameter <a href="chapter_4.2.html#dvrp_host">dvrp_host</a>. If the default values of the dvrp parameters are used, data are send to a so-called <span style="font-style: italic;">streaming server</span> at the
70RRZN. Apart from graphic data an additional html file is created, which
71can be opened by an internet browser to view the data (a special <span style="font-weight: bold;">dvrp</span> plugin is required for this).</p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold;">Quickstart guide for using dvrp on the HLRN/IMUK-System (June 2010):</span></p><p style="line-height: 100%;">In the following, please replace the string<span style="font-family: Courier New,Courier,monospace; font-weight: bold;"> &lt;UNAME&gt; </span>with your IMUK username, wherever it appears. Please also replace the string<span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold;"> &lt;UDIR&gt;</span> </span>with a subdirectory name of your choice. <span style="font-weight: bold;"></span> </p>
72<ol><li>
73Add the following define statements for environment variables to the configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>):<br><br><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"> &nbsp; &nbsp;%dvr_inc&nbsp;&nbsp;
74-I/home/h/niksiraa/dvr_mvapich2/lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
75&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; lcsgih parallel</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;%dvr_lib&nbsp;&nbsp;&nbsp;-L/home/h/niksiraa/dvr_mvapich2/lib:-lDVRP2:-lftp&nbsp; &nbsp; lcsgih
76parallel</span><br><br><br></li><li>Add the dvrp-steering parameters to your NAMELIST-parameter file, e.g.<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp;&amp;d3par &nbsp;end_time = 3600.0,<br>&nbsp; ... &nbsp; &nbsp; /<br><br>&nbsp;&amp;dvrp_graphics_par &nbsp; dvrp_username = '<span style="font-weight: bold;">&lt;UNAME&gt;</span>',<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; dvrp_host = '130.75.105.6',<br>&nbsp;
77&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
78dvrp_directory = '<span style="font-weight: bold;">&lt;UNAME&gt;</span>/<span style="font-weight: bold;">&lt;UDIR&gt;</span>', ... /<br></span><br>For other dvrp-parameters see <a href="chapter_4.2.html#Paketparameter">chapter 4.2</a>. An example parameter file can be found in directory <span style="font-family: Courier New,Courier,monospace;">..../trunk/EXAMPLES/dvr &nbsp;</span>.<span style="font-family: Courier New,Courier,monospace;"><br><br></span></li><li>Ask the IMUK system operator (Notker Fechner) to mount the filesystem<span style="font-family: Courier New,Courier,monospace;"> /dvrdata </span>on your local computer.<br>
79    <br>
80</li>
81  <li>On the IMUK-system (your local computer), create a subdirectory
82in which the dvrp-data are stored and give it access permit for group <span style="font-style: italic;">palm</span>.<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mkdir /dvrdata/<span style="font-weight: bold;">&lt;UNAME&gt;<br>
83</span>&nbsp;&nbsp; chmod g+rwx /dvrdata</span><span style="font-family: Courier New,Courier,monospace;">/<span style="font-weight: bold;">&lt;UNAME&gt;</span></span><br><br><span style="font-weight: bold;">Steps 3. and 4. have to be done only once, before dvrp is used for the first time.</span><br>
84<br></li>
85<li>Submit the job&nbsp; with <span style="font-weight: bold;">mrun</span>-command<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mrun .... -p dvrp_graphics ....</span><br><br></li><li><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">After the job has finished, the dvrp-output can be found on the IMUK-cluster in a subdirectory under <span style="font-family: Courier New,Courier,monospace;">/dvrdata</span>. The name of the subdirectory is determined by the dvrp-parameter <a href="chapter_4.2.html#dvrp_directory">dvrp_directory</a> (see above), i.e. if the user has set <span style="font-family: Courier New,Courier,monospace;">dvrp_directory</span> = <span style="font-style: italic;">'<span style="font-weight: bold;">&lt;UNAME&gt;</span>/movie_1'</span>, the dvrp-data are stored under&nbsp;<span style="font-family: Courier New,Courier,monospace;">/dvrdata/<span style="font-weight: bold;">&lt;UNAME&gt;</span>/movie_1</span>.<br><br></span></span></li><li><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">Change to this subdirectory (e.g. </span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"><span style="font-family: Courier New,Courier,monospace;">/dvrdata/&lt;UNAME&gt;/movie_1</span></span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">) and enter the command<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;process_dvr_output</span><br><br>It will create a file with name <span style="font-family: Courier New,Courier,monospace;">all_streams_streaming.html</span>.<br><br></span></span></li><li><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">Call the opera-browser (i.e. enter the command <span style="font-family: Courier New,Courier,monospace;">opera</span>) and open the file </span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"><span style="font-family: Courier New,Courier,monospace;">all_streams_streaming.html</span>.</span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"></span><br></span><br></li></ol><span style="font-weight: bold;">Further features:<br></span>The script<span style="font-family: Courier New,Courier,monospace;"> process_dvr_output </span>has additional options:<br><br><span style="font-weight: bold; font-family: Courier New,Courier,monospace;">-s</span> &nbsp; &nbsp; : <span style="font-weight: bold;">create sequence output</span>.
86All streams (and static scenes) are collected to one sequence (one
87static scene), which can be displayed with a browser without using the
88streaming server (the so-called sequence mode). This allows e.g. to
89show animations on a notebook without beeing connected to the internet.
90When the script is called with this option, the sequence is generated
91in subdirectory sequence_data. Copy this subdirectory and the file<span style="font-family: Courier New,Courier,monospace;">
92all_streams_sequence.html </span>to a directory on your local computer and
93open the file<span style="font-family: Courier New,Courier,monospace;"> all_streams_sequence.html </span>with your browser. For this,
94you will need to install the the dvr-plugin (see webpage of the <a href="http://www.dsvr-software.de/">dsvr-software</a>) on your local computer, which is also available for Windows.<br><br><span style="font-weight: bold;">-a</span> &nbsp; &nbsp; &nbsp;: <span style="font-weight: bold;">acceleration factor</span>. If, in case of sequence mode, the performance of the animation is to slow, you can accelerate it. E.g., by using <span style="font-family: Courier New,Courier,monospace;">"-a 2</span>", only every second frame of the original streams will be used for the sequence.<br><br><br><br><br><span style="font-weight: bold;">Current limitations (May 09):</span><br>Only a special opera-version on host "bora" can be used. Log-in on "bora" and call &nbsp;<span style="font-family: Courier New,Courier,monospace;">/usr/bin/opera</span>. <span style="font-weight: bold;">Before that(!!!)</span>, enter the command "<span style="font-family: Courier New,Courier,monospace;">export LD_PRELOAD=libXm.so</span>" !
95<hr><p style="line-height: 100%;"><br>
96<font color="#000080"><font color="#000080"><a href="chapter_4.5.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.6.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;">&nbsp;<i>Last
97change:&nbsp;</i> $Id: chapter_4.5.7.html 555 2010-09-07 07:32:53Z raasch $</p>
98</body></html>
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