| 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 } |
|---|
| 8 | --> |
|---|
| 9 | </style></head><body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.7 |
|---|
| 10 | Plots of |
|---|
| 11 | isosurfaces, 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> |
|---|
| 13 | part of the PALM distribution. Currently (May 2009), this software is |
|---|
| 14 | only available on the the HLRN/IMUK system and partly on RIAM's NEC |
|---|
| 15 | system. 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> |
|---|
| 16 | software 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, |
|---|
| 18 | which can be displayed via a special plugin for internet browsers. With |
|---|
| 19 | suitable graphic hardware (e.g. NVIDIA quattro FX cards) even stereoscopic views are |
|---|
| 20 | possible.</p><p style="line-height: 100%;"> |
|---|
| 21 | In contrast to the other kinds of visualization output realized |
|---|
| 22 | in PALM (1d-, 2d-, 3d-NetCDF output), |
|---|
| 23 | where the data |
|---|
| 24 | is 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> |
|---|
| 25 | software is |
|---|
| 26 | integrated in PALM, i.e. respective routines are directly called within |
|---|
| 27 | the PALM code. The |
|---|
| 28 | <span style="font-weight: bold;">dvrp</span> |
|---|
| 29 | routines then output the |
|---|
| 30 | graphic data |
|---|
| 31 | (so-called plot-primitives, e.g. polygones of isosurfaces) in a special |
|---|
| 32 | dvr format. Since the <span style="font-weight: bold;">dvrp</span> |
|---|
| 33 | software is parallelized (i.e. each PE calculates the graphic data for |
|---|
| 34 | its subdomain), the visualization of simulations with very |
|---|
| 35 | large numbers of grid points is possible (which so far failed because |
|---|
| 36 | of |
|---|
| 37 | several problems: volume of the raw data, which rapidly may sum-up to |
|---|
| 38 | several Terabytes; main memory size needed for graphic workstations, on |
|---|
| 39 | which the visualization is to be carried out; the insufficient scalar |
|---|
| 40 | (!) |
|---|
| 41 | computing speed of commercial graphic software in case of such |
|---|
| 42 | large numbers of grid points). </p> |
|---|
| 43 | <p style="line-height: 100%;">The coupling of <span style="font-weight: bold;">dvrp</span> software and |
|---|
| 44 | PALM |
|---|
| 45 | as well as the visualization of the model results via <span style="font-weight: bold;">dvrp</span> has been |
|---|
| 46 | the main focus of the BMBF project "Application of |
|---|
| 47 | tele-immersion in long-distance networks" (2001-2002), |
|---|
| 48 | which was a joint project of RRZN, ZIB and IMUK. This work was |
|---|
| 49 | continued by RRZN in the DFG-funded project "<a href="http://www.rrzn.uni-hannover.de/evita.html">EVITA</a> - Untersuchung |
|---|
| 50 | effizienter |
|---|
| 51 | Methoden zur visuellen und haptischen tele-immersiven |
|---|
| 52 | Exploration |
|---|
| 53 | komplexer Volumen- und Strömungsdaten aus |
|---|
| 54 | parallelisierten, |
|---|
| 55 | dynamischen 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 |
|---|
| 57 | contained within a |
|---|
| 58 | PALM software package (see chapter <a href="chapter_3.7.html">3.7</a>). |
|---|
| 59 | To 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 |
|---|
| 62 | automatically links the |
|---|
| 63 | required libraries. |
|---|
| 64 | Steering of the plot output is done via the package |
|---|
| 65 | parameters (see chapter <a href="chapter_4.2.html">4.2</a>). |
|---|
| 66 | In contrast to all other PALM output, <span style="font-weight: bold;">dvrp</span> |
|---|
| 67 | graphic |
|---|
| 68 | data are not output to local files but directly to a special remote |
|---|
| 69 | computer 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 |
|---|
| 70 | RRZN. Apart from graphic data an additional html file is created, which |
|---|
| 71 | can 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;"> <UNAME> </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;"> <UDIR></span> </span>with a subdirectory name of your choice. <span style="font-weight: bold;"></span> </p> |
|---|
| 72 | <ol><li> |
|---|
| 73 | Add 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;"> %dvr_inc |
|---|
| 74 | -I/home/h/niksiraa/dvr_mvapich2/lib |
|---|
| 75 | lcsgih parallel</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;"> %dvr_lib -L/home/h/niksiraa/dvr_mvapich2/lib:-lDVRP2:-lftp lcsgih |
|---|
| 76 | parallel</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;"> &d3par end_time = 3600.0,<br> ... /<br><br> &dvrp_graphics_par dvrp_username = '<span style="font-weight: bold;"><UNAME></span>',<br> dvrp_host = '130.75.105.6',<br> |
|---|
| 77 | |
|---|
| 78 | dvrp_directory = '<span style="font-weight: bold;"><UNAME></span>/<span style="font-weight: bold;"><UDIR></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 </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 |
|---|
| 82 | in 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;"> mkdir /dvrdata/<span style="font-weight: bold;"><UNAME><br> |
|---|
| 83 | </span> chmod g+rwx /dvrdata</span><span style="font-family: Courier New,Courier,monospace;">/<span style="font-weight: bold;"><UNAME></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 with <span style="font-weight: bold;">mrun</span>-command<br><br><span style="font-family: Courier New,Courier,monospace;"> 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;"><UNAME></span>/movie_1'</span>, the dvrp-data are stored under <span style="font-family: Courier New,Courier,monospace;">/dvrdata/<span style="font-weight: bold;"><UNAME></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/<UNAME>/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;"> 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> : <span style="font-weight: bold;">create sequence output</span>. |
|---|
| 86 | All streams (and static scenes) are collected to one sequence (one |
|---|
| 87 | static scene), which can be displayed with a browser without using the |
|---|
| 88 | streaming server (the so-called sequence mode). This allows e.g. to |
|---|
| 89 | show animations on a notebook without beeing connected to the internet. |
|---|
| 90 | When the script is called with this option, the sequence is generated |
|---|
| 91 | in subdirectory sequence_data. Copy this subdirectory and the file<span style="font-family: Courier New,Courier,monospace;"> |
|---|
| 92 | all_streams_sequence.html </span>to a directory on your local computer and |
|---|
| 93 | open the file<span style="font-family: Courier New,Courier,monospace;"> all_streams_sequence.html </span>with your browser. For this, |
|---|
| 94 | you 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> : <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 <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%;"> <i>Last |
|---|
| 97 | change: </i> $Id: chapter_4.5.7.html 555 2010-09-07 07:32:53Z raasch $</p> |
|---|
| 98 | </body></html> |
|---|
