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source: palm/trunk/DOC/misc/Tsubame.html @ 131

Last change on this file since 131 was 130, checked in by letzel, 17 years ago

DVRP output modifications:

  • The user can now visualize user-defined quantities using dvrp.

data_output_dvrp calls the new user_interface subroutine
user_data_output_dvrp in case of unknown variables (CASE DEFAULT).

  • Two instead of one digit are allowed to specify isosurface and slicer

variables with the parameter mode_dvrp.
  • Property svn:keywords set to Id
File size: 7.5 KB
Line 
1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
2<html><head>
3<xsscleaned_taghttp-equiv ="content-type" content="text/html; charset=windows-1252"></xsscleaned_taghttp-equiv><title>Tsubame</title><style>
4<!--
5@page { size: 21cm 29.7cm }
6-->
7</style></head>
8<body style="direction: ltr;" lang="en-US"> <xsscleaned_tagname ="generator" content="StarOffice 7 (Win32)"></xsscleaned_tagname>
9<xsscleaned_tagname ="author" content="Siegfried Raasch"></xsscleaned_tagname>
10<xsscleaned_tagname ="created" content="20040809;13460943"></xsscleaned_tagname>
11<xsscleaned_tagname ="changed" content="20041112;15085727"></xsscleaned_tagname>
12<xsscleaned_tagname ="keywords" content="parallel LES model"></xsscleaned_tagname>
13<h3 style="line-height: 100%;">Tsubame</h3>
14<p style="line-height: 100%;">This document contains local
15support information for PALM users on the Linux Cluster <span style="font-weight: bold;">Tsubame</span> of the Tokyo
16Institute of Technology, Tokyo, Japan (<a href="http://www.gsic.titech.ac.jp/%7Eccwww">http://www.gsic.titech.ac.jp/~ccwww</a>).
17Japanese and English user manuals are available for download (<a href="http://www.gsic.titech.ac.jp/%7Eccwww/tebiki">http://www.gsic.titech.ac.jp/~ccwww/tebiki</a>).</p><h4>Subversion</h4><p><span style="text-decoration: underline;">Installation:</span><br>The
18following lines should be added to your <code><span style="font-family: Courier New,Courier,monospace;">~/.profile</span></code> (for ksh users - create if necessary) or <code>~/.bashrc</code> (for bash users). These settings will be active from the next login.<span style="font-family: Courier New,Courier,monospace;"></span></p><span style="font-family: Courier New,Courier,monospace;"><code>export
19LD_LIBRARY_PATH=~mkanda/svn/lib</code></span><code><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">
20export PATH=~mkanda/svn/bin:$PATH</span></code><span style="text-decoration: underline;"><br></span><p><span style="text-decoration: underline;">Usage:</span><br>Since
21Tsubame is located behind a firewall, the usual&nbsp;address  <a class="fixed" href="svn://130.75.105.45" target="_blank">svn://130.75.105.45</a>&nbsp;is unreachable from Tsubame. Instead, please login to media-o
22and use&nbsp;<a class="fixed" href="svn://p9c.cc.titech.ac.jp:36900" target="_blank">svn://p9c.cc.titech.ac.jp:36900</a>.
23This port works in both directions, i.e. for <code>svn update</code> as well as <code>svn commit</code> commands.</p><h4>Combine plot fields</h4><p>Please add the following line to the output command (<code>OC:</code>) section of your <code>.mrun.config</code> to ensure correct output of 2D and 3D data for PALM runs on more than one CPU&nbsp;:</p><code>OC:[[ \$( echo \$localhost | cut -c1-3 ) = lct ]]&nbsp; &amp;&amp;&nbsp; combine_plot_fields.x</code><br><h4>Batch system<br></h4><p>The implementation of the <span style="font-weight: bold;">n1ge</span> command on
24Tsubame requires modifications to&nbsp;<span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">subjob</span> for PALM to
25run on Tsubame. Since <span style="font-weight: bold;">mrun</span>
26must be executed on one PE only, a one-PE "submitting job" is created
27when the user calls <span style="font-weight: bold;">mrun</span>.
28At the time when this "submitting job" is actually executed, it starts
29the main PALM job in the foreground. However, this only works if
30enough resources are available at that time. Therefore PALM users on
31Tsubame are advised to consider the queue load of the available queues
32for the main job (<code>qstat -g c</code>) before job submission.</p><p>According
33to the current queue configuration (<a href="http://www.gsic.titech.ac.jp/%7Eccwww/tgc/q_e.html">http://www.gsic.titech.ac.jp/~ccwww/tgc/q_e.html</a>),
34the following <span style="font-weight: bold;">mrun</span>
35options are available:</p><table style="text-align: left; width: 100%;" border="1" cellpadding="2" cellspacing="2"><tbody><tr><td><span style="font-weight: bold;">mrun</span> option</td><td>explanation</td><td>possible
36values</td><td>default value</td></tr><tr><td><code>-q</code></td><td>queue
37name for main job</td><td>novice,&nbsp;sla1, sla2,
38sla3, RAM64GB, RAM128GB</td><td>sla3</td></tr><tr><td><code>-n</code></td><td>queue
39name for "submitting job" (always runs on 1 PE only)</td><td>novice,
40sla1, sla2, sla3</td><td>sla3</td></tr><tr><td><code>-g</code></td><td>group number</td><td>name of the N1GE_GROUP that is required to utilize the bes or sla queues</td><td>none</td></tr></tbody></table><p>Note that the default value "sla3" of the
41<span style="font-weight: bold;">mrun</span> option <code>-q</code> may
42not always be the best choice. For code development, debugging or short
43test runs the value "novice" for both options may be suitable.
44Production runs should use the respective production queues (see <a href="http://www.gsic.titech.ac.jp/%7Eccwww/tgc/q_e.html">http://www.gsic.titech.ac.jp/~ccwww/tgc/q_e.html</a> for details).&nbsp;</p><p>The
45computer center advised us that due to restrictions of the batch system
46the value "novice" should not be mixed with the other queues. Please
47specify either a combination of sla<span style="font-style: italic;">n</span> for <code>-n</code> and sla<span style="font-style: italic;">n</span> or RAM<span style="font-style: italic;">*</span> for <code>-q</code>, or specify the combination "novice" + "novice".</p><p>The group number contains the accounting information. You must specify it using the&nbsp;<span style="font-weight: bold;">mrun</span> option <code>-g</code>. Alternatively, you may set also a default value in your <code><span style="font-family: Courier New,Courier,monospace;">.mrun.config </span></code>file like this:</p><p><code>%group_number&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
4812345678
49&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
50lctit parallel<br></code></p><p>The <span style="font-weight: bold;">mrun</span> option <code><span style="font-family: Courier New,Courier,monospace;">-t</span></code>
51contains the CPU time demand for the main job<span style="font-weight: bold;"> in s</span> which will be
52automatically converted into min for the <span style="font-weight: bold;">n1ge</span> command. The
53option <code><span style="font-family: Courier New,Courier,monospace;">-m</span></code>
54contains the memory demand for the main job <span style="font-weight: bold;">in MB</span> which will be
55automatically converted into GB for the <span style="font-weight: bold;">n1ge</span> command.</p><p>Finally, PALM batch jobs on Tsubame require the&nbsp;<span style="font-weight: bold;">mrun</span> option <code>-b</code>.</p><h4>NetCDF</h4><p>In order to use NetCDF commands like <code>ncdump</code>&nbsp;and the graphical NetCDF tools <a href="http://www.ncl.ucar.edu" target="_top">NCL</a> and <a href="http://meteora.ucsd.edu/%7Epierce/ncview_home_page.html" target="_top">Ncview</a>, please add the following lines to  <code><span style="font-family: Courier New,Courier,monospace;">~/.profile</span></code> (for ksh users) or <code>~/.bashrc</code> (for bash users):</p><p><code># NetCDF<br>export PATH=$PATH:~mkanda/netcdf-3.6.2/bin:~mkanda/netcdf-3.6.2/include<br><br></code><code># NCL<br>export NCARG_ROOT=~mkanda/ncl<br>PATH=~mkanda/ncl/bin:$PATH<br><br># Ncview<br>export PATH=$PATH:~mkanda/ncview/bin<br>export XAPPLRESDIR=~mkanda/.app-defaults</code></p><i><br>Last
56change:</i>&nbsp; $Id: Tsubame.html 130 2007-11-13 14:08:40Z letzel $</body></html>
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