source: palm/trunk/DOC/misc/Tsubame.html @ 2696

Last change on this file since 2696 was 132, checked in by letzel, 14 years ago

Vertical profiles now based on nzb_s_inner; they are divided by
ngp_2dh_s_inner (scalars, procucts of scalars and velocity components) and
ngp_2dh (staggered velocity components and their products), respectively.

Allow new case bc_uv_t = 'dirichlet_0' for channel flow.

  • Property svn:keywords set to Id
File size: 8.1 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 }
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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>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). In the past the queueing system on Tsubame has undergone several changes, so this information may change.</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 <a href="http://www.unidata.ucar.edu/software/netcdf" target="_top">NetCDF</a> commands like <code>ncdump</code>&nbsp;and the graphical NetCDF tools <a href="http://www.ncl.ucar.edu" target="_top">NCL</a>,&nbsp;<a href="http://meteora.ucsd.edu/%7Epierce/ncview_home_page.html" target="_top">Ncview</a> and <a href="http://ferret.pmel.noaa.gov/Ferret" target="_top">Ferret</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><p><code># Ferret<br>export FER_DIR=~mkanda/ferret<br>export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FER_DIR/lib<br>export PATH=$PATH:$FER_DIR:$FER_DIR/bin<br>export FER_DSETS=$FER_DIR<br>export FER_WEB_BROWSER=firefox<br>export FER_EXTERNAL_FUNCTIONS="$FER_DIR/lib"<br>export FER_GO=". $FER_DIR/go $FER_DIR/examples $FER_DIR/contrib"<br>export FER_DATA="."<br>export FER_DESCR="."<br>export FER_GRIDS=". $FER_DSETS/grids"<br>export TMAP="$FER_DIR/fmt"<br>export PLOTFONTS="$FER_DIR/ppl/fonts"<br>export SPECTRA="$FER_DIR/ppl"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # for old ferret versions<br>export FER_PALETTE=". $FER_DIR/ppl"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # palette search list<br></code></p><i><br>Last
56change:</i>&nbsp; $Id: Tsubame.html 132 2007-11-20 09:46:11Z kanani $</body></html>
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