| [127] | 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> |
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| 3 | <xsscleaned_taghttp-equiv ="content-type" content="text/html; charset=windows-1252"></xsscleaned_taghttp-equiv><title>Tsubame</title><style> |
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| 8 | <body style="direction: ltr;" lang="en-US"> <xsscleaned_tagname ="generator" content="StarOffice 7 (Win32)"></xsscleaned_tagname> |
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| 9 | <xsscleaned_tagname ="author" content="Siegfried Raasch"></xsscleaned_tagname> |
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| 10 | <xsscleaned_tagname ="created" content="20040809;13460943"></xsscleaned_tagname> |
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| 11 | <xsscleaned_tagname ="changed" content="20041112;15085727"></xsscleaned_tagname> |
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| 12 | <xsscleaned_tagname ="keywords" content="parallel LES model"></xsscleaned_tagname> |
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| 13 | <h3 style="line-height: 100%;">Tsubame</h3> |
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| 14 | <p style="line-height: 100%;">This document contains local |
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| 15 | support information for PALM users on the Linux Cluster <span style="font-weight: bold;">Tsubame</span> of the Tokyo |
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| 16 | Institute of Technology, Tokyo, Japan (<a href="http://www.gsic.titech.ac.jp/%7Eccwww">http://www.gsic.titech.ac.jp/~ccwww</a>). |
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| [130] | 17 | Japanese 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 |
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| 18 | following 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 |
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| 19 | LD_LIBRARY_PATH=~mkanda/svn/lib</code></span><code><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;"> |
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| 20 | export PATH=~mkanda/svn/bin:$PATH</span></code><span style="text-decoration: underline;"><br></span><p><span style="text-decoration: underline;">Usage:</span><br>Since |
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| [127] | 21 | Tsubame is located behind a firewall, the usual address <a class="fixed" href="svn://130.75.105.45" target="_blank">svn://130.75.105.45</a> is unreachable from Tsubame. Instead, please login to media-o |
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| 22 | and use <a class="fixed" href="svn://p9c.cc.titech.ac.jp:36900" target="_blank">svn://p9c.cc.titech.ac.jp:36900</a>. |
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| [132] | 23 | This 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 |
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| [127] | 24 | Tsubame requires modifications to <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">subjob</span> for PALM to |
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| 25 | run on Tsubame. Since <span style="font-weight: bold;">mrun</span> |
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| 26 | must be executed on one PE only, a one-PE "submitting job" is created |
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| 27 | when the user calls <span style="font-weight: bold;">mrun</span>. |
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| 28 | At the time when this "submitting job" is actually executed, it starts |
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| 29 | the main PALM job in the foreground. However, this only works if |
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| 30 | enough resources are available at that time. Therefore PALM users on |
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| 31 | Tsubame are advised to consider the queue load of the available queues |
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| 32 | for the main job (<code>qstat -g c</code>) before job submission.</p><p>According |
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| 33 | to 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>), |
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| 34 | the following <span style="font-weight: bold;">mrun</span> |
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| 35 | options 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 |
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| 36 | values</td><td>default value</td></tr><tr><td><code>-q</code></td><td>queue |
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| [129] | 37 | name for main job</td><td>novice, sla1, sla2, |
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| 38 | sla3, RAM64GB, RAM128GB</td><td>sla3</td></tr><tr><td><code>-n</code></td><td>queue |
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| [127] | 39 | name for "submitting job" (always runs on 1 PE only)</td><td>novice, |
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| [129] | 40 | sla1, 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 |
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| [127] | 41 | <span style="font-weight: bold;">mrun</span> option <code>-q</code> may |
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| [129] | 42 | not always be the best choice. For code development, debugging or short |
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| 43 | test runs the value "novice" for both options may be suitable. |
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| [132] | 44 | Production 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 |
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| [130] | 45 | computer center advised us that due to restrictions of the batch system |
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| 46 | the value "novice" should not be mixed with the other queues. Please |
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| 47 | specify 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 <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 |
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| 48 | 12345678 |
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| 49 | |
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| 50 | lctit 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> |
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| 51 | contains the CPU time demand for the main job<span style="font-weight: bold;"> in s</span> which will be |
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| [127] | 52 | automatically converted into min for the <span style="font-weight: bold;">n1ge</span> command. The |
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| 53 | option <code><span style="font-family: Courier New,Courier,monospace;">-m</span></code> |
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| [130] | 54 | contains the memory demand for the main job <span style="font-weight: bold;">in MB</span> which will be |
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| [132] | 55 | automatically converted into GB for the <span style="font-weight: bold;">n1ge</span> command.</p><p>Finally, PALM batch jobs on Tsubame require the <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> and the graphical NetCDF tools <a href="http://www.ncl.ucar.edu" target="_top">NCL</a>, <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" # for old ferret versions<br>export FER_PALETTE=". $FER_DIR/ppl" # palette search list<br></code></p><i><br>Last |
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| [127] | 56 | change:</i> $Id: Tsubame.html 132 2007-11-20 09:46:11Z witha $</body></html> |
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