https://wiki.nikhef.nl/lhcb/index.php?title=How_to_setup_the_qsub_tunnel_for_use_with_Ganga_and_the_LHCb_software&feed=atom&action=historyHow to setup the qsub tunnel for use with Ganga and the LHCb software - Revision history2024-03-28T20:43:34ZRevision history for this page on the wikiMediaWiki 1.35.3https://wiki.nikhef.nl/lhcb/index.php?title=How_to_setup_the_qsub_tunnel_for_use_with_Ganga_and_the_LHCb_software&diff=1283&oldid=prevRaaij@nikhef.nl at 15:36, 22 December 20102010-12-22T15:36:59Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:36, 22 December 2010</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Preparing your environment on the submission machine ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Preparing your environment on the submission machine ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* To make <del class="diffchange diffchange-inline">sure </del>your grid proxy <del class="diffchange diffchange-inline">is </del>available on the worker node, set the following environment variable before you create your proxy. It is easiest to put this in your login scripts.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* To make your grid proxy available on the worker node, set the following environment variable before you create your proxy. It is easiest to put this in your login scripts.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The pbs server must also be known (Set this back to allier.nikhef.nl if you want to submit to stoomboot):</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The pbs server must also be known (Set this back to allier.nikhef.nl if you want to submit to stoomboot):</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* For bash-like shells:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* For bash-like shells:</div></td></tr>
</table>Raaij@nikhef.nlhttps://wiki.nikhef.nl/lhcb/index.php?title=How_to_setup_the_qsub_tunnel_for_use_with_Ganga_and_the_LHCb_software&diff=330&oldid=prevRaaij@nikhef.nl at 15:33, 22 December 20102010-12-22T15:33:58Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:33, 22 December 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td>
<td colspan="2" class="diff-lineno">Line 7:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Make sure that you are using Ganga version 5.5.16 (v505r16)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Make sure that you are using Ganga version 5.5.16 (v505r16)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>== Preparing your <del class="diffchange diffchange-inline">proxy </del>==</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== Preparing your <ins class="diffchange diffchange-inline">environment on the submission machine </ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* To make sure your grid proxy is available on the worker node, set the following environment variable before you create your proxy. It is easiest to put this in your login scripts.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* To make sure your grid proxy is available on the worker node, set the following environment variable before you create your proxy. It is easiest to put this in your login scripts.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The pbs server must also be known (Set this back to allier.nikhef.nl if you want to submit to stoomboot):</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The pbs server must also be known (Set this back to allier.nikhef.nl if you want to submit to stoomboot):</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>== Preparing the environment ==</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== Preparing the environment <ins class="diffchange diffchange-inline">for the worker nodes </ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The LHCb software available on the Tier1 worker nodes is not the same installation as is available in the /project/bfys area. The worker nodes have all versions available which are distributed to the Grid by the LHCb production and software management team. Login scripts need to be prepared:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The LHCb software available on the Tier1 worker nodes is not the same installation as is available in the /project/bfys area. The worker nodes have all versions available which are distributed to the Grid by the LHCb production and software management team. Login scripts need to be prepared:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Create a file called .bash_profile in /data/tunnel/user/yourusername.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Create a file called .bash_profile in /data/tunnel/user/yourusername.</div></td></tr>
</table>Raaij@nikhef.nlhttps://wiki.nikhef.nl/lhcb/index.php?title=How_to_setup_the_qsub_tunnel_for_use_with_Ganga_and_the_LHCb_software&diff=329&oldid=prevRaaij@nikhef.nl at 15:32, 22 December 20102010-12-22T15:32:00Z<p></p>
<p><b>New page</b></p><div>== General information ==<br />
The qsub tunnel is a new service supplied by the PDP group that allows Nikhef users to submit directly to the "medium" queue of the Nikhef Tier1. For general information and instructions, see this twiki page: [http://www.nikhef.nl/pub/projects/grid/gridwiki/index.php/Qsub-tunnel qsub tunnel wiki pagina].<br />
<br />
== First steps ==<br />
* Make sure that you are included in the list of people who are allowed to submit jobs using the qsub tunnel by asking the PDP group if you are.<br />
* Make sure that you have a grid proxy if you want to use the Oracle conditions database or if you want to access files on the Nikhef or Sara storage elements.<br />
* Make sure that you are using Ganga version 5.5.16 (v505r16)<br />
<br />
== Preparing your proxy ==<br />
* To make sure your grid proxy is available on the worker node, set the following environment variable before you create your proxy. It is easiest to put this in your login scripts.<br />
* The pbs server must also be known (Set this back to allier.nikhef.nl if you want to submit to stoomboot):<br />
* For bash-like shells:<br />
<pre><br />
export X509_USER_PROXY=/data/tunnel/user/yourusername/.x509tmp<br />
export PBS_SERVER=stro.nikhef.nl<br />
</pre><br />
* For csh-like shells:<br />
<pre><br />
setenv X509_USER_PROXY /data/tunnel/user/yourusername/.x509tmp<br />
setenv PBS_SERVER stro.nikhef.nl<br />
</pre><br />
<br />
== Preparing the environment ==<br />
The LHCb software available on the Tier1 worker nodes is not the same installation as is available in the /project/bfys area. The worker nodes have all versions available which are distributed to the Grid by the LHCb production and software management team. Login scripts need to be prepared:<br />
* Create a file called .bash_profile in /data/tunnel/user/yourusername.<br />
* Put the following lines into it:<br />
<pre><br />
if [ -f ~/.bashrc ]; then<br />
. ~/.bashrc<br />
fi<br />
</pre><br />
* Create a file named .bashrc in /data/tunnel/user/yourusername.<br />
* Put the following lines into it:<br />
<pre><br />
export X509_USER_PROXY=/data/tunnel/user/yourusername/.x509tmp<br />
. $VO_LHCB_SW_DIR/group_login.sh<br />
</pre><br />
<br />
== Ganga configuration ==<br />
Edit your ~/.gangarc file and look for the [PBS] section, put in the following bits:<br />
<pre><br />
postexecute =<br />
import os<br />
env = os.environ<br />
tmpdir = None<br />
if "TMPDIR" in env: tmpdir = env[ "TMPDIR" ].rstrip( "/" )<br />
else: tmpdir = "."<br />
jobnumid = env["PBS_JOBID"]<br />
dir = "%s/%s" % ( tmpdir, jobnumid )<br />
os.chdir( tmpdir )<br />
os.system("rm -rf %s" % dir )<br />
</pre><br />
<pre><br />
preexecute =<br />
import os<br />
env = os.environ<br />
jobnumid = env["PBS_JOBID"]<br />
tmpdir = None<br />
if "TMPDIR" in env: tmpdir = env[ "TMPDIR" ].rstrip( "/" )<br />
else: tmpdir = "."<br />
dir = "%s/%s" % ( tmpdir, jobnumid )<br />
os.system("mkdir %s" % dir )<br />
os.chdir( "%s" % dir )<br />
os.environ["PATH"]+=":."<br />
</pre><br />
<pre><br />
submit_res_pattern = ^(?P<id>\d*)\.\w+\.nikhef\.nl<br />
</pre><br />
<br />
== When using Ganga ==<br />
* When submitting jobs, use the PBS backend with the following settings:<br />
<pre><br />
yourjob.backend = PBS( queue = 'medium' )<br />
</pre></div>Raaij@nikhef.nl