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<span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Dear Einstein Toolkit Users,</span></p>
<p style="text-align: left; text-indent: 0px; text-transform: none;"><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">I am trying to configure SimFactory to submit jobs using PBS on a machine named "Hubble".</span></p>
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<span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Initially, the automatically generated
<code>hubble.ini</code> was configured for a local login node submission. I attempted to modify the submission commands to support our PBS environment, but the jobs are not running properly.</span></p>
<p style="text-align: left; text-indent: 0px; text-transform: none;"><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Here are the modifications I made to the
<code>.ini</code> configuration:</span></p>
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<li style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<p role="presentation"><span style="text-transform: none;"><b>submit:</b> Changed from:
<code>exec nohup @SCRIPTFILE@ < /dev/null > @RUNDIR@/@SIMULATION_NAME@.out 2> @RUNDIR@/@SIMULATION_NAME@.err & echo $!</code> To:
<code>qsub @SCRIPTFILE@</code></span></p>
</li><li style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<p role="presentation"><span style="text-transform: none;"><b>stop:</b> Changed from:
<code>pkill -g $(ps -o pgid= -p @JOB_ID@)</code> To: <code>qdel @JOB_ID@</code></span></p>
</li><li style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<p role="presentation"><span style="text-transform: none;"><b>getstatus:</b> Changed from:
<code>ps @JOB_ID@</code> To: <code>qstat -f @JOB_ID@</code></span></p>
</li></ul>
<p style="text-align: left; text-indent: 0px; text-transform: none;"><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Symptoms:</b></span></p>
<ol start="1" data-path-to-node="11" style="text-align: left;">
<li style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<p role="presentation"><span style="text-transform: none;">When running <code>simfactory/bin/sim submit</code>, no
<code>.out</code> or <code>.err</code> files are generated at all.</span></p>
</li><li style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<p role="presentation"><span style="text-transform: none;">When running <code>simfactory/bin/sim create-submit</code>, the
<code>.out</code> and <code>.err</code> files are generated, but the <code>.out</code> file only contains the PBS job ID, and the
<code>.err</code> file is completely empty.</span></p>
</li><li style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<p role="presentation"><span style="text-transform: none;">No simulation output files or directories are created inside the designated simulation directory.</span></p>
</li></ol>
<p style="text-align: left; text-indent: 0px; text-transform: none; margin-top: 0px; margin-bottom: 0px;">
<span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">As you can see from the symptoms, </span><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><code>create-submit
</code></span><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">successfully captures the job ID, but the simulation does not run and no output is generated.</span></p>
<p style="text-align: left; text-indent: 0px; text-transform: none;"><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Could anyone guide me on the correct way to write the
<code>submit</code> option or the template script for PBS in SimFactory? Any working examples of a PBS configuration (<code>.ini</code> and
<code>.sub</code> files) would be greatly appreciated.</span></p>
<p style="text-align: left; text-indent: 0px;">For your reference, I have attached my .ini file and .sub file that I am currently using.</p>
<p style="text-align: left; text-indent: 0px; text-transform: none;"><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Thank you very much for your help.</span></p>
<p style="text-align: left; text-indent: 0px; text-transform: none;"><span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Best regards,</span></p>
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<span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); text-transform: none;">Taiki Makino</span></p>
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<span style="font-family: Aptos, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Graduate School of Science, Nagoya University</span></p>
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<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 120, 212);"><a href="mailto:makino.taiki.g6@s.mail.nagoya-u.ac.jp" class="ms-outlook-linkify" title="mailto:makino.taiki.g6@s.mail.nagoya-u.ac.jp" data-outlook-id="6d81fc28-cd0c-48ea-aead-675b28048b3b" style="color: rgb(0, 120, 212); margin-top: 0px; margin-bottom: 0px;"><u>makino</u>.taiki.g6@s.mail.nagoya-u.ac.jp</a></span></p>
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