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<div class="moz-cite-prefix">Since several of you claimed that you
saw a marked degradation in your runtimes when I was running code,
and since the long running jobs could use upwards of 800 MB of
memory each, it is probably in your best interest to allocate
everything. However -- I don't recommend a single person "hogging"
hammer -- so run single jobs (not 10 long running executables in a
single job script) and set your wallclock time to something
reasonable -- (like 4 hours maximum).</div>
<div class="moz-cite-prefix"> </div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">If you want to "stage" your jobs to run
one after another you can use the <br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">-W depend=afterok:<job num></div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">on your qsub command line where <job
num> is the job that has to finish before this current job
begins.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">For example, if the job I am waiting on
to finish is 10023 and my pbs script is in the file runbench.pbs
I would use the command</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">qsub runbench.pbs -W
depend=afterok:10023</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 3/4/22 08:01, Brody Mitchell Dutka
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:6ed3a14ff7f04f4facd6a4d51ea450d1@SA1PR01MB6528.prod.exchangelabs.com">
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Hello Dr. Pounds,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Do you want us to allocate all of hammer to ourselves for each
run, or share it?</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Thanks, </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Brody Dutka</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> csc435
<a class="moz-txt-link-rfc2396E" href="mailto:csc435-bounces@theochem.mercer.edu"><csc435-bounces@theochem.mercer.edu></a> on behalf of Andrew
J. Pounds <a class="moz-txt-link-rfc2396E" href="mailto:pounds_aj@mercer.edu"><pounds_aj@mercer.edu></a><br>
<b>Sent:</b> Thursday, March 3, 2022 8:10 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:csc435@theochem.mercer.edu">csc435@theochem.mercer.edu</a>
<a class="moz-txt-link-rfc2396E" href="mailto:csc435@theochem.mercer.edu"><csc435@theochem.mercer.edu></a><br>
<b>Subject:</b> [CSC 435] Specifying long batch runtimes</font>
<div> </div>
</div>
<div>
<p><font face="serif">If you need to run a jobs for more than an
hour, you can just update the value of the allocated
walltime in the PBS jobs script.</font></p>
<p><font face="serif">For example...</font></p>
<p>#PBS -l nodes=1:hammer:ppn=42,walltime=48:00:00<br>
</p>
<p>would allocate ALL of hammer for up to 48 hours<br>
</p>
<div class="x_moz-signature">-- <br>
<b><i>Andrew J. Pounds, Ph.D.</i></b><br>
<i>Professor of Chemistry and Computer Science</i><br>
<i>Director of the Computational Science Program</i><br>
<i>Mercer University, Macon, GA 31207 (478) 301-5627</i></div>
</div>
</blockquote>
<p><br>
</p>
<div class="moz-signature">-- <br>
<b>Andrew J. Pounds, Ph.D.</b><br>
<i>Professor of Chemistry and Computer Science</i><br>
<i>Director of the Computational Science Program</i><br>
<i>Mercer University, Macon, GA, 31207 (478) 301-5627 </i></div>
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