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<p class="MsoNormal">Hi All, We are going through our first setup of ood and have a question regarding environments. If I were to submit a job outside of the ood browser using a submission script like this to PBS:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#!/bin/bash<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -V<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -l select=1:ncpus=2:mpiprocs=2<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -l walltime=01:00<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -N hostname.pbs<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -j oe<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:.5in">module load prun/1.1 gnu7/7.1.0 openmpi/1.10.7 ohpc<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">mpirun hostname<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Resulting in an output file similar to this:<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">compute-0-1<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">compute-0-1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I submit the same job through the ood console using the Job Composer I end up getting this error:<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">/var/spool/pbs/mom_priv/jobs/29.vbcluster1.nor-tech.com.SC: line 9: module: command not found<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">/var/spool/pbs/mom_priv/jobs/29.vbcluster1.nor-tech.com.SC: line 11: mpirun: command not found<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have been able to get around this issue by sourcing the lmod init script inside my job script like this:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#!/bin/bash<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -V<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -l select=1:ncpus=2:mpiprocs=2<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -N hostname.pbs<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">#PBS -j oe<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:.5in">export MODULEPATH=/opt/ohpc/pub/moduledeps/gnu7-openmpi:/opt/ohpc/pub/moduledeps/gnu7:/opt/ohpc/pub/modulefiles<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">source /opt/ohpc/admin/lmod/lmod/init/bash<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">module load prun/1.1 gnu7/7.1.0 openmpi/1.10.7 ohpc<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:.5in">mpirun hostname<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoNormal">Is there a way to pass the user’s full environment to the job so we don’t have to do the sourcing above? Usually in PBS you’d use the ‘#PBS –V’ option but that is not working with the ood.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance, Kyle<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#1F497D">Kyle Gross |
</span><span style="color:#1F497D"><a href="mailto:kyleg@nor-tech.com"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:green">kyleg@nor-tech.com</span></a></span><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D"><br>
</span><span style="font-size:7.5pt;font-family:"Trebuchet MS",sans-serif;color:gray">Senior HPC Technician<br>
901 East Cliff Road, Burnsville, MN 55337<br>
Direct 952-229-2086 | Fax 952-229-2061</span><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Trebuchet MS",sans-serif;color:#1F497D"><img border="0" width="89" height="37" style="width:.927in;height:.3854in" id="Picture_x0020_0" src="cid:image001.jpg@01D3434F.E160C810" alt="NT logo.jpg"></span><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#1F497D">Burnsville,
Minn.<o:p></o:p></span></p>
<p class="MsoNormal"><b><i><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:teal">People Friendly Technology with a Global Reach</span></i></b><span style="font-size:10.0pt;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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