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<div>Ok, we’ll try it with mpiexec. Thanks for your help.</div>
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<div>Karsten</div>
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<div id="divRplyFwdMsg" dir="dir="ltr""><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Carson Holt <carsonhh@gmail.com><br>
<b>Sent:</b> Tuesday, March 12, 2019 11:07 AM<br>
<b>To:</b> Siller, Karsten H (khs3z)<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] Running MAKER with MPI support and SLURM scheduler
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Launch with OpenMPI’s mpiexec command. The slurm stun command you are using won’t launch it as expected.
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<div>—Carson<br>
<div dir="ltr"><br>
On Mar 12, 2019, at 6:39 AM, Siller, Karsten H (khs3z) <<a href="mailto:khs3z@virginia.edu">khs3z@virginia.edu</a>> wrote:<br>
<br>
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<blockquote type="cite">
<div dir="ltr"><span class="" style="font-size:14px">Hi,</span>
<div class=""><span class="" style="font-size:14px"><br class="">
</span></div>
<div class=""><span class="" style="font-size:14px">We have configured and installed MAKER 2.31 with OpenMPI 2.1.5 on our HPC cluster. During build/installation, the MPI libs and mpicc wrapper are found. This is the output of ./Build status</span></div>
<div class=""><span class="" style="font-size:14px"><br class="">
</span></div>
<div class="">
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">==============================================================================</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">STATUS MAKER v2.31.10</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">==============================================================================</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">PERL Dependencies:<span class="Apple-tab-span" style="white-space:pre"></span>VERIFIED</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">External Programs:<span class="Apple-tab-span" style="white-space:pre"></span>VERIFIED</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">External C Libraries:<span class="Apple-tab-span" style="white-space:pre"></span>VERIFIED</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">MPI SUPPORT:<span class="Apple-tab-span" style="white-space:pre"></span>ENABLED</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">MWAS Web Interface:<span class="Apple-tab-span" style="white-space:pre"></span>DISABLED</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">MAKER PACKAGE:<span class="Apple-tab-span" style="white-space:pre"></span>CONFIGURATION OK</span></div>
</div>
<div class=""><span class="" style="font-size:14px"><br class="">
</span></div>
<div class="">
<div class=""><span class="" style="background-color:rgb(255,255,255); font-size:14px"><font color="#2f3941" class="">This is how we run MAKER (the number of nodes and tasks are set via #SBATCH directives):</font></span></div>
<div class=""><span class="" style="background-color:rgb(255,255,255); font-size:14px"><font color="#2f3941" class=""><br class="">
</font></span></div>
<div class="">
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-size:14px"><span class="" style="font-variant-ligatures:no-common-ligatures">srun maker </span><span class="" style="font-variant-ligatures:no-common-ligatures; color:rgb(205,121,35)">></span><span class="" style="font-variant-ligatures:no-common-ligatures"> maker_small_PARALLEL</span></span></div>
</div>
</div>
<div class=""><span class="" style="font-size:14px"><br class="">
</span></div>
<div class=""><span class="" style="font-size:14px">This launches the correct number of MAKER processes across nodes but we’re seeing messages in the output </span><span class="" style="font-size:14px; color:rgb(47,57,65); background-color:rgb(255,255,255)">"WARNING:
Multiple MAKER processes have been started in the same directory.</span><font color="#2f3941" class="" style="font-size:14px">” The processes appear to run ok, but we want to make sure there’s nothing fundamentally wrong with how we run MAKER.</font></div>
<div class=""><span class="" style="color:rgb(47,57,65); background-color:rgb(255,255,255); font-size:14px"><br class="">
</span></div>
<div class=""><span class="" style="background-color:rgb(255,255,255)"><font color="#2f3941" class=""><span class="" style="font-size:14px">Browsing the mailing list, I came across similar posts and it was suggested that there’s an issue either with the MAKER
MPI configuration or with the scheduler. We’re positive that the scheduler is configured properly since many other MPI applications run without problems on the cluster with the same scheduler and MPI implementation. </span></font></span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px"><br class="">
</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">Is it possible that launching MAKER processes via srun is not supported? Or is the warning harmless and can be ignored?</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px"><br class="">
</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">Thanks,</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">Karsten</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px"><br class="">
</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">—</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px"><br class="">
</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-variant-ligatures:no-common-ligatures; font-size:14px">Karsten Siller</span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal; background-color:rgb(255,255,255)">
<span class="" style="font-size:14px">University of Virginia</span></div>
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</blockquote>
<blockquote type="cite">
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