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<p style="margin:0;"><br></p>
<p style="margin:0;">Dear Michael,</p>
<p style="margin:0;"><br></p>
<p style="margin:0;">There are settings within relion for parallel file systems, you should check they are enabled if you have SS underneath.</p>
<p style="margin:0;"><br></p>
<p style="margin:0;">Otherwise, check which version of relion and then try to understand the problem that is being analysed a little more.</p>
<p style="margin:0;"><br></p>
<p style="margin:0;">If the box size is very small and the internal symmetry low then the user may read 100,000s of small "picked particle" files for each iteration opening and closing the files each time.</p>
<p style="margin:0;"><br></p>
<p style="margin:0;">I believe that relion3 has some facility for extracting these small particles from the larger raw images and that is more SS-friendly. Alternatively, the size of the set of picked particles is often only in 50GB range and so staging to one or more local machines is quite feasible...</p>
<p style="margin:0;"><br></p>
<p style="margin:0;">Hope one of those suggestions helps.</p>
<p style="margin:0;">Regards,<br>Robert</p>
<p style="margin:0;"><br></p>
<div class="signature">--<br><br>Dr Robert Esnouf<br><br>University Research Lecturer,<br>Director of Research Computing BDI,<br>Head of Research Computing Core WHG,<br>NDM Research Computing Strategy Officer<br><br>Main office:<br>Room 10/028, Wellcome Centre for Human Genetics,<br>Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK<br><br>Emails:<br><a href="mailto:robert@strubi.ox.ac.uk">robert@strubi.ox.ac.uk</a> / <a href="mailto:robert@well.ox.ac.uk">robert@well.ox.ac.uk</a> / <a href="mailto:robert.esnouf@bdi.ox.ac.uk">robert.esnouf@bdi.ox.ac.uk</a><br><br>Tel: (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)<br> </div>
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<hr size="1">-----Original Message-----<br>From: "Michael Holliday" <<a href="mailto:michael.holliday@crick.ac.uk">michael.holliday@crick.ac.uk</a>><br>To: <a href="mailto:gpfsug-discuss@spectrumscale.org">gpfsug-discuss@spectrumscale.org</a><br>Date: 27/02/19 12:21<br>Subject: [gpfsug-discuss] relion software using GPFS storage<br><br><div class="WordSection1">
<p class="MsoNormal">Hi All,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">We've recently had an issue where a job on our client GPFS cluster caused out main storage to go extremely slowly. The job was running relion using MPI (<a href="https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page">https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page</a>)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">It caused waiters across the cluster, and caused the load to spike on NSDS on at a time. When the spike ended on one NSD, it immediately started on another. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">There were no obvious errors in the logs and the issues cleared immediately after the job was cancelled. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Has anyone else see any issues with relion using GPFS storage?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Michael</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#7F7F7F" lang="EN-GB">Michael Holliday RITTech MBCS</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#7F7F7F" lang="EN-GB">Senior HPC & Research Data Systems Engineer | eMedLab Operations Team</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#767171" lang="EN-GB">Scientific Computing STP | The Francis Crick Institute</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#767171" lang="EN-GB">1, Midland Road | London | NW1 1AT | United Kingdom</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#7F7F7F" lang="EN-GB">Tel: 0203 796 3167</span></p>
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