<div class="socmaildefaultfont" dir="ltr" style="font-family:Arial, Helvetica, sans-serif;font-size:12pt" ><div dir="ltr" >FYI Scale 4.2.3 went out of support in September 2020. DDN may still support it but there are no updates/enhancements being made to that code stream. It is quite old. Scale 5.0.x goes end of support at the end of April 2022. Scale 5.1.2 was just released and if possible I suggest you upgrade your entire cluster to the Scale 5.1.x release stream.</div>
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<div dir="ltr" >The change to the prefetchAggressivenessRead variable should help, but performance may still not be as you require.</div>
<div dir="ltr" ><div class="socmaildefaultfont" dir="ltr" style="font-family:Arial, Helvetica, sans-serif;font-size:10pt" ><div class="socmaildefaultfont" dir="ltr" style="font-family:Arial, Helvetica, sans-serif;font-size:10.5pt" ><div dir="ltr" ><br><font size="2" face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" ><span style="font-size:1.143em;" >Fred<br>_______________________________________________________<br>Fred Stock | Spectrum Scale Development Advocacy | 720-430-8821<br>stockf@us.ibm.com</span></font></div></div></div></div>
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<blockquote data-history-content-modified="1" dir="ltr" style="border-left:solid #aaaaaa 2px; margin-left:5px; padding-left:5px; direction:ltr; margin-right:0px" >----- Original message -----<br>From: "Stuart Barkley" <stuartb@4gh.net><br>Sent by: gpfsug-discuss-bounces@spectrumscale.org<br>To: gpfsug-discuss@spectrumscale.org<br>Cc:<br>Subject: [EXTERNAL] [gpfsug-discuss] alphafold and mmap performance<br>Date: Tue, Oct 19, 2021 1:25 PM<br>
<div><font size="2" face="Default Monospace,Courier New,Courier,monospace" >Over the years there have been several discussions about performance<br>problems with mmap() on GPFS/Spectrum Scale.<br><br>We are currently having problems with mmap() performance on our<br>systems with new alphafold <<a href="https://github.com/deepmind/alphafold" target="_blank">https://github.com/deepmind/alphafold</a> ><br>protein folding software. Things look similar to previous times we<br>have had mmap() problems.<br><br>The software component "hhblits" appears to mmap a large file with<br>genomic data and then does random reads throughout the file. GPFS<br>appears to be doing 4K reads for each block limiting the performance.<br><br>The first run takes 20+ hours to run. Subsequent identical runs<br>complete in just 1-2 hours. After clearing the linux system cache<br>(echo 3 > /proc/sys/vm/drop_caches) the slow performance returns for<br>the next run.<br><br>GPFS Server is 4.2.3-5 running on DDN hardware. CentOS 7.3<br>Default GPFS Client is 4.2.3-22. CentOS 7.9<br><br>We have tried a number of things including Spectrum Scale client<br>version 5.0.5-9 which should have Sven's recent mmap performance<br>improvements. Are the recent mmap performance improvements in the<br>client code or the server code?<br><br>Only now do I notice a suggestion:<br> mmchconfig prefetchAggressivenessRead=0 -i<br>I did not use this. Would a performance change be expected?<br><br>Would the pagepool size be involved in this?<br><br>Stuart Barkley<br>--<br>I've never been lost; I was once bewildered for three days, but never lost!<br> -- Daniel Boone<br>_______________________________________________<br>gpfsug-discuss mailing list<br>gpfsug-discuss at spectrumscale.org<br><a href="http://gpfsug.org/mailman/listinfo/gpfsug-discuss" target="_blank">http://gpfsug.org/mailman/listinfo/gpfsug-discuss</a> </font></div></blockquote>
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