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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Kevin,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I uploaded the master branch with those two changes under code review, plus a work-around for ICC 17beta to github. You can download this version as<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><a href="https://codeload.github.com/rolandschulz/gromacs/zip/knl">https://codeload.github.com/rolandschulz/gromacs/zip/knl</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Besides the general performance tips you might want to try:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">If you benchmark on a single node try to use only OpenMP with a single MPI rank<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Or use 4 OpenMP and the appropriate number of MPI ranks (both for single node as well as multiple nodes)<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Use 2 way Hyper threading (2 thread / core)<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Try ICC17beta<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Use “numactl –m1” when using Flat mode<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Let me know if you have any other questions.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Roland<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></a></p>
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<p class="MsoNormal"><a name="_____replyseparator"></a><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> gromacs.org_gmx-developers-bounces@maillist.sys.kth.se
[mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se] <b>On Behalf Of </b>
Kevin Chen<br>
<b>Sent:</b> Friday, July 15, 2016 7:27 AM<br>
<b>To:</b> gmx-developers@gromacs.org<br>
<b>Subject:</b> Re: [gmx-developers] Gromacs 5.0 benchmarks<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Roland,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for getting back to us. Yes, it will be great if you could share the latest Gromacs development with all available improvements. In the meantime, we will
give 2016RC a try first.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Kevin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
</span><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
[</span><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">]
<b>On Behalf Of </b>Schulz, Roland<br>
<b>Sent:</b> Thursday, July 14, 2016 12:22 PM<br>
<b>To:</b> </span><a href="mailto:gmx-developers@gromacs.org"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">gmx-developers@gromacs.org</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
<b>Subject:</b> Re: [gmx-developers] Gromacs 5.0 benchmarks<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Kevin,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">GROMACS 2016 has already a lot of KNL optimizations included. Including AVX512(+ER) and OpenMP scaling improvements. The RC is out
</span><a href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016-rc1.tar.gz"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016-rc1.tar.gz</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">.
Additionally there are further improvements publically available in the code-review system which will be included in the 2017 version such as<o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://gerrit.gromacs.org/#/c/5841/"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">https://gerrit.gromacs.org/#/c/5841/</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://gerrit.gromacs.org/#/c/6004/"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">https://gerrit.gromacs.org/#/c/6004/</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">If you want to test a version with all available KNL improvements included feel free to contact me.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Roland<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
</span><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
[</span><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">]
<b>On Behalf Of </b>Kevin Chen<br>
<b>Sent:</b> Thursday, July 14, 2016 7:51 AM<br>
<b>To:</b> </span><a href="mailto:gmx-developers@gromacs.org"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">gmx-developers@gromacs.org</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
<b>Subject:</b> Re: [gmx-developers] Gromacs 5.0 benchmarks<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Mark,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for getting back to me! Here at TACC, we are trying to do some Gromacs benchmarking on Stampede and the Stampede 1.5 (our latest KNL machine) and try to
publish the results on conferences/ tutorials. We could easily make some systems for that purpose. However, we feel it’s always better to get the “official” ones from the developer. As such, it will be great if you could share those files with us.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Speaking of KNL, at TACC we have received first 500 nodes from intel a couple month ago. Those nodes will eventually become the Stampede 1.5 and hopefully be
in production later this year. So I was wondering, if you guys have any plan on testing/optimizing Gromacs code no KNLs in the near future? <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Kevin Chen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
</span><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
[</span><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">]
<b>On Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Thursday, July 7, 2016 5:46 AM<br>
<b>To:</b> GROMACS developers <</span><a href="mailto:gmx-developers@gromacs.org"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">gmx-developers@gromacs.org</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Subject:</b> Re: [gmx-developers] Gromacs 5.0 benchmarks<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Yes we've had a few requests for these. I can share e.g. the .tpr files easily enough but attempting to reproduce them requires driver scripts to scan parameters, etc. and I don't have time right now to make those usable in the hands of
others on arbitrary HPC platforms and job schedulers. What's the purpose of the benchmarking? Are you better served by getting examples of actual .tpr files used by your users, and using those?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Mark<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Thu, Jul 7, 2016 at 12:43 PM Vedran Miletiæ <<a href="mailto:vedran@miletic.net">vedran@miletic.net</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">On 07/06/2016 05:54 PM, Kevin Chen wrote:<br>
> Dear GROMACS developers,<br>
><br>
> We are currently in the process of benchmarking GROMACS5.1.2 on our<br>
> local HPC systems. There are some nice results posted online<br>
> (<a href="http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf" target="_blank">http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf</a>). I<br>
> was wondering if anybody can kindly share the files (such as, pdbs,<br>
> mdps, tops and tprs) used for those tests? We’d like to see if we could<br>
> reproduce any of those results.<br>
><br>
><br>
><br>
> Thank you in advance!<br>
><br>
><br>
><br>
> Kevin Chen<br>
><br>
<br>
Hi Kevin,<br>
<br>
for benchmarking, the following files may be what you are looking for:<br>
<a href="ftp://ftp.gromacs.org/pub/benchmarks/" target="_blank">ftp://ftp.gromacs.org/pub/benchmarks/</a><br>
<br>
Regards,<br>
Vedran<br>
<br>
--<br>
Vedran Miletiæ<br>
<a href="http://vedran.miletic.net" target="_blank">vedran.miletic.net</a><br>
--<br>
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