<div dir="ltr"><div dir="ltr"><div>Hi Guido,</div><div><br></div><div>On Fri, Jun 11, 2021 at 3:16 PM Guido Giuntoli <<a href="mailto:guido.giuntoli@huawei.com">guido.giuntoli@huawei.com</a>> wrote:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Thanks Berk and Szilard,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">I am trying to achieve a small system that stills being representative on a single core. If I understood correctly from:
<a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2021-February/011004.html" target="_blank">
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2021-February/011004.html</a> good scaling is achieved typically with setups of 50-1000 atoms/core in order to fit the problem in the LLC.</span></p></div></div></blockquote><div><br></div>*At least in LLC (on CPU-only), in some cases even second-to-last level caches.<br></div><div class="gmail_quote"> <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-US"><div class="gmail-m_2852465987651197902WordSection1"><p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">I am wondering if the water boxes are still representative of this situation without including the bonded forces. Do they use the nbnxn_kernel and the pme computations
in a similar way as a normal use case?</span></p></div></div></blockquote><div><br></div><div>Yes. The only thing different compared to some of the more real-world biomolecular use-cases is the lack of bonded interactions and to some degree a more homogeneous workload distribution (so less tendency for workload-density related imbalance). The latter is hard to "emulate" in systems generated by stacking, but the former would be addressed by either using stacked villin (or to a great extent by using simpler systems like ethanol boxes I mentioned before).<br></div><div> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-US"><div class="gmail-m_2852465987651197902WordSection1"><p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Should I use
<a href="https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-solvate.html" target="_blank">
https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-solvate.html</a> for generating water boxes?</span></p></div></div></blockquote><div><br></div><div>That or just grab a set from here:</div><div><a href="https://ftp.gromacs.org/benchmarks/water_bare_hbonds.tar.gz">https://ftp.gromacs.org/benchmarks/water_bare_hbonds.tar.gz</a></div><div><br></div><div>Cheers,</div><div>--</div><div>Szilárd</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-US"><div class="gmail-m_2852465987651197902WordSection1"><p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Thanks a lot, Guido.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11pt;font-family:"Calibri",sans-serif"> <a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [mailto:<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>]
<b>On Behalf Of </b>Szilárd Páll<br>
<b>Sent:</b> Friday, June 11, 2021 2:55 PM<br>
<b>To:</b> Discussion list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<b>Subject:</b> Re: [gmx-developers] GROMACS uses cases with 50-2K atoms<u></u><u></u></span></p>
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<p class="MsoNormal">Hi,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">RNAse is 18k/24k (dodec/cubic setup), otherwise you can stack the 5k villin and get 10k, 20k,... systems (using "gmx genconf -nbox N M K").<u></u><u></u></p>
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<p class="MsoNormal">Additionally to water boxes, I do have some water + ethanol boxes too which do have bonded interactions, but that will only be useful if you really want the granularity of system sizes beyond what the villing stacking allows. I can share
these if you are interested.<u></u><u></u></p>
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<p class="MsoNormal">Cheers,<u></u><u></u></p>
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<p class="MsoNormal">--<br>
Szilárd<u></u><u></u></p>
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<p class="MsoNormal">On Fri, Jun 11, 2021 at 10:54 AM Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi,<br>
<br>
I don't think we have much else in that range.<br>
<br>
I would use water boxes of different size. They don't have bonded interactions, so you don't test everything, but it is anyhow unrealistic to use a single thread, as synchronization between threads and cache sharing have large effects on the performance of
GROMACS.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 6/9/21 5:37 PM, Guido Giuntoli wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hello,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I would like to know if there are GROMACS use cases/inputs that simulate about 50 – 2K atoms.
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Is there any benchmark hard coded in GROMACS that allows parametrization and test different problem sizes?
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The nonbonded-benchmark helps but I need something that executes all the typical GROMACS algorithms (PME, NxN computations, etc.). I need such a small case for a single-core simulator
where I don’t have any threading facility.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The smallest case (ready to use) that I found up to now is called “villin” with 5K atoms.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thanks a lot, Guido.<u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:10pt;color:rgb(102,102,102)"> </span></b><u></u><u></u></p>
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