<p dir="ltr">Hi,</p>
<p dir="ltr">Some work has started, but it will take a while to complete.</p>
<p dir="ltr">Mark</p>
<div class="gmail_quote">On Aug 16, 2014 8:00 AM, "Yorquant Wang" <<a href="mailto:wangykoo@gmail.com">wangykoo@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><span style="color:rgb(0,0,0);font-family:'lucida Grande',Verdana;font-size:14px;line-height:19.16666603088379px">Hi,</span><br style="color:rgb(0,0,0);font-family:'lucida Grande',Verdana;font-size:14px;line-height:19.16666603088379px">
<span style="color:rgb(0,0,0);font-family:'lucida Grande',Verdana;font-size:14px;line-height:19.16666603088379px"> So, if the size of the simulation is big enough, FMM can be faster than PME. Even though I heard that FMM is very hard to be coded into program, I just want to know the state of implement of FMM to GMX5.x . </span><br style="color:rgb(0,0,0);font-family:'lucida Grande',Verdana;font-size:14px;line-height:19.16666603088379px">
<span style="color:rgb(0,0,0);font-family:'lucida Grande',Verdana;font-size:14px;line-height:19.16666603088379px"> It seems that FMM probabily can behave better than PME in massively parallelled architecture hardware, for example the mutliple GPU or CPU or MIC nodes clusters. I quite look forword that. </span><br>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-08-15 4:42 GMT+08:00 Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Thu, Aug 14, 2014 at 1:42 PM, Smart Eagle <span dir="ltr"><<a href="mailto:wangykoo@gmail.com" target="_blank">wangykoo@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hi,</div><div> I just notice that GMX have plan to implement FMM in to GMX to calculate long-term forces for MD. You know PME will suffer FFT NxN all communactiom problems and FMM seemly can scale much better than FME. Indeed there have been a progrom called MODYLAS which have implement FMM to MD (J. Chem. Theory Comput. 2013, 9, 3201−3209<span style="line-height:0px"></span>). </div>
<div> I just want to know therotically, which is larger between FMM and PME for the time cost of long-term forces calculation in one MD steps in one nodes ? (means the basic calculation load for each method without consideration of communications between nodes). <span style="line-height:0px"></span><span style="line-height:0px"></span><span style="line-height:0px"></span></div>
</blockquote><div><br></div></div></div><div>Theoretically - it depends on the size of the simulation (which fixes N) and the quality of the implementations (which fix the prefactors in the asymptotic analysis of O(N) vs O(N log N)).</div>
<div><br></div><div>Practically - you could analyze the total flops on a given problem, but it would tell you little about the performance on a single node, because how well the implementation handles data flow is what dominates performance (now, and more so in the future). Adding inter-node parallelism makes that worse.</div>
<div><br></div><div>Mark</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>cheers up</div><div><br></div><span><font color="#888888"><br>
--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
</font></span></blockquote></div><br></div></div>
<br>--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><span><font color="#888888">Yukun Wang <br>PhD candidate<br><span style="text-align:center">Institute of Natural Sciences && College of Life Science, Shanghai Jiao Tong University</span><br>
Cell phone: 13621806236.<br>China Shanghai</font></span>
</div>
<br>--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
</blockquote></div>