<div dir="ltr">Hi,<div><br></div><div>Indeed. I missed this email when Michael wrote it, but I have added a little more flesh on the bones of a provably reproducible build type at <a href="http://redmine.gromacs.org/issues/1587#note-6">http://redmine.gromacs.org/issues/1587#note-6</a></div><div><br></div><div>Mark</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 2, 2014 at 6:20 AM, Shirts, Michael R. (mrs5pt) <span dir="ltr"><<a href="mailto:mrs5pt@eservices.virginia.edu" target="_blank">mrs5pt@eservices.virginia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div><span class="">
<div>> So one can have fully deterministic forces in MD by simply paying a couple of flops per force component in each inner loop.</div>
<div><br>
</div>
</span><div>If there was a way to overload functions in such a way as to make this a compile time option, it might be pretty useful for validation . . .</div>
<div>
<div><br>
</div>
~~~~~~~~~~~~<br>
Michael Shirts<br>
Associate Professor<br>
Department of Chemical Engineering<br>
University of Virginia<br>
<a href="http://michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a><br>
(434) 243-1821</div>
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<div style="font-family:Calibri;font-size:14pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span>Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, November 30, 2014 at 5:40 AM<br>
<span style="font-weight:bold">To: </span>Discussion list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [gmx-developers] reproducability of md sims<br>
</div><div><div class="h5">
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<div dir="ltr"><br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Nov 30, 2014 at 12:03 PM, Carsten Kutzner <span dir="ltr">
<<a href="mailto:ckutzne@gwdg.de" target="_blank">ckutzne@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi,<br>
<span><br>
On 30 Nov 2014, at 11:17, Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>> wrote:<br>
<br>
> Hi,<br>
><br>
> There is documentation on this somewhere.<br>
> Even when running with MPI and/or OpenMP simulations should be reproducible when ran on an identical run<br>
</span>But reductions of several summands into a sum do not yield a bit-identical result across runs.<br>
Therefore I think at least with MPI and/or OpenMP we will never get bit-identical<br>
trajectories unless the order of summation is fixed somehow for such operations.<br>
</blockquote>
<div><br>
</div>
<div>True, but not the whole story. You can leave the order free if you pre-round the operands such that the result is provably insensitive to the order of the operations. See <a href="http://htor.inf.ethz.ch/publications/img/arteaga-fuhrer-hoefler-reproducible-apps-ipdps14.pdf" target="_blank">http://htor.inf.ethz.ch/publications/img/arteaga-fuhrer-hoefler-reproducible-apps-ipdps14.pdf</a>.
So one can have fully deterministic forces in MD by simply paying a couple of flops per force component in each inner loop.</div>
<div><br>
</div>
<div>Mark</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Best,<br>
Carsten<br>
<div>
<div><br>
<br>
> setup. The only things that usually matter, and which -reprod should turn off, are dynamic load balancing and FFTW kernel choice by timing.<br>
> You can mail me your tpr and I can have a look.<br>
><br>
> Cheers,<br>
><br>
> BerkOn Nov 30, 2014 9:05 AM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>> wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> I'm trying to test reproducibility of simulations of liquids. The<br>
>> simulation systems are flexible (no constraints) and run with the<br>
>> -reprod flag, starting from the same tpr, on a single core. However<br>
>> after a few hundred fs the energy starts to diverge.<br>
>><br>
>> Are there factors impacting the reproducibility that are not controlled<br>
>> by the -reprod flag?<br>
>><br>
>> --<br>
>> David van der Spoel, Ph.D., Professor of Biology<br>
>> Dept. of Cell & Molec. Biol., Uppsala University.<br>
>> Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">
+46184714205</a>.<br>
>> <a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">
http://folding.bmc.uu.se</a><br>
>> --<br>
>> Gromacs Developers mailing list<br>
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