<div>Thank you, Szilárd.</div>
<div> </div>
<div>Do you know where (say, in a piece of code or some documentation) I can be sure about that?<br></div>
<div>Cheers,</div>
<div> </div>
<div>Pedro.<br></div>
<div class="gmail_quote">Em 17 de abril de 2012 15:43, Szilárd Páll <span dir="ltr"><<a href="mailto:szilard.pall@cbr.su.se">szilard.pall@cbr.su.se</a>></span> escreveu:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro <<a href="mailto:palaplou@gmail.com">palaplou@gmail.com</a>>:<br>
<div>
<div class="h5">> Hi,<br>><br>> I've come across a discussion about the "single X double precision" issue in<br>> a NAMD users list e-mail<br>> (<a href="http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9166.html" target="_blank">http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9166.html</a>).<br>
> I would like to know what do you think about these 3 specific points:<br>><br>> 1) "there are some places where single precision (FFT, force/energy<br>> computation), where single precision can be applied, but in other<br>
> places (summations) where even double precision may result in<br>> artefacts, due to limited numerical accuracy for large enough<br>> systems. there are some applications that show little sensitivity<br>> to single/double precision issues (homogeneous bulk lennard-jones<br>
> systems), but others are notoriously difficult (systems with<br>> significant potential drops in one or two dimensions, e.g. metal<br>> surface slabs or lipid bilayers) since you don't have that much<br>> error cancellation anymore."<br>
><br>> 2) "if you store coordinates in single precision, you have to take<br>> extra precautions for handling very large systems, since you<br>> would store coordinates with different relative precision,<br>
> depending on how close you are to the origin. e.g., with domain<br>> decomposition, you can define per domain offsets, but that<br>> would work only well in case of a large enough number of domains. "<br>><br>
> 3) "the best way to study the impact of single vs. double would be<br>> by running tests with the gromacs code. gromacs _can_ be compiled<br>> in single or double precision. for a proper comparison, you'll have<br>
> to turn off the assembly innerloops though, since they may use single<br>> precision even in double precision mode."<br>><br>> Specifically this last point startled me. In fact, is this true?<br><br></div>
</div>AFAIK no, the assembly (SSE intrinsic in 4.6) kernels have both single<br>and double versions. If double precision is requested that's always<br>respected in the code.<br><br>Additionally, single precision in GROMACS is in fact not *pure* single<br>
precision, in some parts of the code where needed double precision is<br>used (e.g. constraints). Therefore, technically what we call single<br>corresponds to what some MD packages call mixed precision.<br><br>--<br>Szilárd<br>
<br><br>> Cheers,<br>><br>> Pedro.<br>><br><span class="HOEnZb"><font color="#888888">><br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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</font></span></blockquote></div><br>