Manual Appendix A.2; note that the last one among the reasons listed for needing double will soon not be the case anymore (see verlet scheme in 4.6 http://www.gromacs.org/Documentation/Cut-off_schemes).
-- Szilárd 2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro <[email protected]>: > Thank you, Szilárd. > > Do you know where (say, in a piece of code or some documentation) I can be > sure about that? > Cheers, > > Pedro. > Em 17 de abril de 2012 15:43, Szilárd Páll <[email protected]> > escreveu: > >> 2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro >> <[email protected]>: >> > Hi, >> > >> > I've come across a discussion about the "single X double precision" >> > issue in >> > a NAMD users list e-mail >> > (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9166.html). >> > I would like to know what do you think about these 3 specific points: >> > >> > 1) "there are some places where single precision (FFT, force/energy >> > computation), where single precision can be applied, but in other >> > places (summations) where even double precision may result in >> > artefacts, due to limited numerical accuracy for large enough >> > systems. there are some applications that show little sensitivity >> > to single/double precision issues (homogeneous bulk lennard-jones >> > systems), but others are notoriously difficult (systems with >> > significant potential drops in one or two dimensions, e.g. metal >> > surface slabs or lipid bilayers) since you don't have that much >> > error cancellation anymore." >> > >> > 2) "if you store coordinates in single precision, you have to take >> > extra precautions for handling very large systems, since you >> > would store coordinates with different relative precision, >> > depending on how close you are to the origin. e.g., with domain >> > decomposition, you can define per domain offsets, but that >> > would work only well in case of a large enough number of domains. " >> > >> > 3) "the best way to study the impact of single vs. double would be >> > by running tests with the gromacs code. gromacs _can_ be compiled >> > in single or double precision. for a proper comparison, you'll have >> > to turn off the assembly innerloops though, since they may use single >> > precision even in double precision mode." >> > >> > Specifically this last point startled me. In fact, is this true? >> >> AFAIK no, the assembly (SSE intrinsic in 4.6) kernels have both single >> and double versions. If double precision is requested that's always >> respected in the code. >> >> Additionally, single precision in GROMACS is in fact not *pure* single >> precision, in some parts of the code where needed double precision is >> used (e.g. constraints). Therefore, technically what we call single >> corresponds to what some MD packages call mixed precision. >> >> -- >> Szilárd >> >> >> > Cheers, >> > >> > Pedro. >> > >> > >> > -- >> > gmx-users mailing list [email protected] >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to [email protected]. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
