[gmx-users] single X double precision
Pedro Alexandre de Araújo Gomes Lapido Loureiro
palaplou at gmail.com
Tue Apr 17 20:52:58 CEST 2012
Thank you, Szilárd.
Do you know where (say, in a piece of code or some documentation) I can be
sure about that?
Em 17 de abril de 2012 15:43, Szilárd Páll <szilard.pall at cbr.su.se>escreveu:
> 2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro <
> palaplou at gmail.com>:
> > 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.
> > Cheers,
> > Pedro.
> > --
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