[gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...

[Szilárd Páll]

On Thu, Mar 7, 2013 at 2:02 PM, Berk Hess <gmx3 at hotmail.com> wrote:

>
> Hi,
>
> This was only a note, not a fix.
> I was just trying to say that what linear algebra library you use for
> Gromacs is irrelevant in more than 99% of the cases.
> But having said that, the choice of library should not complicate the
> configure stage of Gromacs.
>

I guess Evren assumed that GROMACS has an explicit dependency on an
external linear algebra library.

To be concrete, you can simply use the GROMACS internal linear algebra code
by setting -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF.

--
Szilárd

PS: This issue sounds like a valid reason to consider switching external
BLAS/LAPACK off by default.



> Cheers,
>
> Berk
>
> ----------------------------------------
> > Date: Thu, 7 Mar 2013 14:54:39 +0200
> > From: eyurtese at abo.fi
> > To: gmx-users at gromacs.org
> > Subject: RE: [gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA
> detection problems...
> >
> >
> >
> > On Thu, 7 Mar 2013, Berk Hess wrote:
> >
> > >
> > > Hi,
> > >
> > > Note that the linear algebra in Gromacs is limited to eigenvalue
> solving in two analysis tools,
> > > the MD engine does not use any (large) linear algebra.
> > > So linear algebra library performance is irrelevant, except for the
> cases where users
> > > would want to repeated uses one of the two tools with large systems.
> > > Even then, our built-in code is not bad.
> > >
> > > Cheers,
> > >
> > > Berk
> >
> > Hello,
> >
> > I am not sure what you are suggesting as a fix to the problem? Do you
> mean
> > the support for ATLAS should/will be removed as a fix because it is not
> > very useful performancewise (and non-functional) anyway?
> >
> > Thanks,
> > Evren
> > --
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