[gmx-users] Intel and GNU compiler
spoel at xray.bmc.uu.se
Wed Aug 10 09:48:47 CEST 2005
On Wed, 2005-08-10 at 00:32 -0700, leafyoung81-group at yahoo.com wrote:
> --- David <spoel at xray.bmc.uu.se> wrote:
> > > > Topologies shall mean trajectory and end
> > structure.
> > > If I use Cut-off instead of PME for coulomb (no
> > FFT), the trajectories
> > > are the same.
> > It is actually more surprising that they are the
> > same than that they
> > would be different, since small numerical
> > differences quickly diverge.
> Sorry for misleading. Cut-off trajectories are the
> same between different runs. They are different from
> those "PME" runs.
> I did another test that, by turning "optimize_fft"
> off, PME trajectories are the same between different
> runs. Are those code in gromacs "compiler specific"?
That algorithm (part of FFTW) tests different ways of computing the FFT
you need and chooses the fastest one. This may give different results
depending on compiler, and hence different trajectories. The average
energies and densities should be identical over a long trajectory.
> > --
> > David.
> > David van der Spoel, PhD, Assoc. Prof., Molecular
> > Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala
> > University.
> > Husargatan 3, Box 596, 75124 Uppsala,
> > Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org
> > http://xray.bmc.uu.se/~spoel
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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