[gmx-users] Gromacs Version 5.0.2 - Bug #1603
sdasett at g.clemson.edu
Wed Oct 8 20:24:36 CEST 2014
Thank You Mark for the reply.
Now that clears my confusion about the values in the PP-PME load part of
the log file. However, I am still a little bit confused about how to
distinguish between a normal-but-not-guranteed change and the normal
change, though I understood that for a normal change we can compare the
densities obtained from GPU runs and the CPU only runs to verify the
Also, I have a general question about using vdwtype as PME.
Is it advisable to use vdwtype as PME when I am using GPU runs?
On Wed, Oct 8, 2014 at 12:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
> On Wed, Oct 8, 2014 at 4:29 PM, Siva Dasetty <sdasett at g.clemson.edu>
> > Dear All,
> > I am using gpu enabled gromacs version 5.0.2 and I am checking if my
> > simulation is still affected by bug #1603
> > http://redmine.gromacs.org/issues/1603.
> > Below is the PP-PME load balancing part of my log file
> > PP/PME load balancing changed the cut-off and PME settings:
> > particle-particle PME
> > rcoulomb rlist grid spacing 1/beta
> > initial 1.000 nm 1.092 nm 108 108 120 0.119 nm 0.320 nm
> > final 1.482 nm 1.574 nm 72 72 80 0.178 nm 0.475 nm
> > cost-ratio 3.00 0.30
> > (note that these numbers concern only part of the total PP and PME load)
> > The release notes says,
> > If, for your simulation, the final rcoulomb value (1.368 here) is
> > from the initial one (1.000 here), then so was the LJ cutoff for
> > short-ranged interactions, and the model physics was not what you asked
> > for.
> > Does that mean the initial and final values are supposed to be the same?
> No. The point of the tuning is to change the rcoulomb value to maximize
> performance while maintaining the quality of the electrostatic
> approximation you chose in the .mdp file. If you were using one of the
> affected versions (5.0 or 5.0.1), then the normal-but-not-guaranteed change
> of rcoulomb led to an inappropriate change of rvdw, which is why it is a
> relevant diagnostic for whether an actual simulation from the versions with
> wrong code was affected in practice.
> But the normal change of rcoulomb neither confirms nor denies that the bug
> is fixed in 5.0.2. You could observe that the NPT density in 5.0.2 agrees
> with a CPU-only (or 4.6.x GPU) calculation, for example.
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