Hi Ben,
Did you try with bugfix 20? -
http://ambermd.org/bugfixes11.html
All the best
Ross
> -----Original Message-----
> From: Ben Roberts [mailto:ben.roberts.geek.nz]
> Sent: Friday, December 30, 2011 4:14 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error
>
>
> On 30/12/2011, at 7:08 p.m., Ben Roberts wrote:
>
> > Hi again,
> >
> > On 12/12/2011, at 4:19 p.m., Ben Roberts wrote:
> >
> >> Hi Ross,
> >>
> >> On 12/12/2011, at 1:51 p.m., Ross Walker wrote:
> >>
> >>> Hi Ben,
> >>>
> >>> I believe this is a known (and fixed in the development tree) bug.
> A patch
> >>> will be released in a bit when I have dealt with some pending
> deadlines.
> >>>
> >>> If this is the same bug it is actually due to problems with the
> system
> >>> itself. If the code gets a cell with zero atoms in it crashes. This
> happens
> >>> only when you have huge vacuum bubbles in your system. Ideally the
> code
> >>> should probably quit with a message about the system being very
> >>> inhomogenous. Either way if it is this bug fixing it probably won't
> help you
> >>> much as your system is probably messed up with vacuum bubbles. Try
> looking
> >>> at the restart file carefully and see if you have some void spaces
> in your
> >>> system.
> >>>
> >>> Then try running a much shorter NVT heating stage before switching
> on NPT.
> >>> Maybe do a short pressure equilibration on the CPU to equilibrate
> out any
> >>> vacuum bubbles and then switch to the GPU code.
> >>>
> >>> If this isn't the issue, I.e. your system looks fine then please
> post the
> >>> necessary files to reproduce it and we can take a look at it.
> >>
> >> I'm currently running an NVT simulation to do further equilibration.
> When I looked at the system, though, there didn't seem to be any
> dishing or bubbling. The only part of the solvent that looked a bit
> thin to me was where I might have expected the solute's periodic image
> to be.
> >
> > I've done a bit more investigation, incorporating Scott and Ross'
> suggestions for debugging. Specifically, I ran with a known "ig" value
> (viz., 123456), and I asked for coordinates and velocities to be saved,
> and energies to be logged, at every step.
> >
> > I got the output results shown at the end of this email.
>
> I forgot to mention: I'm willing to supply my input files on request,
> via an appropriate channel. Because my inpcrd file is some 22 MB and my
> prmtop weighs in at 54 MB, I didn't want to attach them to any old
> email to the list.
>
> B.
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Received on Fri Dec 30 2011 - 17:30:02 PST
