Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error

From: Ben Roberts <>
Date: Mon, 12 Dec 2011 16:19:14 -0500

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.

However, I'll see how the NVT looks on completion, and possibly try again, before getting too concerned.

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Received on Mon Dec 12 2011 - 13:30:02 PST
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