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

From: Ben Roberts <>
Date: Fri, 30 Dec 2011 19:14:02 -0500

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.

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Received on Fri Dec 30 2011 - 16:30:04 PST
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