Re: [AMBER] pmemd.cuda incomplete output file

From: David Case <>
Date: Sun, 18 Dec 2016 08:45:01 -0500

On Sun, Dec 18, 2016, Andreas Tosstorff wrote:
> The error is not fully reproducible, meaning that the equilibration stops at
> different times. Sometimes after 90 ps sometimes after 200 ps.
> I set ntpr=100 and printed out stderr with "pmemd.cuda .... > out 2>error"
> but no error messages were printed neither in the error file nor the output.

First, how big is your system? pmemd.cuda has a limit on the range of forces
that can be fit into a fixed-point representation, and larger systems have
larger fluctuations that can violate this. Having a fully equilibrated system
would reduce the likelihood of this.

Having said that, pmemd.cuda jobs are supposed to be reproducible. (Perhaps
not after a fixed-point overflow.) But a job that runs for 200ps once, should
give identical results for that long every time, and not sometimes crash after
90 ps. [Here I am assuming that you are re-running the exact job.] Have you
ruled out hardware failure, e.g by seeing the same thing on a different GPU,
and/or by noting that all your other simulations seem to run fine on this GPU?


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Received on Sun Dec 18 2016 - 06:00:04 PST
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