Hi Jason,
Thanks for you answer.
1) The script runs in serial from the command line (MMPBSA.py) but the
MMPBSA.py.MPI does not run in parallel.
2) There is no problem with the strip mask since the exact same script runs
with older versions of AmberTools and runs on the serial form.
Could the error be something related to the cluster I'm using?
Ahmed Ayoub
Message: 3
> Date: Tue, 4 Mar 2014 16:41:31 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA TrajError
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3p3o4VJKYPD5UAcorh0DeGUB3yz-=
> apmq-kmQCrCLmsbA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Mar 3, 2014 at 6:08 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
>
> > Dear Amber Developers,
> >
> > I have been trying to submit an MMPBSA parallel job. The job works
> > perfectly fine on AmberTools 12 perfectly fine. But on AmberTools 13 it
> > keeps giving me this error although the trajectory files are fine:
> >
>
> Does it work in serial?
>
>
> > TrajError: start frame (1) > total frames (0)
> >
> > Error occured on rank 0.
> >
> > Exiting. All files have been retained.
> >
>
> There are a number of things that might be going wrong here. First,
> strip_mask may be set incorrectly (do you have any water molecules or ions
> that you included as part of your receptor?) Second, you might be asking
> for more processors than you have snapshots in your trajectory. Since
> MMPBSA.py.MPI parallelizes by splitting up frames, you could wind up with
> these kinds of errors.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Research
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Received on Wed Mar 05 2014 - 21:00:03 PST
