Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI

From: Erin Kelly <>
Date: Wed, 15 Jun 2011 14:24:58 -0500

Sorry that BATCH_ERRORS file is incorrect from a previous run; the correct
output is simply what is pasted in the main text of the file. Sorry for the

I should mention that these simulations fail immediately when I submit them,
I don't even have time to see it listed in the job que, so I'm not sure that
shorter runs would help.


On Wed, Jun 15, 2011 at 2:15 PM, David A Case <>wrote:

> On Wed, Jun 15, 2011, Erin Kelly wrote:
> >
> > I've been attempting to complete "Tutorial 1: Molecular dynamics
> simulation
> > of protein" with 3OGP.pdb I was able to make it through the minimizaton,
> > heating, and equilibration steps but was stopped at the production step.
> I
> > was given the following error in an BATCH_ERROR file:
> The output file says this:
> peek_ewald_inpcrd: SHOULD NOT BE HERE
> This indicates that the program could not process your inpcrd file
> (3OGP_equil.rst) correctly. Are you sure that this is really a restart
> file
> from a previous MD (not minimization) run? Is there any chance that your
> file
> naming scheme got mixed up, or something like that?
> It's worth running a very short attempt with the serial code, just to rule
> out any parallel problems, but you will probably see the same error.
> Look at the inpcrd file, especially the last few lines (you might want to
> post
> those). Compare to a restart file from some run that works.
> [In the BATCH_ERRORS file you posted, there is an addition message:
> Unit 5 Error on OPEN:
> This would indicate that the program could not even find the file.
> But since it is reprinted in the output file, it guessing(!!?!) that this
> is
> the BATCH_ERRORS file from some other run. When you have problems, try a
> short interactive run so that errors and warnings don't get lost or
> confused
> with earlier errors, and so on.]
> ...good luck....dac
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Received on Wed Jun 15 2011 - 12:30:05 PDT
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