Dear Jason,
Thanks for your help!
I didn't get mdout file, and there are no steps completed since the run was
terminated.
I just got an uncompleted output file, the last few lines in this file are:
--------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> default_name
>
> begin time read from input coords = 0.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> ERROR: No "wt" namelist with TYPE=END found
>
Best Regards,
Alaa
On Fri, Jul 24, 2015 at 3:28 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Jul 24, 2015, at 8:28 AM, Amber mail <amber.auc14.gmail.com> wrote:
> >
> > Dear AMBER community,
> >
> > I was running a MD parallel simulation using AMBER12 with pmemd.MPI on a
> > cluster, and I got the error below:
> >
> >
> --------------------------------------------------------------------------
> >> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >> with errorcode 1.
> >>
> >> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >> You may or may not see output from other processes, depending on
> >> exactly when Open MPI kills them.
> >>
> --------------------------------------------------------------------------
> >>
> --------------------------------------------------------------------------
> >> mpirun has exited due to process rank 0 with PID 21536 on
> >> node e01 exiting improperly. There are two reasons this could occur:
> >>
> >> 1. this process did not call "init" before exiting, but others in
> >> the job did. This can cause a job to hang indefinitely while it waits
> >> for all processes to call "init". By rule, if one process calls "init",
> >> then ALL processes must call "init" prior to termination.
> >>
> >> 2. this process called "init", but exited without calling "finalize".
> >> By rule, all processes that call "init" MUST call "finalize" prior to
> >> exiting or it will be considered an "abnormal termination"
> >>
> >> This may have caused other processes in the application to be
> >> terminated by signals sent by mpirun (as reported here).
> >>
> --------------------------------------------------------------------------
> >> ~
> >
> > I have checked my input files and everything were correct.
>
> This error message is very generic and basically only says "something went
> wrong" -- not nearly enough to tell us WHAT went wrong.
>
> Do you see any other error messages in your mdout file? If not, how many
> steps completed? Can you try a short serial simulation to see if you get a
> better error report?
>
> HTH,
> Jason
>
> >
> > I appreciate If you could help me
> >
> > Thanks for your time!
> >
> > Best Regards,
> > Alaa
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 24 2015 - 07:00:02 PDT
