From: Jason Swails <>
Date: Fri, 24 Jul 2015 09:28:11 -0400

> On Jul 24, 2015, at 8:28 AM, Amber mail <> 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?


> I appreciate If you could help me
> Thanks for your time!
> Best Regards,
> Alaa
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 24 2015 - 06:30:03 PDT
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