Dear AMBER community,
I just want to point out that some other simulations were completed
successfully on the cluster without any problems, so I am sure that
pmemd.MPI is working.
Best Regards,
Alaa
On Fri, Jul 24, 2015 at 2:28 PM, 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.
>
> I appreciate If you could help me
>
> Thanks for your time!
>
> Best Regards,
> Alaa
>
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Received on Fri Jul 24 2015 - 06:00:04 PDT
