where you able to run OTHER sander or pmemd multi core files ?
Run some of them as found in the test directory of the amber
installation. That way we can figure out if this is a problem with
constant pH or if it is related to amber itself.
Thanks
adrian
On 2/17/16 9:22 AM, Elisa Pieri wrote:
> Dear all,
>
> I'm experiencing problems running pH-REMD on my computer. I have these
> machine: Intel® Xeon(R) CPU E5-2623 v3 @ 3.00GHz × 16, and I ran
> simulations using pmemd.MPI with no problems (I have Amber14). Now I'm
> using this command:
>
> mpirun -np 16 pmemd.MPI -ng 8 -groupfile prova.grpfile &
>
> Unfortunately, I get this error:
>
> Running multipmemd version of pmemd Amber12
> Total processors = 16
> Number of groups = 8
>
> --------------------------------------------------------------------------
> 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 12 with PID 4994 on
> node agachon 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).
> --------------------------------------------------------------------------
> [agachon:04981] 7 more processes have sent help message help-mpi-api.txt /
> mpi-abort
> [agachon:04981] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
> Can you help me?
>
> Elisa
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Feb 17 2016 - 07:00:04 PST
