Hi,
Can you post the exact cpptraj input you used? Do all of the test
cases pass in parallel?
-Dan
On Wed, Nov 21, 2018 at 4:35 AM Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:
>
> Dear Amber users and developers,
>
> when I tried to extract forces in parallel (cpptraj.MPI) from
> a trajectory, the following error occured:
>
> CPPTRAJ: Trajectory Analysis. V18.01 MPI
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Running on 8 threads
> | Date/time: 11/18/18 23:37:33
> | Available memory: 11.006 GB
>
> ************************************************************************
>
> BEGIN PARALLEL TRAJECTORY PROCESSING:
> [2] PNetCDF Error: NetCDF: Action prohibited on NC_GLOBAL varid
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
> with errorcode -50.
>
> 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.
> ________________________________________________________________
>
> What could be the source of this error and how is it possible to overcome
> it?
> I am using Amber18/AmberTools18, gcc (SUSE Linux) 7.3.1 compiler.
> Trajectory processing in serial was OK.
>
> Kind regards,
> Nick
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Received on Mon Nov 26 2018 - 07:00:03 PST
