On Mon, Jul 1, 2013 at 9:01 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Dear users,
>
> I am trying to rum MMPBSA.py.MPI on 5 cores for 1000 frames of simulation.
> The serial version of the same is running properly on the machine, but when
> i 'm trying to submit the same script in parallel, i 'm getting this
> message :
>
>
> 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.
> --------------------------------------------------------------------------
> ImportError: cannot import name run_calculations
> Exiting. All files have been retained.
> ImportError: cannot import name run_calculations
> Exiting. All files have been retained.
> ImportError: cannot import name run_calculations
> Exiting. All files have been retained.
> ImportError: cannot import name run_calculations
> Exiting. All files have been retained.
> ImportError: cannot import name run_calculations
> Exiting. All files have been retained.
>
> -----------------------------------------------------------------------------
>
> Is this has got to do with mpi4py installation?
>
Are your serial and parallel programs installed to different locations?
This error message says that some of the modules inside MMPBSA_mods cannot
be imported. The only reason I can think of that this would happen in
parallel and not serial is if somebody moved all the .MPI programs to a
different folder after they were installed, but never copied over
MMPBSA_mods alongside MMPBSA.py.MPI.
As a general note, MMPBSA.py.MPI is useless without a serial installation
of Amber, since it only calls serial Amber programs (e.g., cpptraj,
mmpbsa_py_energy, sander, etc.)
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 01 2013 - 16:00:02 PDT
