What version of amber are you using? If you're using amber11, pmemd.MPI
should be installed automatically alongside sander.MPI. Moreover, if
pmemd.MPI was not installed, you'd see something about "command not found",
not
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
MPI version of PMEMD must be used with 2 or more processors!
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
I still think my previous response is the most likely. The above messages
are basically 4 threads of pmemd.MPI that are unaware of any kind of MPI
world. i.e. mpirun from, say, openMPI not playing nice with pmemd.MPI
compiled from an mpich2 mpif90. Do you have MPI_HOME set? What is
$MPI_HOME/bin/mpirun and `which mpirun` ? Are they different?
Good luck!
Jason
On Thu, Sep 16, 2010 at 1:46 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I'd like to retract the previous message.
>
> It seems that pmemd.MPI was not installed during the installation.
> sander.MPI was
>
> So my question is whether there's a special procedure to install it?
>
> George
>
>
> On Sep 16, 2010, at 7:35 PM, George Tzotzos wrote:
>
> > Hi everybody
> >
> > amber11 parallel has been installed and passed all tests.
> >
> > I'm running OSX on a 4 Core 2.8 GHz Intel Core i7 machine.
> >
> > Running: mpirun -np 4 sander.MPI etc. works smoothly
> >
> > Running: mpirun -np 4 pmemd.MPI produces the following error.
> >
> > MPI version of PMEMD must be used with 2 or more processors!
> > MPI version of PMEMD must be used with 2 or more processors!
> > MPI version of PMEMD must be used with 2 or more processors!
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > MPI version of PMEMD must be used with 2 or more processors!
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >
> > Any ideas as to why?
> >
> > Thanks in advance and regards
> >
> > George
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 16 2010 - 11:00:07 PDT
