mpirun -np 4 $AMBERHOME/bin/sander.MPI -O -i blah.in -o blah.out ...
The variable after -np allows you to choose the number of processors you wish to run for your mpi task.
You may need to set MPI_HOME to your MPI directory and export the path.
Charlie
________________________________________
From: Sreemol G [sreemolinfo.gmail.com]
Sent: Tuesday, April 05, 2016 9:31 PM
To: david.case.rutgers.edu; AMBER Mailing List
Subject: Re: [AMBER] General question
Thanks for your suggestions. I have configured using -mpi gnu and installed
ambertools15. But I dont have Amber14 installed. I'm running sander.MPI
even now it is running in single node (| Running AMBER/MPI version on 1
nodes) . What could I do to run in 4 nodes??
On Mon, Apr 4, 2016 at 6:31 PM, David A Case <david.case.rutgers.edu> wrote:
> On Mon, Apr 04, 2016, Sreemol G wrote:
>
> > configure: error: could not find mpi library for --enable-mpi"
> >
> > my system has mpi/openmpi-x86_64 installed in it.
>
> It's almost sure that the system mpi is using a different compiler than the
> one you specified in the configure step (which was gnu 5.3). You can check
> this by typing
>
> mpicc -show
>
> (or something similar). The simplest way to get a compatible mpi is
> to cd to $AMBERHOME/AmberTools/src and run "configure_mpich" -- see the
> comments at the top of this file for instructions.
>
> An alternative (depending on your experience and the type of computer you
> are
> running on) is to figure out which compiler your system mpi is using, and
> configure with that option.
>
> Also, you will almost certainly get better performance by running pmemd.MPI
> in place of sander.MPI (if you have Amber14 installed).
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Tue Apr 05 2016 - 22:00:04 PDT
