Hi Jason,
I figured this out. The solution is simple, given by standard output of
one of the mpiexec commands:
cd $HOME
touch .mpd.conf
chmod 600 .mpd.conf
vim .mpd.conf #insert your secretword here:
SECRETWORD=your_secret_word_here
mpd &
./Run &
Just in case anyone else runs into this error in the future.
Thanks so much for your help Jason!
Have a happy 2012,
-Dave
On Tue, Dec 27, 2011 at 6:00 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Dec 27, 2011 at 12:20 PM, David Condon <dec986.gmail.com> wrote:
>
> > Hello,
> >
> > I am trying to make AMBER11 parallel for PMEMD production runs on my
> lab's
> > 8-cpu desktop computer, following instructions on
> > http://ambermd.org/ubuntu.html The installation completed.
> >
> > However, I am trying to run PMEMD with the following:
> >
> > mpirun -np 8 pmemd -O -i md3.in -o 18.out -p prmtop -c 17.rst -r 18.rst
> -x
> > > 18.mdcrd
> >
>
> This doesn't sound like it'll solve the issue you're having, but pmemd is
> the serial version of pmemd in Amber 11. Now, pmemd.MPI is the parallel
> version.
>
> >
> >
> > as I have done successfully on other AMBER11 installations.
> >
> > This time, however, I get the error:
> >
> > mpiexec failed: gethostbyname_ex failed for zip.chem.rochester.edu
> > >
> >
> > I don't think this is an AMBER-specific problem but something wrong with
> > /etc/hosts; but I have no idea how to fix it.
> >
> > What changes can I make so I run PMEMD in parallel?
> >
> > thanks for your expertise,
> > -Dave
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 27 2011 - 16:00:02 PST
