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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 27 2011 - 15:30:02 PST
