AMBER Archive (2007)

Subject: Re: AMBER: Problem with running Sander

From: Lili Peng (lilipeng_at_gmail.com)
Date: Tue Jul 10 2007 - 16:50:45 CDT

Hi Dr. Case,

I tried running the AMBER advanced tutorial A2 with the NMA file, and I
receive the same error message. I've tried Googling the error but nothing
relevant came up. I'm not sure what MPI I'm using. I'm running AMBER 9 on
a Linux machine via ssh to the SDSC Teragrid machine, and I don't know if
the MPI can be changed through that.

Thanks,
Lili

On 7/7/07, David A. Case <case_at_scripps.edu> wrote:
>
> On Sat, Jul 07, 2007, Lili Peng wrote:
> >
> > I'm trying to do a classical MD simulation for a pdb file using
> Sander. I
> > have generated the .inpcrd and .prmtop files but when I try to run the
> > initial energy minimization, I get this error:
> >
> > "*Need to obtain the job magic number in GMPI_MAGIC ! Broken pipe*"
>
> This is not an Amber error message: it comes from your MPI implementation.
> It has nothing to do with how you built your topology files, and so on.
>
> Can you run the parallel test cases? If not, that is the place to start,
> and you may have to consult your MPI documentation (what MPI are you
> using?)
> If you can run the parallel test cases, look carefully to see if there is
> anything different in the way you are running those, and the way you are
> running this job (the one that fails).
>
> Others on the list may recognize the exact error message, and be able to
> suggest a specific fix....
>
> ...regards...dac
>
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