AMBER Archive (2007)

Subject: Re: AMBER: Problem with running Sander

From: Lili Peng (lilipeng_at_gmail.com)
Date: Tue Jul 10 2007 - 18:01:11 CDT

sorry i meant "sander.1cpu"

On 7/10/07, Lili Peng <lilipeng_at_gmail.com> wrote:
>
> Hi Dr. Case,
>
> By test case do you mean the tutorial? I was running the simulation with
> the NMA tutorial. But I actually called SDSC, and they were able to help me
> resolve the problem. Basically the problem had to do something with that
> the tutorial was written for a single user, and with my case I was running
> it on different nodes. All I had to do was to replaced the "sander" with
> the executable file " sander1.cpu" and the program was executed
> successfully.
>
> Thanks for your response,
> LIli
>
> On 7/10/07, David A. Case < case_at_scripps.edu> wrote:
> >
> > On Tue, Jul 10, 2007, Lili Peng wrote:
> > >
> > > 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.
> >
> > Again: this message has nothing to do with Amber: it doesn't depend on
> > on what molecule or system you are running.
> >
> > Now that we know you are trying to run on SDSC Tergrid, people on the
> > list
> > may know more about how to help you. If not, contact the support people
> > at SDSC.
> >
> > I note that you did not reply to my earlier question: "Can you run the
> > test
> > cases?" It's always good to check this out, since we know that the test
> > cases
> > should work, and we can rule out user error in creating the input files.
> >
> > ...dac
> > -----------------------------------------------------------------------
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> >
>
>

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