Hi.
It is okay now! I have to type 'bsub' in front of it.
Thanks for your help!
x
Hello death, hello oblivion.
On 14/01/2008, David A. Case <case.scripps.edu> wrote:
>
> On Mon, Jan 14, 2008, Neko Maryam. wrote:
> >
> > I'm following amber workshop's tutorial two, and I'm thwarted at the
> energy
> > minimisation step.
> >
> >
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_two/section2.htm
> >
> > When I type:
> > $AMBERHOME/exe/sander -O -i min.in -o min_complex.out -p complex.prmtop-c
> > complex.inpcrd -r complex_min.crd &
> > (using the tutorial files)
> >
> > I get:
> >
> > [1] 5092
> > ELAN_EXCEPTION . --: 6 (Initialisation error)
> > elan_init: Can't get capability from environment : 0 : Success
> >
> > [1]+ Aborted $AMBERHOME/exe/sander -O -i min.in -o
> > min_complex.out -p complex.prmtop -c complex.inpcrd -r complex_min.crd
> >
>
> You can Google on "ELAN_EXCEPTION" to find that this appears to be an
> mpi-related problem. My wild guess is that you might be running Amber
> 8(?),
> and that you compiled for a parallel machine. If so, you want to remove
> that
> parallel sander (or rename it), and re-create the single-cpu (serial)
> version.
>
> [Of course, if you are using Amber 9, then something else must be going
> on.]
>
> Is this the first time you have run sander? I suspect that it has nothing
> to
> do with the tutorial files at all. That is, if you just typed
>
> $AMBERHOME/exe/sander
>
> would you get a similar initialization error?
>
> So, make sure the test cases work for the sander executable you have.
>
> ....dac
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Received on Wed Jan 16 2008 - 06:07:10 PST
