Oh no, it still doesn't work.
now the file lsf.out says:
ELAN_EXCEPTION . --: 6 (Initialisation error)
elan_init: Can't get capability from environment : 0 : Success
/home/me/.lsbatch/1200292919.340815: line 8: 16755 Aborted
(core dumped) /usr/local/amber/exe/sander -O -i min.in -o min_complex.out -p
complex.prmtop -c complex.inpcrd -r complex_min.crd
ie. it still doesn't work.
when i type
$AMBERHOME/exe/sander
yes, the same thing happens.
I believe I'm running Amber 8. i'll try Amber 9.
x
Hello death, hello oblivion.
On 14/01/2008, Neko Maryam. <neko.nekoai.com> wrote:
>
> 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
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
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> >
>
>
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Received on Wed Jan 16 2008 - 06:07:31 PST
