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
