AMBER Archive (2008)

Subject: Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error)

From: David A. Case (
Date: Mon Jan 14 2008 - 00:16:31 CST

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.
> When I type:
> $AMBERHOME/exe/sander -O -i -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 -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


would you get a similar initialization error?

So, make sure the test cases work for the sander executable you have.

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