Re: [AMBER-Developers] Third (final?) release candidate for Amber 12

From: Jason Swails <>
Date: Mon, 02 Apr 2012 09:06:36 -0400

On Mon, 2012-04-02 at 05:03 -0400, wrote:
> g03 is in my PATH and in GAUSS_EXEDIR, therefore check_GAUSSIAN.x returns 0.
> But the test still tries to call g09 (which does not exist) and I could
> not figure out where in e.g.
> amber12/test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN/Run.h2o.blyp_sto-3g
> the actual name of the Gaussian executable is set. It looks like it checks
> for g03 or g09, but then assumes g09 is installed.

The check for g09/g03 is done inside the sander source code itself. For
lack of a better alternative, it just uses a system call `which g03` and
`which g09`. It then analyzes the return value of that system call to
determine if and where the executable exists.

Can you give us the output of:

which g09
echo $?
which g03
echo $?

(this assumes bash/sh, I don't know the csh-equivalent).

> I reran this one with 400MB stack space and it still segfaulted. If that
> is expected, then ok, I guess...

This is actually fixed in the current version (forgot to allocate an

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Apr 02 2012 - 06:30:02 PDT
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