Re: [AMBER-Developers] Fwd: Amber 'configure' now forcing miniconda?

From: Hai Nguyen <>
Date: Wed, 21 Dec 2016 14:02:14 -0500

On Wed, Dec 21, 2016 at 1:23 PM, David Case <> wrote:

> On Wed, Dec 21, 2016, Hai Nguyen wrote:
> > I actually updated configure2 to follow your option A (which I agree with
> > too).
> ...thx...that means we automatically advance to option D!

> A few questions:
> 1. do we know which programs require scipy? Can we try to get rid of that?

Pengfei Li's pymsmt package. He is using scipy for some minimization
If he agrees, we can make scipy optional since user can install via
'amber.conda install scipy' in 5 seconds.

> 2. are we actually set up so that users don't need cython?

User don't need Cython (thanks to Jason suggestion to pre-compile pyx
But developers still need to install Cython.

> 3. What does "optional" mean in your new configure2 script? I think we
> would
> be better off referring users to a web page/wiki for info about which
> python
> packages are needed for what, rather than to try to cram all that
> information
> into a configure2 usage statement that will quickly get out of date.

"Optional" means they are only useful for a small number of users (e.g: if
someone wants to use jupyter notebook for interactive computing or
Hard requirement means "must have". numpy is hard requirement for both
ParmEd and pytraj.

> 4. Has anyone (e.g. Dan) tried a soft-link to have their
> $AMBERHOME/miniconda directory point to a common anaconda tree? This
> might be
> a simple way for developers to have many amber trees without having many
> miniconda installations. (Not sure this will work, but it seems worth
> trying...)
I myself say no to soft/hard/alias/... link. Just install Anaconda or
Miniconda in your $HOME folder and then use --with-python flag

bash configure --with-python $HOME/anaconda/bin/python gnu

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Received on Wed Dec 21 2016 - 11:30:03 PST
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