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

From: Scott Brozell <>
Date: Wed, 21 Dec 2016 12:03:17 -0500


In summary, I second Dan's suggestions on both python and fftw.

In particular, i appreciate that we should have a simple path for
the (perhaps vast) majority of Amber installers (who just want to
get it installed without checking the prerequisites list twice, thrice,
etc.). But we should also support the advanced installers. And while
there may be far fewer of us some of us (like me) are installing
for a large number of Amber end users.

I don't want to dive into the python muck, but i claim that it
should be suffcient for Amber's installation mechanism that my local
python expert has installed several pythons. Say python -V yields:
Python 3.4.2 :: Anaconda 2.0.1 (64-bit)
If Amber's installation mechanism finds faults then it should give
explicit details so that i can go to my python expert with them
and get the matter resolved without headaches.

Has there been an investigation and classification of these python
problems? It seems that this is a persistent issue.

On a historical bent, I recall a time not so long ago when the Amber
powers that be frowned upon C++ because of apparent portability/
installability/etc. issues. Perhaps we need to revisit our python
usage from that perspective.


On Wed, Dec 21, 2016 at 11:12:58AM -0500, Daniel Roe wrote:
> Hi All,
> Recently when configuring Amber I get this message:
> ```
> We highly recommend to let AMBER install Python with all prerequisites inside
> $AMBERHOME via Continuum Miniconda distribution.
> This will only need to be done once.
> This may take several minutes and will require Internet access.
> - Amber requires Python version 2.7 or higher:
> - You can also install missing packages (e.g., numpy and matplotlib) yourself
> and then use --with-python </path/to/python> to specify a particular Python
> interpreter to use for Amber's Python-requiring programs.
> - Use --skip-python if you do not want to build any parts of Amber that
> require Python.
> Should I download and install Miniconda for you? [y/n] n
> ```
> This is despite the fact that I'm currently employing a full Anaconda
> install (4.2.9, python 2.7), which up until recently Amber's configure
> was quite happy with. When I say "no", I get this message:
> ```
> OK. I will try to use /mnt/local/droe/anaconda2/bin/python, but not
> all Python components
> in Amber will work correctly...
> ```
> Install then appears to proceed as normal. However, certain python
> components like pytraj are silently skipped. Digging a little deeper
> the issue appears to be that the script '' checks
> to see if Amber's miniconda is in use, and if not it skips installing
> certain python components (without much fanfare). According to the
> notes in the script this was due to some libgfortran bug that was in
> conda a while back. However, if I comment out the check in the script
> everything appears to install OK, and python tests pass. So I think
> this check is no longer needed, but I'd also like to bring up a few
> points.
> I think a better solution for situations like this in the future will
> be to have 'configure' check if downloading Amber's miniconda is
> actually needed to make programs run. IMO the proper time to check for
> these things is *before* compile time, not during. It took me a couple
> of minutes to realize that certain python components were skipped. The
> current configure message is really vague and just says 'certain
> components won't work correctly' without telling me which ones. The
> message also implies I might have missing packages when in fact I
> don't.
> Having a built-in miniconda is great, unless you need to have several
> versions of Amber installed on the same system (for e.g. different
> compilers/parallel libraries), and then it can become cumbersome.
> (Related to this, we really should make it so that we can specify an
> external FFTW3). I think, 'configure' needs to 1) check that the
> current python installation will work, 2) if it won't work, tell me
> exactly why, and what I might do to make my python install
> Amber-compatible (what packages etc), and 3) if certain python
> components are going to be skipped and others not, tell me up-front
> which ones.

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Received on Wed Dec 21 2016 - 09:30:02 PST
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