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

From: Hai Nguyen <>
Date: Wed, 21 Dec 2016 11:45:10 -0500


1. I absolutely agree that the message is vague. I made change to the
current behavior without update the message.
We (Dave, me and Scott) had very long discussion about checking Python.
However, Dave and I have the same consensus that the checking is not always
reliable, especially user uses system Python (e.g on Mac).
To avoid spending time on debug different Python distributions, we just
force user to use Miniconda (much lighter than Anaconda) as we (me, Dave,
Jason, ...) use it in production.

So I think the configure2 should exit you user saying "N" to force him/her
to use --with-python or --skip-python flag.

If you have different amber dirs, just simply

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

For guys who do need Python
bash configure --skip-python gnu

2. I agree that we can skip the gfortran checking since it's a quick hack a
year ago.
This script is intended for OSX.

> (Related to this, we really should make it so that we can specify an
external FFTW3).


> 3) if certain python
components are going to be skipped and others not, tell me up-front
which ones.


thanks for raise this issue again. :D


On Wed, Dec 21, 2016 at 11:12 AM, 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...
> ```
I will take this message out.

> 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.
> Sorry for the long post.
> -Dan
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> _______________________________________________
> AMBER-Developers mailing list
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Received on Wed Dec 21 2016 - 09:00:03 PST
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