Re: [AMBER-Developers] Latest configure script seems to want to install tons of third party dependencies?

From: Gerald Monard <>
Date: Thu, 28 Jan 2016 15:50:38 +0100


There's already some "configure_mpich" and "configure_openmpi" in
AmberTools/src. What about having a "configure_python" also?


On 01/28/2016 03:44 PM, Jason Swails wrote:
> On Thu, Jan 28, 2016 at 8:59 AM, Ross Walker <> wrote:
>> What is going on here? Should we downloading all this stuff and installing
>> it? It seems like this could be a serious security concern for some people
>> and also extremely fragile.
> ​We are trying out some ideas for providing a reliable Python environment
> for an improved user experience. The main goals here are to provide an
> environment where our Python scripts can run in a version-compatible Python
> *and* so that we can expose our Python functionality that others would like
> to hook into more easily and reliably (for instance, through pysander,
> pytraj, etc.)​. This is already being done through some collaborations,
> like improving xtal refinement through Phenix.
> This workflow is currently utilized by many automated services and is
> fairly robust. It is also secure -- Continuum's business depends on it.
> It also polutes the git tree and a make clean / make dist clean does not
>> clear this up.
> ​Everything it does is put inside $AMBERHOME/miniconda. This is hardly
> polluting. We can have make clean/make distclean clear this stuff out
> quite easily ("make clean" should definitely not touch this, but there's an
> argument to be made that distclean should). I can expand on why I *didn't*
> have distclean remove this if you want my explanation.
> In my opinion we really really really should not be depending on tons of
>> external libraries and the configure script in AMBER should definitely NOT
>> be connecting to any external sites EXCEPT
> You're certainly entitled to your opinion, but mine is that this stance is
> rather arbitrarily purist. The reason I say it's arbitrary is because it
> would be easy to simply host those files on -- but why not take
> advantage of their (i.e., Continuum's) better web infrastructure (more
> reliable web service, more bandwidth, faster connection to more areas, ...
> etc.)?
> It also should not be doing this for a configure that does not involve an
>> AMBERTools build.
> ​I've fixed this. I've also improved the CUDA configure so it doesn't try
> to configure (an unused) FFTW-3.
> A couple other notes -- it seems you're using an outdated version of the
> tree. configure no longer goes off and does this on its own. It's smarter
> about figuring out when it should do this and then asking for permission.
> It's also circumvented entirely by specifying a python to use with Amber.
> For instance, if you do `./configure --with-python /usr/bin/python gnu`, it
> will simply use /usr/bin/python and never attempt to build its own.
> ​Feedback is appreciated, and is how we will hopefully provide the best and
> easiest experience for both users and developers.
> I will also fix this to not be a fatal issue when connectivity is a problem.
> Thanks,
> Jason​

  Prof. Gerald MONARD
  SRSMC, Université de Lorraine, CNRS
  Boulevard des Aiguillettes B.P. 70239
  F-54506 Vandoeuvre-les-Nancy, FRANCE
  e-mail :
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Received on Thu Jan 28 2016 - 07:00:04 PST
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