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

From: Jason Swails <>
Date: Thu, 22 Dec 2016 16:48:53 -0500

On Wed, Dec 21, 2016 at 11:12 AM, Daniel Roe <> wrote:

> 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.

‚ÄčA few (late) comments here:

1. I think we should support users having anaconda or Miniconda on their
system and use that installation if available. This can be as simple as
just checking to see if there is a "conda" executable in the same directory
where `which python` is located.

I thought I added some code in configure2 to do this, but maybe it was

We should make *some* attempt to play nicely with experienced Python users'
environments (although probably the best way of doing this is to just make
Amber conda-installable, which I believe Hai is working on).

2. Allowing users to link to external libraries is a good thing, IMO. I
briefly tried tackling FFTW3 around the same time I added the --with-netcdf
flag several years ago. But strangely enough, the bundled FFTW3 version
was actually more integrated into the standard build scripts than NetCDF
was, and therefore harder to extricate.

Bundling 3rd-party libraries is good (especially for NetCDF, where the
fortran libs need to be built with the same fortran compiler we're using),
but allowing system libraries to be used is beneficial IMO.

‚ÄčAll the best,

Jason M. Swails
AMBER-Developers mailing list
Received on Thu Dec 22 2016 - 14:00:03 PST
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