Re: [AMBER-Developers] python dependency

From: Jason Swails <>
Date: Fri, 23 Jun 2017 17:01:17 -0400

On Fri, Jun 23, 2017 at 2:41 PM, Brent Krueger <> wrote:

> I know we had a lot of discussions about python back earlier this year, but
> I'm not sure whether this point came up exactly.
> We've been doing some work installing AMBER onto very bare-bones Linux
> machines and have found that python is required in order to complete the
> configure process. This is true even when one wishes to use the MINICONDA
> that will lie within the amber tree.
> Maybe I'm misunderstanding what MINICONDA is (is it not a full python
> install on its own?) but it seems a little silly to me to require python to
> already exist on the system when our recommended installation will, in
> fact, not use it at all.
> I realize that this will not impact most users and that it is trivial to
> install a system-wide python, so this isn't worth spending a lot of time
> on. But if there is a simple way around this, perhaps it is worth
> implementing?

​As Dave mentioned, the Python dependency comes from the update_amber
script. There's a little bit of a chicken-and-the-egg problem here.
Miniconda *does* set up a full Python installation, but in principle
configure should be able to apply updates and upgrades *before* running the
actual configure process. So update_amber (and therefore configure) needs
to use Python at least once before Miniconda gets a chance to get installed.

The reason for installing Miniconda is that it's difficult (and
counterproductive) to support a wide range of Python versions in each of
our Python components -- most of them have already dropped Python 2.6 and
below as well as Python 3.2 and below. update_amber is an exception -- I
wrote it specifically to support anything higher than 2.4 using only stdlib
modules that were available in each of those versions so that it will run
with the system Python ​sans 3rd-party packages. After all, it's the only
Python package you simply *can't* refuse to use in Amber :). [1]

All the best,

[1] Except, of course, if you use --no-updates (must be first argument
after ./configure), as Dave also mentioned.

Jason M. Swails
AMBER-Developers mailing list
Received on Fri Jun 23 2017 - 14:30:02 PDT
Custom Search