Re: [AMBER-Developers] Tests Errors in AmberTools

From: Hai Nguyen <>
Date: Wed, 8 Jun 2016 13:40:33 -0400

Looking at the log, I think Claudia used system python:

> /usr/bin/python

I agree that we should always suggest users to install miniconda (with Y/N)
I will go ahead make that change. If anyone has strong objection, please
reply here. thanks.


On Wed, Jun 8, 2016 at 1:33 PM, David A Case <> wrote:

> On Wed, Jun 08, 2016, Claudia Ramírez wrote:
> >
> > I did a git pull on Monday (June 6), with gnu 4.8 compilers and doing
> just
> > ./configure gnu (serial for now) in Ubuntu 14.04 LTS. And it has 4 tests
> on
> > AmberTools that aren't working (this is without my modifications), and I
> > don't know why. I'm attaching the log file to see if anyone could help me
> > make it work.
> All the problems are python-related problems, related either to pytraj or
> to the sander api interface.
> What is the PYTHON variable in your config.h? If you are not already
> using a miniconda python, try going to $AMBERHOME/AmberTools/src and
> running
> configure_python. Then go back to AMBERHOME and re-run configure.
> [I still am pushing the (so-far, minority) viewpoint that all users should
> be offered the choice to install the miniconda python. Users that have
> both
> experience with python, and the desire/need to use a different interpreter,
> are welcome to decline the offer. But configure2 is still prone to
> deciding
> that the python in a user's path is OK when it is in fact not OK. So,
> letting
> us know which python your Amber installation is using would be a help
> here.]
> ....dac
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Received on Wed Jun 08 2016 - 11:00:02 PDT
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