Re: [AMBER-Developers] Should we add more troubleshooting to the Makefile?

From: Hai Nguyen <>
Date: Mon, 6 Feb 2017 20:20:49 -0500

I agree.

And it would be great if you (and any one) can post the error logs related
to python stuff here
so we can keep track/solve that. (I know we have bugs tracking but not sure
if any one is still using it. :D
Keep track in email seems better way to me).


On Mon, Feb 6, 2017 at 7:44 PM, David Cerutti <> wrote:

> I had a messy problem with remaking amber last week, but there seems to be
> an overall trend that I see on various systems: works at first, then over
> time (months to a year or more) rebuilding, even if from a fresh clone of
> the repository, becomes harder to do successfully. This happens, I am
> pretty sure, as new software or versions get installed by sysadmins, and
> various pointers in my environment or files that Amber depends on retain
> their old settings. If you've downloaded miniconda, "make clean ; make
> uninstall" doesn't get rid of it, but changing to a different compiler and
> trying to rebuild might be a problem (haven't quite seen that happen, but
> it's conceivable to me). The particular problem I hit was that my
> $PYTHONPATH had, in front of the miniconda amber installation, a path to
> another pre-installed python library, and the compilation was going there
> before checking the amber-downloaded python, then hitting a problem with
> intel versus gnu compiler mismatch.
> Perhaps we should discuss ways to add features to the installation script
> that will detect common errors or vulnerabilities we can foresee, then
> prompt the user to take specific actions to rememdy them. Some of this is
> already in place, such as suggestions to source and
> when encountering certain problems. In the case of my python problem, it
> would have been helpful for the installation to show me my actual
> $PYTHONPATH. Should we make an effort to broaden the scope of these hints?
> Dave
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Received on Mon Feb 06 2017 - 17:30:02 PST
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