[AMBER] Problems with the miniconda installation

From: David Case <david.case.rutgers.edu>
Date: Wed, 3 Jul 2019 18:34:05 +0000

General announcement, still tentative:

With AmberTools19, one may get (on Linux) an configure error message like this:

Done. Miniconda installed in /scratch/jenkins/workspace/AmberGitlab/AmberMergeGatePipeline/miniconda
Traceback (most recent call last):
 File "/scratch/jenkins/workspace/AmberGitlab/AmberMergeGatePipeline/miniconda/bin/conda", line 7, in <module>
   from conda.cli import main
ModuleNotFoundError: No module named 'conda'
Problem installing Miniconda... see error above.
Configure failed due to the errors above!

What we think has happened: something at continuum.io (host for
MiniConda) has changed that makes older scripts no longer function the
way they did up until about a day or so ago. The behavior change does
not seem to affect the OSX scripts.

Here is a trial fix: edit $AMBERHOME/AmberTools/src/configure_python
and find the line that sets MINICONDA_VERSION -- this is line 34 for
AmberTools19, may be slightly different for older releases.

Change that line to read:


(Note: no spaces before or after the "=" sign.) Remove any
AMBERHOME/miniconda folder you may have from a failed installation, then
re-run configure.

This has *not* been tested very extensively yet, so an alternative is to
just wait for a day or so, and we'll get more definitive information
(and, hopefully, a bugfix update) posted here. But I don't think the
change above will cause any real problems, although there is certainly a
chance that it won't work in every environment.

We apologize for the problems...this behavior change has caught us all
by surprise.


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Received on Wed Jul 03 2019 - 12:00:03 PDT
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