Re: [AMBER] compiling Amber Tools 19

From: David A Case <>
Date: Tue, 28 May 2019 07:38:55 -0400

On Tue, May 28, 2019, Vlad Cojocaru wrote:
>The first time I got the error was during the first configure step
>(serial compilation). The error appears when building package
>subprocess32 during the compilation of miniconda (I run configure with
>minicoda compilation). Parts of the error are below.

Can you say exactly what arguments you gave to the configure script? Did
you say "yes" to downloading miniconda? As far as I know, there is
nothing that is supposed to be compiled at that step, and I've never
seen an error like this before. It doesn't sound like anything that
changed between AmberTools18 and AmberTools19.

As you found out, you can use the --with-python flag: it can point to
your system python, or to the minconda python that was downloaded in
your AmberTools18 install. That way, you will have all the needed

[Aside: I'm not sure whether everything in Amber actually works with
Python 3.7, althought the things you are most likely to use are.]

If you wish, can you post the entire output of running
AMBERHOME/AmberTools/src/configure_python (this is what the configure
script is running)? This seems like a miniconda problem--still our
problem, since we ask users to rely on that--but one that involves third
party codes that we don't control.


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Received on Tue May 28 2019 - 05:00:03 PDT
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