Re: [AMBER] compiling Amber Tools 19

From: Vlad Cojocaru <>
Date: Tue, 28 May 2019 14:37:07 +0200

Sorry for not being completely clear ...

Basically I just did a simple "./configure gnu" from $AMBERHOME and said
"Yes" when configure was asking me whether to download and install
miniconda ....

See attached the output of "$AMBERHOME/AmberTools/src/configure_python "

It does look to me like some python packages get compiled at this stage
and the error pops up during these compilations (e.g. line 1299 in the
attached file) ...

This may or may not be different between Tools 18 and 19. I forgot I
performed an OS update before compiling Tools 19 (did not try to
recompile 18 after this update) ... So, the error might have something
to do with that OS update ... And of course, with software that is not
under your control ...

But maybe this thread helps to track this down or at least to point
people with the solution with using the system's python just in case
anybody gets similar issues ...


On 5/28/19 1:38 PM, David A Case wrote:
> 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
> modules.
> [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.
> ...thanks....dac
> _______________________________________________
> AMBER mailing list

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]

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Received on Tue May 28 2019 - 06:00:02 PDT
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