Re: [AMBER] compiling Amber Tools 19

From: Vlad Cojocaru <>
Date: Tue, 28 May 2019 10:33:15 +0200

Dear David,

First, thanks for answering ....

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.

When ignoring this error during configure, the compilation ("make
install") failed with the same error when building parmed (second error

Now I should add that last night I managed to compile successfully using
the system python 3.7 (using the --with-python flag for configure)
without compiling miniconda from Amber (of course after installing all
required python modules for python 3.7).

So, it seems that the issue is somehow between the python distributed
with Amber and my system (openSUSE tumbleweed, gcc 7 or gcc 8) So, for
now things seem to work for me, but the way I compiled requires the use
of the system python and all the modules needed should be installed ...

Best wishes Vlad

........... error during "configure gnu" ..................

Building wheels for collected packages: subprocess32
   Building wheel for subprocess32 ( started
   Building wheel for subprocess32 ( finished with status 'error'
   ERROR: Complete output from command
/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/bin/python -u
-c 'import setuptools,
'"'"'open'"'"', open)(__file__);'"'"'\r\n'"'"',
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
bdist_wheel -d /tmp/pip-wheel-zaCsru --python-tag cp27:
   ERROR: running bdist_wheel

.... error during "make install" .........

make[2]: Entering directory
(cd parmed &&

/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/bin/amber.python install -f
--prefix=/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1 > build.log)
warning: no files found matching ''
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
C/ObjC but not for C++
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
C/ObjC but not for C++

/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
initialize decompress status for section .debug_aranges

On 5/28/19 3:45 AM, David Case wrote:
> On Mon, May 27, 2019, Vlad Cojocaru wrote:
>> I am trying to compile Amber Tools 19 on a computer with openSUSE
>> Tumbleweed (x86_64). Both when using gcc 7.4.1 and gcc 8.3.1 I get
>> errors like the one below (crti.o: file not recognized: file format not
>> recognized).
> No clue, but can you say more about your exact toolchain (why is
> everything under a miniconda directory path?) and where are you in the
> configure/compile step? That is, what part of the code is being
> built, or what was the last thing that built correctly?
>> I have previously compiled and used successfully Amber Tools 18 on the
>> same machine (both compile gcc 8 and gcc 7)
> My problem is that I can't tell from the snippets of error message you
> gave even where to look, that is, which part of AmberTools19 fails.
> ..thx...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]
AMBER mailing list
Received on Tue May 28 2019 - 02:00:02 PDT
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