[Chimera-users] How to correct this error: ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4)

[Greg Couch]

That looks like a problem between libopenbabel and Chimera.  The bug is 
that libopenbabel.so was compiled with a newer compiler than what 
Chimera was compiled with.  You can try renaming 
chimera-1.12/lib/libgomp.so.1 (eg., to libgomp.so.1.save) to see if it 
fixes the problem.  While I consider this a bug with the Python 
openbabel package, it should be bundling and using a libopenbabel.so 
that is compatible with the Python "manylinux1" ABI (based on CentOS 5), 
we will investigate incorporating a workaround.

     -- Greg


On 11/13/2018 5:53 PM, Francois Berenger wrote:
> Hello,
>
> On a Ubuntu 18.04.1 LTS, I get this error message when I start chimera.
>
> Is there a known fix?
>
> Am I running a too old version of chimera or should I run
> a version specially compiled for Ubuntu computers?
>
> Here is the full error message:
> ---
> # chimera
> Error while importing plipgui from 
> /home/berenger/.local/lib/python2.7/site-packages:
> Traceback (most recent call last):
>   File 
> "/home/berenger/usr/chimera-1.12/share/chimera/extension/base.py", 
> line 349, in _importExtension
>     __import__(module)
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/ChimeraExtension.py", 
> line 8, in <module>
>     from plipgui.core import cmd_plip, cmd_unplip
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/core.py", 
> line 50, in <module>
>     from plip.modules.preparation import PDBComplex
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/preparation.py", 
> line 13, in <module>
>     from .detection import *
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/detection.py", 
> line 12, in <module>
>     from .supplemental import *
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/supplemental.py", 
> line 26, in <module>
>     import pybel
>   File "/home/berenger/.local/lib/python2.7/site-packages/pybel.py", 
> line 53, in <module>
>     import openbabel as ob
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line 
> 21, in <module>
>     _openbabel = swig_import_helper()
>   File 
> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line 
> 20, in swig_import_helper
>     return importlib.import_module('_openbabel')
>   File 
> "/home/berenger/usr/chimera-1.12/lib/python2.7/importlib/__init__.py", 
> line 37, in import_module
>     __import__(name)
> ImportError: /home/berenger/usr/chimera-1.12/lib/libgomp.so.1: version 
> `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4)
> ---
>
> Thanks a lot,
> F.
>
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