On 11/15/18 9:51 AM, Francois Berenger wrote:

-------- Original Message -------- Subject: Re: [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) Date: 14/11/2018 18:42 From: Greg Couch <gregc@cgl.ucsf.edu> To: Francois Berenger <mlists@ligand.eu>, chimera <chimera-users@cgl.ucsf.edu>

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.

Yes, this workaround works: mv ~/usr/chimera-1.13/lib/libgomp.so.1.bck ~/usr/chimera-1.13/lib/libgomp.so.1.bck And I also needed to issue that one: mv ~/usr/chimera-1.13/lib/libz.so.1 ~/usr/chimera-1.13/lib/libz.so.1.bck

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.

Thanks a lot. Francois.

    -- 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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