[Chimera-users] Fwd: Re: 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)

[Francois Berenger]

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 at cgl.ucsf.edu>
> To: Francois Berenger <mlists at ligand.eu>, chimera
> <chimera-users at 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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