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#2693 closed defect (fixed)

Problem importing surface module due to missing libstdc++.so.6

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Platform	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        Linux-4.18.0-80.11.2.el8_0.x86_64-x86_64-with-centos-8.0.1905-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Surface' custom initialization failed  
warnings | 'clip' is a prefix of an existing command 'clipper'  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 548, in get_module  
m = importlib.import_module(self.package_name)  
File
"/programs/x86_64-linux/chimerax/0.9/lib/python3.7/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import  
File "<frozen importlib._bootstrap>", line 983, in _find_and_load  
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 728, in exec_module  
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 431, in initialize  
api = self._get_api(session.logger)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 574, in _get_api  
m = self.get_module()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 550, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Surface's module:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  

[_many_ of these deleted]

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in  
from ._surface import subdivide_triangles, vertex_areas  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 59, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
ImportError:
/nfs/sbgrid/programs/x86_64-linux/chimerax/0.9/bin/../lib/libstdc++.so.6:
version `CXXABI_1.3.9' not found (required by /lib64/libGLU.so.1)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in




OpenGL version: 3.3.0 NVIDIA 390.132
OpenGL renderer: Quadro 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Platform
Description:	modified (diff)
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Problem importing surface module due to missing libstdc++.so.6

comment:2 by Greg Couch, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

This should have been fixed by switching to use CentOS 7 binary bundles on all Linux variants.

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