Opened 5 years ago

Closed 5 years ago

#4395 closed defect (worksforme)

libGLU.so.1: cannot open shared object file: No such file or directory

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: high 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-3.10.0-957.1.3.el7.x86_64-x86_64-with-redhat-7.9-Nitrogen
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Surface' custom initialization failed  
warning | Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File
"/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, 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: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 60, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 60, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 60, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  

[many repetitions deleted]

ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 60, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 60, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/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/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 60, in draw_new_frame  
from chimerax import surface  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in <module>  
from ._surface import subdivide_triangles, vertex_areas  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
ImportError: libGLU.so.1: cannot open shared object file: No such file or
directory  
  
File "/programs/x86_64-linux/chimerax/1.1.1/ChimeraX/lib/python3.7/site-
packages/chimerax/surface/__init__.py", line 19, in




OpenGL version: 3.3.0 NVIDIA 410.73
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Scientific Linux 7.9 Nitrogen
Architecture: 64bit ELF
CPU: 24 Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
Cache Size: 30720 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        6.9G        606M        680M        118G        117G
	Swap:          8.0G          0B        8.0G

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:119e]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Description: modified (diff)
Owner: set to Greg Couch
Platform: → all
Priority: normal → high
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → libGLU.so.1: cannot open shared object file: No such file or directory

comment:2 by Greg Couch, 5 years ago

Resolution: → worksforme
Status: assigned → closed

Without an email address, it is impossible to find out what really happened or to help the user. libGLU.so.1 is installed if the ChimeraX rpm is used to install ChimeraX (through the dependency on mesa-libGLU). So maybe, the generic version was installed?

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