Opened 5 years ago

Last modified 5 years ago

#3748 closed defect

ChimeraX bug report submission — at Version 1

Reported by: goddard@… Owned by:
Priority: critical Milestone: 1.2
Component: Build System Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Tom Goddard) 

The following bug report has been submitted:
Platform:        Linux-5.4.0-47-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.2.dev202009220514 (2020-09-22 05:14:36 UTC)
Description
ChimeraX starts with errors, cannot open libatomstruct.so

Log:
Startup Errors  
---  
errors | Bundle 'ChimeraX-DistMonitor' custom initialization failed  
Bundle 'ChimeraX-Atomic' custom initialization failed  
Bundle 'ChimeraX-SwapRes' custom initialization failed  
Bundle 'ChimeraX-ChemGroup' custom initialization failed  
Bundle 'ChimeraX-Markers' custom initialization failed  
warnings | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/dist_monitor/__init__.py", line 15, in <module>  
from .cmd import SimpleMeasurable, ComplexMeasurable  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/dist_monitor/cmd.py", line 27, in <module>  
from chimerax.atomic import Atom  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax-daily/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-
DistMonitor's module: libatomstruct.so: cannot open shared object file: No
such file or directory  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax-daily/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-Atomic's
module: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/swap_res/__init__.py", line 14, in <module>  
from .swap_res import swap_aa, get_rotamers  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/swap_res/swap_res.py", line 17, in <module>  
from chimerax.atomic import AtomicStructure  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax-daily/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-
SwapRes's module: libatomstruct.so: cannot open shared object file: No such
file or directory  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/chem_group/__init__.py", line 14, in <module>  
from .chem_group import find_group  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/chem_group/chem_group.py", line 18, in <module>  
from chimerax.atomic.idatm import type_info, tetrahedral, planar, linear,
single  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax-daily/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-
ChemGroup's module: libatomstruct.so: cannot open shared object file: No such
file or directory  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/markers/__init__.py", line 67, in <module>  
from .markers import MarkerSet, create_link, selected_markers, selected_links  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/markers/markers.py", line 14, in <module>  
from chimerax.atomic import Structure  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax-daily/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-
Markers's module: libatomstruct.so: cannot open shared object file: No such
file or directory  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1251, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/model_panel/__init__.py", line 21, in start_tool  
return model_panel(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 350, in model_panel  
_mp = ModelPanel(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 100, in __init__  
from chimerax import atomic  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 379, in start_tools  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Model Panel
in bundle ChimeraX-ModelPanel:  
libatomstruct.so: cannot open shared object file: No such file or directory  
  
Tool "Model Panel" failed to start:  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Model Panel
in bundle ChimeraX-ModelPanel:  
libatomstruct.so: cannot open shared object file: No such file or directory  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
UCSF ChimeraX version: 1.2.dev202009220514 (2020-09-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 56, in draw_new_frame  
from chimerax import atomic  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in  
from .lib import _load_libs  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 56, in draw_new_frame  
from chimerax import atomic  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in  
from .lib import _load_libs  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 56, in draw_new_frame  
from chimerax import atomic  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in  
from .lib import _load_libs  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback  
drew = self.draw_new_frame()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 56, in draw_new_frame  
from chimerax import atomic  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/__init__.py", line 15, in <module>  
import chimerax.atomic_lib  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic_lib/__init__.py", line 34, in <module>  
from .lib import _load_libs  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory  
  
ImportError: libatomstruct.so: cannot open shared object file: No such file or
directory

Change History (1)

comment:1 by Tom Goddard, 5 years ago

Description: modified (diff)
Platform: → all
Project: → ChimeraX

Here are the libraries in atomic_lib/lib

/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/atomic_lib/lib:

total used in directory 2004 available 197759388
drwxr-xr-x 3 root root 4096 Sep 22 18:13 .
drwxr-xr-x 6 root root 4096 Sep 22 18:13 ..
-rw-r--r-- 1 root root 0 Sep 22 02:50 init.py
-rwxr-xr-x 1 root root 1946512 Sep 22 02:50 libatomstruct.so
-rwxr-xr-x 1 root root 63792 Sep 22 02:50 libelement.so
-rwxr-xr-x 1 root root 9344 Sep 22 02:50 libpyinstance.so
-rwxr-xr-x 1 root root 10400 Sep 22 02:50 _load_libs.so
drwxr-xr-x 2 root root 4096 Sep 22 18:13 pycache

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