Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3745 closed defect (duplicate)

Can't find split-off atomic lib on Linux

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: critical Milestone: 1.2
Component: Platform Version:
Keywords: Cc: chimera-programmers
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-5.4.0-47-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.2.dev202009211759 (2020-09-21 17:59:04 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
errors | Bundle 'ChimeraX-SwapRes' custom initialization failed  
Bundle 'ChimeraX-Markers' custom initialization failed  
Bundle 'ChimeraX-DistMonitor' custom initialization failed  
Bundle 'ChimeraX-Atomic' custom initialization failed  
Bundle 'ChimeraX-ChemGroup' 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/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 . 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/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 . 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 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 . 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 . 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/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 . 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 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 . 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.dev202009211759 (2020-09-21)  
© 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 . 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 . 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 . 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 . 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 . 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 . import _load_libs  
  
See log for complete Python traceback.  
  

[lots of these deleted]

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 . 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 . 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 . 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 . 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 . 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 . 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 . 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 . 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 . 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 . 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 . 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 . 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 . 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




OpenGL version: 4.6 (Core Profile) Mesa 20.0.8
OpenGL renderer: Mesa Intel(R) HD Graphics 630 (KBL GT2)
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: XPS 15 9560
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       7.5Gi       1.5Gi       1.5Gi        22Gi        21Gi
	Swap:          15Gi       2.4Gi        13Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:591b] (rev 04)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell HD Graphics 630 [1028:07be]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    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
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    ChimeraX-AlignmentMatrices: 2.0
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    ChimeraX-Atomic: 1.8.2
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    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-BasicActions: 1.1
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    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
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    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
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    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202009211759
    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
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    ChimeraX-ExperimentalCommands: 1.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    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-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
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    ChimeraX-MapEraser: 1.0
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    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
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    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
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    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
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    ChimeraX-Movie: 1.0
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    ChimeraX-Nucleotides: 2.0
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    ChimeraX-PDB: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
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    ChimeraX-PubChem: 2.0.1
    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
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    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: 2.2.1
    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: 2.0.1
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    ChimeraX-SpaceNavigator: 1.0
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    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: 1.3
    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
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Change History (9)

comment:1 by Eric Pettersen, 5 years ago

Cc: chimera-programmers added
Component: Unassigned → Platform
Description: modified (diff)
Milestone: → 1.2
Owner: set to Greg Couch
Platform: → all
Priority: normal → critical
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Can't find split-off atomic lib on Linux

The ChimeraX daily build works on Mac, but fails as per this report on Linux. I guess the first question is whether lib/libatomstruct.so is in the atomic_lib bundle with a daily build installed on Linux...

comment:2 by Greg Couch, 5 years ago

The CentOS 7 daily build is installed on plato:~chimera/chimerax_daily.

In site-packages/chimerax/atomic_lib/lib, I see libatomstruct.so, libelement.so, and libpyinstance.so. libatomstruct.so needs libelement.so, libpyinstance.so, libappdirs.so, liblogger.so, and libarrays.so to already be loaded. Is that the case?

comment:3 by Greg Couch, 5 years ago

Looking at it a bit closer. _load_libs.so does not have RPATH nor RUNPATH set in it, so it expects all of the libraries to be in the same directory as it. If you put _load_libs.so in the same directory as the others, it should work.

comment:4 by Eric Pettersen, 5 years ago

Okay, moved _load_libs.so into the same dir as the other libraries. Had to jigger around some path-fixing code for the Mac to compensate for the change. Seems to work on Mac. Need you (Greg) to check on Linux tomorrow.

comment:5 by Eric Pettersen, 5 years ago

Greg, have you had a chance to test if the current daily build starts on Linux?

comment:6 by Eric Pettersen, 5 years ago

Tap, tap, is this thing on? Greg?

in reply to:  7 ; comment:7 by goddard@…, 5 years ago 

I tried the current daily build (9/22) on Ubuntu 18.04, failed loading atomic libraries, new ticket #3748

comment:8 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: assigned → closed

comment:9 by Greg Couch, 5 years ago

For future reference, you can test this kind of issue with the daily build on plato:
[[[
~chimera/chimerax_daily/bin/ChimeraX --offscreen
]]]

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