Opened 6 years ago

Closed 6 years ago

#2247 closed defect (duplicate)

Residue::find_atom missing from _ISOLDES_ libmolc.so?!?

Reported by: chimerax-bug-report@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-07-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-07-03)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open cis22a.mol2

Opened cis22a.mol2 containing 1 structures (54 atoms, 57 bonds)  

> toolshed show "Basic Actions"

> toolshed show Toolbar

> toolshed show ISOLDE

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 9.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, 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 1511, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/__init__.py", line 48, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 307, in __init__  
self._start_gui(gui)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 444, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 543, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 947, in _update_model_list  
from .restraints import MDFF_Mgr  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import Restraint_Change_Tracker  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 41, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 23, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/ctypes/__init__.py", line
356, in __init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
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/ui/gui.py", line 1135, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2646, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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 ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> toolshed show ISOLDE

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 9.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, 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 1511, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/__init__.py", line 48, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 307, in __init__  
self._start_gui(gui)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 444, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 543, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 947, in _update_model_list  
from .restraints import MDFF_Mgr  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import Restraint_Change_Tracker  
File "/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 41, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 23, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/ctypes/__init__.py", line
356, in __init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
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/ui/gui.py", line 1135, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2646, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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 ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/micael/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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.  
  




OpenGL version: 3.3.0 NVIDIA 390.116
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 6 years ago

Cc: Tristan Croll added
Component: Unassigned → Tool Shed
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Residue::find_atom missing from _ISOLDES_ libmolc.so?!?

comment:2 by pett, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #2161, which in turn is really because of #1673 (incompatible ABI)

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