id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3748 Can't find split-off atomic lib on Linux goddard@… Eric Pettersen "{{{ 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 """", line 1006, in _gcd_import File """", line 983, in _find_and_load File """", line 967, in _find_and_load_unlocked File """", line 677, in _load_unlocked File """", line 728, in exec_module File """", 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 from .cmd import SimpleMeasurable, ComplexMeasurable File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/dist_monitor/cmd.py"", line 27, in from chimerax.atomic import Atom File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/__init__.py"", line 15, in import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 """", line 1006, in _gcd_import File """", line 983, in _find_and_load File """", line 967, in _find_and_load_unlocked File """", line 677, in _load_unlocked File """", line 728, in exec_module File """", 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 """", line 1006, in _gcd_import File """", line 983, in _find_and_load File """", line 967, in _find_and_load_unlocked File """", line 677, in _load_unlocked File """", line 728, in exec_module File """", 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 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 from chimerax.atomic import AtomicStructure File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/__init__.py"", line 15, in import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 """", line 1006, in _gcd_import File """", line 983, in _find_and_load File """", line 967, in _find_and_load_unlocked File """", line 677, in _load_unlocked File """", line 728, in exec_module File """", 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 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 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 """", line 1006, in _gcd_import File """", line 983, in _find_and_load File """", line 967, in _find_and_load_unlocked File """", line 677, in _load_unlocked File """", line 728, in exec_module File """", 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 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 from chimerax.atomic import Structure File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/__init__.py"", line 15, in import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 import chimerax.atomic_lib File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic_lib/__init__.py"", line 34, in 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 " defect closed critical 1.2 Build System fixed chimera-programmers all ChimeraX