id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7728 chimerax daily logs many errors in nogui mode Greg Couch Zach Pearson "On plato, running chimerax --nogui, which is encapsulated in a CentOS 8 container, generates many errors on startup: {{{ Open-command provider in bundle ArtiaX specified unknown data format 'Artiatomi Motivelist'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Generic Particle List'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Dynamo Table'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'RELION STAR file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Coords file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'PEET mod/csv'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'ArtiaX geometric model'; skipping Open-command provider in bundle SEQCROW specified unknown data format 'Q-Chem output file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Artiatomi Motivelist'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Generic Particle List'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Dynamo Table'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'RELION STAR file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Coords file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'PEET mod/csv'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'ArtiaX geometric model'; skipping Open-command provider in bundle SEQCROW specified unknown data format 'Q-Chem output file'; skipping Open-command provider in bundle SEQCROW specified unknown data format 'Q-Chem output file'; skipping Open-command provider in bundle SEQCROW specified unknown data format 'Q-Chem output file'; skipping Open-command provider in bundle SEQCROW specified unknown data format 'Q-Chem output file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Artiatomi Motivelist'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Generic Particle List'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Dynamo Table'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'RELION STAR file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'Coords file'; skipping Open-command provider in bundle ArtiaX specified unknown data format 'PEET mod/csv'; skipping Traceback (most recent call last): File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/dicom/__init__.py"", line 18, in from .dicom import DICOM, DICOMMapFormat File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/dicom/dicom.py"", line 28, in from chimerax.core.decorators import requires_gui File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/core/decorators.py"", line 8, in import chimerax.ui File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/ui/__init__.py"", line 21, in from .gui import MainToolWindow, initialize_qt, menu_capitalize File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 29, in from Qt.QtWidgets import QApplication File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/Qt/__init__.py"", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: 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 ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/home/socr/a/chimera/chimerax_daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's module: libQt6Core.so.6: cannot open shared object file: No such file or directory Bundle 'ChimeraX-Dicom' custom initialization failed UCSF ChimeraX version: 1.5.dev202210040701 (2022-10-04) © 2016-2022 Regents of the University of California. All rights reserved. cmd> }}} Qt won't load because the runtime loader will not load the Qt shared library. And that is because of the underlying old kernel (the CentOS 7 kernel) used by the CentOS 8 singularity image." defect closed blocker DICOM fixed Greg Couch all ChimeraX