id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2880 GCC 7.3 breaks ISOLDE Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.4.13-201.fc31.x86_64-x86_64-with-fedora-31-Thirty_One ChimeraX Version: 0.92 (2020-02-23) Description Looks like the recent generic-Linux daily builds are now using GCC 7.3: strings -a libmolc.so |grep ""GCC: ("" GCC: (GNU) 7.3.1 20180303 (Red Hat 7.3.1-5) This will leave ISOLDE broken for all ChimeraX builds except RedHat-7, until there's either an OpenMM plugin built with the same compiler or I can work out some dual-compiler build pipeline. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.92 (2020-02-23) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Traceback (most recent call last): File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 297, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1616, in register_command return cls._get_func(api, ""register_command"")(ci.name, logger) File ""/home/tic20/.local/share/ChimeraX/0.92/site- packages/chimerax/isolde/__init__.py"", line 137, in register_command cmd.register_isolde(logger) File ""/home/tic20/.local/share/ChimeraX/0.92/site- packages/chimerax/isolde/cmd.py"", line 259, in register_isolde from chimerax.isolde.restraints.cmd import register_isolde_restrain File ""/home/tic20/.local/share/ChimeraX/0.92/site- packages/chimerax/isolde/restraints/__init__.py"", line 11, in from ..molobject import RestraintChangeTracker File ""/home/tic20/.local/share/ChimeraX/0.92/site- packages/chimerax/isolde/molobject.py"", line 41, in _c_functions = CFunctions(os.path.splitext(libfile)[0]) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 23, in __init__ self._c_lib = ctypes_open(library_path) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 261, in ctypes_open lib = ctypes.PyDLL(lib_path) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/ctypes/__init__.py"", line 364, in __init__ self._handle = _dlopen(self._name, mode) OSError: /home/tic20/.local/share/ChimeraX/0.92/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 ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2125, in lazy_register deferred.call() File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2056, in call return self.proxy() File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 287, in cb s._register_cmd(ci, l) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 300, in _register_cmd ""register_command() failed for command %s in bundle %s:\n%s"" % (ci.name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: register_command() failed for command isolde in bundle ChimeraX-ISOLDE: /home/tic20/.local/share/ChimeraX/0.92/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 ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2778, in run self._find_command_name(final, used_aliases=_used_aliases) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2521, in _find_command_name what.lazy_register(cmd_name) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2127, in lazy_register raise RuntimeError(""delayed command registration for %r failed (%s)"" % (cmd_name, e)) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: /home/tic20/.local/share/ChimeraX/0.92/site- packages/chimerax/isolde/libmolc.so: undefined symbol: _ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: /home/tic20/.local/share/ChimeraX/0.92/site- packages/chimerax/isolde/libmolc.so: undefined symbol: _ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE) File ""/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2127, in lazy_register raise RuntimeError(""delayed command registration for %r failed (%s)"" % (cmd_name, e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.44 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Build System fixed Conrad Huang Tom Goddard all ChimeraX