id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3034 Infrequent ISOLDE crash Tristan Croll Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.93 (2020-04-03) Description I'm still getting a *very* occasional (I estimate less than 1 in 100) segmentation fault when preparing a model for ISOLDE. Being so rare makes it really difficult to pin down exactly which step is causing it, and so far I haven't managed to ever trigger it when running under GDB (which makes me suspect some subtle race condition). As best I can tell, it happens when ISOLDE is started just after doing e.g. ""clipper assoc #2 to #1"" to assign a cryo-EM map to a model. The tracebacks I get *suggest* it has to do with some Drawing being improperly deleted. Here's an example from a crash *within* ChimeraX: {{{ Fatal Python error: Aborted Current thread 0x00007f931a7ed700 (most recent call first): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 134 in make_current File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/drawing.py"", line 1122 in delete File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py"", line 88 in delete File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/drawing.py"", line 1113 in __del__ File ""/home/tic20/.local/share/ChimeraX/0.93/site-packages/chimerax/isolde/openmm/forcefields.py"", line 66 in _background_load_ff File ""/opt/UCSF/ChimeraX/lib/python3.7/concurrent/futures/thread.py"", line 57 in run File ""/opt/UCSF/ChimeraX/lib/python3.7/concurrent/futures/thread.py"", line 80 in _worker File ""/opt/UCSF/ChimeraX/lib/python3.7/threading.py"", line 870 in run File ""/opt/UCSF/ChimeraX/lib/python3.7/threading.py"", line 926 in _bootstrap_inner File ""/opt/UCSF/ChimeraX/lib/python3.7/threading.py"", line 890 in _bootstrap Thread 0x00007f9414d99740 (most recent call first): File ""/home/tic20/.local/share/ChimeraX/0.93/site-packages/chimerax/clipper/symmetry.py"", line 1459 in _update_box File ""/home/tic20/.local/share/ChimeraX/0.93/site-packages/chimerax/clipper/symmetry.py"", line 1605 in _model_changed_cb File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 213 in _activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 182 in activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 348 in activate_trigger File ""/home/tic20/.local/share/ChimeraX/0.93/site-packages/chimerax/clipper/symmetry.py"", line 622 in _structure_change_cb File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 213 in _activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 182 in activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 348 in activate_trigger File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/changes.py"", line 31 in check_for_changes File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/__init__.py"", line 79 in File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 213 in _activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 182 in activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 348 in activate_trigger File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/cli.py"", line 2948 in command_trigger File ""/opt/UCSF/ChimeraX/lib/python3.7/contextlib.py"", line 119 in __exit__ File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/cli.py"", line 2866 in run File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/cmd_line/tool.py"", line 258 in execute File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/cmd_line/tool.py"", line 112 in keyPressEvent File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 268 in event_loop File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py"", line 771 in init File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py"", line 903 in File ""/opt/UCSF/ChimeraX/lib/python3.7/runpy.py"", line 85 in _run_code File ""/opt/UCSF/ChimeraX/lib/python3.7/runpy.py"", line 193 in _run_module_as_main [8341:8345:0100/000000.235334:ERROR:broker_posix.cc(40)] Recvmsg error: Connection reset by peer (104) Aborted (core dumped) }}} Line 1459 of clipper/symmetry.py is: {{{ atoms = self.structure.atoms atoms.hides |=HIDE_ISOLDE # 1459 }}} Line 66 of isolde/openmm/forcefields.py is {{{ forcefield, cached_openmm_version, cached_isolde_version = pickle.load(infile) }}} ... where forcefield is an OpenMM ForceField object and the other two variables are simple strings. As the method name suggests, this is running in a Python thread. Most likely coincidental that it happened to be in progress when the crash occurred. While repeatedly looping through the commands: {{{ open 6kpf open 0744 from emdb clipper assoc #2 to #1 isolde start }}} ... to try to reproduce it I didn't get any hard crashes, but in one instance I got a traceback on *closing* ChimeraX: {{{ Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/drawing.py"", line 1113, in __del__ self.delete() File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py"", line 88, in delete Drawing.delete(self) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/drawing.py"", line 1122, in delete c.make_current() # Make OpenGL context current for deleting OpenGL resources. File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 135, in make_current raise OpenGLError(""Could not make graphics context current"") chimerax.graphics.opengl.OpenGLError: Could not make graphics context current Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/drawing.py"", line 1113, in __del__ self.delete() File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py"", line 88, in delete Drawing.delete(self) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/drawing.py"", line 1122, in delete c.make_current() # Make OpenGL context current for deleting OpenGL resources. File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 135, in make_current raise OpenGLError(""Could not make graphics context current"") chimerax.graphics.opengl.OpenGLError: Could not make graphics context current Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""position"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""normal"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""tex_coord"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""position"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""normal"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/opengl.py"", line 2484, in __del__ % self.shader_variable_name) chimerax.graphics.opengl.OpenGLError: OpenGL buffer ""tex_coord"" was not deleted before graphics.Buffer destroyed ObjectCache: Leaked 0004 refs to

Segmentation fault (core dumped) }}} This has been niggling at me for weeks now, and I'm more-or-less at a loss as to where to go from here. Any suggestions? OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia }}} " defect closed normal Third Party fixed Eric Pettersen all ChimeraX