id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4587 Python shell: ERROR:tornado.general:Uncaught exception in zmqstream callback Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14 ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC) Description This started happening again while I was messing around in the shell... once it's happened, shell interaction is pretty much broken for the remainder of the session. Not sure what triggered it... the only thing of note that I can think of is that it started soon after I came back after leaving it alone for an hour-long meeting. Seems pretty clearly an iPython bug. Log: > alias preview_toolshed toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu; toolshed reload available > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu; > toolshed reload available > alias st isolde step $* > alias aw isolde add water $* > alias awsf isolde add water sim false > alias al isolde add ligand $* > alias so setattr sel atoms occupancy $* UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Shell /opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > open > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/class1b_26A.mrc > format mrc Opened class1b_26A.mrc as #1, grid size 400,400,400, pixel 0.999, shown at level 0.0224, step 2, values float32 ERROR:tornado.general:Uncaught exception in ZMQStream callback Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 434, in _run_callback callback(*args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 120, in _handle_event event_f() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 214, in self.schedule(lambda : self._really_send(*args, **kwargs)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 222, in _really_send self.socket.send_multipart(msg, *args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/socket.py"", line 62, in send_multipart self.message_sent += 1 File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 604, in __set__ self.set(obj, value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 593, in set obj._notify_trait(self.name, old_value, new_value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1217, in _notify_trait self.notify_change(Bunch( File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1227, in notify_change return self._notify_observers(change) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1264, in _notify_observers c(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/ipkernel.py"", line 130, in _io_dispatch ident, msg = self.session.recv(self.iopub_socket, copy=False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/jupyter_client/session.py"", line 807, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 246, in __getattr__ warnings.warn(""Accessing zmq Socket attribute %s on BackgroundSocket"" % attr, DeprecationWarning: Accessing zmq Socket attribute recv_multipart on BackgroundSocket ERROR:tornado.general:Uncaught exception in zmqstream callback Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 451, in _handle_events self._handle_recv() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 480, in _handle_recv self._run_callback(callback, msg) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 434, in _run_callback callback(*args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 120, in _handle_event event_f() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 214, in self.schedule(lambda : self._really_send(*args, **kwargs)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 222, in _really_send self.socket.send_multipart(msg, *args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/socket.py"", line 62, in send_multipart self.message_sent += 1 File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 604, in __set__ self.set(obj, value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 593, in set obj._notify_trait(self.name, old_value, new_value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1217, in _notify_trait self.notify_change(Bunch( File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1227, in notify_change return self._notify_observers(change) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1264, in _notify_observers c(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/ipkernel.py"", line 130, in _io_dispatch ident, msg = self.session.recv(self.iopub_socket, copy=False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/jupyter_client/session.py"", line 807, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 246, in __getattr__ warnings.warn(""Accessing zmq Socket attribute %s on BackgroundSocket"" % attr, DeprecationWarning: Accessing zmq Socket attribute recv_multipart on BackgroundSocket ERROR:asyncio:Exception in callback BaseAsyncIOLoop._handle_events(122, 1) handle: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/asyncio/events.py"", line 81, in _run self._context.run(self._callback, *self._args) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/tornado/platform/asyncio.py"", line 189, in _handle_events handler_func(fileobj, events) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 451, in _handle_events self._handle_recv() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 480, in _handle_recv self._run_callback(callback, msg) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 434, in _run_callback callback(*args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 120, in _handle_event event_f() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 214, in self.schedule(lambda : self._really_send(*args, **kwargs)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 222, in _really_send self.socket.send_multipart(msg, *args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/socket.py"", line 62, in send_multipart self.message_sent += 1 File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 604, in __set__ self.set(obj, value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 593, in set obj._notify_trait(self.name, old_value, new_value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1217, in _notify_trait self.notify_change(Bunch( File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1227, in notify_change return self._notify_observers(change) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1264, in _notify_observers c(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/ipkernel.py"", line 130, in _io_dispatch ident, msg = self.session.recv(self.iopub_socket, copy=False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/jupyter_client/session.py"", line 807, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 246, in __getattr__ warnings.warn(""Accessing zmq Socket attribute %s on BackgroundSocket"" % attr, DeprecationWarning: Accessing zmq Socket attribute recv_multipart on BackgroundSocket OpenGL version: 3.3.0 NVIDIA 455.32.00 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 9.0G 38G 388M 14G 52G Swap: 4.9G 0B 4.9G 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 Locale: ('en_GB', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.4 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.12 ChimeraX-AtomicLibrary: 3.0 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202103310726 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-DevelExtras: 0.4.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.dev38 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.2 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.1 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 }}} " defect closed normal General Controls fixed Tom Goddard all ChimeraX