Crash adding then deleting residue

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1rc202009022202 (2020-09-02 22:02:29 UTC)
Description
Adding a residue to the N-terminus of a chain and then deleting it causes a segmentation fault in _make_ribbon_graphics() (possibly at other positions in the chain as well - haven't tried). Looks like somehow the deleted residue is still being queried?

(command line)
open 3fhr
sel /A:33

(shell)
m = session.models.list()[0]
from chimerax.isolde.atomic.building.build_utils import add_amino_acid_residue
from chimerax.atomic import selected_residues
add_amino_acid_residue(m, 'PRO', next_res=selected_residues(session)[0])

(command line)
del /A:32

<segfault>

Current thread 0x00007f55055c9740 (most recent call first):
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py", line 195 in get_prop
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/ribbon.py", line 96 in _make_ribbon_graphics
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/ribbon.py", line 588 in compute_ribbons
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/structure.py", line 559 in _create_ribbon_graphics
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/structure.py", line 302 in update_graphics_if_needed
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/structure.py", line 1567 in _update_graphics_if_needed
  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 350 in activate_trigger
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/view.py", line 269 in check_for_drawing_change
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/updateloop.py", line 138 in _redraw_timer_callback
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line 269 in event_loop
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py", line 772 in init
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py", line 919 in <module>
  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

Program received signal SIGSEGV, Segmentation fault.
0x00007fffb072b55a in residue_secondary_structure_id () from /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/libmolc.so
Missing separate debuginfos, use: debuginfo-install ucsf-chimerax-1.1-0.2020.09.02.el7.x86_64
(gdb) bt
#0  0x00007fffb072b55a in residue_secondary_structure_id ()
    at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/libmolc.so
#1  0x00007fffe760de2c in ffi_call_unix64 () at /lib64/libffi.so.6
#2  0x00007fffe760d755 in ffi_call () at /lib64/libffi.so.6
#3  0x00007fffe78221fa in _ctypes_callproc (argcount=3, resmem=0x7fffffffa6d0, restype=<optimized out>, atypes=<optimized out>, avalues=0x7fffffffa6a0, pProc=0x7fffb072b240 <residue_secondary_structure_id>, flags=4357) at ./tmp/Python-3.7.8/Modules/_ctypes/callproc.c:829
#4  0x00007fffe78221fa in _ctypes_callproc (pProc=pProc@entry=0x7fffb072b240 <residue_secondary_structure_id>, argtuple=argtuple@entry=0x7ffe9110cb40, 


Log:
UCSF ChimeraX version: 1.1rc202009022202 (2020-09-02)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 450.51.06
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
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        4.9G         48G        255M        9.7G         57G
	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
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1rc202009022202
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.0.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-Phenix: 0.1
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    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
    graphviz: 0.14.1
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    objgraph: 3.4.1
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.2
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Apparently asking for the secondary-structure ID of a dead residue. Which means that the Residues collection being used by the ribbon code hasn't yet been cleared of dead residues when used -- which implies a timing issue.

[Tom Goddard]

The crash happens after a redraw timer goes off so ChimeraX is back to the event loop. So this does not look like at timing issue -- it looks like the residue delete simply does not remove the residue from the Residues collection. I don't know what the timing is of residues being removed from arrays, Eric knows that, but it certainly cannot be delayed until after the event loop gets control.

[Tom Goddard]

Thanks for the precise steps to reproduce the crash. Does it happen every time for you?

The crash does not happen in ChimeraX 1.0 following the exact steps, tried 2 times. I do not have ISOLDE for ChimeraX 1.1 RC so I cannot reproduce the problem. Can you provide wheels for ISOLDE and Clipper (if needed) so I can reproduce the crash with 1.1 rc?

[Eric Pettersen]

The Array_Updater class in molc.cpp is a direct DestructionObserver, so it isn't waiting for any Python-level triggers for sure.

[Tom Goddard]

Skipping the ISOLDE adding of a residue and just deleting the terminal /A:33 does not cause a crash. If that does not cause a crash for you I would be concerned that the ISOLDE code that added the residue did not add it properly. Do you add it purely from Python or do you use C++?

[Tristan Croll]

Reproduced 4 times in a row on my Linux machine (first 3 with ISOLDE running; 4th from a fresh start using only the steps described). Can provide wheels in the morning- I take it you’d prefer Mac?

[Tristan Croll]

The addition code only uses Python. I also tried simply deleting a terminal residue and didn’t trigger a crash, so it’s something about the sequential addition then deletion that does it.

[Tristan Croll]

The add_amino_acid_residue() method lives at 
https://github.com/tristanic/isolde/blob/874878bbc4699ec4811760379af3a83c03742064/isolde/src/atomic/building/build_utils.py#L110. 
It's pretty much independent from the rest of ISOLDE (requires 
new_residue_from_template() from 
https://github.com/tristanic/isolde/blob/874878bbc4699ec4811760379af3a83c03742064/isolde/src/atomic/building/place_ligand.py#L153 
and set_new_atom_style() from 
https://github.com/tristanic/isolde/blob/874878bbc4699ec4811760379af3a83c03742064/isolde/src/atomic/building/__init__.py#L9; 
all other dependencies are ChimeraX or vanilla Python stuff) so if you 
wanted to test urgently it wouldn't be too difficult to cut these out 
into a standalone script.

On 2020-09-08 20:06, ChimeraX wrote:

[goddard@…]

Thanks, I'll wait for the wheels.  Mac would be best.  If it does not reproduce on Mac then I can try Linux.

[Tristan Croll]

Mac builds are on my Google Drive.

Clipper: 
https://drive.google.com/file/d/123n5On8WrCv7Itqh8Vragb_sx8JDttpm/view?usp=sharing
ISOLDE: 
https://drive.google.com/file/d/1R0agQle24wQlftEjiDDnz9lh21T1oiMW/view?usp=sharing

Also crashes here, albeit subtly different. First time didn't crash 
until I repeated the add-residue step (i.e. added, deleted, then added 
again). Second time crashed right on cue.

On 2020-09-08 22:27, ChimeraX wrote:

[Eric Pettersen]

Beginning to feel like a memory-trashing problem.

[Tom Goddard]

After adding and deleting residue pro:32 the Chain object c = m.residues[0].chain still has a dead residue c[18] = pro:32 and any use of that residue causes a crash. Somehow the Chain object is not removing the deleted residue. Eric develops the C++ atomic data structures so reassigning to him.

[Eric Pettersen]

For the specific case of a residue being added into the missing-structure part of a chain, the residue's 'chain' attribute wasn't being set.