(ISOLDE?) segmentation fault

[andrea.smith@…]

The following bug report has been submitted:
Platform:        Linux-5.11.0-38-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Fatal Python error: Fatal Python error: Segmentation faultSegmentation faultSegmentation fault





Thread 0x00007fa50ff83740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/smith/Documents/Srp_structures/PTI-Chy-Try_PP/Refine_13/PTI-Chy-
> Try_PP_refine_13.pdb

Chain information for PTI-Chy-Try_PP_refine_13.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> isolde start

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 10.1 - if installed, please make sure this is
on your library path before starting ChimeraX.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 19 residues in model #1 to IUPAC-IUB
standards.  
Chain information for PTI-Chy-Try_PP_refine_13.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
  
Done loading forcefield  

> addh hbond true

Summary of feedback from adding hydrogens to PTI-Chy-Try_PP_refine_13.pdb #1.2  
---  
warnings | Not adding hydrogens to /A LYS 36 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 79 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B ASN 97 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C LYS 132 CB because it is missing heavy-atom bond
partners  
3 messages similar to the above omitted  
notes | No usable SEQRES records for PTI-Chy-Try_PP_refine_13.pdb (#1.2) chain
A; guessing termini instead  
No usable SEQRES records for PTI-Chy-Try_PP_refine_13.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for PTI-Chy-Try_PP_refine_13.pdb (#1.2) chain C;
guessing termini instead  
Chain-initial residues that are actual N termini: /A CYS 1, /B ILE 1, /C PRO 7  
Chain-initial residues that are not actual N termini: /A ILE 16, /A THR 151,
/C GLN 77, /C PHE 162  
Chain-final residues that are actual C termini: /A ASN 245, /B ASN 223, /C GLN
193  
Chain-final residues that are not actual C termini: /A LEU 10, /A ARG 145, /C
SER 71, /C VAL 148  
682 hydrogen bonds  
Adding 'H' to /A ILE 16  
Adding 'H' to /A THR 151  
Adding 'H' to /C GLN 77  
Adding 'H' to /C PHE 162  
4722 hydrogens added  
  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLA A  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLB A  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLC A  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLD A  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level 0.337, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level -0.123,0.123, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_9 as #1.1.1.4, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level 0.306, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-
included)) F-model, PHIF-model as #1.1.1.5, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level -0.517,0.517, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 50,46,44, pixel 0.544,0.557,0.568, shown at level 0.384, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 50,46,44, pixel 0.544,0.557,0.568, shown at level
0.366, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 50,46,44, pixel 0.544,0.557,0.568, shown at level -0.258,0.258, step 1,
values float32  
Opened (LIVE) MDFF potential as #1.1.1.9, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level 0.281, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 5856, resource id:
17165627, major code: 40 (TranslateCoords), minor code: 0  

> set bgColor white

> clipper spotlight radius 11.00

> clipper spotlight radius 10.00

> clipper spotlight radius 11.00

> clipper spotlight radius 12.00

ISOLDE: started sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  

> hide #1.3 models

ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 21.0.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CML GT2)
OpenGL vendor: Intel
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B460MDS3HV2
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       7.9Gi        10Gi       1.5Gi        13Gi        21Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:9bc5] (rev 05)	
	DeviceName: Onboard - Video	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:d000]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
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    Sphinx: 4.2.0
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    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tristan Croll]

Hi Andrea,

There's not enough information in the log to say exactly what caused the crash, but I'm afraid the system that you're running on isn't really set up to run ISOLDE well - see the warning message early in the log:

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed.

While the lightweight Intel graphics card you're using is capable of running OpenCL, you currently don't have the right libraries installed to support it. This might be a good place to start: ​https://stackoverflow.com/questions/57954533/using-opencl-with-intel-uhd-graphics-on-linux. Performance won't be great, but at least it shouldn't crash. To make it really shine, ideally you'll want to work on a machine with a reasonably recent Nvidia GPU (GTX 10-series or later).

[andrea.smith@…]

Hi,

the specification of my PC should be as follows:
CPU s PassMark Benchmark > 15000, 32GB RAM, 1000GB SSD
INTEL Core i7-10700 / ASRock MB Sc LGA1200 H410M-HDV / 32GB DDR4 2666MHz / 1TB SSD / Intel® UHD Graphics 630 / DVD-RW / Tower /

So I guess my system is not good enough to run ISOLDE?

Thank you, best,
Andrea

Pondelok, Február 07, 2022 19:08 CET, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> napísal:#6095: (ISOLDE?) segmentation fault
-------------------------------------+---------------------------
Reporter: andrea.smith@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+---------------------------

Comment (by Tristan Croll):

Hi Andrea,

There's not enough information in the log to say exactly what caused the
crash, but I'm afraid the system that you're running on isn't really set
up to run ISOLDE well - see the warning message early in the log:

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please
check
that you have the recommended drivers from the manufacturer installed.

While the lightweight Intel graphics card you're using is capable of
running OpenCL, you currently don't have the right libraries installed to
support it. This might be a good place to start:
https://stackoverflow.com/questions/57954533/using-opencl-with-intel-uhd-
graphics-on-linux. Performance won't be great, but at least it shouldn't
crash. To make it really shine, ideally you'll want to work on a machine
with a reasonably recent Nvidia GPU (GTX 10-series or later).

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6095#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

Hi Andrea,

That should still be able to run ISOLDE if you’re able to install the correct drivers to support OpenCL on your GPU. All the specs are great other than the GPU itself - if you were able to get your hands on even, say, a GTX 1060 it would make a world of difference.

— Tristan