Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#6951 closed defect (fixed)

Crash masking volume

Reported by: gimshan.jayawardena@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.18.0-305.12.1.el8_4.x86_64-x86_64-with-glibc2.28
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: Segmentation fault

Current thread 0x00007f73a258f740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/mask/depthmask.py", line 244 in project_and_mask
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/mask/depthmask.py", line 104 in masked_volume
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/mask/maskcommand.py", line 46 in mask
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 297 in execute
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 134 in keyPressEvent
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== 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 /data/mcm14/nadishka/wiv_modelling/modelling/postprocess_zflip_3_54.mrc

Opened postprocess_zflip_3_54.mrc as #1, grid size 1600,1600,1600, pixel 1.36,
shown at step 1, values float32  

> volume #1 region 0,0,0,1599,1599,1599 step 8

> volume #1 step 1

> ui tool show "Map Eraser"

> open
> /data/mcm14/nadishka/wiv_modelling/modelling/phenix/new_penton/maps/old_maps/pentons_5fold_12042022.mrc

Opened pentons_5fold_12042022.mrc as #3, grid size 83,98,63, pixel
1.36,1.36,1.36, shown at level 0.0164, step 1, values float32  

> volume #3 level 0.003738

> hide #!3 models

> volume erase #1 center 741.94,1090.2,1648.2 radius 378.62 outside true

Opened postprocess_zflip_3_54.mrc copy as #4, grid size 1600,1600,1600, pixel
1.36, shown at step 1, values float32  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log  
h.show_data(log(counts + 1))  

> close #1

> hide #2 models

> volume #3 level 0.001128

> volume mask #4 surfaces #3 fullMap true


===== 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: 3.3.0 NVIDIA 470.63.01
OpenGL renderer: NVIDIA GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D04
OS: AlmaLinux 8.5 Arctic Sphynx
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i9-11900KF @ 3.50GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        15Gi        46Gi       107Mi       1.0Gi        46Gi
	Swap:          31Gi       2.5Gi        28Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:8736]	
	Kernel driver in use: nvidia
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-Phenix: 0.3
    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
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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

Change History (5)

comment:1 by pett, 3 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash masking volume

Reported by Nadishka Jayawardena

comment:2 by Tom Goddard, 3 years ago

I think this ChimeraX crash was caused by trying to mask a very large map 1600 by 1600 by 1600 grid points, 4 GVoxels with float32 values, so 16 Gbytes in size. It is possible it was caused by a memory allocation failure . But the machine has 64 Gbytes of memory so it probably can handle this size (two copies of map = 32 Gbytes). More likely I think the code might somewhere be using int32 indices into the map array which only can handle 2Gvoxels before negative indices are produced. I can test this and if that is the problem I can improve the code to use int64 indices as I have done for other volume code when this large map problem arose (e.g. computing contour surfaces).

comment:3 by Tom Goddard, 3 years ago

I get the same crash using commands on macOS with ChimeraX daily build

volume new size 1600 value uint8
volume #1 level -1
volume mask #1 surface #1

I see the ChimeraX C++ code is using an int32 array index to fill the new volume, so I will change that to int64.

Last edited 3 years ago by Tom Goddard (previous) (diff)

comment:4 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in daily build, not in ChimeraX 1.4.

After changing the array index to int64 my test case works without crashing.

in reply to:  5 ; comment:5 by GIMSHAN.JAYAWARDENA@…, 3 years ago 

Dear Tom,

Many thanks for fixing this issue. I will test it out.

Best,
Nadishka
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, May 26, 2022 1:55 PM
Cc: Nadishka Jayawardena <GIMSHAN.JAYAWARDENA@OIST.JP>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6951: Crash masking volume

#6951: Crash masking volume
--------------------------------------------+-------------------------
          Reporter:  gimshan.jayawardena@…  |      Owner:  Tom Goddard
              Type:  defect                 |     Status:  closed
          Priority:  normal                 |  Milestone:
         Component:  Volume Data            |    Version:
        Resolution:  fixed                  |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Fixed in daily build, not in ChimeraX 1.4.

 After changing the array index to int64 my test case works without
 crashing.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6951#comment:4>
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