Changes between Initial Version and Version 1 of Ticket #6023


Ignore:
Timestamp:
Jan 26, 2022, 1:44:10 PM (4 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #6023

    • Property Component Unassigned → Structure Prediction
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash running multiple AlphaFold predictions

  • Ticket #6023 – Description

    initial v1  
    1616Thread 0x000000031bc85000 (most recent call first):
    1717  File "/private/var/folders/dd/c4gl6td53g5d6br70_sz3pd40000gn/T/AppTranslocation/93D92606-AA62-47A6-966F-6A360C66B290/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py528_handle_tasks/private/var/folders/dd/c4gl6td53g5d6br70_sz3pd40000gn/T/AppTranslocation/93D92606-AA62-47A6-966F-6A360C66B290/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py910run/private/var/folders/dd/c4gl6td53g5d6br70_sz3pd40000gn/T/AppTranslocation/93D92606-AA62-47A6-966F-6A360C66B290/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py973_bootstrap_inner/private/var/folders/dd/c4gl6td53g5d6br70_sz3pd40000gn/T/AppTranslocation/93D92606-AA62-47A6-966F-6A360C66B290/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py930_bootstrap
     18
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     20{
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     22  "procLaunch" : "2022-01-26 02:30:44.6885 +0100",
     23  "procRole" : "Background",
     24  "version" : 2,
     25  "userID" : 501,
     26  "deployVersion" : 210,
     27  "modelCode" : "MacBookAir10,1",
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     33    "releaseType" : "User"
     34  },
     35  "captureTime" : "2022-01-26 17:44:19.5567 +0100",
     36  "incident" : "80DEFBBD-A6FE-4DA3-A78B-88FC04052B5D",
     37  "bug_type" : "309",
     38  "pid" : 30019,
     39  "procExitAbsTime" : 4160652861858,
     40  "translated" : true,
     41  "cpuType" : "X86-64",
     42  "procName" : "ChimeraX",
     43  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
     44  "parentProc" : "launchd",
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     48  "wakeTime" : 88,
     49  "sleepWakeUUID" : "03056DF8-B48B-40C6-99C4-9B66C10DADC5",
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     52  "isCorpse" : 1,
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     54  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":30019},
     55  "ktriageinfo" : "VM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\n",
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     121  "vmSummary" : "ReadOnly portion of Libraries: Total=206.0M resident=0K(0%) swapped_out_or_unallocated=206.0M(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1024K        8 \nActivity Tracing                   256K        1 \nCG backing stores                 2176K        4 \nCG image                           492K       51 \nColorSync                          240K       28 \nCoreAnimation                      232K       20 \nCoreGraphics                        12K        2 \nCoreUI image data                 4880K       36 \nFoundation                          36K        2 \nKernel Alloc Once                 1388K        6 \nMALLOC                           593.6M      117 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         784.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        24K        6 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   2244K      558 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               780K       78 \nRosetta Thread Context             780K       78 \nSTACK GUARD                         40K       10 \nStack                            325.6M       40 \nStack Guard                       56.1M       30 \nVM_ALLOCATE                      102.4M      199 \nVM_ALLOCATE (reserved)           160.0M        8         reserved VM address space (unallocated)\n__DATA                             355K       45 \n__DATA_CONST                      3028K       39 \n__DATA_DIRTY                        79K       24 \n__LINKEDIT                       193.1M        7 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                            12.9M       50 \n__UNICODE                          588K        1 \ndyld private memory               1024K        1 \nmapped file                        6.9G      898 \nshared memory                     5348K       37 \nunshared pmap                     11.1M        7 \n===========                     =======  ======= \nTOTAL                              9.7G     2420 \nTOTAL, minus reserved VM space     8.4G     2420 \n",
     122  "legacyInfo" : {
     123  "threadTriggered" : {
     124    "name" : "CrBrowserMain",
     125    "queue" : "com.apple.main-thread"
     126  }
     127},
     128  "trialInfo" : {
     129  "rollouts" : [
     130    {
     131      "rolloutId" : "607844aa04477260f58a8077",
     132      "factorPackIds" : {
     133        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
     134      },
     135      "deploymentId" : 240000066
     136    },
     137    {
     138      "rolloutId" : "60da5e84ab0ca017dace9abf",
     139      "factorPackIds" : {
     140
     141      },
     142      "deploymentId" : 240000008
     143    },
     144    {
     145      "rolloutId" : "602ad4dac86151000cf27e46",
     146      "factorPackIds" : {
     147        "SIRI_DICTATION_ASSETS" : "61a80a438feb033580c2778b"
     148      },
     149      "deploymentId" : 240000290
     150    },
     151    {
     152      "rolloutId" : "5fc94383418129005b4e9ae0",
     153      "factorPackIds" : {
     154
     155      },
     156      "deploymentId" : 240000207
     157    },
     158    {
     159      "rolloutId" : "601d9415f79519000ccd4b69",
     160      "factorPackIds" : {
     161        "SIRI_TEXT_TO_SPEECH" : "61c11dcd2cb6041dc630dc63"
     162      },
     163      "deploymentId" : 240000369
     164    },
     165    {
     166      "rolloutId" : "5ffde50ce2aacd000d47a95f",
     167      "factorPackIds" : {
     168
     169      },
     170      "deploymentId" : 240000098
     171    }
     172  ],
     173  "experiments" : [
     174    {
     175      "treatmentId" : "c4ac6461-f0e0-47b0-a630-f7739342ca3b",
     176      "experimentId" : "60c785f07aa5af21f0101872",
     177      "deploymentId" : 400000012
     178    }
     179  ]
     180}
     181}
     182===== Log before crash start =====
     183Startup Messages 
     184--- 
     185note | available bundle cache has not been initialized yet 
     186 
     187UCSF ChimeraX version: 1.3 (2021-12-08) 
     188© 2016-2021 Regents of the University of California. All rights reserved. 
     189How to cite UCSF ChimeraX 
     190
     191> ui tool show AlphaFold
     192
     193> alphafold predict
     194> MVSSSPAAPNIVFILSDDQGPWALGCAGNDEIHTPVLDTLAAGGTRLENFFCVSPVCSPARASLMTGQIPSRHGVHDYLTGVEVGAQAPDYLAGQAIFTDVLAEHGYRMGLAGKWHLGANDAPRKGFVHWYGLEGGGSPYLGATMYRNGEREDVTDYLTDIITDDAHAFLDREAAREEPFFLAVNYTAPHKPWKGQHPQKFEDLYADCAFDSCPQEEPHPWQPTVDGVAIGGEPDVRAALVGYFAAVSAMDAAIGSLLEHLEKLGIAENTLVIFSSDNGFNCGHHGVWGKGNGTFPQNMYDSSVKVPAIFHWPGRIAAGQVREELLSAYDVAATILELTGLDPAPFETGPGSSFAPLLRADDGTGDAAGRAENAVVVYDEYGPVRMIRTPEFKYVHRHPHGPHELYHLAADPGERHNLMDDAVPHPALVGLRAQLAGWFSRHGVPDFDGAALPVAGAGQHSPLRPPGGQTDPLGAFTAPNWDGI
     195
     196Running AlphaFold prediction 
     197
     198> alphafold predict
     199> MVSSSPAAPNIVFILSDDQGPWALGCAGNDEIHTPVLDTLAAGGTRLENFFCVSPVCSPARASLMTGQIPSRHGVHDYLTGVEVGAQAPDYLAGQAIFTDVLAEHGYRMGLAGKWHLGANDAPRKGFVHWYGLEGGGSPYLGATMYRNGEREDVTDYLTDIITDDAHAFLDREAAREEPFFLAVNYTAPHKPWKGQHPQKFEDLYADCAFDSCPQEEPHPWQPTVDGVAIGGEPDVRAALVGYFAAVSAMDAAIGSLLEHLEKLGIAENTLVIFSSDNGFNCGHHGVWGKGNGTFPQNMYDSSVKVPAIFHWPGRIAAGQVREELLSAYDVAATILELTGLDPAPFETGPGSSFAPLLRADDGTGDAAGRAENAVVVYDEYGPVRMIRTPEFKYVHRHPHGPHELYHLAADPGERHNLMDDAVPHPALVGLRAQLAGWFSRHGVPDFDGAALPVAGAGQHSPLRPPGGQTDPLGAFTAPNWDGI
     200
     201Running AlphaFold prediction 
     202
     203> alphafold predict
     204> MVSSSPAAPNIVFILSDDQGPWALGCAGNDEIHTPVLDTLAAGGTRLENFFCVSPVCSPARASLMTGQIPSRHGVHDYLTGVEVGAQAPDYLAGQAIFTDVLAEHGYRMGLAGKWHLGANDAPRKGFVHWYGLEGGGSPYLGATMYRNGEREDVTDYLTDIITDDAHAFLDREAAREEPFFLAVNYTAPHKPWKGQHPQKFEDLYADCAFDSCPQEEPHPWQPTVDGVAIGGEPDVRAALVGYFAAVSAMDAAIGSLLEHLEKLGIAENTLVIFSSDNGFNCGHHGVWGKGNGTFPQNMYDSSVKVPAIFHWPGRIAAGQVREELLSAYDVAATILELTGLDPAPFETGPGSSFAPLLRADDGTGDAAGRAENAVVVYDEYGPVRMIRTPEFKYVHRHPHGPHELYHLAADPGERHNLMDDAVPHPALVGLRAQLAGWFSRHGVPDFDGAALPVAGAGQHSPLRPPGGQTDPLGAFTAPNWDGI
     205
     206Running AlphaFold prediction 
     207
     208
     209===== Log before crash end =====
     210
     211Log:
     212UCSF ChimeraX version: 1.3 (2021-12-08) 
     213© 2016-2021 Regents of the University of California. All rights reserved. 
     214How to cite UCSF ChimeraX 
     215
     216
     217
     218
     219OpenGL version: 4.1 Metal - 76.3
     220OpenGL renderer: Apple M1
     221OpenGL vendor: AppleHardware:
     222
     223    Hardware Overview:
     224
     225      Model Name: MacBook Air
     226      Model Identifier: MacBookAir10,1
     227      Processor Name: Unknown
     228      Processor Speed: 2.4 GHz
     229      Number of Processors: 1
     230      Total Number of Cores: 8
     231      L2 Cache: 8 MB
     232      Memory: 16 GB
     233
     234Software:
     235
     236    System Software Overview:
     237
     238      System Version: macOS 12.1 (21C52)
     239      Kernel Version: Darwin 21.2.0
     240      Time since boot: 4 days 18:35
     241
     242Graphics/Displays:
     243
     244    Apple G13G:
     245
     246      Chipset Model: Apple G13G
     247      Type: GPU
     248      Bus: Built-In
     249      Total Number of Cores: 8
     250      Vendor: Apple (0x106b)
     251      Metal Family: Supported, Metal GPUFamily Apple 7
     252      Displays:
     253        Color LCD:
     254          Display Type: Built-In Retina LCD
     255          Resolution: 2560 x 1600 Retina
     256          Main Display: Yes
     257          Mirror: Off
     258          Online: Yes
     259          Automatically Adjust Brightness: No
     260          Connection Type: Internal
     261
     262Locale: (None, 'UTF-8')
     263PyQt5 5.15.2, Qt 5.15.2
     264Installed Packages:
     265    alabaster: 0.7.12
     266    appdirs: 1.4.4
     267    appnope: 0.1.2
     268    Babel: 2.9.1
     269    backcall: 0.2.0
     270    blockdiag: 2.0.1
     271    certifi: 2021.5.30
     272    cftime: 1.5.1.1
     273    charset-normalizer: 2.0.9
     274    ChimeraX-AddCharge: 1.2.2
     275    ChimeraX-AddH: 2.1.11
     276    ChimeraX-AlignmentAlgorithms: 2.0
     277    ChimeraX-AlignmentHdrs: 3.2
     278    ChimeraX-AlignmentMatrices: 2.0
     279    ChimeraX-Alignments: 2.2.3
     280    ChimeraX-AlphaFold: 1.0
     281    ChimeraX-AltlocExplorer: 1.0.1
     282    ChimeraX-AmberInfo: 1.0
     283    ChimeraX-Arrays: 1.0
     284    ChimeraX-Atomic: 1.31
     285    ChimeraX-AtomicLibrary: 4.2
     286    ChimeraX-AtomSearch: 2.0
     287    ChimeraX-AtomSearchLibrary: 1.0
     288    ChimeraX-AxesPlanes: 2.0
     289    ChimeraX-BasicActions: 1.1
     290    ChimeraX-BILD: 1.0
     291    ChimeraX-BlastProtein: 2.0
     292    ChimeraX-BondRot: 2.0
     293    ChimeraX-BugReporter: 1.0
     294    ChimeraX-BuildStructure: 2.6.1
     295    ChimeraX-Bumps: 1.0
     296    ChimeraX-BundleBuilder: 1.1
     297    ChimeraX-ButtonPanel: 1.0
     298    ChimeraX-CageBuilder: 1.0
     299    ChimeraX-CellPack: 1.0
     300    ChimeraX-Centroids: 1.2
     301    ChimeraX-ChemGroup: 2.0
     302    ChimeraX-Clashes: 2.2.2
     303    ChimeraX-ColorActions: 1.0
     304    ChimeraX-ColorGlobe: 1.0
     305    ChimeraX-ColorKey: 1.5
     306    ChimeraX-CommandLine: 1.1.5
     307    ChimeraX-ConnectStructure: 2.0
     308    ChimeraX-Contacts: 1.0
     309    ChimeraX-Core: 1.3
     310    ChimeraX-CoreFormats: 1.1
     311    ChimeraX-coulombic: 1.3.2
     312    ChimeraX-Crosslinks: 1.0
     313    ChimeraX-Crystal: 1.0
     314    ChimeraX-CrystalContacts: 1.0
     315    ChimeraX-DataFormats: 1.2.2
     316    ChimeraX-Dicom: 1.0
     317    ChimeraX-DistMonitor: 1.1.5
     318    ChimeraX-DistUI: 1.0
     319    ChimeraX-Dssp: 2.0
     320    ChimeraX-EMDB-SFF: 1.0
     321    ChimeraX-ExperimentalCommands: 1.0
     322    ChimeraX-FileHistory: 1.0
     323    ChimeraX-FunctionKey: 1.0
     324    ChimeraX-Geometry: 1.1
     325    ChimeraX-gltf: 1.0
     326    ChimeraX-Graphics: 1.1
     327    ChimeraX-Hbonds: 2.1.2
     328    ChimeraX-Help: 1.2
     329    ChimeraX-HKCage: 1.3
     330    ChimeraX-IHM: 1.1
     331    ChimeraX-ImageFormats: 1.2
     332    ChimeraX-IMOD: 1.0
     333    ChimeraX-IO: 1.0.1
     334    ChimeraX-ItemsInspection: 1.0
     335    ChimeraX-Label: 1.1
     336    ChimeraX-ListInfo: 1.1.1
     337    ChimeraX-Log: 1.1.4
     338    ChimeraX-LookingGlass: 1.1
     339    ChimeraX-Maestro: 1.8.1
     340    ChimeraX-Map: 1.1
     341    ChimeraX-MapData: 2.0
     342    ChimeraX-MapEraser: 1.0
     343    ChimeraX-MapFilter: 2.0
     344    ChimeraX-MapFit: 2.0
     345    ChimeraX-MapSeries: 2.1
     346    ChimeraX-Markers: 1.0
     347    ChimeraX-Mask: 1.0
     348    ChimeraX-MatchMaker: 2.0.4
     349    ChimeraX-MDcrds: 2.6
     350    ChimeraX-MedicalToolbar: 1.0.1
     351    ChimeraX-Meeting: 1.0
     352    ChimeraX-MLP: 1.1
     353    ChimeraX-mmCIF: 2.4
     354    ChimeraX-MMTF: 2.1
     355    ChimeraX-Modeller: 1.2.6
     356    ChimeraX-ModelPanel: 1.2.1
     357    ChimeraX-ModelSeries: 1.0
     358    ChimeraX-Mol2: 2.0
     359    ChimeraX-Morph: 1.0
     360    ChimeraX-MouseModes: 1.1
     361    ChimeraX-Movie: 1.0
     362    ChimeraX-Neuron: 1.0
     363    ChimeraX-Nucleotides: 2.0.2
     364    ChimeraX-OpenCommand: 1.7
     365    ChimeraX-PDB: 2.6.5
     366    ChimeraX-PDBBio: 1.0
     367    ChimeraX-PDBLibrary: 1.0.2
     368    ChimeraX-PDBMatrices: 1.0
     369    ChimeraX-PickBlobs: 1.0
     370    ChimeraX-Positions: 1.0
     371    ChimeraX-PresetMgr: 1.0.1
     372    ChimeraX-PubChem: 2.1
     373    ChimeraX-ReadPbonds: 1.0.1
     374    ChimeraX-Registration: 1.1
     375    ChimeraX-RemoteControl: 1.0
     376    ChimeraX-ResidueFit: 1.0
     377    ChimeraX-RestServer: 1.1
     378    ChimeraX-RNALayout: 1.0
     379    ChimeraX-RotamerLibMgr: 2.0.1
     380    ChimeraX-RotamerLibsDunbrack: 2.0
     381    ChimeraX-RotamerLibsDynameomics: 2.0
     382    ChimeraX-RotamerLibsRichardson: 2.0
     383    ChimeraX-SaveCommand: 1.5
     384    ChimeraX-SchemeMgr: 1.0
     385    ChimeraX-SDF: 2.0
     386    ChimeraX-Segger: 1.0
     387    ChimeraX-Segment: 1.0
     388    ChimeraX-SelInspector: 1.0
     389    ChimeraX-SeqView: 2.4.6
     390    ChimeraX-Shape: 1.0.1
     391    ChimeraX-Shell: 1.0
     392    ChimeraX-Shortcuts: 1.1
     393    ChimeraX-ShowAttr: 1.0
     394    ChimeraX-ShowSequences: 1.0
     395    ChimeraX-SideView: 1.0
     396    ChimeraX-Smiles: 2.1
     397    ChimeraX-SmoothLines: 1.0
     398    ChimeraX-SpaceNavigator: 1.0
     399    ChimeraX-StdCommands: 1.6.1
     400    ChimeraX-STL: 1.0
     401    ChimeraX-Storm: 1.0
     402    ChimeraX-Struts: 1.0
     403    ChimeraX-Surface: 1.0
     404    ChimeraX-SwapAA: 2.0
     405    ChimeraX-SwapRes: 2.1
     406    ChimeraX-TapeMeasure: 1.0
     407    ChimeraX-Test: 1.0
     408    ChimeraX-Toolbar: 1.1
     409    ChimeraX-ToolshedUtils: 1.2
     410    ChimeraX-Tug: 1.0
     411    ChimeraX-UI: 1.13.7
     412    ChimeraX-uniprot: 2.2
     413    ChimeraX-UnitCell: 1.0
     414    ChimeraX-ViewDockX: 1.0.1
     415    ChimeraX-VIPERdb: 1.0
     416    ChimeraX-Vive: 1.1
     417    ChimeraX-VolumeMenu: 1.0
     418    ChimeraX-VTK: 1.0
     419    ChimeraX-WavefrontOBJ: 1.0
     420    ChimeraX-WebCam: 1.0
     421    ChimeraX-WebServices: 1.0
     422    ChimeraX-Zone: 1.0
     423    colorama: 0.4.4
     424    cxservices: 1.1
     425    cycler: 0.11.0
     426    Cython: 0.29.24
     427    decorator: 5.1.0
     428    docutils: 0.17.1
     429    filelock: 3.0.12
     430    funcparserlib: 0.3.6
     431    grako: 3.16.5
     432    h5py: 3.6.0
     433    html2text: 2020.1.16
     434    idna: 3.3
     435    ihm: 0.21
     436    imagecodecs: 2021.4.28
     437    imagesize: 1.3.0
     438    ipykernel: 5.5.5
     439    ipython: 7.23.1
     440    ipython-genutils: 0.2.0
     441    jedi: 0.18.0
     442    Jinja2: 3.0.1
     443    jupyter-client: 6.1.12
     444    jupyter-core: 4.9.1
     445    kiwisolver: 1.3.2
     446    lxml: 4.6.3
     447    lz4: 3.1.3
     448    MarkupSafe: 2.0.1
     449    matplotlib: 3.4.3
     450    matplotlib-inline: 0.1.3
     451    msgpack: 1.0.2
     452    netCDF4: 1.5.7
     453    networkx: 2.6.3
     454    numexpr: 2.8.0
     455    numpy: 1.21.2
     456    openvr: 1.16.801
     457    packaging: 21.0
     458    ParmEd: 3.2.0
     459    parso: 0.8.3
     460    pexpect: 4.8.0
     461    pickleshare: 0.7.5
     462    Pillow: 8.3.2
     463    pip: 21.2.4
     464    pkginfo: 1.7.1
     465    prompt-toolkit: 3.0.23
     466    psutil: 5.8.0
     467    ptyprocess: 0.7.0
     468    pycollada: 0.7.1
     469    pydicom: 2.1.2
     470    Pygments: 2.10.0
     471    PyOpenGL: 3.1.5
     472    PyOpenGL-accelerate: 3.1.5
     473    pyparsing: 3.0.6
     474    PyQt5-commercial: 5.15.2
     475    PyQt5-sip: 12.8.1
     476    PyQtWebEngine-commercial: 5.15.2
     477    python-dateutil: 2.8.2
     478    pytz: 2021.3
     479    pyzmq: 22.3.0
     480    qtconsole: 5.1.1
     481    QtPy: 1.11.3
     482    RandomWords: 0.3.0
     483    requests: 2.26.0
     484    scipy: 1.7.1
     485    setuptools: 57.5.0
     486    sfftk-rw: 0.7.1
     487    six: 1.16.0
     488    snowballstemmer: 2.2.0
     489    sortedcontainers: 2.4.0
     490    Sphinx: 4.2.0
     491    sphinx-autodoc-typehints: 1.12.0
     492    sphinxcontrib-applehelp: 1.0.2
     493    sphinxcontrib-blockdiag: 2.0.0
     494    sphinxcontrib-devhelp: 1.0.2
     495    sphinxcontrib-htmlhelp: 2.0.0
     496    sphinxcontrib-jsmath: 1.0.1
     497    sphinxcontrib-qthelp: 1.0.3
     498    sphinxcontrib-serializinghtml: 1.1.5
     499    suds-jurko: 0.6
     500    tifffile: 2021.4.8
     501    tinyarray: 1.2.3
     502    tornado: 6.1
     503    traitlets: 5.1.1
     504    urllib3: 1.26.7
     505    wcwidth: 0.2.5
     506    webcolors: 1.11.1
     507    wheel: 0.37.0
     508    wheel-filename: 1.3.0
     509
     510}}}