Cannot download AlphaFold model

[jagadish.mangu@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Since last week I am unable to use the alfafold modeling on the chimera? It shows unable to download the model? I have previously reported this error and was able to get an update. 

I would be glad if you can help in this regard.

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MIRAYEQNPQHDIEDLEKVRVEQLTGHGSSVLEELVQLVKDKNIDISIKYDPRKDSEVFANRVITDDIELLKKILAYFLPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVIHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSGGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQEGETEKKIVSIKNFLESEKKRTGALGNLKDSYSYNKDNNELSHFATTCSDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDDTSGK

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\jach0015/Downloads/ChimeraX/AlphaFold/prediction_23  

Downloaded prediction file not found:
C:\Users\jach0015/Downloads/ChimeraX/AlphaFold/prediction_23\best_model.pdb  




OpenGL version: 3.3.0 NVIDIA 474.26
OpenGL renderer: NVIDIA GeForce GT 630/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: sv_SE.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Hewlett-Packard
Model: HP EliteDesk 800 G1 TWR
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 17,081,643,008
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 0.2
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
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    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
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    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
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    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
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    sphinxcontrib-devhelp: 1.0.2
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    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
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    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Tom Goddard]

This probably means the AlphaFold prediction failed. Did you look in the AlphaFold Run window to see if there were any error messages? Copy and paste the full text of that window if you want some advice on what happened.

[Tom Goddard]

I tried running your sequence and got an error

"INTERNAL: Failed to launch CUDA kernel: fusion_31"

This seems to be some new Google Colab problem. The CUDA version is still 12.0.

Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions.
INFO:main__:Starting prediction on 2023-11-06 UTC time
INFO:main__:Installing ColabFold on Google Colab virtual machine.
Installing ColabFold
Using Tesla T4 graphics processor
Downloading alphafold2 weights to .: 100%|██████████| 3.47G/3.47G [00:21<00:00, 177MB/s]
2023-11-06 21:19:36,293 Running on GPU
2023-11-06 21:19:36,603 Found 4 citations for tools or databases
2023-11-06 21:19:36,603 Query 1/1: af326 (length 326)
COMPLETE: 100%|██████████| 150/150 [elapsed: 00:01 remaining: 00:00]
2023-11-06 21:19:38,227 Setting max_seq=273, max_extra_seq=1
2023-11-06 21:20:16,116 Could not predict af326. Not Enough GPU memory? INTERNAL: Failed to launch CUDA kernel: fusion_31 with block dimensions: 1024x1x1 and grid dimensions: 273x1x1: CUDA_ERROR_ILLEGAL_ADDRESS: an illegal memory access was encountered
2023-11-06 21:20:16,117 Done
Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold
cp: cannot stat '*_unrelaxed_rank_001_*.pdb': No such file or directory
cp: cannot stat '*_scores_rank_001_*.json': No such file or directory

[Tom Goddard]

This is the same error from two weeks ago, ticket #10067. I made a fix back then for the Google Colab update to CUDA 12.0 and it was working. So I am puzzled by how it is broken again. The same CUDA 12.0 and same Nvidia driver 525.105.17 is in use. Needs more investigation.

[Tom Goddard]

Here's the installation log showing it installed jax for cuda 11.

+ set -e
+ pip install --no-warn-conflicts 'colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2'
Collecting colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2

Cloning ​https://github.com/sokrypton/ColabFold (to revision dc9fc3d03379d23784e796f4c7fd31d173bafaa2) to /tmp/pip-install-xso37kg8/colabfold_76d40bdc14d44b95b9760f8dd3421a5e
Running command git clone --filter=blob:none --quiet ​https://github.com/sokrypton/ColabFold /tmp/pip-install-xso37kg8/colabfold_76d40bdc14d44b95b9760f8dd3421a5e
Running command git rev-parse -q --verify 'sha^{dc9fc3d03379d23784e796f4c7fd31d173bafaa2'
Running command git fetch -q ​https://github.com/sokrypton/ColabFold dc9fc3d03379d23784e796f4c7fd31d173bafaa2
Running command git checkout -q dc9fc3d03379d23784e796f4c7fd31d173bafaa2
Resolved ​https://github.com/sokrypton/ColabFold to commit dc9fc3d03379d23784e796f4c7fd31d173bafaa2
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'}

Requirement already satisfied: absl-py<2.0.0,>=1.0.0 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (1.4.0)
Requirement already satisfied: appdirs<2.0.0,>=1.4.4 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (1.4.4)
Collecting dm-haiku<0.0.10,>=0.0.9 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading dm_haiku-0.0.9-py3-none-any.whl (352 kB)

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Collecting importlib-metadata<5.0.0,>=4.8.2 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading importlib_metadata-4.13.0-py3-none-any.whl (23 kB)

Requirement already satisfied: matplotlib<4.0.0,>=3.2.2 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (3.7.1)
Requirement already satisfied: numpy<2.0.0,>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (1.23.5)
Requirement already satisfied: pandas<2.0.0,>=1.3.4 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (1.5.3)
Collecting py3Dmol<3.0.0,>=2.0.1 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading py3Dmol-2.0.4-py2.py3-none-any.whl (12 kB)

Requirement already satisfied: requests<3.0.0,>=2.26.0 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (2.31.0)
Collecting tensorflow-cpu<3.0.0,>=2.11.0 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading tensorflow_cpu-2.14.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (198.2 MB)

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Requirement already satisfied: tqdm<5.0.0,>=4.62.2 in /usr/local/lib/python3.10/dist-packages (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (4.66.1)
Collecting alphafold-colabfold==v2.3.5 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading alphafold_colabfold-2.3.5-py3-none-any.whl (242 kB)

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Collecting biopython (from alphafold-colabfold==v2.3.5->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)

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Requirement already satisfied: chex in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (0.1.7)
Requirement already satisfied: dm-tree in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2) (0.1.8)
Collecting docker (from alphafold-colabfold==v2.3.5->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading docker-6.1.3-py3-none-any.whl (148 kB)

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Collecting immutabledict (from alphafold-colabfold==v2.3.5->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading immutabledict-3.0.0-py3-none-any.whl (4.0 kB)

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Collecting ml-collections (from alphafold-colabfold==v2.3.5->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading ml_collections-0.1.1.tar.gz (77 kB)

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Preparing metadata (setup.py): started
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Collecting jmp>=0.0.2 (from dm-haiku<0.0.10,>=0.0.9->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@dc9fc3d03379d23784e796f4c7fd31d173bafaa2)

Downloading jmp-0.0.4-py3-none-any.whl (18 kB)

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Building wheels for collected packages: colabfold, ml-collections

Building wheel for colabfold (pyproject.toml): started
Building wheel for colabfold (pyproject.toml): finished with status 'done'
Created wheel for colabfold: filename=colabfold-1.5.2-py3-none-any.whl size=58098 sha256=ea8b44c2246cb61efb8f33341f96ca308c5d5fa94d78eb42018fb97e21540373
Stored in directory: /root/.cache/pip/wheels/07/47/79/0bb338a0be5217a8ee6f58ee45dffc567940d99c82e20acb1f
Building wheel for ml-collections (setup.py): started
Building wheel for ml-collections (setup.py): finished with status 'done'
Created wheel for ml-collections: filename=ml_collections-0.1.1-py3-none-any.whl size=94506 sha256=fcf0b341b98b775cb748695b823979eb33ad22498269cb7e369cac0ba2f51b2e
Stored in directory: /root/.cache/pip/wheels/7b/89/c9/a9b87790789e94aadcfc393c283e3ecd5ab916aed0a31be8fe

Successfully built colabfold ml-collections
Installing collected packages: py3Dmol, ml-collections, jmp, importlib-metadata, immutabledict, biopython, docker, dm-haiku, tensorflow-cpu, colabfold, alphafold-colabfold

Attempting uninstall: importlib-metadata

Found existing installation: importlib-metadata 6.8.0
Uninstalling importlib-metadata-6.8.0:

Successfully uninstalled importlib-metadata-6.8.0

Successfully installed alphafold-colabfold-2.3.5 biopython-1.81 colabfold-1.5.2 dm-haiku-0.0.9 docker-6.1.3 immutabledict-3.0.0 importlib-metadata-4.13.0 jmp-0.0.4 ml-collections-0.1.1 py3Dmol-2.0.4 tensorflow-cpu-2.14.0
+ pip uninstall jax jaxlib -y
Found existing installation: jax 0.4.16
Uninstalling jax-0.4.16:

Successfully uninstalled jax-0.4.16

Found existing installation: jaxlib 0.4.16+cuda11.cudnn86
Uninstalling jaxlib-0.4.16+cuda11.cudnn86:

Successfully uninstalled jaxlib-0.4.16+cuda11.cudnn86

+ pip install 'jax[cuda]==0.3.25' -f ​https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
Looking in links: ​https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
Collecting jax[cuda]==0.3.25

Downloading jax-0.3.25.tar.gz (1.1 MB)

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Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'

Requirement already satisfied: numpy>=1.20 in /usr/local/lib/python3.10/dist-packages (from jax[cuda]==0.3.25) (1.23.5)
Requirement already satisfied: opt_einsum in /usr/local/lib/python3.10/dist-packages (from jax[cuda]==0.3.25) (3.3.0)
Requirement already satisfied: scipy>=1.5 in /usr/local/lib/python3.10/dist-packages (from jax[cuda]==0.3.25) (1.11.3)
Requirement already satisfied: typing_extensions in /usr/local/lib/python3.10/dist-packages (from jax[cuda]==0.3.25) (4.5.0)
Collecting jaxlib==0.3.25+cuda11.cudnn82 (from jax[cuda]==0.3.25)

Downloading ​https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.25%2Bcuda11.cudnn82-cp310-cp310-manylinux2014_x86_64.whl (154.5 MB)

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Building wheels for collected packages: jax

Building wheel for jax (setup.py): started
Building wheel for jax (setup.py): finished with status 'done'
Created wheel for jax: filename=jax-0.3.25-py3-none-any.whl size=1308493 sha256=f1aec69aeea8392b89213390744efc76965762a3323cd39f0efda1a7e2079fa3
Stored in directory: /root/.cache/pip/wheels/41/0b/45/1acffcaf4c863a6d0d0e910e56ae6502ca8d16300e39e1dab2

Successfully built jax
Installing collected packages: jaxlib, jax
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
chex 0.1.7 requires jax>=0.4.6, but you have jax 0.3.25 which is incompatible.
flax 0.7.4 requires jax>=0.4.2, but you have jax 0.3.25 which is incompatible.
orbax-checkpoint 0.4.1 requires jax>=0.4.9, but you have jax 0.3.25 which is incompatible.
Successfully installed jax-0.3.25 jaxlib-0.3.25+cuda11.cudnn82
+ touch COLABFOLD_READY

[Tom Goddard]

Fixed.

Since jaxlib depends on CUDA and the CUDA version gets updated by Google Colab periodically, we need jaxlib to sometimes update to remain compatible. Google Colab includes a jaxlib (currently version 0.4.16). But our install script was uninstalling the default jaxlib and trying to use 0.3.25. I think we have to use the Google Colab jaxlib to remain compatible with the system CUDA. This is what the ColabFold web server does. So I changed the ChimeraX ColabFold install script to not install jax or jaxlib and instead use the system versions. The script installs dm-haiku which also needs to be compatible with jax but my old ColabFold uses an old dm-haiku which fails with the current jax, so I also put in a pip update of dm-haiku. This is what the ColabFold web server does. I'm not sure what caused the current breakage. This all seems fragile and likely to break in the future, but we are at the mercy of Google Colab.

In summary ChimeraX was using this for setup

pip uninstall jax jaxlib -y
pip install "jax[cuda]==0.3.25" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

and now uses

pip install --upgrade dm-haiku

Let's see how long before this breaks.