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Opened 2 months ago
Last modified 2 months ago
#18490 assigned defect
Boltz: no supported GPU
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.4-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508200109 (2025-08-20 01:09:36 UTC)
Description
Hi, I got an error when I use Blotz prediciton on mac. My Mac version is 12.4, chip Apple M2, memory RAM 24G. The error as below "Attempted to run Boltz on the GPU but no supported GPU device could be found. To avoid this error specify the compute device as "cpu" in the ChimeraX Boltz options panel, or using the ChimeraX boltz command "device cpu" option. Boltz supports Nvidia GPUs with CUDA and Mac M series GPUs. On Windows the Boltz installation installs torch with no GPU support, so using Nvidia GPUs on Windows requires reinstalling gpu-enabled torch with Boltz which we plan to support in the future."
The boltz intalled log as below:
boltz install /Users/wangxiang/boltz22
Successfully created Boltz Python virtual environment /Users/wangxiang/boltz22. Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba... /Users/wangxiang/boltz22/bin/python -m pip install git+https://github.com/RBVI/boltz@chimerax_boltz22 Collecting git+https://github.com/RBVI/boltz@chimerax_boltz22 Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz22) to /private/var/folders/88/khqb5kbj0n78n9xv0_v13zk40000gn/T/pip-req-build-t2fgo3gq Running command git clone --filter=blob:none --quiet https://github.com/RBVI/boltz /private/var/folders/88/khqb5kbj0n78n9xv0_v13zk40000gn/T/pip-req-build-t2fgo3gq Running command git checkout -b chimerax_boltz22 --track origin/chimerax_boltz22 Switched to a new branch 'chimerax_boltz22' Branch 'chimerax_boltz22' set up to track remote branch 'chimerax_boltz22' from 'origin'. Resolved https://github.com/RBVI/boltz to commit f1638c67006f656dc78fa7062f852077e7016018 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' Collecting torch>=2.2 (from boltz==2.2.0) Using cached torch-2.8.0-cp311-none-macosx_11_0_arm64.whl.metadata (30 kB) Requirement already satisfied: numpy<2.0,>=1.26 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from boltz==2.2.0) (1.26.4) Collecting hydra-core==1.3.2 (from boltz==2.2.0) Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB) Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0) Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB) Collecting rdkit>=2024.3.2 (from boltz==2.2.0) Using cached rdkit-2025.3.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.1 kB) Collecting dm-tree==0.1.8 (from boltz==2.2.0) Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl.metadata (1.9 kB) Collecting requests==2.32.3 (from boltz==2.2.0) Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) Collecting pandas>=2.2.2 (from boltz==2.2.0) Using cached pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB) Collecting types-requests (from boltz==2.2.0) Using cached types_requests-2.32.4.20250809-py3-none-any.whl.metadata (2.0 kB) Collecting einops==0.8.0 (from boltz==2.2.0) Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB) Collecting einx==0.3.0 (from boltz==2.2.0) Using cached einx-0.3.0-py3-none-any.whl.metadata (6.9 kB) Collecting fairscale==0.4.13 (from boltz==2.2.0) Using cached fairscale-0.4.13-py3-none-any.whl Collecting mashumaro==3.14 (from boltz==2.2.0) Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB) Collecting modelcif==1.2 (from boltz==2.2.0) Using cached modelcif-1.2-py3-none-any.whl Collecting wandb==0.18.7 (from boltz==2.2.0) Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl.metadata (9.7 kB) Collecting click==8.1.7 (from boltz==2.2.0) Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting pyyaml==6.0.2 (from boltz==2.2.0) Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.1 kB) Collecting biopython==1.84 (from boltz==2.2.0) Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB) Collecting scipy==1.13.1 (from boltz==2.2.0) Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (60 kB) Collecting numba==0.61.0 (from boltz==2.2.0) Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.7 kB) Collecting gemmi==0.6.5 (from boltz==2.2.0) Using cached gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.3 kB) Collecting scikit-learn==1.6.1 (from boltz==2.2.0) Using cached scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (31 kB) Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0) Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9 kB) Collecting cuequivariance_torch>=0.5.0 (from boltz==2.2.0) Using cached cuequivariance_torch-0.6.0-py3-none-any.whl.metadata (15 kB) Requirement already satisfied: setuptools>=46.4.0 in /Users/wangxiang/boltz22/lib/python3.11/site-packages (from chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0) Collecting sympy (from einx==0.3.0->boltz==2.2.0) Using cached sympy-1.14.0-py3-none-any.whl.metadata (12 kB) Collecting frozendict (from einx==0.3.0->boltz==2.2.0) Using cached frozendict-2.4.6-py311-none-any.whl.metadata (23 kB) Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0) Using cached omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB) Collecting antlr4-python3-runtime==4.9.* (from hydra-core==1.3.2->boltz==2.2.0) Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl Requirement already satisfied: packaging in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz==2.2.0) (25.0) Requirement already satisfied: typing-extensions>=4.1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from mashumaro==3.14->boltz==2.2.0) (4.14.1) Requirement already satisfied: ihm>=1.7 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from modelcif==1.2->boltz==2.2.0) (2.2) Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.2.0) Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.8 kB) Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0) Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB) Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0) Using cached torchmetrics-1.8.1-py3-none-any.whl.metadata (22 kB) Collecting lightning-utilities>=0.10.0 (from pytorch-lightning==2.5.0->boltz==2.2.0) Using cached lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (3.4.3) Requirement already satisfied: idna<4,>=2.5 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (2025.7.14) Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0) Using cached joblib-1.5.1-py3-none-any.whl.metadata (5.6 kB) Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0) Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB) Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0) Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.2.0) Using cached gitpython-3.1.45-py3-none-any.whl.metadata (13 kB) Requirement already satisfied: platformdirs in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from wandb==0.18.7->boltz==2.2.0) (4.3.8) Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==2.2.0) Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl.metadata (592 bytes) Requirement already satisfied: psutil>=5.0.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from wandb==0.18.7->boltz==2.2.0) (7.0.0) Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.2.0) Using cached sentry_sdk-2.35.0-py2.py3-none-any.whl.metadata (10 kB) Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0) Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl.metadata (10 kB) Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0) Using cached cuequivariance-0.6.0-py3-none-any.whl.metadata (15 kB) Requirement already satisfied: python-dateutil>=2.8.2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2) Requirement already satisfied: tzdata>=2022.7 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2) Requirement already satisfied: Pillow in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz==2.2.0) (10.4.0) Requirement already satisfied: filelock in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==2.2.0) (3.18.0) Requirement already satisfied: networkx in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==2.2.0) (3.3) Requirement already satisfied: jinja2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==2.2.0) (3.1.6) Requirement already satisfied: six>=1.4.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0) Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl.metadata (7.7 kB) Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0) Using cached gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB) Requirement already satisfied: msgpack in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz==2.2.0) (1.1.0) Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.2.0) Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB) Collecting opt-einsum (from cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.2.0) Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB) Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz==2.2.0) (3.0.2) Collecting aiohappyeyeballs>=2.5.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB) Collecting aiosignal>=1.4.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB) Collecting attrs>=17.3.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB) Collecting frozenlist>=1.1.1 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (18 kB) Collecting multidict<7.0,>=4.5 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached multidict-6.6.4-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.3 kB) Collecting propcache>=0.2.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB) Collecting yarl<2.0,>=1.17.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (73 kB) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0) Using cached smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB) Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB) Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB) Using cached click-8.1.7-py3-none-any.whl (97 kB) Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB) Using cached einops-0.8.0-py3-none-any.whl (43 kB) Using cached einx-0.3.0-py3-none-any.whl (102 kB) Using cached gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl (3.0 MB) Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB) Using cached mashumaro-3.14-py3-none-any.whl (92 kB) Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB) Using cached pytorch_lightning-2.5.0-py3-none-any.whl (819 kB) Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB) Using cached requests-2.32.3-py3-none-any.whl (64 kB) Using cached scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl (11.1 MB) Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB) Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB) Using cached cuequivariance_torch-0.6.0-py3-none-any.whl (214 kB) Using cached pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB) Using cached rdkit-2025.3.5-cp311-cp311-macosx_11_0_arm64.whl (28.7 MB) Using cached torch-2.8.0-cp311-none-macosx_11_0_arm64.whl (73.6 MB) Using cached types_requests-2.32.4.20250809-py3-none-any.whl (20 kB) Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB) Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB) Using cached gitpython-3.1.45-py3-none-any.whl (208 kB) Using cached joblib-1.5.1-py3-none-any.whl (307 kB) Using cached lightning_utilities-0.15.2-py3-none-any.whl (29 kB) Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB) Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB) Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB) Using cached sentry_sdk-2.35.0-py2.py3-none-any.whl (363 kB) Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB) Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Using cached torchmetrics-1.8.1-py3-none-any.whl (982 kB) Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) Using cached cuequivariance-0.6.0-py3-none-any.whl (266 kB) Using cached frozendict-2.4.6-py311-none-any.whl (16 kB) Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB) Using cached aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl (471 kB) Using cached gitdb-4.0.12-py3-none-any.whl (62 kB) Using cached mpmath-1.3.0-py3-none-any.whl (536 kB) Using cached opt_einsum-3.4.0-py3-none-any.whl (71 kB) Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB) Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB) Using cached attrs-25.3.0-py3-none-any.whl (63 kB) Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl (47 kB) Using cached multidict-6.6.4-cp311-cp311-macosx_11_0_arm64.whl (44 kB) Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (43 kB) Using cached smmap-5.0.2-py3-none-any.whl (24 kB) Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB) Building wheels for collected packages: boltz Building wheel for boltz (pyproject.toml): started Building wheel for boltz (pyproject.toml): finished with status 'done' Created wheel for boltz: filename=boltz-2.2.0-py3-none-any.whl size=268910 sha256=63392dd4dbf4bcf7abdfe3647446726e128f43f32c405e8c1f748928187057db Stored in directory: /private/var/folders/88/khqb5kbj0n78n9xv0_v13zk40000gn/T/pip-ephem-wheel-cache-7cwi6_m7/wheels/a2/57/a2/680a7866e1b7f1dc290112e8f82241f58511d33c66a8818e3d Successfully built boltz Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy, requests, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict, mashumaro, llvmlite, lightning-utilities, joblib, gemmi, fsspec, frozenlist, frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs, yarl, torch, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb, einx, cuequivariance, chembl_structure_pipeline, aiosignal, torchmetrics, hydra-core, gitpython, fairscale, cuequivariance_torch, aiohttp, wandb, pytorch-lightning, boltz Attempting uninstall: scipy Found existing installation: scipy 1.14.0 Not uninstalling scipy at /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages, outside environment /Users/wangxiang/boltz22 Can't uninstall 'scipy'. No files were found to uninstall. Attempting uninstall: requests Found existing installation: requests 2.32.4 Not uninstalling requests at /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages, outside environment /Users/wangxiang/boltz22 Can't uninstall 'requests'. No files were found to uninstall. Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0 antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-2.2.0 chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.6.0 cuequivariance_torch-0.6.0 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 frozenlist-1.7.0 fsspec-2025.7.0 gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.1 lightning-utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.6.4 numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.1 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.3.5 requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1 sentry-sdk-2.35.0 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 threadpoolctl-3.6.0 torch-2.8.0 torchmetrics-1.8.1 tqdm-4.67.1 types-requests-2.32.4.20250809 wandb-0.18.7 yarl-1.20.1 [notice] A new release of pip is available: 24.0 -> 25.2 [notice] To update, run: /Users/wangxiang/boltz22/bin/python -m pip install --upgrade pip Downloading Boltz model parameters (4 GB) and chemical component database (1.8 GB) to ~/.boltz /Users/wangxiang/boltz22/bin/python /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/boltz/download_weights_and_ccd.py Boltz model parameters and CCD database are installed in ~/.boltz Successfully installed Boltz.
Log:
> ui tool show clix
Error running startup command 'ui tool show clix': No running or installed
tool named "clix"
UCSF ChimeraX version: 1.11.dev202508200109 (2025-08-20)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Boltz
> boltz install /Users/wangxiang/boltz22
Successfully created Boltz Python virtual environment
/Users/wangxiang/boltz22.
Now installing Boltz and required packages from PyPi. This may take tens of of
minutes since Boltz uses many other packages totaling about 1 Gbyte of disk
space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb,
numba...
/Users/wangxiang/boltz22/bin/python -m pip install
git+https://github.com/RBVI/boltz@chimerax_boltz22
Collecting git+https://github.com/RBVI/boltz@chimerax_boltz22
Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz22) to
/private/var/folders/88/khqb5kbj0n78n9xv0_v13zk40000gn/T/pip-req-
build-t2fgo3gq
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz
/private/var/folders/88/khqb5kbj0n78n9xv0_v13zk40000gn/T/pip-req-
build-t2fgo3gq
Running command git checkout -b chimerax_boltz22 --track
origin/chimerax_boltz22
Switched to a new branch 'chimerax_boltz22'
Branch 'chimerax_boltz22' set up to track remote branch 'chimerax_boltz22'
from 'origin'.
Resolved https://github.com/RBVI/boltz to commit
f1638c67006f656dc78fa7062f852077e7016018
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'
Collecting torch>=2.2 (from boltz==2.2.0)
Using cached torch-2.8.0-cp311-none-macosx_11_0_arm64.whl.metadata (30 kB)
Requirement already satisfied: numpy<2.0,>=1.26 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from boltz==2.2.0) (1.26.4)
Collecting hydra-core==1.3.2 (from boltz==2.2.0)
Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0)
Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)
Collecting rdkit>=2024.3.2 (from boltz==2.2.0)
Using cached rdkit-2025.3.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.1
kB)
Collecting dm-tree==0.1.8 (from boltz==2.2.0)
Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl.metadata (1.9 kB)
Collecting requests==2.32.3 (from boltz==2.2.0)
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting pandas>=2.2.2 (from boltz==2.2.0)
Using cached pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB)
Collecting types-requests (from boltz==2.2.0)
Using cached types_requests-2.32.4.20250809-py3-none-any.whl.metadata (2.0 kB)
Collecting einops==0.8.0 (from boltz==2.2.0)
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting einx==0.3.0 (from boltz==2.2.0)
Using cached einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)
Collecting fairscale==0.4.13 (from boltz==2.2.0)
Using cached fairscale-0.4.13-py3-none-any.whl
Collecting mashumaro==3.14 (from boltz==2.2.0)
Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB)
Collecting modelcif==1.2 (from boltz==2.2.0)
Using cached modelcif-1.2-py3-none-any.whl
Collecting wandb==0.18.7 (from boltz==2.2.0)
Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl.metadata (9.7 kB)
Collecting click==8.1.7 (from boltz==2.2.0)
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting pyyaml==6.0.2 (from boltz==2.2.0)
Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.1 kB)
Collecting biopython==1.84 (from boltz==2.2.0)
Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB)
Collecting scipy==1.13.1 (from boltz==2.2.0)
Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (60 kB)
Collecting numba==0.61.0 (from boltz==2.2.0)
Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.7 kB)
Collecting gemmi==0.6.5 (from boltz==2.2.0)
Using cached gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.3 kB)
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)
Using cached scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (31
kB)
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0)
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9
kB)
Collecting cuequivariance_torch>=0.5.0 (from boltz==2.2.0)
Using cached cuequivariance_torch-0.6.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: setuptools>=46.4.0 in
/Users/wangxiang/boltz22/lib/python3.11/site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0)
Collecting sympy (from einx==0.3.0->boltz==2.2.0)
Using cached sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
Collecting frozendict (from einx==0.3.0->boltz==2.2.0)
Using cached frozendict-2.4.6-py311-none-any.whl.metadata (23 kB)
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0)
Using cached omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)
Collecting antlr4-python3-runtime==4.9.* (from hydra-
core==1.3.2->boltz==2.2.0)
Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl
Requirement already satisfied: packaging in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from hydra-core==1.3.2->boltz==2.2.0) (25.0)
Requirement already satisfied: typing-extensions>=4.1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from mashumaro==3.14->boltz==2.2.0) (4.14.1)
Requirement already satisfied: ihm>=1.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from modelcif==1.2->boltz==2.2.0) (2.2)
Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.2.0)
Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.8
kB)
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB)
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)
Using cached torchmetrics-1.8.1-py3-none-any.whl.metadata (22 kB)
Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (3.4.3)
Requirement already satisfied: idna<4,>=2.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (2.5.0)
Requirement already satisfied: certifi>=2017.4.17 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (2025.7.14)
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0)
Using cached joblib-1.5.1-py3-none-any.whl.metadata (5.6 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0)
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0)
Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.2.0)
Using cached gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: platformdirs in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==2.2.0) (4.3.8)
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from
wandb==0.18.7->boltz==2.2.0)
Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl.metadata
(592 bytes)
Requirement already satisfied: psutil>=5.0.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==2.2.0) (7.0.0)
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.2.0)
Using cached sentry_sdk-2.35.0-py2.py3-none-any.whl.metadata (10 kB)
Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0)
Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl.metadata (10
kB)
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)
Using cached cuequivariance-0.6.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: python-dateutil>=2.8.2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2)
Requirement already satisfied: Pillow in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from rdkit>=2024.3.2->boltz==2.2.0) (10.4.0)
Requirement already satisfied: filelock in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==2.2.0) (3.18.0)
Requirement already satisfied: networkx in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==2.2.0) (3.3)
Requirement already satisfied: jinja2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==2.2.0) (3.1.6)
Requirement already satisfied: six>=1.4.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0)
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl.metadata (7.7
kB)
Collecting gitdb<5,>=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)
Using cached gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
Requirement already satisfied: msgpack in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ihm>=1.7->modelcif==1.2->boltz==2.2.0) (1.1.0)
Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.2.0)
Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting opt-einsum (from
cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.2.0)
Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Requirement already satisfied: MarkupSafe>=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from jinja2->torch>=2.2->boltz==2.2.0) (3.0.2)
Collecting aiohappyeyeballs>=2.5.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
Collecting aiosignal>=1.4.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
Collecting attrs>=17.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)
Collecting frozenlist>=1.1.1 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (18
kB)
Collecting multidict<7.0,>=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached multidict-6.6.4-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.3
kB)
Collecting propcache>=0.2.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (12
kB)
Collecting yarl<2.0,>=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (73 kB)
Collecting smmap<6,>=3.0.1 (from
gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)
Using cached smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB)
Using cached click-8.1.7-py3-none-any.whl (97 kB)
Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB)
Using cached einops-0.8.0-py3-none-any.whl (43 kB)
Using cached einx-0.3.0-py3-none-any.whl (102 kB)
Using cached gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl (3.0 MB)
Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB)
Using cached mashumaro-3.14-py3-none-any.whl (92 kB)
Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB)
Using cached pytorch_lightning-2.5.0-py3-none-any.whl (819 kB)
Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB)
Using cached requests-2.32.3-py3-none-any.whl (64 kB)
Using cached scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl (11.1 MB)
Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB)
Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB)
Using cached cuequivariance_torch-0.6.0-py3-none-any.whl (214 kB)
Using cached pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB)
Using cached rdkit-2025.3.5-cp311-cp311-macosx_11_0_arm64.whl (28.7 MB)
Using cached torch-2.8.0-cp311-none-macosx_11_0_arm64.whl (73.6 MB)
Using cached types_requests-2.32.4.20250809-py3-none-any.whl (20 kB)
Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB)
Using cached gitpython-3.1.45-py3-none-any.whl (208 kB)
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Using cached lightning_utilities-0.15.2-py3-none-any.whl (29 kB)
Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB)
Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB)
Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB)
Using cached sentry_sdk-2.35.0-py2.py3-none-any.whl (363 kB)
Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB)
Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Using cached torchmetrics-1.8.1-py3-none-any.whl (982 kB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
Using cached cuequivariance-0.6.0-py3-none-any.whl (266 kB)
Using cached frozendict-2.4.6-py311-none-any.whl (16 kB)
Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB)
Using cached aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl (471 kB)
Using cached gitdb-4.0.12-py3-none-any.whl (62 kB)
Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)
Using cached opt_einsum-3.4.0-py3-none-any.whl (71 kB)
Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
Using cached attrs-25.3.0-py3-none-any.whl (63 kB)
Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl (47 kB)
Using cached multidict-6.6.4-cp311-cp311-macosx_11_0_arm64.whl (44 kB)
Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (43 kB)
Using cached smmap-5.0.2-py3-none-any.whl (24 kB)
Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB)
Building wheels for collected packages: boltz
Building wheel for boltz (pyproject.toml): started
Building wheel for boltz (pyproject.toml): finished with status 'done'
Created wheel for boltz: filename=boltz-2.2.0-py3-none-any.whl size=268910
sha256=63392dd4dbf4bcf7abdfe3647446726e128f43f32c405e8c1f748928187057db
Stored in directory:
/private/var/folders/88/khqb5kbj0n78n9xv0_v13zk40000gn/T/pip-ephem-wheel-
cache-7cwi6_m7/wheels/a2/57/a2/680a7866e1b7f1dc290112e8f82241f58511d33c66a8818e3d
Successfully built boltz
Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy,
requests, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict,
mashumaro, llvmlite, lightning-utilities, joblib, gemmi, fsspec, frozenlist,
frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs,
yarl, torch, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb, einx,
cuequivariance, chembl_structure_pipeline, aiosignal, torchmetrics, hydra-
core, gitpython, fairscale, cuequivariance_torch, aiohttp, wandb, pytorch-
lightning, boltz
Attempting uninstall: scipy
Found existing installation: scipy 1.14.0
Not uninstalling scipy at
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/wangxiang/boltz22
Can't uninstall 'scipy'. No files were found to uninstall.
Attempting uninstall: requests
Found existing installation: requests 2.32.4
Not uninstalling requests at
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/wangxiang/boltz22
Can't uninstall 'requests'. No files were found to uninstall.
Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0
antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-2.2.0
chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.6.0
cuequivariance_torch-0.6.0 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0
einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 frozenlist-1.7.0 fsspec-2025.7.0
gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.1
lightning-utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2
mpmath-1.3.0 multidict-6.6.4 numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0
pandas-2.3.1 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.5.0
pyyaml-6.0.2 rdkit-2025.3.5 requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1
sentry-sdk-2.35.0 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0
threadpoolctl-3.6.0 torch-2.8.0 torchmetrics-1.8.1 tqdm-4.67.1 types-
requests-2.32.4.20250809 wandb-0.18.7 yarl-1.20.1
[notice] A new release of pip is available: 24.0 -> 25.2
[notice] To update, run: /Users/wangxiang/boltz22/bin/python -m pip install
--upgrade pip
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz
/Users/wangxiang/boltz22/bin/python
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py
Boltz model parameters and CCD database are installed in ~/.boltz
Successfully installed Boltz.
> open 1tw7 format mmcif fromDatabase pdb
1tw7 title:
Wide Open 1.3A Structure of a Multi-drug Resistant HIV-1 Protease Represents a
Novel Drug Target [more info...]
Chain information for 1tw7 #1
---
Chain | Description
A B | protease
Non-standard residues in 1tw7 #1
---
NA — sodium ion
54 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1890 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> boltz predict protein
> MSQQVGNSIRRKLVIVGDGACGKTCLLIVFSKGQFPEVYVPTVFENYVADVEVDGRRVELALWDTAGQEDYDRLRPLSYPDSNVVLICFSIDLPDSLENVQEKWIAEVLHFCQGVPIILVGCKVDLRNDPQTIEQLRQEGQQPVTSQEGQSVADQIGATGYYECSAKTGYGVREVFEAATRASLMGKSKTNGKAKKNTTEKKKKKCVLL
> ligandCcd GTP affinity GTP
Running Boltz prediction of protein with 209 residues, 1 ligands GTP on gpu
Using multiple sequence alignment server https://api.colabfold.com
Attempted to run Boltz on the GPU but no supported GPU device could be found.
To avoid this error specify the compute device as "cpu" in the ChimeraX Boltz
options panel, or using the ChimeraX boltz command "device cpu" option. Boltz
supports Nvidia GPUs with CUDA and Mac M series GPUs. On Windows the Boltz
installation installs torch with no GPU support, so using Nvidia GPUs on
Windows requires reinstalling gpu-enabled torch with Boltz which we plan to
support in the future.
> cpu
Unknown command: device cpu
> boltz predict protein
> MSQQVGNSIRRKLVIVGDGACGKTCLLIVFSKGQFPEVYVPTVFENYVADVEVDGRRVELALWDTAGQEDYDRLRPLSYPDSNVVLICFSIDLPDSLENVQEKWIAEVLHFCQGVPIILVGCKVDLRNDPQTIEQLRQEGQQPVTSQEGQSVADQIGATGYYECSAKTGYGVREVFEAATRASLMGKSKTNGKAKKNTTEKKKKKCVLL
> ligandCcd GTP device gpu affinity GTP
Running Boltz prediction of protein with 209 residues, 1 ligands GTP on gpu
Using multiple sequence alignment server https://api.colabfold.com
Attempted to run Boltz on the GPU but no supported GPU device could be found.
To avoid this error specify the compute device as "cpu" in the ChimeraX Boltz
options panel, or using the ChimeraX boltz command "device cpu" option. Boltz
supports Nvidia GPUs with CUDA and Mac M series GPUs. On Windows the Boltz
installation installs torch with no GPU support, so using Nvidia GPUs on
Windows requires reinstalling gpu-enabled torch with Boltz which we plan to
support in the future.
> boltz predict protein
> MSQQVGNSIRRKLVIVGDGACGKTCLLIVFSKGQFPEVYVPTVFENYVADVEVDGRRVELALWDTAGQEDYDRLRPLSYPDSNVVLICFSIDLPDSLENVQEKWIAEVLHFCQGVPIILVGCKVDLRNDPQTIEQLRQEGQQPVTSQEGQSVADQIGATGYYECSAKTGYGVREVFEAATRASLMGKSKTNGKAKKNTTEKKKKKCVLL
> ligandCcd GTP device cpu affinity GTP
Running Boltz prediction of protein with 209 residues, 1 ligands GTP on cpu
Using multiple sequence alignment server https://api.colabfold.com
Running boltz prediction failed with exit code 0:
command:
/Users/wangxiang/boltz22/bin/boltz predict
/Users/wangxiang/Desktop/boltz_3/boltz_3.yaml --use_msa_server --accelerator
cpu --no_kernels
stdout:
Boltz version 2.2.0
Running on CPU, this will be slow. Consider using a GPU.
MSA server enabled: https://api.colabfold.com
MSA server authentication: no credentials provided
Checking input data.
Processing 1 inputs with 1 threads.
Generating MSA for /Users/wangxiang/Desktop/boltz_3/boltz_3.yaml with 1
protein entities.
Calling MSA server for target boltz_3 with 1 sequences
MSA server URL: https://api.colabfold.com
MSA pairing strategy: greedy
No authentication provided for MSA server
Failed to process /Users/wangxiang/Desktop/boltz_3/boltz_3.yaml. Skipping.
Error: MMseqs2 API is giving errors. Please confirm your input is a valid
protein sequence. If error persists, please try again an hour later..
stderr:
0%| | 0/1 [00:00<?, ?it/s]
0%| | 0/150 [elapsed: 00:00 remaining: ?][A
SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?][AServer didn't reply with json: <html>
<head><title>403 Forbidden</title></head>
<body>
<center><h1>403 Forbidden</h1></center>
<hr><center>nginx</center>
</body>
</html>
SUBMIT: 0%| | 0/150 [elapsed: 00:01 remaining: ?]
Traceback (most recent call last):
File "/Users/wangxiang/boltz22/lib/python3.11/site-packages/boltz/main.py",
line 581, in process_input
compute_msa(
File "/Users/wangxiang/boltz22/lib/python3.11/site-packages/boltz/main.py",
line 477, in compute_msa
unpaired_msa = run_mmseqs2(
^^^^^^^^^^^^
File "/Users/wangxiang/boltz22/lib/python3.11/site-
packages/boltz/data/msa/mmseqs2.py", line 215, in run_mmseqs2
raise Exception(msg)
Exception: MMseqs2 API is giving errors. Please confirm your input is a valid
protein sequence. If error persists, please try again an hour later.
100%|██████████| 1/1 [00:01<00:00, 1.82s/it] 100%|██████████| 1/1
[00:01<00:00, 1.82s/it]
GPU available: False, used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/Users/wangxiang/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76:
Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the
`pytorch_lightning` package, due to potential conflicts with other packages in
the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the
default logger, unless the `tensorboard` or `tensorboardX` packages are found.
Please `pip install lightning[extra]` or one of them to enable TensorBoard
support by default
> boltz predict protein
> MSQQVGNSIRRKLVIVGDGACGKTCLLIVFSKGQFPEVYVPTVFENYVADVEVDGRRVELALWDTAGQEDYDRLRPLSYPDSNVVLICFSIDLPDSLENVQEKWIAEVLHFCQGVPIILVGCKVDLRNDPQTIEQLRQEGQQPVTSQEGQSVADQIGATGYYECSAKTGYGVREVFEAATRASLMGKSKTNGKAKKNTTEKKKKKCVLL
> ligandCcd GTP device gpu affinity GTP
Running Boltz prediction of protein with 209 residues, 1 ligands GTP on gpu
Using multiple sequence alignment server https://api.colabfold.com
Attempted to run Boltz on the GPU but no supported GPU device could be found.
To avoid this error specify the compute device as "cpu" in the ChimeraX Boltz
options panel, or using the ChimeraX boltz command "device cpu" option. Boltz
supports Nvidia GPUs with CUDA and Mac M series GPUs. On Windows the Boltz
installation installs torch with no GPU support, so using Nvidia GPUs on
Windows requires reinstalling gpu-enabled torch with Boltz which we plan to
support in the future.
Populating font family aliases took 182 ms. Replace uses of missing font
family "Roboto" with one that exists to avoid this cost.
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 7459.121.3
OS Loader Version: 7459.121.3
Software:
System Software Overview:
System Version: macOS 12.4 (21F2081)
Kernel Version: Darwin 21.5.0
Time since boot: 21 days 15:29
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.4
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.12
ChimeraX-AtomicLibrary: 14.1.22
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508200109
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.10.4
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.2
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.1
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.4.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 5.3.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.1
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.5
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (4)
comment:1 by , 2 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Boltz: no supported GPU |
comment:2 by , 2 months ago
Strange, I've never seen this error on an M2 Mac. Can you send the stderr file in Desktop/boltz_1. Apparently it says in that file "No supported gpu backend found" which is why ChimeraX reports the error message you see, but maybe something else in the stderr file explains what is going on.
comment:3 by , 2 months ago
My Mac M2 ChimeraX Boltz install uses the same torch version (2.8.0) and same torch_lightning version (2.5.0) as yours. The one thing that stands out as different is you are running macOS 12.4 and I am running macOS 15.6. The machine learning package torch added Mac GPU support in 2022 and your macOS 12 is from 2021 so it may be that torch requires a newer macOS version to use Mac GPUs (torch calls this Metal Performance Shaders).
I don't have a Mac with an old version of macOS so I am not able to test this theory.
comment:4 by , 2 months ago
Apple claims PyTorch works with macOS 12.3 or newer (https://developer.apple.com/metal/pytorch/).
Huggingface suggests macOS 12.6 is needed (newer than your 12.4) and that macOS 13 is recommended (https://huggingface.co/docs/diffusers/en/optimization/mps) although that may be just for their "diffusers" code.
I didn't find any definitive source that said torch MPS won't work with macOS 12.4. But I would still bet that is your problem.
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Reported by Xiang