Boltz: The GPU device instance has been suspended

[biq2001@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.dev202508150726 (2025-08-15 07:26:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x00002704 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\site-packages\chimerax\boltz\install.py", line 250 in _queue_output_in_thread
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\threading.py", line 1002 in _bootstrap

Current thread 0x00002b14 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
  File "C:\Program Files\ChimeraX 1.11.dev202508150726\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202508150726 (2025-08-15)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

> boltz install C:\Users\annie/boltz2

Successfully created Boltz Python virtual environment C:\Users\annie/boltz2.  
Now installing machine learning package torch.  
C:\Users\annie/boltz2\Scripts\python.exe -m pip install torch --index-url
https://download.pytorch.org/whl/cu126  
Looking in indexes: https://download.pytorch.org/whl/cu126  
  
Collecting torch  
  
Using cached
https://download.pytorch.org/whl/cu126/torch-2.8.0%2Bcu126-cp311-cp311-win_amd64.whl.metadata
(29 kB)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from torch) (3.18.0)  
  
Requirement already satisfied: typing-extensions>=4.10.0 in c:\program
files\chimerax 1.11.dev202508150726\bin\lib\site-packages (from torch)
(4.14.1)  
  
Collecting sympy>=1.13.3 (from torch)  
  
Using cached https://download.pytorch.org/whl/sympy-1.13.3-py3-none-
any.whl.metadata (12 kB)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from torch) (3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from torch) (3.1.6)  
  
Collecting fsspec (from torch)  
  
Using cached https://download.pytorch.org/whl/fsspec-2024.6.1-py3-none-
any.whl.metadata (11 kB)  
  
Collecting mpmath=1.1.0 (from sympy>=1.13.3->torch)  
  
Using cached https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl
(536 kB)  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from jinja2->torch) (3.0.2)  
  
Downloading
https://download.pytorch.org/whl/cu126/torch-2.8.0%2Bcu126-cp311-cp311-win_amd64.whl
(2915.5 MB)  
  
\---------------------------------------- 2.9/2.9 GB 21.8 MB/s eta 0:00:00  
  
Using cached https://download.pytorch.org/whl/sympy-1.13.3-py3-none-any.whl
(6.2 MB)  
  
Using cached https://download.pytorch.org/whl/fsspec-2024.6.1-py3-none-any.whl
(177 kB)  
  
Installing collected packages: mpmath, sympy, fsspec, torch  
  
Successfully installed fsspec-2024.6.1 mpmath-1.3.0 sympy-1.13.3
torch-2.8.0+cu126  
  
  
  
[notice] A new release of pip is available: 24.0 -> 25.2  
  
[notice] To update, run: C:\Users\annie\boltz2\Scripts\python.exe -m pip
install --upgrade pip  
  
Successfully installed torch.  
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...  
C:\Users\annie/boltz2\Scripts\python.exe -m pip install
git+https://github.com/RBVI/boltz@chimerax_boltz2  
Collecting git+https://github.com/RBVI/boltz@chimerax_boltz2  
  
Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz2) to
c:\users\annie\appdata\local\temp\pip-req-build-fxif7l41  
  
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz 'C:\Users\annie\AppData\Local\Temp\pip-req-
build-fxif7l41'  
  
Running command git checkout -b chimerax_boltz2 --track origin/chimerax_boltz2  
  
branch 'chimerax_boltz2' set up to track 'origin/chimerax_boltz2'.  
  
Switched to a new branch 'chimerax_boltz2'  
  
Resolved https://github.com/RBVI/boltz to commit
6e47badce94c472cd66b543781a3fea9ee9186b9  
  
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: torch>=2.2 in c:\users\annie\boltz2\lib\site-
packages (from boltz==2.1.1) (2.8.0+cu126)  
  
Requirement already satisfied: numpy=1.26 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from boltz==2.1.1) (1.26.4)  
  
Collecting hydra-core==1.3.2 (from boltz==2.1.1)  
  
Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)  
  
Collecting pytorch-lightning==2.5.0 (from boltz==2.1.1)  
  
Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)  
  
Collecting rdkit>=2024.3.2 (from boltz==2.1.1)  
  
Using cached rdkit-2025.3.5-cp311-cp311-win_amd64.whl.metadata (4.2 kB)  
  
Collecting dm-tree==0.1.8 (from boltz==2.1.1)  
  
Using cached dm_tree-0.1.8-cp311-cp311-win_amd64.whl.metadata (2.0 kB)  
  
Collecting requests==2.32.3 (from boltz==2.1.1)  
  
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)  
  
Collecting pandas>=2.2.2 (from boltz==2.1.1)  
  
Using cached pandas-2.3.1-cp311-cp311-win_amd64.whl.metadata (19 kB)  
  
Collecting types-requests (from boltz==2.1.1)  
  
Using cached types_requests-2.32.4.20250809-py3-none-any.whl.metadata (2.0 kB)  
  
Collecting einops==0.8.0 (from boltz==2.1.1)  
  
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)  
  
Collecting einx==0.3.0 (from boltz==2.1.1)  
  
Using cached einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)  
  
Collecting fairscale==0.4.13 (from boltz==2.1.1)  
  
Using cached fairscale-0.4.13-py3-none-any.whl  
  
Collecting mashumaro==3.14 (from boltz==2.1.1)  
  
Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB)  
  
Collecting modelcif==1.2 (from boltz==2.1.1)  
  
Using cached modelcif-1.2-py3-none-any.whl  
  
Collecting wandb==0.18.7 (from boltz==2.1.1)  
  
Using cached wandb-0.18.7-py3-none-win_amd64.whl.metadata (9.7 kB)  
  
Collecting click==8.1.7 (from boltz==2.1.1)  
  
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)  
  
Collecting pyyaml==6.0.2 (from boltz==2.1.1)  
  
Using cached PyYAML-6.0.2-cp311-cp311-win_amd64.whl.metadata (2.1 kB)  
  
Collecting biopython==1.84 (from boltz==2.1.1)  
  
Using cached biopython-1.84-cp311-cp311-win_amd64.whl.metadata (13 kB)  
  
Collecting scipy==1.13.1 (from boltz==2.1.1)  
  
Using cached scipy-1.13.1-cp311-cp311-win_amd64.whl.metadata (60 kB)  
  
Collecting numba==0.61.0 (from boltz==2.1.1)  
  
Using cached numba-0.61.0-cp311-cp311-win_amd64.whl.metadata (2.8 kB)  
  
Collecting gemmi==0.6.5 (from boltz==2.1.1)  
  
Using cached gemmi-0.6.5-cp311-cp311-win_amd64.whl.metadata (2.3 kB)  
  
Collecting scikit-learn==1.6.1 (from boltz==2.1.1)  
  
Using cached scikit_learn-1.6.1-cp311-cp311-win_amd64.whl.metadata (15 kB)  
  
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.1.1)  
  
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9
kB)  
  
Collecting cuequivariance_torch>=0.5.0 (from boltz==2.1.1)  
  
Using cached cuequivariance_torch-0.6.0-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: setuptools>=46.4.0 in
c:\users\annie\boltz2\lib\site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.1.1) (65.5.0)  
  
Requirement already satisfied: colorama in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from click==8.1.7->boltz==2.1.1)
(0.4.6)  
  
Requirement already satisfied: sympy in c:\users\annie\boltz2\lib\site-
packages (from einx==0.3.0->boltz==2.1.1) (1.13.3)  
  
Collecting frozendict (from einx==0.3.0->boltz==2.1.1)  
  
Using cached frozendict-2.4.6-py311-none-any.whl.metadata (23 kB)  
  
Collecting omegaconf=2.2 (from hydra-core==1.3.2->boltz==2.1.1)  
  
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==2.1.1)  
  
Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl  
  
Requirement already satisfied: packaging in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from hydra-
core==1.3.2->boltz==2.1.1) (25.0)  
  
Requirement already satisfied: typing-extensions>=4.1.0 in c:\program
files\chimerax 1.11.dev202508150726\bin\lib\site-packages (from
mashumaro==3.14->boltz==2.1.1) (4.14.1)  
  
Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from modelcif==1.2->boltz==2.1.1)
(2.2)  
  
Collecting llvmlite=0.44.0dev0 (from numba==0.61.0->boltz==2.1.1)  
  
Using cached llvmlite-0.44.0-cp311-cp311-win_amd64.whl.metadata (5.0 kB)  
  
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.1.1)  
  
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)  
  
Requirement already satisfied: fsspec>=2022.5.0 in
c:\users\annie\boltz2\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1) (2024.6.1)  
  
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.1.1)  
  
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==2.1.1)  
  
Using cached lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)  
  
Requirement already satisfied: charset-normalizer=2 in c:\program
files\chimerax 1.11.dev202508150726\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (3.4.3)  
  
Requirement already satisfied: idna=2.5 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (3.10)  
  
Requirement already satisfied: urllib3=1.21.1 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (2.5.0)  
  
Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (2025.8.3)  
  
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.1.1)  
  
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==2.1.1)  
  
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==2.1.1)  
  
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==2.1.1)  
  
Using cached gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)  
  
Requirement already satisfied: platformdirs in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from wandb==0.18.7->boltz==2.1.1)
(4.3.8)  
  
Collecting protobuf!=4.21.0,!=5.28.0,=3.19.0 (from
wandb==0.18.7->boltz==2.1.1)  
  
Using cached protobuf-5.29.5-cp310-abi3-win_amd64.whl.metadata (592 bytes)  
  
Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from wandb==0.18.7->boltz==2.1.1)
(7.0.0)  
  
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.1.1)  
  
Using cached sentry_sdk-2.35.0-py2.py3-none-any.whl.metadata (10 kB)  
  
Collecting setproctitle (from wandb==0.18.7->boltz==2.1.1)  
  
Using cached setproctitle-1.3.6-cp311-cp311-win_amd64.whl.metadata (10 kB)  
  
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.1.1)  
  
Using cached cuequivariance-0.6.0-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax 1.11.dev202508150726\bin\lib\site-packages (from
pandas>=2.2.2->boltz==2.1.1) (2.9.0.post0)  
  
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.1.1)
(2025.2)  
  
Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.1.1)
(2025.2)  
  
Requirement already satisfied: Pillow in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from
rdkit>=2024.3.2->boltz==2.1.1) (10.4.0)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from torch>=2.2->boltz==2.1.1)
(3.18.0)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from torch>=2.2->boltz==2.1.1)
(3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from torch>=2.2->boltz==2.1.1)
(3.1.6)  
  
Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from docker-
pycreds>=0.4.0->wandb==0.18.7->boltz==2.1.1) (1.17.0)  
  
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Using cached aiohttp-3.12.15-cp311-cp311-win_amd64.whl.metadata (7.9 kB)  
  
Collecting gitdb=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.1.1)  
  
Using cached gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)  
  
Requirement already satisfied: msgpack in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from
ihm>=1.7->modelcif==1.2->boltz==2.1.1) (1.1.0)  
  
Requirement already satisfied: mpmath=1.1.0 in
c:\users\annie\boltz2\lib\site-packages (from
sympy->einx==0.3.0->boltz==2.1.1) (1.3.0)  
  
Collecting opt-einsum (from
cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.1.1)  
  
Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages (from
jinja2->torch>=2.2->boltz==2.1.1) (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==2.1.1)  
  
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==2.1.1)  
  
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==2.1.1)  
  
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==2.1.1)  
  
Using cached frozenlist-1.7.0-cp311-cp311-win_amd64.whl.metadata (19 kB)  
  
Collecting multidict=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Using cached multidict-6.6.4-cp311-cp311-win_amd64.whl.metadata (5.4 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==2.1.1)  
  
Using cached propcache-0.3.2-cp311-cp311-win_amd64.whl.metadata (12 kB)  
  
Collecting yarl=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Using cached yarl-1.20.1-cp311-cp311-win_amd64.whl.metadata (76 kB)  
  
Collecting smmap=3.0.1 (from
gitdb=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.1.1)  
  
Using cached smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)  
  
Using cached biopython-1.84-cp311-cp311-win_amd64.whl (2.8 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-win_amd64.whl (101 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-win_amd64.whl (2.3 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-win_amd64.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-win_amd64.whl (161 kB)  
  
Using cached requests-2.32.3-py3-none-any.whl (64 kB)  
  
Using cached scikit_learn-1.6.1-cp311-cp311-win_amd64.whl (11.1 MB)  
  
Using cached scipy-1.13.1-cp311-cp311-win_amd64.whl (46.2 MB)  
  
Using cached wandb-0.18.7-py3-none-win_amd64.whl (15.5 MB)  
  
Using cached cuequivariance_torch-0.6.0-py3-none-any.whl (214 kB)  
  
Using cached pandas-2.3.1-cp311-cp311-win_amd64.whl (11.3 MB)  
  
Using cached rdkit-2025.3.5-cp311-cp311-win_amd64.whl (23.5 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 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-win_amd64.whl (30.3 MB)  
  
Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB)  
  
Using cached protobuf-5.29.5-cp310-abi3-win_amd64.whl (434 kB)  
  
Using cached sentry_sdk-2.35.0-py2.py3-none-any.whl (363 kB)  
  
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-win_amd64.whl (12 kB)  
  
Using cached aiohttp-3.12.15-cp311-cp311-win_amd64.whl (453 kB)  
  
Using cached gitdb-4.0.12-py3-none-any.whl (62 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-win_amd64.whl (44 kB)  
  
Using cached multidict-6.6.4-cp311-cp311-win_amd64.whl (46 kB)  
  
Using cached propcache-0.3.2-cp311-cp311-win_amd64.whl (41 kB)  
  
Using cached smmap-5.0.2-py3-none-any.whl (24 kB)  
  
Using cached yarl-1.20.1-cp311-cp311-win_amd64.whl (86 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-2.1.1-py3-none-any.whl size=264958
sha256=6740b884253eddfef651d4fcfe00690829306f8cea23a5ee57d50deb3ce5c066  
  
Stored in directory: C:\Users\annie\AppData\Local\Temp\pip-ephem-wheel-cache-
kooea_yb\wheels\eb\6b\e8\b8f2318f04e510ea3091105ed50c6e2ff4fa900e16361241f7  
  
Successfully built boltz  
  
Installing collected packages: dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, smmap, setproctitle, sentry-sdk, scipy,
requests, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict,
mashumaro, llvmlite, lightning-utilities, joblib, gemmi, frozenlist,
frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs,
yarl, 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 c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages, outside environment
C:\Users\annie\boltz2  
  
Can't uninstall 'scipy'. No files were found to uninstall.  
  
Attempting uninstall: requests  
  
Found existing installation: requests 2.32.4  
  
Not uninstalling requests at c:\program files\chimerax
1.11.dev202508150726\bin\lib\site-packages, outside environment
C:\Users\annie\boltz2  
  
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-2.1.1
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 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 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 threadpoolctl-3.6.0 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: C:\Users\annie\boltz2\Scripts\python.exe -m pip
install --upgrade pip  
  
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz  
C:\Users\annie/boltz2\Scripts\python.exe C:\Program Files\ChimeraX
1.11.dev202508150726\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py  
Downloading the CCD data to C:\Users\annie\\.boltz\mols.tar. This may take a
bit of time. You may change the cache directory with the --cache flag.  
  
Extracting the CCD data to C:\Users\annie\\.boltz\mols. This may take a bit of
time. You may change the cache directory with the --cache flag.  
  

Failed to create 2D texture: COM error 0x887a0005: The GPU device instance has
been suspended. Use GetDeviceRemovedReason to determine the appropriate
action.  

QQuickWidget: failed to create resized output texture of size 1929x81  

Failed to create depth-stencil buffer: COM error 0x887a0005: The GPU device
instance has been suspended. Use GetDeviceRemovedReason to determine the
appropriate action.  

QQuickWidget: failed to create resized depth/stencil buffer of size 1929x81  

Device loss detected in ResizeBuffers()  

QDxgiVSyncService: DXGI Factory is no longer Current  

VSyncService: Failed to find adapter (via EnumAdapters1), skipping  

Failed to create 2D texture: COM error 0x887a0005: The GPU device instance has
been suspended. Use GetDeviceRemovedReason to determine the appropriate
action.  


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

Log:
UCSF ChimeraX version: 1.11.dev202508150726 (2025-08-15)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows

Manufacturer: Alienware
Model: Alienware Aurora R7
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 68,517,203,968
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.4
    blockdiag: 3.0.0
    blosc2: 3.7.1
    build: 1.2.2.post1
    certifi: 2025.8.3
    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.dev202508150726
    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
    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: 1.1.4
    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: 0.1
    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: 1.48.1
    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
    comtypes: 1.4.11
    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
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    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
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    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
    pywin32: 310
    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
    WMI: 1.5.1

[pett]

Reported by Biao Qiu

[Tom Goddard]

The ChimeraX log shows the error from Windows "The GPU device instance has been suspended." Searching online for this message there are many pages and most say it is a problem with your graphics driver and suggest updating your graphics driver. I've seen it reported with ChimeraX before several times. It only happens on Windows.

Your GTX 1070 graphics card is from 2016 and the Nvidia driver you are using 457.51 is from 2020, almost 5 years old. Probably graphics driver support is poor for such an old graphics card.

Also with 8 GB of graphics memory it will probably be limited to very small predictions, 100-200 amino acids with Boltz. You may want to use "Device CPU" under the ChimeraX Boltz Options panel which will allow you to run larger predictions, but will be very slow. Details on the speed are here

https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_help.html#runtimes