Hi,
I have set the accelerator to cpu (boltz predict examples/ligand.fasta --accelerator cpu), but the following erros still happened:
Running on CPU, this will be slow. Consider using a GPU.
Checking input data.
Running predictions for 1 structure
Processing input data.
Found a manifest file at output directory: boltz_results_ligand
All examples in data are processed. Updating the manifest
GPU available: True (cuda), used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/setup.py:177: GPU available but not used. You can set it by doing Trainer(accelerator='gpu').
/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:75: 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
Traceback (most recent call last):
File "/home/wangjw/programs/miniconda3/envs/boltz/bin/boltz", line 8, in
sys.exit(cli())
^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/boltz/main.py", line 679, in predict
trainer.predict(
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 858, in predict
return call._call_and_handle_interrupt(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/call.py", line 47, in _call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 897, in _predict_impl
results = self._run(model, ckpt_path=ckpt_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 981, in _run
results = self._run_stage()
^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 1020, in _run_stage
return self.predict_loop.run()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/loops/utilities.py", line 178, in _decorator
return loop_run(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/loops/prediction_loop.py", line 107, in run
self.reset()
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/loops/prediction_loop.py", line 181, in reset
iter(data_fetcher) # creates the iterator inside the fetcher
^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/loops/fetchers.py", line 104, in iter
super().iter()
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/loops/fetchers.py", line 51, in iter
self.iterator = iter(self.combined_loader)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/utilities/combined_loader.py", line 351, in iter
iter(iterator)
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/utilities/combined_loader.py", line 155, in iter
self._load_current_iterator()
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/pytorch_lightning/utilities/combined_loader.py", line 173, in _load_current_iterator
self.iterators = [iter(self.iterables[self._iterator_idx])]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 491, in iter
return self._get_iterator()
^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 422, in _get_iterator
return _MultiProcessingDataLoaderIter(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 1163, in init
current_device = torch.cuda.current_device() # choose cuda for default
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/torch/cuda/init.py", line 971, in current_device
_lazy_init()
File "/home/wangjw/programs/miniconda3/envs/boltz/lib/python3.11/site-packages/torch/cuda/init.py", line 319, in _lazy_init
torch._C._cuda_init()
RuntimeError: The NVIDIA driver on your system is too old (found version 11070). Please update your GPU driver by downloading and installing a new version from the URL: http://www.nvidia.com/Download/index.aspx Alternatively, go to: https://pytorch.org to install a PyTorch version that has been compiled with your version of the CUDA driver.
jwohlwend
