I have installed Boltz 2 in a Python environment called boltz-env and installed it with the command pip3 install boltz -U. It installs correctly, but when I run the example code, I get the following errors:
boltz predict multimer.yaml --use_msa_server
Checking input data.
Processing 1 inputs with 1 threads.
0%| | 0/1 [00:00<?, ?it/s]Generating MSA for multimer.yaml with 2 protein entities.
COMPLETE: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [elapsed: 00:01 remaining: 00:00]
COMPLETE: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [elapsed: 00:02 remaining: 00:00]
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:04<00:00, 4.02s/it]
/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/lightning_fabric/plugins/environments/slurm.py:204: The srun command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with srun like so: srun python3 /home/aperezs/Documents/Recerca/Boltz2/boltz-env/bi ...
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/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
Running structure prediction for 1 input.
/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/utilities/migration/utils.py:56: The loaded checkpoint was produced with Lightning v2.5.0.post0, which is newer than your current Lightning version: v2.5.0
You are using a CUDA device ('NVIDIA GeForce RTX 4090') that has Tensor Cores. To properly utilize them, you should set torch.set_float32_matmul_precision('medium' | 'high') which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
Predicting DataLoader 0: 0%| | 0/1 [00:00<?, ?it/s]Traceback (most recent call last):
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/bin/boltz", line 8, in
sys.exit(cli())
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/main.py", line 1186, in predict
trainer.predict(
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 859, in predict
return call._call_and_handle_interrupt(
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 47, in _call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 898, in _predict_impl
results = self._run(model, ckpt_path=ckpt_path)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 982, in _run
results = self._run_stage()
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1021, in _run_stage
return self.predict_loop.run()
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/loops/utilities.py", line 179, in _decorator
return loop_run(self, *args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/loops/prediction_loop.py", line 125, in run
self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/loops/prediction_loop.py", line 255, in _predict_step
predictions = call._call_strategy_hook(trainer, "predict_step", *step_args)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 323, in _call_strategy_hook
output = fn(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 438, in predict_step
return self.lightning_module.predict_step(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/model/models/boltz2.py", line 1049, in predict_step
out = self(
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/model/models/boltz2.py", line 616, in forward
s_inputs = self.input_embedder(feats, affinity=True)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/model/modules/trunkv2.py", line 175, in forward
profile = feats["profile_affinity"]
KeyError: 'profile_affinity'
Predicting DataLoader 0: 0%| | 0/1 [00:11<?, ?it/s]
boltz predict ligand.yaml
Checking input data.
All inputs are already processed.
/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/lightning_fabric/plugins/environments/slurm.py:204: The srun command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with srun like so: srun python3 /home/aperezs/Documents/Recerca/Boltz2/boltz-env/bi ...
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/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
Running structure prediction for 1 input.
/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/utilities/migration/utils.py:56: The loaded checkpoint was produced with Lightning v2.5.0.post0, which is newer than your current Lightning version: v2.5.0
You are using a CUDA device ('NVIDIA GeForce RTX 4090') that has Tensor Cores. To properly utilize them, you should set torch.set_float32_matmul_precision('medium' | 'high') which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
Predicting DataLoader 0: 0%| | 0/1 [00:00<?, ?it/s]Traceback (most recent call last):
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/bin/boltz", line 8, in
sys.exit(cli())
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/main.py", line 1186, in predict
trainer.predict(
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 859, in predict
return call._call_and_handle_interrupt(
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 47, in _call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 898, in _predict_impl
results = self._run(model, ckpt_path=ckpt_path)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 982, in _run
results = self._run_stage()
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1021, in _run_stage
return self.predict_loop.run()
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/loops/utilities.py", line 179, in _decorator
return loop_run(self, *args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/loops/prediction_loop.py", line 125, in run
self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/loops/prediction_loop.py", line 255, in _predict_step
predictions = call._call_strategy_hook(trainer, "predict_step", *step_args)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 323, in _call_strategy_hook
output = fn(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 438, in predict_step
return self.lightning_module.predict_step(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/model/models/boltz2.py", line 1049, in predict_step
out = self(
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/model/models/boltz2.py", line 616, in forward
s_inputs = self.input_embedder(feats, affinity=True)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
File "/home/aperezs/Documents/Recerca/Boltz2/boltz-env/lib/python3.10/site-packages/boltz/model/modules/trunkv2.py", line 175, in forward
profile = feats["profile_affinity"]
KeyError: 'profile_affinity'
Predicting DataLoader 0: 0%| | 0/1 [00:45<?, ?it/s]
jwohlwend
