hysonlab / protein_redesign Goto Github PK

Creating the env from the yaml file makes it so that the versions of pytorch and pytorch lightning are incompatible, giving the error: undefined symbol: iJIT_NotifyEvent. I was able to manually edit to switch to pytorch 1.7.1, but that caused issues of its own. Sorry if a solution to this is in the works.

Traceback (most recent call last):
  File "/home/ubuntu/Protein_Redesign/generate.py", line 11, in <module>
    import pytorch_lightning as pl
  File "/home/ubuntu/miniconda3/envs/ProteinReDiff/lib/python3.9/site-packages/pytorch_lightning/__init__.py", line 34, in <module>
    from pytorch_lightning.callbacks import Callback  # noqa: E402
  File "/home/ubuntu/miniconda3/envs/ProteinReDiff/lib/python3.9/site-packages/pytorch_lightning/callbacks/__init__.py", line 14, in <module>
    from pytorch_lightning.callbacks.callback import Callback
  File "/home/ubuntu/miniconda3/envs/ProteinReDiff/lib/python3.9/site-packages/pytorch_lightning/callbacks/callback.py", line 21, in <module>
    from torch import Tensor
  File "/home/ubuntu/miniconda3/envs/ProteinReDiff/lib/python3.9/site-packages/torch/__init__.py", line 202, in <module>
    from torch._C import *  # noqa: F403
ImportError: /home/ubuntu/miniconda3/envs/ProteinReDiff/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent

~/Protein_Redesign$ python generate.py     --ckpt_path "checkpoints/ProteinReDiff_v1.ckpt"     --output_dir "workdir/generate/example_ProteinReDiff"     --protein "LSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD"     --ligand "Cc1ccc2c(c1c3cc(cc4c3nc([nH]4)C5CC5)c6c(noc6C)C)cccn2"     --num_samples 8
Traceback (most recent call last):
  File "/home/ubuntu/Protein_Redesign/generate.py", line 16, in <module>
    from dpl.data import RepeatDataset, collate_fn, ligand_to_data, protein_to_data
ModuleNotFoundError: No module named 'dpl'

It looks like the the conda environment setup doesn't include dpl. I've tried to clone the DPL repo directly and use the directory inside there, but that doesn't seem to be the same one as expected in this repo. Would be great if there's a way to fix this installation.

Error:
g: Starting from v1.9.0,tensorboardXhas been removed as a dependency of thepytorch_lightningpackage, due to potential conflicts with other packages in the ML ecosystem. For this reason,logger=Truewill useCSVLoggeras the default logger, unless thetensorboardortensorboardXpackages are found. Pleasepip install lightning[extra]or one of them to enable TensorBoard support by default "Starting from v1.9.0,tensorboardXhas been removed as a dependency of thepytorch_lightning`"
Missing logger folder: workdir/inference/example_ProteinReDiff/gen5/lightning_logs
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
Predicting DataLoader 0: 0%| | 0/3 [00:00<?, ?it/s]Using cache found in /home/ubuntu/.cache/torch/hub/facebookresearch_esm_main

File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/trainer/call.py", line 38, in _call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 938, in _predict_impl
results = self._run(model, ckpt_path=self.ckpt_path)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1112, in _run
results = self._run_stage()
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1190, in _run_stage
return self._run_predict()
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1244, in _run_predict
return self.predict_loop.run()
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/loops/dataloader/prediction_loop.py", line 101, in advance
dataloader_iter, self.current_dataloader_idx, dl_max_batches, self.num_dataloaders
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/loops/epoch/prediction_epoch_loop.py", line 100, in advance
self._predict_step(batch, batch_idx, dataloader_idx)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/loops/epoch/prediction_epoch_loop.py", line 129, in _predict_step
predictions = self.trainer._call_strategy_hook("predict_step", *step_kwargs.values())
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1494, in _call_strategy_hook
output = fn(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/pytorch_lightning/strategies/strategy.py", line 408, in predict_step
return self.model.predict_step(*args, **kwargs)
File "/home/ubuntu/BOLTPRO/Chirag/Protein_Redesign/ProteinReDiff/model.py", line 251, in predict_step
x, seq_t = self.sample(batch)
File "/home/ubuntu/anaconda3/envs/pr_design/lib/python3.7/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "/home/ubuntu/BOLTPRO/Chirag/Protein_Redesign/ProteinReDiff/model.py", line 387, in sample
batch = self.prepare_batch(batch)
File "/home/ubuntu/BOLTPRO/Chirag/Protein_Redesign/ProteinReDiff/model.py", line 443, in prepare_batch
residue_esm_tokens = batch["residue_esm_tokens"]
KeyError: 'residue_esm_tokens'
Predicting DataLoader 0: 0%| | 0/3 [00:11<?, ?it/s]
`

There is n attribute of "residue_esm_tokens" in the object "batch"
Please mention the python version as well the dependencies version you are using because it is working in other deprecated version