pdb files not exist in mmcif dir

[ozsolomon]

Hi, Thank for the last time it helped me. However, now I have another error. After running the training from ProteinNet input:

python /data/openfold/train_openfold.py /data/af_databases/pdb_mmcif/mmcif_files/ /home/ubuntu/ProteinNet_parsed/ProteinNet_lc/ /data/af_databases/pdb_mmcif/mmcif_files/ /home/ubuntu/OF_train_from_Protein_Net/try_1_Dec29_2021/ 2021-10-10 --template_release_dates_cache_path /data/af_databases/pdb_mmcif/mmcif_cache.json --precision 16 --replace_sampler_ddp=True--deepspeed_config /data/deepspeed_config.json --default_root_dir /home/ubuntu/OF_train_from_Protein_Net/try_1_Dec29_2021/ --gpus 1 --seed 44

I got this error: ###############

Epoch 0: 0%| | 0/50939 [00:00<?, ?it/s]Traceback (most recent call last): File "/data/openfold/train_openfold.py", line 336, in main(args) File "/data/openfold/train_openfold.py", line 196, in main ckpt_path=ckpt_path, File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 736, in fit self._fit_impl, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 682, in _call_and_handle_interrupt return trainer_fn(*args, **kwargs) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 770, in _fit_impl self._run(model, ckpt_path=ckpt_path) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1193, in _run self._dispatch() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1272, in _dispatch self.training_type_plugin.start_training(self) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/plugins/training_type/training_type_plugin.py", line 202, in start_training self._results = trainer.run_stage() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1282, in run_stage return self._run_train() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1312, in _run_train self.fit_loop.run() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/loops/base.py", line 145, in run self.advance(*args, **kwargs) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/loops/fit_loop.py", line 234, in advance self.epoch_loop.run(data_fetcher) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/loops/base.py", line 140, in run self.on_run_start(*args, **kwargs) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/loops/epoch/training_epoch_loop.py", line 141, in on_run_start self._dataloader_iter = _update_dataloader_iter(data_fetcher, self.batch_idx + 1) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/loops/utilities.py", line 121, in _update_dataloader_iter dataloader_iter = enumerate(data_fetcher, batch_idx) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 199, in iter self.prefetching(self.prefetch_batches) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 258, in prefetching self._fetch_next_batch() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 300, in _fetch_next_batch batch = next(self.dataloader_iter) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/supporters.py", line 536, in next return self.request_next_batch(self.loader_iters) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/trainer/supporters.py", line 548, in request_next_batch return apply_to_collection(loader_iters, Iterator, next) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/pytorch_lightning/utilities/apply_func.py", line 92, in apply_to_collection return function(data, *args, **kwargs) File "/data/openfold/openfold/data/data_modules.py", line 350, in _batch_prop_gen for batch in iterator: File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 521, in next data = self._next_data() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 1203, in _next_data return self._process_data(data) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 1229, in _process_data data.reraise() File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/_utils.py", line 434, in reraise raise exception FileNotFoundError: Caught FileNotFoundError in DataLoader worker process 0. Original Traceback (most recent call last): File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 287, in _worker_loop data = fetcher.fetch(index) File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/data/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 49, in data = [self.dataset[idx] for idx in possibly_batched_index] File "/data/openfold/openfold/data/data_modules.py", line 178, in getitem chain_id=chain_id, File "/data/openfold/openfold/data/data_pipeline.py", line 577, in process_pdb with open(pdb_path, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/data/af_databases/pdb_mmcif/mmcif_files/4l6v_9.pdb'

Epoch 0: 0%| | 0/50939 [00:00<?, ?it/s]

Thanks, Oz

[gahdritz]

This looks like it's related to #4.

[ozsolomon]

No, I don't have this file. Indeed, it looks similar I will examine the fix you suggested in the other post. Thanks

[gahdritz]

Since this is a .pdb file, this may be affected by a commit I just pushed (1c3d31b). Re-pull and try again.