jonathanking / protein-transformer Goto Github PK

hello
i get the following error while training :
Traceback (most recent call last): File "train.py", line 681, in <module> main() File "train.py", line 676, in main device, args, log_writer, scheduler, drmsd_worker_pool) File "train.py", line 149, in train pool=drmsd_worker_pool) File "train.py", line 50, in train_epoch pred, tgt_crds, step, validation_datasets, model, device) File "/media/data2/ameenali/protein-transformer/protein_transformer/log.py", line 199, in do_train_batch_logging commit=False, log_angs=False, struct_name=f"V{split}") File "/media/data2/ameenali/protein-transformer/protein_transformer/log.py", line 340, in log_structure_and_angs gltf_out_path = os.path.join(args.gltf_dir, f"{wandb.run.step:05}_{struct_name}.gltf") AttributeError: 'RunManaged' object has no attribute 'step'
any idea?

Hello,
Im trying to run a training and I get the following error :
training command : python train.py --data casp12_200218_30.pt --name model01 -lr 0.01 -e 30 -b 12 -m conv-enc -dm 256 -l drmsd

`wandb: Currently logged in as: theterminator (use wandb login --relogin to force relogin)
wandb: ERROR Error while calling W&B API: project koes-group/protein-transformer not found (<Response [404]>)
Exception in thread wandb_send:
Traceback (most recent call last):
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/old/retry.py", line 95, in call
result = self._call_fn(*args, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/internal_api.py", line 122, in execute
six.reraise(*sys.exc_info())
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/six.py", line 703, in reraise
raise value
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/internal_api.py", line 116, in execute
return self.client.execute(*args, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/gql/client.py", line 52, in execute
result = self._get_result(document, *args, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/gql/client.py", line 60, in _get_result
return self.transport.execute(document, *args, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/gql/transport/requests.py", line 39, in execute
request.raise_for_status()
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/requests/models.py", line 941, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://api.wandb.ai/graphql

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/apis/normalize.py", line 25, in wrapper
return func(*args, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/internal_api.py", line 801, in upsert_run
mutation, variable_values=variable_values, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/old/retry.py", line 102, in call
if not check_retry_fn(e):
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/util.py", line 511, in no_retry_auth
raise CommError("Permission denied, ask the project owner to grant you access")
wandb.errors.error.CommError: Permission denied, ask the project owner to grant you access

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/threading.py", line 926, in _bootstrap_inner
self.run()
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/threading.py", line 870, in run
self._target(*self._args, **self._kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/internal.py", line 113, in wandb_send
sh.send(i)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/sender.py", line 72, in send
handler(i)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/sender.py", line 121, in handle_run
sweep_name=run.sweep_id or None,
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/apis/normalize.py", line 57, in wrapper
message, err), sys.exc_info()[2])
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/six.py", line 702, in reraise
raise value.with_traceback(tb)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/apis/normalize.py", line 25, in wrapper
return func(*args, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/internal/internal_api.py", line 801, in upsert_run
mutation, variable_values=variable_values, **kwargs)
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/old/retry.py", line 102, in call
if not check_retry_fn(e):
File "/home/ameenali/anaconda3/envs/Transformer/lib/python3.7/site-packages/wandb/util.py", line 511, in no_retry_auth
raise CommError("Permission denied, ask the project owner to grant you access")
wandb.errors.error.CommError: Permission denied, ask the project owner to grant you access`

`[ Epoch 0 ]

• (Train) drmsd=16.16, lndrmsd=0.0587509, rmse=0.4618, c=12.13, res/s=258: 0%| | 0/996 [00:07<?, ?batch/s]
  PyMOL not running, entering library mode (experimental)
  Traceback (most recent call last):
  File "train.py", line 624, in
  main()
  File "train.py", line 619, in main
  device, args, log_writer, scheduler, drmsd_worker_pool)
  File "train.py", line 148, in train
  pool=drmsd_worker_pool)
  File "train.py", line 49, in train_epoch
  pred, tgt_crds, step, validation_datasets, model, device)
  File "/data2/hadxu/protein-transformer/protein_transformer/log.py", line 199, in do_train_batch_logging
  commit=False, log_angs=False, struct_name=f"V{split}")
  File "/data2/hadxu/protein-transformer/protein_transformer/log.py", line 345, in log_structure_and_angs
  pse_out_path=f"{cur_struct_path}/{wandb.run.step:05}_both.pse")
  File "/data2/hadxu/protein-transformer/protein_transformer/protein/PDB_Creator.py", line 196, in save_gltfs
  pymol.cmd.save(gltf_out_path, f"{wandb.run.step:05}.gltf")
  File "/data2/hadxu/anaconda3/envs/py36/lib/python3.6/site-packages/pymol/exporting.py", line 892, in save
  raise pymol.CmdException('File format not supported for export')
  pymol.CmdException: Error: File format not supported for export`

thank you!

when I run your code and use casp12_200123_100.pt occur follow error

Traceback (most recent call last): File "train.py", line 624, in <module> main() File "train.py", line 559, in main angle_means = data["settings"]["angle_means"] KeyError: 'angle_means'