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huhlim / cg2all

Convert coarse-grained protein structure to all-atom model
https://huggingface.co/spaces/huhlim/cg2all
Apache License 2.0
34 stars 9 forks source link

error in runing cg2all #10

Closed ntxxt closed 8 months ago

ntxxt commented 8 months ago

I encountered this error during the conversion.

Traceback (most recent call last): File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/bin/convert_cg2all", line 8, in sys.exit(main()) ^^^^^^ File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/cg2all/script/convert_cg2all.py", line 190, in main batch = next(iter(input_s)).to(device) ^^^^^^^^^^^^^^^^^^^ File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 628, in next data = self._next_data() ^^^^^^^^^^^^^^^^^ File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 1333, in _next_data return self._process_data(data) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 1359, in _process_data data.reraise() File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/_utils.py", line 543, in reraise raise exception RuntimeError: Caught RuntimeError in DataLoader worker process 0. Original Traceback (most recent call last): File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/utils/data/_utils/worker.py", line 302, in _worker_loop data = fetcher.fetch(index) ^^^^^^^^^^^^^^^^^^^^ File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/utils/data/_utils/fetch.py", line 58, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/torch/utils/data/_utils/fetch.py", line 58, in data = [self.dataset[idx] for idx in possibly_batched_index]


  File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/cg2all/lib/libdata.py", line 347, in __getitem__
    node_feat = cg.geom_to_feature(geom_s, cg.continuous, dtype=self.dtype)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/nmrbox/0035/xiaxu/anaconda3/envs/cg2all/lib/python3.11/site-packages/cg2all/lib/libcg.py", line 213, in geom_to_feature
    f_in["0"] = torch.as_tensor(torch.cat(f_in["0"], axis=1), dtype=dtype)  # 17
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: Sizes of tensors must match except in dimension 1. Expected size 111 but got size 113 for tensor number 1 in the list.

What could be the reason for this?