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sacdallago / bio_embeddings

Get protein embeddings from protein sequences
http://docs.bioembeddings.com
MIT License
463 stars 65 forks source link

Crash in PLUS with GPU #96

Closed konstin closed 3 years ago

konstin commented 3 years ago

Needs further investigation:

  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/bio_embeddings/embed/embedder_interfaces.py", line 113, in embed_many
    yield from self.embed_batch(batch)
  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/bio_embeddings/embed/plus_rnn_embedder.py", line 71, in embed_batch
    trainer.embed(batch, {"data_parallel": False})
  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/plus/train.py", line 108, in embed
    embeddings = self.get_loss(batch, self.models_dict, args)
  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/plus/model/plus_rnn.py", line 225, in get_embedding
    z, r = model(tokens, lengths)
  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/torch/nn/modules/module.py", line 727, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/plus/model/plus_rnn.py", line 49, in forward
    h = pack_padded_sequence(h, lengths, batch_first=True)
  File "/mnt/project/seqvec-search/.venv/lib/python3.8/site-packages/torch/nn/utils/rnn.py", line 244, in pack_padded_sequence
    _VF._pack_padded_sequence(input, lengths, batch_first)
RuntimeError: 'lengths' argument should be a 1D CPU int64 tensor, but got 1D cuda:0 Long tensor