Description
Traceback (most recent call last):
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/hpcfs/fhome/yangchh/.vscode-server/extensions/ms-python.debugpy-2024.2.0-linux-x64/bundled/libs/debugpy/adapter/../../debugpy/launcher/../../debugpy/main.py", line 39, in
cli.main()
File "/hpcfs/fhome/yangchh/.vscode-server/extensions/ms-python.debugpy-2024.2.0-linux-x64/bundled/libs/debugpy/adapter/../../debugpy/launcher/../../debugpy/../debugpy/server/cli.py", line 430, in main
run()
File "/hpcfs/fhome/yangchh/.vscode-server/extensions/ms-python.debugpy-2024.2.0-linux-x64/bundled/libs/debugpy/adapter/../../debugpy/launcher/../../debugpy/../debugpy/server/cli.py", line 284, in run_file
runpy.run_path(target, run_name="main")
File "/hpcfs/fhome/yangchh/.vscode-server/extensions/ms-python.debugpy-2024.2.0-linux-x64/bundled/libs/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 321, in run_path
return _run_module_code(code, init_globals, run_name,
File "/hpcfs/fhome/yangchh/.vscode-server/extensions/ms-python.debugpy-2024.2.0-linux-x64/bundled/libs/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 135, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/hpcfs/fhome/yangchh/.vscode-server/extensions/ms-python.debugpy-2024.2.0-linux-x64/bundled/libs/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 124, in _run_code
exec(code, run_globals)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/aa.py", line 9, in
embeddings = model.get_embeddings(seqs)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/_auto.py", line 171, in get_embeddings
outputs = self.model.forward(**batch, output_hidden_states=True)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/modeling_encodon.py", line 1298, in forward
outputs = self.bert(
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/modeling_encodon.py", line 1199, in forward
encoder_outputs = self.encoder(
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/modeling_encodon.py", line 959, in forward
layer_outputs = layer_module(
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/modeling_encodon.py", line 896, in forward
self_attention_outputs = self.attention(
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/modeling_encodon.py", line 824, in forward
attn_outputs = self.self_attention(
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/hpcfs/fhome/yangchh/ai/finetuneFMs/FMs/cdsFM/cdsfm/encodon/modeling_encodon.py", line 612, in forward
attention_scores = einsum(q, k, "b q h d, b k h d -> b h q k")
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/functional.py", line 361, in einsum
equation = ','.join(''.join(parse_subscript(s) for s in l) for l in args[1::2])
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/functional.py", line 361, in
equation = ','.join(''.join(parse_subscript(s) for s in l) for l in args[1::2])
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/functional.py", line 361, in
equation = ','.join(''.join(parse_subscript(s) for s in l) for l in args[1::2])
File "/hpcfs/fhome/yangchh/software/anaconda/envs/bioseq/lib/python3.8/site-packages/torch/functional.py", line 354, in parse_subscript
if n >= 0 and n < 26:
RuntimeError: Boolean value of Tensor with more than one value is ambiguous