Closed Khas-Erdene-1 closed 1 month ago
having the same issues for some pdb files
Turned out our machine graphics memory is not enough for bigger proteins like bigger than 1200 amino acids, so I'm closing this issue. Also RF2 doesn't allow multi graphics unit to predict.
Hi,
I'm having following problem. I run with the example files, it was fine but when I input following fasta, it gives the error. Any suggestions?
/data2/apps/RoseTTAFold2/run_RF2.sh /home/khasaa/projects/RoseTTAfold_ADAMTS13/Q76LX8.fasta -o Q76LX8 Running RoseTTAFold2 to predict structures -> Running command: python /data2/apps/RoseTTAFold2/network/predict.py -inputs Q76LX8/Q76LX8_1.msa0.a3m -prefix Q76LX8/models/model -model /data2/apps/RoseTTAFold2/network/weights/RF2_jan24.pt -db /data2/apps/RoseTTAFold2/pdb100_2021Mar03/pdb100_2021Mar03 -symm C1 Running on GPU N=2048 L=1427 recycle 0 plddt 0.308 pae 28.391 rmsd 34.750 Traceback (most recent call last): File "/data2/apps/RoseTTAFold2/network/predict.py", line 623, in
pred.predict(
File "/data2/apps/RoseTTAFold2/network/predict.py", line 425, in predict
self.run_prediction(
File "/data2/apps/RoseTTAFold2/network/predict.py", line 510, in run_prediction
logits, , _, logits_pae, p_bind, xyz_prev, alpha, symmsub, pred_lddt, msa_prev, pair_prev, state_prev = self.model(
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, *kwargs)
File "/data2/apps/RoseTTAFold2/network/RoseTTAFoldModel.py", line 115, in forward
msa, pair, R, T, alpha, state, symmsub = self.simulator(
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, kwargs)
File "/data2/apps/RoseTTAFold2/network/Track_module.py", line 792, in forward
msa_full, pair, R_in, T_in, state, alpha, symmsub = self.extra_block[i_m](
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, *kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(args, kwargs)
File "/data2/apps/RoseTTAFold2/network/Track_module.py", line 690, in forward
R, T, state, alpha = self.str2str(
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, *kwargs)
File "/data2/apps/RoseTTAFold2/network/Track_module.py", line 600, in forward
shift = self.se3(G, node, l1_feats, edge_feats)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 16, in decorate_autocast
return func(*args, *kwargs)
File "/data2/apps/RoseTTAFold2/network/SE3_network.py", line 86, in forward
return self.se3(G, node_features, edge_features)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/transformer.py", line 187, in forward
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, *kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/transformer.py", line 47, in forward
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, *kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/layers/attention.py", line 158, in forward
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/layers/convolution.py", line 358, in forward
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/layers/convolution.py", line 245, in
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, *kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/layers/convolution.py", line 181, in forward
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, *kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/se3_transformer-1.2.0-py3.10.egg/se3_transformer/model/layers/convolution.py", line 119, in forward
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(args, kwargs)
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
RuntimeError: The following operation failed in the TorchScript interpreter.
Traceback of TorchScript (most recent call last):
File "/home/khasaa/miniconda3/envs/RF2/lib/python3.10/site-packages/torch/nn/modules/container.py", line 217, in forward
def forward(self, input):
for module in self:
input = module(input)