Comments (5)
maybe you can try our pre-compiled wheel (https://github.com/dptech-corp/Uni-Core/releases/tag/0.0.1), we also use the wheel in the colab server.
For the docker version, you can try:
docker pull dptechnology/unifold:latest-pytorch1.11.0-cuda11.3
docker run -d -it --gpus all --net=host --name unifold dptechnology/unifold:latest-pytorch1.11.0-cuda11.3
docker attach unifold
to use GPU in docker, you need to install nvidia-docker-2 https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker
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it is quite simple, first download the wheel according to your python, pytorch, cuda version, and then run
pip3 -q install "unicore-0.0.1+cu113torch1.12.1-cp37-cp37m-linux_x86_64.whl"
the "unicore-0.0.1+cu113torch1.12.1-cp37-cp37m-linux_x86_64.whl" could be replaced to your downloaded one.
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I managed to install the whl and successfully complete the first part of the multimer prediction, but then I get this error in the second part:
Starting prediction...
/usr/lib/python3/dist-packages/requests/__init__.py:87: RequestsDependencyWarning: urllib3 (2.0.6) or chardet (4.0.0) doesn't match a supported version!
warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported "
start to load params /home/petmedix/Uni-Fold/multimer.unifold.pt
Traceback (most recent call last):
File "/home/petmedix/Uni-Fold/unifold/inference.py", line 266, in <module>
main(args)
File "/home/petmedix/Uni-Fold/unifold/inference.py", line 91, in main
model.load_state_dict(state_dict)
File "/home/petmedix/.local/lib/python3.10/site-packages/torch/nn/modules/module.py", line 2041, in load_state_dict
raise RuntimeError('Error(s) in loading state_dict for {}:\n\t{}'.format(
RuntimeError: Error(s) in loading state_dict for AlphaFold:
Missing key(s) in state_dict: "template_pair_embedder.linear.weight", "template_pair_embedder.linear.bias", "template_pointwise_att.mha.linear_q.weight", "template_pointwise_att.mha.
linear_k.weight", "template_pointwise_att.mha.linear_v.weight", "template_pointwise_att.mha.linear_o.weight", "template_pointwise_att.mha.linear_o.bias", "structure_module.ipa.linear_q.bias"
, "structure_module.ipa.linear_kv.weight", "structure_module.ipa.linear_kv.bias", "structure_module.ipa.linear_kv_points.weight", "structure_module.ipa.linear_kv_points.bias".
Unexpected key(s) in state_dict: "template_proj.output_linear.weight", "template_proj.output_linear.bias", "template_pair_embedder.z_layer_norm.weight", "template_pair_embedder.z_lay
er_norm.bias", "template_pair_embedder.z_linear.weight", "template_pair_embedder.z_linear.bias", "template_pair_embedder.linear.0.weight", "template_pair_embedder.linear.0.bias", "template_p
air_embedder.linear.1.weight", "template_pair_embedder.linear.1.bias", "template_pair_embedder.linear.2.weight", "template_pair_embedder.linear.2.bias", "template_pair_embedder.linear.3.weig
ht", "template_pair_embedder.linear.3.bias", "template_pair_embedder.linear.4.weight", "template_pair_embedder.linear.4.bias", "template_pair_embedder.linear.5.weight", "template_pair_embedd
er.linear.5.bias", "template_pair_embedder.linear.6.weight", "template_pair_embedder.linear.6.bias", "template_pair_embedder.linear.7.weight", "template_pair_embedder.linear.7.bias", "struct
ure_module.ipa.linear_k.weight", "structure_module.ipa.linear_v.weight", "structure_module.ipa.linear_k_points.weight", "structure_module.ipa.linear_k_points.bias", "structure_module.ipa.lin
ear_v_points.weight", "structure_module.ipa.linear_v_points.bias", "aux_heads.pae.linear.weight", "aux_heads.pae.linear.bias".
size mismatch for input_embedder.linear_tf_z_i.weight: copying a param with shape torch.Size([128, 21]) from checkpoint, the shape in current model is torch.Size([128, 22]).
size mismatch for input_embedder.linear_tf_z_j.weight: copying a param with shape torch.Size([128, 21]) from checkpoint, the shape in current model is torch.Size([128, 22]).
size mismatch for input_embedder.linear_tf_m.weight: copying a param with shape torch.Size([256, 21]) from checkpoint, the shape in current model is torch.Size([256, 22]).
size mismatch for input_embedder.linear_relpos.weight: copying a param with shape torch.Size([128, 73]) from checkpoint, the shape in current model is torch.Size([128, 65]).
size mismatch for template_angle_embedder.linear_1.weight: copying a param with shape torch.Size([256, 34]) from checkpoint, the shape in current model is torch.Size([256, 57]).
size mismatch for aux_heads.masked_msa.linear.weight: copying a param with shape torch.Size([22, 256]) from checkpoint, the shape in current model is torch.Size([23, 256]).
size mismatch for aux_heads.masked_msa.linear.bias: copying a param with shape torch.Size([22]) from checkpoint, the shape in current model is torch.Size([23]).
Any ideas? Does this mean I need to somehow convert the alphafold models, or am I already using the correct model in model_2_ft
?
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Answering my own question: it works if I use model_name multimer_ft rather than model_2_ft.
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Related Issues (20)
- Missing import in Colab HOT 1
- colab error HOT 8
- Is total_step fixed? HOT 2
- import_jax_weights_ failed on AlphaFold-Multimer 2.3.0 HOT 3
- parameters are missing in the pretrained weights HOT 4
- Multi node training HOT 3
- Could not find path to the "hhblits" binary
- Run Uni-Fold with Bohrium Apps
- FileNotFoundError: No such file or directory: '/C.feature.pkl.gz' HOT 1
- questions on installing on Ubuntu Linux 22.04 HOT 1
- recreating homo_search.py output -- minimal version HOT 3
- competition multimer analysis -- does chain order matter? HOT 7
- model name for all alphafold parameters HOT 1
- multi-gpu inference
- convert_unifold_to_alphafold.py?
- UniFold crash: unable to find SCOPdata (a bug that has popped up in ColabFold, & there is a straightforward reason and patch) HOT 2
- Training with linkers
- Symmetry code doesnβt work HOT 4
- Unifold-Musse training and finetuning scripts as well as the ability to use PDB templates
- Unifold on custom a3m MSA files
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