Closed jl-marin closed 1 year ago
luwei0917
commented
1 year ago torch_scatter is part of PyG. could try to re-install the version that match your cuda. following the instruction described in "https://github.com/pyg-team/pytorch_geometric"
pip install torch-scatter -f https://data.pyg.org/whl/torch-1.12.0+${CUDA}.html
pip install torch-sparse -f https://data.pyg.org/whl/torch-1.12.0+${CUDA}.html
pip install torch-geometricHope this help. Wei
jl-marin
commented
1 year ago Thank you very much; your suggestion put me in the right direction. And since I'll admit I am biased against Conda's shotgun approach to dependency management, I decided to:
With this in mind, the following installation procedure worked for me. My Host environment is Ubuntu 22.04LTS and Nvidia driver 510 (CUDA 11.6). I had to install Python 3.9 (I use pyenv for this) because TorchDrug requires a version < 3.10. Then, on a clean venv, I installed everything as follows:
MY_VENV=tb_venv
CUDA=cu116
################################
# Install TankBind deps
################################
#
# Install PyTorch (latest stable is PyTorch 1.13, but PyG only supports up to 1.12):
pip install torch==1.12.1 --extra-index-url https://download.pytorch.org/whl/${CUDA}
# Install Torch Geometric (needs PyTorch <=1.12)
pip install torch-scatter -f https://data.pyg.org/whl/torch-1.12.1+${CUDA}.html
pip install torch-sparse -f https://data.pyg.org/whl/torch-1.12.1+${CUDA}.html
pip install torch-geometric
# Install TorchDrug (Requires: Python >=3.7, <3.10)
pip install torch-cluster -f https://data.pyg.org/whl/torch-1.12.1+${CUDA}.html
pip install torchdrug
# The rest didn't give me any trouble:
pip install torchmetrics biopython jupyterlab nglview tqdm mlcrate pyarrow
####################
# Install TankBind
###################
#
# Clone the TankBind repo:
rm -rf TankBind
git clone https://github.com/luwei0917/TankBind.git
# Dowload and install p2rank
cd TankBind
wget https://github.com/rdk/p2rank/releases/download/2.4/p2rank_2.4.tar.gz
tar zxf p2rank_2.4.tar.gz
So this gives me an apparently flawless install. Then I tried to run TankBind, but I found an error. Here's the output when running examples/high_throughput_virtual_screening_LRRK2_WDR.ipynb (I extracted this Notebook's code to a script, in order to run it from the console):
(tb_venv) marinjl@darwin:~/TANKBIND/TankBind/examples$ python virtual_screening_test_tankbind.py
Reading protein...
Protein PDB read and formatted.
----------------------------------------------------------------------------------------------
P2Rank 2.4
----------------------------------------------------------------------------------------------
predicting pockets for proteins from dataset [protein_list.ds]
processing [6dlo.pdb] (1/1)
predicting pockets finished in 0 hours 0 minutes 8.083 seconds
results saved to directory [/data/home/marinjl/TANKBIND/TankBind/examples/HTVS/p2rank]
----------------------------------------------------------------------------------------------
finished successfully in 0 hours 0 minutes 9.751 seconds
----------------------------------------------------------------------------------------------
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10000/10000 [00:01<00:00, 7913.11it/s]
Pocketing succesfully done.
Processing...
Done!
['HTVS/dataset/processed/data.pt', 'HTVS/dataset/processed/protein.pt']
Constructing dataset...
12:30:57 5 stack, readout2, pred dis map add self attention and GVP embed, compound model GIN
Loading model...
Ready to start inference.
0%| | 0/2000 [00:00<?, ?it/s]
/home/marinjl/.pyenv/versions/tb_venv/lib/python3.9/site-packages/torchdrug/utils/decorator.py:189: UserWarning: from_smiles(): argument `node_feature` is deprecated in favor of `atom_feature`
warnings.warn("%s(): argument `%s` is deprecated in favor of `%s`" % (obj.__name__, key, value))
[... a few more deprecation warnings like this from TorchDrug, which look harmless ...]
0%| | 0/2000 [00:19<?, ?it/s]
Traceback (most recent call last):
File "/data/home/marinjl/TANKBIND/TankBind/examples/virtual_screening_test_tankbind.py", line 169, in <module>
y_pred, affinity_pred = model(data)
File "/home/marinjl/.pyenv/versions/tb_venv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/data/home/marinjl/TANKBIND/TankBind/examples/../tankbind/model.py", line 343, in forward
compound_out = self.conv_compound(compound_edge_index,edge_weight,compound_edge_feature,compound_x.shape[0],compound_x)['node_feature']
File "/home/marinjl/.pyenv/versions/tb_venv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/data/home/marinjl/TANKBIND/TankBind/examples/../tankbind/GINv2.py", line 182, in forward
hidden = layer(edge_list, edge_weight, edge_feature, num_node, layer_input)
File "/home/marinjl/.pyenv/versions/tb_venv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/data/home/marinjl/TANKBIND/TankBind/examples/../tankbind/GINv2.py", line 110, in forward
update = self.message_and_aggregate(edge_list, edge_weight, edge_feature, num_node, input)
File "/data/home/marinjl/TANKBIND/TankBind/examples/../tankbind/GINv2.py", line 91, in message_and_aggregate
edge_update = self.edge_linear(edge_update)
File "/home/marinjl/.pyenv/versions/tb_venv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/home/marinjl/.pyenv/versions/tb_venv/lib/python3.9/site-packages/torch/nn/modules/linear.py", line 114, in forward
return F.linear(input, self.weight, self.bias)
RuntimeError: mat1 and mat2 shapes cannot be multiplied (123x18 and 19x56)Any ideas? Do you guys have a sort of minimal working example in order to test if TankBind is installed correctly?
luwei0917
commented
1 year ago "RuntimeError: mat1 and mat2 shapes cannot be multiplied (123x18 and 19x56)" occurs when using newer version of torchdrug. Please ensure that you are using v0.1.2.
jl-marin
commented
1 year ago Thanks, the example is working now. Just out of curiosity (and because I have the whole install process scripted), I went backwards testing all previous versions of TorchDrug in sequence (see https://pypi.org/project/torchdrug/#history). It was only after I arrived at torchdrug version 0.1.2.post1 that the error went away. In turn, this version needed a downgrade to Python 3.8.
Any chance you guys will upgrade your code to the latest TorchDrug soon?
Anyway, I'm closing this issue since everything seems to be working fine. Thanks for your help!
luwei0917
commented
1 year ago Glad to hear that you resolve the problem. We plan to drop the dependency of torchdrug in the future. it was mainly used to extract features from the small molecule, but it's a bit too heavily loaded with other modules that we don't need.
We installed miniconda (user-level install), then activated a new conda environment for tankbind, and we installed TankBind following the instructions to the letter. We found the following error:
This library
libtorch_cuda_cu.sois nowhere to be found. Any ideas?For what is worh, the host has nvidia kernel driver version 510.85.02 (I'm not sure if this influences conda to install different versions of CUDA libs).