Closed GsGithub17 closed 2 years ago
Hi, Could you provide a bit more of the error messages? I do not know why this is happening. Are you potentially trying to run this with python 2?
Thanks!
Yes, python version was the issue. That is now resolved by creating py37 env. However, I'm now getting a new error.
python inference.py --config=configs_clean/inference.yml
[10:55:12] /opt/dgl/src/runtime/tensordispatch.cc:43: TensorDispatcher: dlopen failed: libtorch_cuda.so: cannot open shared object file: No such file or directory
Using backend: pytorch
[2022-02-13 10:55:13.079302] [ Using Seed : 1 ]
Traceback (most recent call last):
File "inference.py", line 506, in
Could it be that you do not have a CUDA GPU?
I now added a environment_cpuonly.yml
which you can use if you do not have a CUDA enabled GPU.
You can install the environment as described in the README:
conda env create -f environment_cpuonly.yml
Thank you! Yes, the current machine doesn't have CUDA. I'll try recreating a new conda env without GPU and let you know.
Successfully, installed without CUDA. But, when I run a prediction, it's looking for ligand files in sdf format, I thought pdbqt files are also supported.
python inference.py --config=configs_clean/inference.yml
Using backend: pytorch
[2022-02-13 13:11:42.865877] [ Using Seed : 1 ]
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "inference.py", line 506, in
I converted the pdbqt ligand file to sdf using openbabel <obabel -ipdbqt vo_ligand.pdbqt -osdf -Ovo_ligand.sdf> and rerun the prediction, now I'm getting the following error associated to the receptor, it sounds like it is looking for
python inference.py --config=configs_clean/inference.yml
Using backend: pytorch
[2022-02-13 13:29:14.882930] [ Using Seed : 1 ]
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "inference.py", line 506, in
I tried to change the receptor file to
python inference.py --config=configs_clean/inference.yml
Using backend: pytorch
[2022-02-13 13:34:06.153129] [ Using Seed : 1 ]
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "inference.py", line 506, in
Thank you for pointing out the issue with the different file formats. I fixed it and updated the description in the README.
I am not sure what exactly causes your error dgl._ffi.base.DGLError: /opt/dgl/src/array/cpu/./spmm_blocking_libxsmm.h:267: Failed to generate libxsmm kernel for the SpMM operation!
But DGL has this issue on it: #3459 Is that related to your situation?
That is right, I'll try two other machines in addition, just to make sure this is machine dependent. I'll let you know asap.
Closing the issue since there is no follow up.
would love to hear about a follow-up @GsGithub17 - currently setting up a very simple dockerfile for this project at labdao/lab-equibind and ran into this error when running CPU-only on my M1 Mac locally. Will ask another community member to run it on their infrastructure soon.
python inference.py --config=configs_clean/inference.yml File "inference.py", line 119 sys.stdout = Logger(logpath=os.path.join(os.path.dirname(args.checkpoint), f'inference.log'), syspart=sys.stdout) ^ SyntaxError: invalid syntax