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google-deepmind / alphafold

Open source code for AlphaFold 2.
Apache License 2.0
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docker.errors.APIError: 500 Server Error for http+docker://localhost/v1.43/containers/ee2565cd6294bdf23537e9fb81814d89cb240f8c02b23f24a0926e3c66b44aea/start: Internal Server Error ("could not select device driver "nvidia" with capabilities: [[gpu]]") #886

Open khanhtomiu opened 9 months ago

khanhtomiu commented 9 months ago

Had successfully built GPU environment and the alphafold docker image (AlphaFold V2.3.2) on the Centos8.

image

When I run the alphafold by the following command: python3 docker/run_docker.py --fasta_paths=/myshare/khanh/projects/alphafold/1cxz.fasta --max_template_date=2022-01-01 --data_dir=/myshare/database/alphafold --output_dir=/myshare/khanh/projects/alphafold/

I got the following error:**** I0118 09:22:00.403837 140362355152704 run_docker.py:113] Mounting /myshare/khanh/projects/alphafold -> /mnt/fasta_path_0 I0118 09:22:00.404139 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/uniref90 -> /mnt/uniref90_database_path I0118 09:22:00.404336 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/mgnify -> /mnt/mgnify_database_path I0118 09:22:00.404402 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold -> /mnt/data_dir I0118 09:22:00.404542 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir I0118 09:22:00.404651 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/pdb_mmcif -> /mnt/obsolete_pdbs_path I0118 09:22:00.404766 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/pdb70 -> /mnt/pdb70_database_path I0118 09:22:00.404883 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/uniref30 -> /mnt/uniref30_database_path I0118 09:22:00.404992 140362355152704 run_docker.py:113] Mounting /myshare/database/alphafold/bfd -> /mnt/bfd_database_path Traceback (most recent call last): File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/api/client.py", line 265, in _raise_for_status response.raise_for_status() File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/requests/models.py", line 1021, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: http+docker://localhost/v1.43/containers/ee2565cd6294bdf23537e9fb81814d89cb240f8c02b23f24a0926e3c66b44aea/start

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "docker/run_docker.py", line 264, in app.run(main) File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 308, in run _run_main(main, args) File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 254, in _run_main sys.exit(main(argv)) File "docker/run_docker.py", line 234, in main container = client.containers.run( File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/models/containers.py", line 880, in run container.start() File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/models/containers.py", line 417, in start return self.client.api.start(self.id, *kwargs) File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/utils/decorators.py", line 19, in wrapped return f(self, resource_id, args, **kwargs) File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/api/container.py", line 1135, in start self._raise_for_status(res) File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/api/client.py", line 267, in _raise_for_status raise create_api_error_from_http_exception(e) from e File "/home/khanh/biosoft/miniconda3/envs/alphafold/lib/python3.8/site-packages/docker/errors.py", line 39, in create_api_error_from_http_exception raise cls(e, response=response, explanation=explanation) from e docker.errors.APIError: 500 Server Error for http+docker://localhost/v1.43/containers/ee2565cd6294bdf23537e9fb81814d89cb240f8c02b23f24a0926e3c66b44aea/start: Internal Server Error ("could not select device driver "nvidia" with capabilities: [[gpu]]")

wenz1xv commented 9 months ago

Installing the NVIDIA Container Toolkit may solve this problem. https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html

sherryliu987 commented 9 months ago

If you're struggling to install AlphaFold locally, feel free to try https://www.tamarind.bio/alphafold, a website which offers a no-code interface for bioinformatics tools including protein structure prediction with AlphaFold for free.