google-deepmind / google-deepmind/alphafold
400 Client Error: Bad Request for url: http+docker://localhost/v1.43/containers/create
- Dominant language
- Python
- Stars
- 14.9k
- Forks
- 2.9k
- PR merge metrics
- No merged PRs in 30d
Description
Trying to build a Alphafold2 VM (Ubuntu22.04) on Azure. Had successfully built GPU environment and the alphafold docker image (AlphaFold V2.3.2).
### Output from `docker images`:
_REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold latest f1fca93d3422 2 hours ago 10.3GB
nvidia/cuda 11.0.3-base 4f3e95122fab 2 years ago 122MB_
### Output from `docker run --rm --gpus all nvidia/cuda:11.0.3-base nvidia-smi` (Please be aware that cuda:11.0 has been moved):
_Sun Dec 3 02:00:22 2023
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.54.03 Driver Version: 535.54.03 CUDA Version: 12.2 |
|-----------------------------------------+----------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+======================+======================|
| 0 Tesla V100-PCIE-16GB On | 00000001:00:00.0 Off | 0 |
| N/A 28C P0 24W / 250W | 0MiB / 16384MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
+---------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=======================================================================================|
| No running processes found |
+---------------------------------------------------------------------------------------+_
### When I run the alphafold by the following command:
`nohup python3 $run --fasta_paths= \
--max_template_date=2023-11-15 \
--data_dir= \
--output_dir= &`
### I got the following error:
_I1203 01:45:49.190692 140572338368512 run_docker.py:116] Mounting /data/input -> /mnt/fasta_path_0
I1203 01:45:49.190894 140572338368512 run_docker.py:116] Mounting /data/af_download_data/uniref90 -> /mnt/uniref90_database_path
I1203 01:45:49.191008 140572338368512 run_docker.py:116] Mounting /data/af_download_data/mgnify -> /mnt/mgnify_database_path
I1203 01:45:49.191097 140572338368512 run_docker.py:116] Mounting /data/af_download_data -> /mnt/data_dir
I1203 01:45:49.191181 140572338368512 run_docker.py:116] Mounting /data/af_download_data/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
I1203 01:45:49.191273 140572338368512 run_docker.py:116] Mounting /data/af_download_data/pdb_mmcif -> /mnt/obsolete_pdbs_path
I1203 01:45:49.191371 140572338368512 run_docker.py:116] Mounting /data/af_download_data/pdb70 -> /mnt/pdb70_database_path
I1203 01:45:49.191466 140572338368512 run_docker.py:116] Mounting /data/af_download_data/uniref30 -> /mnt/uniref30_database_path
I1203 01:45:49.191560 140572338368512 run_docker.py:116] Mounting /data/af_download_data/bfd -> /mnt/bfd_database_path
Traceback (most recent call last):
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/usr/lib/python3/dist-packages/requests/models.py", line 943, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: http+docker://localhost/v1.43/containers/create
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jingqiduan/alphafold/docker/run_docker.py", line 267, in
app.run(main)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/home/jingqiduan/alphafold/docker/run_docker.py", line 237, in main
container = client.containers.run(
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/models/containers.py", line 811, in run
container = self.create(image=image, command=command,
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/models/containers.py", line 870, in create
resp = self.client.api.create_container(**create_kwargs)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/api/container.py", line 430, in create_container
return self.create_container_from_config(config, name)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/api/container.py", line 441, in create_container_from_config
return self._result(res, True)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/api/client.py", line 274, in _result
self._raise_for_status(response)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
File "/home/jingqiduan/.local/lib/python3.10/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.APIError: 400 Client Error for http+docker://localhost/v1.43/containers/create: Bad Request ("invalid mount config for type "bind": field Source must not be empty")_
I went through the alphafold issues threads and found the same issue had been raised before. But the resolutions did not work for me, like 'sudo mkdir /tmp/alphafold'. And change the docker daemon.json file, I even don't have the file under /etc/docker. Please help me with it. Thanks.
Contributor guide
Assessment
This issue has not been assessed yet.