wasserth
commented
3 weeks ago You can manually download the weights using totalseg_download_weights on your local machine with internet. Then all weights will get downloaded to ~/.totalsegmentator. Then you can copy this folder to the same location on your HPC cluster. If you want to set a different location you can set the environment variable: TOTALSEG_HOME_DIR, e.g. export TOTALSEG_HOME_DIR=/mnt/nor/software/.totalsegmentator
How do I get around the error below that I get when I try to run the ‘TotalSegmentator -i ct.nii.gz -o segmentations’ command on a SLURM-managed HPC cluster/a system without internet access? The main issue clearly is that the script attempts to make the HTTP request for the ‘download_url_and_unpack’ function, but the network connection fails because the system cannot access the internet. Has anyone experienced the same? Please can someone help? Thanks.
Error message is: Traceback (most recent call last): File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connection.py", line 198, in _new_conn sock = connection.create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) OSError: [Errno 101] Network is unreachable
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connectionpool.py", line 793, in urlopen response = self._make_request( ^^^^^^^^^^^^^^^^^^^ File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connectionpool.py", line 491, in _make_request raise new_e File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connectionpool.py", line 467, in _make_request self._validate_conn(conn) File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1099, in _validate_conn conn.connect() File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connection.py", line 616, in connect self.sock = sock = self._new_conn() ^^^^^^^^^^^^^^^^ File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connection.py", line 213, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x2ade890d33e0>: Failed to establish a new connection: [Errno 101] Network is unreachable
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/requests/adapters.py", line 589, in send resp = conn.urlopen( ^^^^^^^^^^^^^ File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/connectionpool.py", line 847, in urlopen retries = retries.increment( ^^^^^^^^^^^^^^^^^^ File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/urllib3/util/retry.py", line 515, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /wasserth/TotalSegmentator/releases/download/v2.0.0-weights/Dataset291_TotalSegmentator_part1_organs_1559subj.zip (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2ade890d33e0>: Failed to establish a new connection: [Errno 101] Network is unreachable'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/xxxx/.conda/envs/myenvr/bin/TotalSegmentator", line 8, in
sys.exit(main())
^^^^^^
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/totalsegmentator/bin/TotalSegmentator.py", line 138, in main
totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/totalsegmentator/python_api.py", line 392, in totalsegmentator
download_pretrained_weights(tid)
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/totalsegmentator/libs.py", line 333, in download_pretrained_weights
download_url_and_unpack(WEIGHTS_URL, config_dir)
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/totalsegmentator/libs.py", line 129, in download_url_and_unpack
raise e
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/totalsegmentator/libs.py", line 112, in download_url_and_unpack
with requests.get(url, stream=True) as r:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/xxxx/.conda/envs/myenvr/lib/python3.12/site-packages/requests/adapters.py", line 622, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /wasserth/TotalSegmentator/releases/download/v2.0.0-weights/Dataset291_TotalSegmentator_part1_organs_1559subj.zip (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2ade890d33e0>: Failed to establish a new connection: [Errno 101] Network is unreachable'))
srun: error: indigo51: task 0: Exited with exit code 1