wasserth
TotalSegmentator command HTTP request failure, network unreachable
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
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
I set the pretrained weight file in the computing equipment to be used, which path is like '/Projects/TotalSegmentator/.totalsegmentator/nnunet/results', I set all the zip and unzip files(because i dont know whether it need to be zipped, so i put both), and i export the env path: 'export TOTALSEG_HOME_DIR=/Projects/TotalSegmentator/.totalsegmentator', but it occur the same error which shows 'requests.exceptions.ConnectionError: HTTPSConnectionPool', it looks like it doesnt find my manually download pretrain weight file, do i need to do anything else except putting them to target location and doing export env path operation? Looking forward to your answer, THX :)
The files need to be unzipped. But if you did this it is hard to say what the problem might without seeing your system.
Nice to see your reply! I find the mistake not because of the env path, just when I need to use task_id=258(lung_vessel), the manually downloaded pretained weights filename did not match its require, it needs the lunng_vessel's weight path named 'Dataset258_lung_vessels....', but the manually downloaded one named 'Task258_lung_vessels...', just a little problem. And now i meet another problem that when i finish the inference(maybe have not finished),it showed me the progress bar'100%|██████████| 1/1 [00:06<00:00, 6.86s/it]', and jump a error telling me that it can not find the dataset.json file, I find other my manually download weight files, in dataset008(HepaticVessel), it has datast.json file and have a correct file path, even in dataset258, the target file path is not matched with needed one, so just a suggestion, there are some tasks pretrain file, its name or file in it or file path do not match with the codes, if you still mainntain this project, maybe check all these tasks file. Best wishes