Bugs during inferences (urlopen error [Errno 101] Network is unreachable>)

[lalalalala-ai]

Dear sir,

Thx for your awesome work. I followed the instruction and set up the env. when I tried to run the inference test on sever (slurm), I got the error message below. Do you have any suggestions to fix it?

Downloading the CCD dictionary to /home/nnn/.boltz/ccd.pkl. You may change the cache directory with the --cache flag. Traceback (most recent call last): File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 1344, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1336, in request self._send_request(method, url, body, headers, encode_chunked) File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1382, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1331, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1091, in _send_output self.send(msg) File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1035, in send self.connect() File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1470, in connect super().connect() File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/http/client.py", line 1001, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/socket.py", line 865, in create_connection raise exceptions[0] File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/socket.py", line 850, in create_connection sock.connect(sa) OSError: [Errno 101] Network is unreachable

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/bin/boltz", line 8, in sys.exit(cli()) ^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/click/core.py", line 1157, in call return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/boltz/main.py", line 547, in predict download(cache) File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/lightning_utilities/core/rank_zero.py", line 42, in wrapped_fn return fn(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/site-packages/boltz/main.py", line 77, in download urllib.request.urlretrieve(CCD_URL, str(ccd)) # noqa: S310 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 240, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: ^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 215, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 515, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 532, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 492, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 1392, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nnn/scratch/conda_scratch_pkg/env/boltz_env/lib/python3.12/urllib/request.py", line 1347, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno 101] Network is unreachable>

[simmed00]

Same thing happen to me, waiting for a solution

[caglaaokyay]

I have the same problem

[haoecust]

confirm whether you can access the "https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl" and "https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1_conf.ckpt" in your server? Otherwise, you can manualy download the two files and deposit in the --cache folder.

[nick-youngblut]

I ran into the same issue. It appears that the code does not retry with backoff. It should be an easy feature to add.

[ChengQin01]

@haoecust I manualy download the files you mentioned， but still get the same error. could you give some idea?

confirm whether you can access the "https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl" and "https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1_conf.ckpt" in your server? Otherwise, you can manualy download the two files and deposit in the --cache folder.