genomescan / gsport

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Gsport server side stopped working? #12

Open mmterpstra opened 6 months ago

mmterpstra commented 6 months ago

Around 30 april the server side stopped responding and didn't returned ever since:

> gsport -a -r -p $GSID -t 4 
Traceback (most recent call last):
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 703, in urlopen
    httplib_response = self._make_request(
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 449, in _make_request
    six.raise_from(e, None)
  File "<string>", line 3, in raise_from
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 444, in _make_request
    httplib_response = conn.getresponse()
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/http/client.py", line 1374, in getresponse
    response.begin()
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/http/client.py", line 318, in begin
    version, status, reason = self._read_status()
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/http/client.py", line 287, in _read_status
    raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/requests/adapters.py", line 440, in send
    resp = conn.urlopen(
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 785, in urlopen
    retries = retries.increment(
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/util/retry.py", line 550, in increment
    raise six.reraise(type(error), error, _stacktrace)
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/packages/six.py", line 769, in reraise
    raise value.with_traceback(tb)
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 703, in urlopen
    httplib_response = self._make_request(
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 449, in _make_request
    six.raise_from(e, None)
  File "<string>", line 3, in raise_from
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/urllib3/connectionpool.py", line 444, in _make_request
    httplib_response = conn.getresponse()
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/http/client.py", line 1374, in getresponse
    response.begin()
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/http/client.py", line 318, in begin
    version, status, reason = self._read_status()
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/http/client.py", line 287, in _read_status
    raise RemoteDisconnected("Remote end closed connection without"
urllib3.exceptions.ProtocolError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/scratch/p313191/apps/versions/2023.01/rocky8/x86_64/amd/zen3/software/gsport/1.6.2-GCCcore-11.3.0-Python-3.10.4/bin/gsport", line 8, in <module>
    sys.exit(main())
  File "/scratch/p313191/apps/versions/2023.01/rocky8/x86_64/amd/zen3/software/gsport/1.6.2-GCCcore-11.3.0-Python-3.10.4/lib/python3.10/site-packages/gsport.py", line 455, in main
    download_all(session)
  File "/scratch/p313191/apps/versions/2023.01/rocky8/x86_64/amd/zen3/software/gsport/1.6.2-GCCcore-11.3.0-Python-3.10.4/lib/python3.10/site-packages/gsport.py", line 354, in download_all
    response = requests.get(session.options.host + '/data_api_recursive/' +
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/requests/api.py", line 75, in get
    return request('get', url, params=params, **kwargs)
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/requests/api.py", line 61, in request
    return session.request(method=method, url=url, **kwargs)
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/requests/sessions.py", line 529, in request
    resp = self.send(prep, **send_kwargs)
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/requests/sessions.py", line 645, in send
    r = adapter.send(request, **kwargs)
  File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/requests/adapters.py", line 501, in send
    raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
[1]+  Exit 1                  gsport -a -r -p $GSID -t 4

Idk why though.....

Maybe a firewall issue on our side idk?

SHajema commented 6 months ago

The amount of files in the directory is probably the issue (more than 40k). I will zip these files for now so it's easier. In the new version of this tool we have an idea to mitigate this limit.