Cannot launch experiments for some datasets (PATTERN/CLUSTER/Peptides-func/Peptides-struct)

[wsjeon]

Hi, thanks for your nice work.

I tried running GraphGPS for all datasets, but I could find out the following errors for the datasets below:

• PATTERN (from configs/GPS/pattern-GPS.yaml) / CLUSTER (from configs/GPS/cluster-GPS.yaml)

  Traceback (most recent call last):
  File "/usr2/wjeon/scratch/GraphGPS/main.py", line 143, in <module>
  loaders = create_loader()
  File "/opt/conda/lib/python3.10/site-packages/torch_geometric/graphgym/loader.py", line 311, in create_loader
  dataset = create_dataset()
  File "/opt/conda/lib/python3.10/site-packages/torch_geometric/graphgym/loader.py", line 242, in create_dataset
  dataset = load_dataset()
  File "/opt/conda/lib/python3.10/site-packages/torch_geometric/graphgym/loader.py", line 187, in load_dataset
  dataset = func(format, name, dataset_dir)
  File "/local/mnt/workspace/scratch/wjeon/GraphGPS/graphgps/loader/master_loader.py", line 110, in load_dataset_master
  dataset = preformat_GNNBenchmarkDataset(dataset_dir, name)
  File "/local/mnt/workspace/scratch/wjeon/GraphGPS/graphgps/loader/master_loader.py", line 287, in preformat_GNNBenchmarkDataset
  return dataset
  UnboundLocalError: local variable 'dataset' referenced before assignment

• peptides-func (from configs/GPS/peptides-func) / peptides-struct (from configs/GPS/peptides-struct)

  
  Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/urllib/request.py", line 1348, in do_open
  h.request(req.get_method(), req.selector, req.data, headers,
  File "/opt/conda/lib/python3.10/http/client.py", line 1282, in request
  self._send_request(method, url, body, headers, encode_chunked)
  File "/opt/conda/lib/python3.10/http/client.py", line 1328, in _send_request
  self.endheaders(body, encode_chunked=encode_chunked)
  File "/opt/conda/lib/python3.10/http/client.py", line 1277, in endheaders
  self._send_output(message_body, encode_chunked=encode_chunked)
  File "/opt/conda/lib/python3.10/http/client.py", line 1037, in _send_output
  self.send(msg)
  File "/opt/conda/lib/python3.10/http/client.py", line 975, in send
  self.connect()
  File "/opt/conda/lib/python3.10/http/client.py", line 1454, in connect
  self.sock = self._context.wrap_socket(self.sock,
  File "/opt/conda/lib/python3.10/ssl.py", line 513, in wrap_socket
  return self.sslsocket_class._create(
  File "/opt/conda/lib/python3.10/ssl.py", line 1071, in _create
  self.do_handshake()
  File "/opt/conda/lib/python3.10/ssl.py", line 1342, in do_handshake
  self._sslobj.do_handshake()
  ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:997)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr2/wjeon/scratch/GraphGPS/main.py", line 142, in loaders = create_loader() File "/opt/conda/lib/python3.10/site-packages/torch_geometric/graphgym/loader.py", line 312, in create_loader dataset = create_dataset() File "/opt/conda/lib/python3.10/site-packages/torch_geometric/graphgym/loader.py", line 243, in create_dataset dataset = load_dataset() File "/opt/conda/lib/python3.10/site-packages/torch_geometric/graphgym/loader.py", line 188, in load_dataset dataset = func(format, name, dataset_dir) File "/local/mnt/workspace/scratch/wjeon/GraphGPS/graphgps/loader/master_loader.py", line 160, in load_dataset_master dataset = preformat_Peptides(dataset_dir, name) File "/local/mnt/workspace/scratch/wjeon/GraphGPS/graphgps/loader/master_loader.py", line 522, in preformat_Peptides dataset = PeptidesFunctionalDataset(dataset_dir) File "/local/mnt/workspace/scratch/wjeon/GraphGPS/graphgps/loader/dataset/peptides_functional.py", line 56, in init super().init(self.folder, transform, pre_transform) File "/opt/conda/lib/python3.10/site-packages/torch_geometric/data/in_memory_dataset.py", line 55, in init super().init(root, transform, pre_transform, pre_filter, log) File "/opt/conda/lib/python3.10/site-packages/torch_geometric/data/dataset.py", line 91, in init self._download() File "/opt/conda/lib/python3.10/site-packages/torch_geometric/data/dataset.py", line 185, in _download self.download() File "/local/mnt/workspace/scratch/wjeon/GraphGPS/graphgps/loader/dataset/peptides_functional.py", line 75, in download if decide_download(self.url): File "/opt/conda/lib/python3.10/site-packages/ogb/utils/url.py", line 12, in decide_download d = ur.urlopen(url) File "/opt/conda/lib/python3.10/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) File "/opt/conda/lib/python3.10/urllib/request.py", line 519, in open response = self._open(req, data) File "/opt/conda/lib/python3.10/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "/opt/conda/lib/python3.10/urllib/request.py", line 496, in _call_chain result = func(*args) File "/opt/conda/lib/python3.10/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, File "/opt/conda/lib/python3.10/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:997)>

May I ask how we can launch the code for those datasets?

Thanks!

[wsjeon]

For peptides-func and peptides-struct, I could resolve issues by following this link.

[rampasek]

Hi! Thanks for reporting the issue! It was indeed a bug from accumulated edits to preformat_GNNBenchmarkDataset() function, it is now fixed by PR #26 Please let me know if there are still any other issues!

[wsjeon]

Thanks for resolving and closing this issue! Everything works well on my end 👍