Cannot download pretrained model (GCSFS failed)

[jwasswa2023]

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Is there an existing issue for this?

• [X] I have searched the existing issues and found nothing

Bug description

Hello here, thank you for your efforts.

I have been using Molfeat but failed to run through a tutorial for fine-tuning a pre-trained model. When I try to define the featurizer and load a transformer model using the code below, I get an error,

"featurizer = PretrainedHFTransformer(kind="ChemBERTa-77M-MLM", pooling="bert", preload=True)"

This is the error below.

ERROR:gcsfs:_request out of retries on exception: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7f583491b8b0>)
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py", line 111, in refresh
    self._retrieve_info(request)
  File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py", line 87, in _retrieve_info
    info = _metadata.get_service_account_info(
  File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/_metadata.py", line 234, in get_service_account_info
    return get(request, path, params={"recursive": "true"})
  File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/_metadata.py", line 182, in get
    raise exceptions.TransportError(
google.auth.exceptions.TransportError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7f583491b8b0>)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.10/site-packages/gcsfs/retry.py", line 114, in retry_request
    return await func(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/gcsfs/core.py", line 414, in _request
    headers=self._get_headers(headers),
  File "/usr/local/lib/python3.10/site-packages/gcsfs/core.py", line 393, in _get_headers
    self.credentials.apply(out)
  File "/usr/local/lib/python3.10/site-packages/gcsfs/credentials.py", line 187, in apply
    self.maybe_refresh()
  File "/usr/local/lib/python3.10/site-packages/gcsfs/credentials.py", line 182, in maybe_refresh
    self.credentials.refresh(req)
  File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py", line 117, in refresh
    six.raise_from(new_exc, caught_exc)
  File "<string>", line 3, in raise_from
google.auth.exceptions.RefreshError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7f583491b8b0>)
---------------------------------------------------------------------------
TransportError                            Traceback (most recent call last)
[/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py](https://localhost:8080/#) in refresh(self, request)
    110         try:
--> 111             self._retrieve_info(request)
    112             self.token, self.expiry = _metadata.get_service_account_token(

25 frames
TransportError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7f583491b8b0>)
The above exception was the direct cause of the following exception:

RefreshError                              Traceback (most recent call last)
<decorator-gen-121> in _request(self, method, path, headers, json, data, *args, **kwargs)

/usr/local/lib/python3.10/dist-packages/six.py in raise_from(value, from_value)

RefreshError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7f583491b8b0>)

How to reproduce the bug

No response

Error messages and logs

# Error messages and logs here please

Environment

Current environment

#- Molfeat version (e.g., 0.1.0):
#- PyTorch Version (e.g., 1.10.0):
#- RDKit version (e.g., 2022.09.5): 
#- scikit-learn version (e.g.,  1.2.1): 
#- OS (e.g., Linux):
#- How you installed Molfeat (`conda`, `pip`, source):

Additional context

No response

[jstlaurent]

@jwasswa2023 : Thanks for reporting this! I'm taking a look.

[jstlaurent]

@jwasswa2023: It seems to be a transient issue with Google Cloud Platform, who hosts the bucket in which the files are located. Could you try it again and tell me if you still have an issue? And if so, are you running your Python code from a terminal where your user is logged in to GCP?

Thank you.

[jwasswa2023]

Hello Julien, Sorry for the delayed response. I am running my code in Colab where I am logged in. I have run the tutorial again and I am getting a similar error but with a modified warning message. see below.

2023-06-16 01:48:32 | WARNING | google.auth._default | No project ID could be determined. Consider running gcloud config set project or setting the GOOGLE_CLOUD_PROJECT environment variable 2023-06-16 01:49:08 | ERROR | gcsfs | _request out of retries on exception: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7fd861c2d5d0>) Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py", line 111, in refresh self._retrieve_info(request) File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py", line 87, in _retrieve_info info = _metadata.get_service_account_info( File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/_metadata.py", line 234, in get_service_account_info return get(request, path, params={"recursive": "true"}) File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/_metadata.py", line 182, in get raise exceptions.TransportError( google.auth.exceptions.TransportError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7fd861c2d5d0>)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/lib/python3.10/site-packages/gcsfs/retry.py", line 114, in retry_request return await func(*args, **kwargs) File "/usr/local/lib/python3.10/site-packages/gcsfs/core.py", line 414, in _request headers=self._get_headers(headers), File "/usr/local/lib/python3.10/site-packages/gcsfs/core.py", line 393, in _get_headers self.credentials.apply(out) File "/usr/local/lib/python3.10/site-packages/gcsfs/credentials.py", line 187, in apply self.maybe_refresh() File "/usr/local/lib/python3.10/site-packages/gcsfs/credentials.py", line 182, in maybe_refresh self.credentials.refresh(req) File "/usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py", line 117, in refresh six.raise_from(new_exc, caught_exc) File "", line 3, in raise_from google.auth.exceptions.RefreshError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7fd861c2d5d0>)

TransportError Traceback (most recent call last) /usr/local/lib/python3.10/dist-packages/google/auth/compute_engine/credentials.py in refresh(self, request) 110 try: --> 111 self._retrieve_info(request) 112 self.token, self.expiry = _metadata.get_service_account_token(

25 frames TransportError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7fd861c2d5d0>)

The above exception was the direct cause of the following exception:

RefreshError Traceback (most recent call last) in _request(self, method, path, headers, json, data, *args, **kwargs)

/usr/local/lib/python3.10/dist-packages/six.py in raise_from(value, from_value)

RefreshError: ("Failed to retrieve http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/?recursive=true from the Google Compute Engine metadata service. Status: 404 Response:\nb''", <google.auth.transport.requests._Response object at 0x7fd861c2d5d0>)

[azkalot1]

Hi all!

Having the same problem here. Is there a solution?

[maclandrol]

Hi @azkalot1, from what we have gathered so far, this is often either:

• some temporary issues with GCP
• the user having some existing credentials that interfere with access to the bucket or a wrong setup of gcloud service.

Can you ls the bucket with some tool like gsutil ? (gsutil ls gs://molfeat-store-prod/)

Also how did you install molfeat through pip or conda ?

[azkalot1]

installed from pip

gsutil ls gs://molfeat-store-prod/
gs://molfeat-store-prod/artifacts/
gs://molfeat-store-prod/checkpoints/

[maclandrol]

So it seems that you do have access through gsutil but your installed gcsfs can't assess it.

Two other questions:

1. Could you confirm the above hypothesis with the following code in the same environment as your molfeat installation ?

import datamol as dm

mapper = dm.fs.get_mapper("gs://molfeat-store-prod/")
mapper.fs.ls("gs://molfeat-store-prod/")

2. Are you on a local machine ?

[azkalot1]

import datamol as dm

mapper = dm.fs.get_mapper("gs://molfeat-store-prod/")
mapper.fs.ls("gs://molfeat-store-prod/")

gives

['molfeat-store-prod/artifacts', 'molfeat-store-prod/checkpoints']

2 - no, instance from Saturn Cloud (AWS instance)

[maclandrol]

Everything seems to indicate that it should be working in theory.

I will investigate during the weekend. In the meantime, you might want to try temporary removing any previous gcp credentials you have and check again.

[azkalot1]

I think the issue is different and the exception is a bit misleading.

from molfeat.store.modelstore import ModelStore
from molfeat.store.modelstore import ModelStoreError

store = ModelStore()
store.search(name='GPT2-Zinc480M-87M')[0]

will give

     83 def match(self, new_card: Union["ModelInfo", dict], match_only: Optional[List[str]] = None):
     84     """Compare two model card information and returns True if they are the same
     85 
     86     Args:
     87         new_card: card to search for in the modelstore
     88         match_only: list of minimum attribute that should match between the two model information
     89     """
---> 91     self_content = self.model_dump().copy()
     92     if not isinstance(new_card, dict):
     93         new_card = new_card.model_dump()

AttributeError: 'ModelInfo' object has no attribute 'model_dump'

this is the actual error, not loading from the cloud

This happens on molfeat 0.9.2

When I install 0.8.9

features = transformer(['CCCCC'])

works!

[maclandrol]

I haven’t had the time to look yet, sorry. We recently moved to pydantic 2.0, maybe something in the migration that didn’t work. If the error is the model store, then not forwarding the proper error is a bug that needs fixing.

[cwognum]

@azkalot1 Could you share your Pydantic version? Besides a too broad except statement (here?), it seems to me that we are lacking a lower bound for the pydantic version in the pyproject.toml, causing issues when not installing with a conda-like dependency manager.

[miladrayka]

Does anyone find a solution for this bug?

[peiyaoli]

same issues here

[Jessyjias]

Any update to this? Tried to run molfeat on colab but still having this issue. Would appreciate if there's any advice around using molfeat on colab.

[maclandrol]

I will investigate this further. It seems to be something around colab notebooks and authentication in gcsfs.

[maclandrol]

So this is really an issue with google colab and gcsfs.

When in a google colab, it seems that the authentication does not work (even though the bucket accepts anonymous request by default). You therefore needs to be authenticated to access the bucket.

The following works for me

from google.colab import auth
auth.authenticate_user()
credentials, project_id = google.auth.default()

then

from molfeat.trans.pretrained import PretrainedHFTransformer
featurizer = PretrainedHFTransformer(kind="ChemBERTa-77M-MLM", pooling="bert", preload=True)

Does this address the issues of everyone else ? I will try to find a definitive solution where in the colab, user do not need to run the authentication part.

[orgw]

hi i'm having issues

WARNING:google.auth.compute_engine._metadata:Compute Engine Metadata server unavailable on attempt 1 of 3. Reason: timed out