Immediate crash upon running ColabFold's AF2 w/ MMseqs2

[jfbazan]

Below are the error messages that result, centering on import errors in loading the different parts of the Colab. Perhaps there's updating of AF2 to 2.1.1? Thx, FB

ImportError Traceback (most recent call last) in () 5 from colabfold.download import download_alphafold_params, default_data_dir 6 from colabfold.utils import setup_logging ----> 7 from colabfold.batch import get_queries, run, set_model_type 8 9 from colabfold.colabfold import plot_protein

9 frames /usr/local/lib/python3.7/dist-packages/colabfold/batch.py in () 41 ) 42 from alphafold.data.tools import hhsearch ---> 43 from alphafold.model import model 44 45 from colabfold.alphafold.models import load_models_and_params

/usr/local/lib/python3.7/dist-packages/alphafold/model/model.py in () 18 from absl import logging 19 from alphafold.common import confidence ---> 20 from alphafold.model import features 21 from alphafold.model import modules 22 from alphafold.model import modules_multimer

/usr/local/lib/python3.7/dist-packages/alphafold/model/features.py in () 17 from typing import List, Mapping, Tuple 18 ---> 19 from alphafold.model.tf import input_pipeline 20 from alphafold.model.tf import proteins_dataset 21

/usr/local/lib/python3.7/dist-packages/alphafold/model/tf/input_pipeline.py in () 15 """Feature pre-processing input pipeline for AlphaFold.""" 16 ---> 17 from alphafold.model.tf import data_transforms 18 from alphafold.model.tf import shape_placeholders 19 import tensorflow.compat.v1 as tf

/usr/local/lib/python3.7/dist-packages/alphafold/model/tf/data_transforms.py in () 16 17 from alphafold.common import residue_constants ---> 18 from alphafold.model.tf import shape_helpers 19 from alphafold.model.tf import shape_placeholders 20 from alphafold.model.tf import utils

/usr/local/lib/python3.7/dist-packages/alphafold/model/tf/shape_helpers.py in () 14 15 """Utilities for dealing with shapes of TensorFlow tensors.""" ---> 16 import tensorflow.compat.v1 as tf 17 18

/usr/local/lib/python3.7/dist-packages/tensorflow/init.py in () 35 import typing as _typing 36 ---> 37 from tensorflow.python.tools import module_util as _module_util 38 from tensorflow.python.util.lazy_loader import LazyLoader as _LazyLoader 39

/usr/local/lib/python3.7/dist-packages/tensorflow/python/init.py in () 35 36 from tensorflow.python import pywrap_tensorflow as _pywrap_tensorflow ---> 37 from tensorflow.python.eager import context 38 39 # pylint: enable=wildcard-import

/usr/local/lib/python3.7/dist-packages/tensorflow/python/eager/context.py in () 33 from tensorflow.python import pywrap_tfe 34 from tensorflow.python import tf2 ---> 35 from tensorflow.python.client import pywrap_tf_session 36 from tensorflow.python.eager import executor 37 from tensorflow.python.eager import monitoring

/usr/local/lib/python3.7/dist-packages/tensorflow/python/client/pywrap_tf_session.py in () 17 # pylint: disable=invalid-import-order,g-bad-import-order, wildcard-import, unused-import 18 from tensorflow.python import pywrap_tensorflow ---> 19 from tensorflow.python.client._pywrap_tf_session import * 20 from tensorflow.python.client._pywrap_tf_session import _TF_SetTarget 21 from tensorflow.python.client._pywrap_tf_session import _TF_SetConfig

ImportError: SystemError: <built-in method contains of dict object at 0x7ffa9203aeb0> returned a result with an error set

[jfbazan]

And I forgot to mention that Deepmind's AF Colab seems to run well (albeit sooo slowly, as usual) and isn't affected by the other ColabFold import problems

[milot-mirdita]

I can reproduce the issue, but I am not sure whats broken. I'll update you once we know more.

[jfbazan]

Thanks Milot! And also, is an update to AF2.1.2 imminent? Cheers, FB

Sent from my iPhone

On Feb 2, 2022, at 1:38 PM, Milot Mirdita @.***> wrote:

I can reproduce the issue, but I am not sure whats broken. I'll update you once we know more.

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[milot-mirdita]

I don't think there are a lot of relevant changes for ColabFold in 2.1.2, we don't use the JackHMMer based pairing pipeline. The amber GPU relaxation is something that we tried before that we could. I think we will take a closer look in the next few days.

[milot-mirdita]

The notebook should work again (you might have to do a colab factory reset under Runtime->Factory reset runtime first).