"Install third-party software" gets stuck at 17%

[JD-Crick]

Hi, I'm trying to predict a structure with AlphaFold, but Colab gets stuck trying to Install the third party software:

# Set environment variables before running any other code.
import os
os.environ['TF_FORCE_UNIFIED_MEMORY'] = '1'
os.environ['XLA_PYTHON_CLIENT_MEM_FRACTION'] = '4.0'

#@title 1. Install third-party software

#@markdown Please execute this cell by pressing the _Play_ button
#@markdown on the left to download and import third-party software
#@markdown in this Colab notebook. (See the [acknowledgements](https://github.com/deepmind/alphafold/#acknowledgements) in our readme.)

#@markdown **Note**: This installs the software on the Colab
#@markdown notebook in the cloud and not on your computer.

from IPython.utils import io
import os
import subprocess
import tqdm.notebook

TQDM_BAR_FORMAT = '{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} remaining: {remaining}]'

try:
  with tqdm.notebook.tqdm(total=100, bar_format=TQDM_BAR_FORMAT) as pbar:
    with io.capture_output() as captured:
      # Uninstall default Colab version of TF.
      %shell pip uninstall -y tensorflow

      %shell sudo apt install --quiet --yes hmmer
      pbar.update(6)

      # Install py3dmol.
      %shell pip install py3dmol
      pbar.update(2)

      # Install OpenMM and pdbfixer.
      %shell rm -rf /opt/conda
      %shell wget -q -P /tmp \
        https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
          && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
          && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
      pbar.update(9)

      PATH=%env PATH
      %env PATH=/opt/conda/bin:{PATH}
      %shell conda install -qy conda==23.5.2 \
          && conda install -qy -c conda-forge \
            python=3.10 \
            openmm=7.7.0 \
            pdbfixer
      pbar.update(80)

      # Create a ramdisk to store a database chunk to make Jackhmmer run fast.
      %shell sudo mkdir -m 777 --parents /tmp/ramdisk
      %shell sudo mount -t tmpfs -o size=9G ramdisk /tmp/ramdisk
      pbar.update(2)

      %shell wget -q -P /content \
        https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
      pbar.update(1)
except subprocess.CalledProcessError:
  print(captured)
  raise

executed_cells = set([1])

Installation always freezes at 17% with "17/100 [elapsed: 00:31 remaining: 02:53]"

[Irideus]

Same problem here... Any solutions?

[geoff919]

Same issue and this seems to have worked for me. Just some trial and error, unsure why it has fixed it but seems to run fine now.

replace: PATH=%env PATH %env PATH=/opt/conda/bin:{PATH} %shell conda install -qy conda==23.5.2 \ && conda install -qy -c conda-forge \ python=3.10 \ openmm=7.7.0 \ pdbfixer pbar.update(80)

with: PATH=%env PATH %env PATH=/opt/conda/bin:{PATH} %shell conda update -qy conda \ && conda install -qy -c conda-forge \ python=3.10 \ openmm=7.7.0 \ pdbfixer pbar.update(80)