Openforcefield package import error occurs wiith missing 'GLIBCXX_3.4.26'

user_17612085 0
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I installed openmm package by miniconda with following code. It was executed on colab

import sys
print(sys.version)
!wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.10.3-Linux-x86_64.sh
!bash Miniconda3-py*.sh -bfp /usr/local
!conda config --set always_yes yes
!conda config --add channels conda-forge
!conda create -n openmm python=3.7 cudatoolkit=10.0 git jupyterlab numpy pandas scipy matplotlib ipympl rdkit openbabel openmm mdtraj pymbar pdbfixer parmed openff-toolkit openmoltools openmmforcefields
sys.path.append('/usr/local/envs/openmm/lib/python3.7/site-packages')
import openmm.testInstallation
openmm.testInstallation.main()

since openmm package contains openff package, the following code should be executed.

from openff.toolkit.topology import Molecule
from openforcefield.utils.toolkits import RDKitToolkitWrapper, AmberToolsToolkitWrapper
from openforcefield.topology import Topology
from openforcefield.typing.engines.smirnoff import ForceField
biar = Molecule.from_smiles('c1ccccc1-c1c(C)ccnc1')
#Gerates conformers, default number of generated conformers is 10.
biar.generate_conformers()
biar.compute_partial_charges_am1bcc()

I know that the 2nd-4th line have errors, however, the first line shouldn't have any problems.

The error was following.

ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /usr/local/lib/python3.7/site-packages/openmm/../../../libOpenMM.so.7.7)

I tried downgrading RDkit and adding GLIBCXX_3.4.26 by the following.

!add-apt-repository ppa:ubuntu-toolchain-r/test
!apt-get update --fix-missing
!apt-get dist-upgrade

None of them was worked.

Is there any possible way to resolve this error? I'm really frustrating now...

google-colaboratory linux python
1 Answers

I resolved this error by the following code!

import sys
import os
import requests
import subprocess
import shutil
from logging import getLogger, StreamHandler, INFO


logger = getLogger(__name__)
logger.addHandler(StreamHandler())
logger.setLevel(INFO)


def install(
        chunk_size=4096,
        file_name="Miniconda3-latest-Linux-x86_64.sh",
        url_base="https://repo.continuum.io/miniconda/",
        conda_path=os.path.expanduser(os.path.join("~", "miniconda")),
        rdkit_version='2020.03.3',
        add_python_path=True,
        force=False):
    """install rdkit from miniconda
    ```
    import rdkit_installer
    rdkit_installer.install()
    ```
    """

    python_path = os.path.join(
        conda_path,
        "lib",
        "python{0}.{1}".format(*sys.version_info),
        "site-packages",
    )

    if add_python_path and python_path not in sys.path:
        logger.info("add {} to PYTHONPATH".format(python_path))
        sys.path.append(python_path)

    if os.path.isdir(os.path.join(python_path, "rdkit")):
        logger.info("rdkit is already installed")
        if not force:
            return

        logger.info("force re-install")

    url = url_base + file_name
    python_version = "{0}.{1}.{2}".format(*sys.version_info)

    logger.info("python version: {}".format(python_version))

    if os.path.isdir(conda_path):
        logger.warning("remove current miniconda")
        shutil.rmtree(conda_path)
    elif os.path.isfile(conda_path):
        logger.warning("remove {}".format(conda_path))
        os.remove(conda_path)

    logger.info('fetching installer from {}'.format(url))
    res = requests.get(url, stream=True)
    res.raise_for_status()
    with open(file_name, 'wb') as f:
        for chunk in res.iter_content(chunk_size):
            f.write(chunk)
    logger.info('done')

    logger.info('installing miniconda to {}'.format(conda_path))
    subprocess.check_call(["bash", file_name, "-b", "-p", conda_path])
    logger.info('done')

    logger.info("installing rdkit")
    subprocess.check_call([
        os.path.join(conda_path, "bin", "conda"),
        "install",
        "--yes",
        "-c", "rdkit",
        "python==3.7.9",
        "rdkit" if rdkit_version is None else "rdkit=={}".format(rdkit_version)])
    logger.info("done")

    import rdkit
    logger.info("rdkit-{} installation finished!".format(rdkit.__version__))


install()

but still, biar.compute_partial_charges_am1bcc() function does not work...

user_176120850
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