OpenFF toolkit

[laraPPr]

• link to support ticket: #2024041860000927
• website: https://docs.openforcefield.org/projects/toolkit/en/stable/index.html
• installation docs: https://docs.openforcefield.org/projects/toolkit/en/stable/installation.html#installing-from-source
• toolchain: 2023a
• easyblock to use: PythonBundle?
• required dependencies:
  • [x] openmm
  • [x] openff-inerchange
  • [x] openff-units
  • [x] openff-utilities
  • [x] openff-amberports
  • [x] openff-forcefield
  • [x] SMIRNOFF99Frosst
  • [x] rdkit
  • [x] ambertools
• optional dependencies:
  • [x] ...
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: yes (https://docs.openforcefield.org/projects/toolkit/en/stable/installation.html#installing-via-mamba)
  • container image: no
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: no

[pavelToman]

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20840
• https://github.com/easybuilders/easybuild-easyconfigs/pull/20824

[pavelToman]

PR

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20852

[pavelToman]

The newest version 0.16.1 does not work - it checks some deps through conda - failing sanity_checks

[boegel]

@pavelToman Can you clarify the latter? How does it check deps exactly? Is that baked into a script somewhere? Can we patch it out?

[pavelToman]

The log from unsuccessful installation of v0.16.1 is:

== 2024-06-19 15:14:58,229 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-f
ramework/easybuild/base/exceptions.py:126 in __init__): Sanity check failed: sanity check command python -c
 'from openff.toolkit import Molecule, Topology, ForceField' exited with code 1 (output: Traceback (most re
cent call last):
  File "<string>", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 1231, in _handle_fromlist
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit
/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/__init__.py", line 81, in __getattr__
    mod = importlib.import_module(obj_mod)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/importlib/__in
it__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/topology/__init__.py", line 1, in <module>
    from openff.toolkit.topology.molecule import (
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/topology/molecule.py", line 57, in <module>
    from openff.toolkit.utils.constants import DEFAULT_AROMATICITY_MODEL
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/utils/__init__.py", line 9, in <module>
    from openff.toolkit.utils.toolkits import (
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/utils/toolkits.py", line 102, in <module>
    GLOBAL_TOOLKIT_REGISTRY = ToolkitRegistry(
                              ^^^^^^^^^^^^^^^^
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/utils/toolkit_registry.py", line 127, in __init__
    self.register_toolkit(
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/utils/toolkit_registry.py", line 314, in register_toolkit
    _toolkit_wrapper = toolkit_wrapper()
                       ^^^^^^^^^^^^^^^^^
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Toolkit/0.16.1-foss-2023a/lib/python3.11/site-packages/openff/toolkit/utils/ambertools_wrapper.py", line 73, in __init__
    self._toolkit_version = get_ambertools_version()
                            ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Utilities/0.1.12-GCC-12.3.0/lib/python3.11/site-packages/openff/utilities/provenance.py", line 42, in get_ambertools_version
    return _get_conda_list_package_versions().get("ambertools", None)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenForceField-Utilities/0.1.12-GCC-12.3.0/lib/python3.11/site-packages/openff/utilities/provenance.py", line 19, in _get_conda_list_package_versions
    raise CondaExecutableNotFoundError()
openff.utilities.exceptions.CondaExecutableNotFoundError

[laraPPr]

@pavelToman Could you add the following deadline to this request: End of August?

[pavelToman]

There is a problem with RDKit PR - one test is failing - https://github.com/easybuilders/easybuild-easyconfigs/pull/20824 https://github.com/rdkit/rdkit/discussions/7588 We should ignore this failing test