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OpenFF toolkit #328

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laraPPr opened this issue May 6, 2024 · 7 comments · Fixed by easybuilders/easybuild-easyconfigs#20852 or easybuilders/easybuild-easyconfigs#20824
Closed
10 tasks done

OpenFF toolkit #328

laraPPr opened this issue May 6, 2024 · 7 comments · Fixed by easybuilders/easybuild-easyconfigs#20852 or easybuilders/easybuild-easyconfigs#20824
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@pavelToman
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conda Is supported in conda difficulty: medium software that likely require a fair amount of effort to support new new software priority: medium Python site:ugent Software installation request for UGent Tier-2

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@laraPPr
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laraPPr commented May 6, 2024 •
edited by pavelToman
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@laraPPr laraPPr added difficulty: easy software that should be easy to support new new software priority: medium Python site:ugent Software installation request for UGent Tier-2 conda Is supported in conda difficulty: medium software that likely require a fair amount of effort to support and removed difficulty: easy software that should be easy to support labels May 6, 2024
@pavelToman pavelToman self-assigned this Jun 13, 2024
pavelToman added a commit that referenced this issue Jun 13, 2024
@pavelToman
#328 deps
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pavelToman added a commit that referenced this issue Jun 14, 2024
@pavelToman
#328 rdkit pre-PR version
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pavelToman added a commit that referenced this issue Jun 14, 2024
@pavelToman
#328 rdkit PR version
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pavelToman added a commit that referenced this issue Jun 17, 2024
@pavelToman
#328 working AmberTools-23.6
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pavelToman added a commit that referenced this issue Jun 17, 2024
@pavelToman
#328 PR version of AmberTools + nagl-models
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pavelToman added a commit that referenced this issue Jun 18, 2024
@pavelToman
#328 pr-PR version
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pavelToman added a commit that referenced this issue Jun 18, 2024
@pavelToman
#328 PR vesrion
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pavelToman added a commit that referenced this issue Jun 19, 2024
@pavelToman
#328 test Ambertolls v24
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@pavelToman
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PR

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

@boegel
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boegel commented Jun 19, 2024

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

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pavelToman commented Jun 19, 2024 •
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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

@pavelToman pavelToman mentioned this issue Jun 27, 2024
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@laraPPr
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laraPPr commented Jul 5, 2024

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

@pavelToman
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pavelToman commented Jul 8, 2024 •
edited
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There is a problem with RDKit PR - one test is failing - easybuilders/easybuild-easyconfigs#20824
rdkit/rdkit#7588
We should ignore this failing test

@pavelToman pavelToman mentioned this issue Jul 8, 2024
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pavelToman added a commit that referenced this issue Jul 10, 2024
@pavelToman
#328 rdkit - ignore failing test
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pavelToman added a commit that referenced this issue Aug 6, 2024
@pavelToman
#328 update checksum + sources
1b7bf46
pavelToman added a commit that referenced this issue Aug 9, 2024
@pavelToman
#328 cleanup
57e3060
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conda Is supported in conda difficulty: medium software that likely require a fair amount of effort to support new new software priority: medium Python site:ugent Software installation request for UGent Tier-2
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