The toolkit showcase stochastically fails with OMP_NUM_THREADS=1 and AmberToolsToolkitWrapper

[Yoshanuikabundi]

Describe the bug Assigning charges with AmberTools can fail when OMP_NUM_THREADS is set to 1 (but not other values or when it is unset). This only happens for some inputs - for instance, simply changing the atom indexing for the test molecule can fix the issue.

I found this trying to fix the OpenFF Docs cookbook - see https://github.com/openforcefield/openff-docs/actions/runs/8342106212/job/22829552667#step:7:249

To Reproduce

from openff.toolkit import Molecule

# %env OMP_NUM_THREADS=2
%env OMP_NUM_THREADS=1

mol1 = Molecule.from_smiles('[H][O][C@@]1([H])[c]2[c]([c]([O][c]3[c]([H])[c]([F])[c]([H])[c]([C]#[N])[c]3[H])[c]([H])[c]([H])[c]2[S](=[O])(=[O])[C]([H])([H])[H])[C]([H])([H])[C]1([F])[F]')
# mol1 = Molecule.from_smiles('CS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2')
mol2 = Molecule.from_mapped_smiles('[O:1]([C@:2]1([H:28])[C:3]([F:24])([F:25])[C:4]([H:29])([H:30])[c:5]2[c:6]1[c:7]([S:20](=[O:21])(=[O:22])[C:23]([H:36])([H:37])[H:38])[c:8]([H:31])[c:9]([H:32])[c:10]2[O:11][c:12]1[c:13]([H:33])[c:14]([F:15])[c:16]([H:34])[c:17]([C:18]#[N:26])[c:19]1[H:35])[H:27]')

assert mol1 == mol2

mol1.assign_partial_charges('am1bcc')
mol2.assign_partial_charges('am1bcc')

mol2.partial_charges

Output

Output for the above code is:

[/home/joshmitchell/Documents/openff/openff-docs/.soap/examples/bin/wrapped_progs/antechamber](http://localhost:8888/home/joshmitchell/Documents/openff/openff-docs/.soap/examples/bin/wrapped_progs/antechamber): Fatal Error!
Cannot properly run "[/home/joshmitchell/Documents/openff/openff-docs/.soap/examples/bin/sqm](http://localhost:8888/home/joshmitchell/Documents/openff/openff-docs/.soap/examples/bin/sqm) -O -i sqm.in -o sqm.out".

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[2], line 13
     10 assert mol1 == mol2
     12 mol1.assign_partial_charges('am1bcc')
---> 13 mol2.assign_partial_charges('am1bcc')
     15 mol2.partial_charges

File [~/Documents/openff/openff-docs/.soap/examples/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py:2629](http://localhost:8888/home/joshmitchell/Documents/openff/openff-docs/.soap/examples/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py#line=2628), in FrozenMolecule.assign_partial_charges(self, partial_charge_method, strict_n_conformers, use_conformers, toolkit_registry, normalize_partial_charges)
   2615         warnings.warn(
   2616             f"Warning! Partial charge method '{partial_charge_method}' is not designed "
   2617             "for use on large (i.e. > 150 atoms) molecules and may crash or take hours to "
   (...)
   2621             stacklevel=2,
   2622         )
   2624 if isinstance(toolkit_registry, ToolkitRegistry):
   2625     # We may need to try several toolkitwrappers to find one
   2626     # that supports the desired partial charge method, so we
   2627     # tell the ToolkitRegistry to continue trying ToolkitWrappers
   2628     # if one raises an error (raise_exception_types=[])
-> 2629     toolkit_registry.call(
   2630         "assign_partial_charges",
   2631         molecule=self,
   2632         partial_charge_method=partial_charge_method,
   2633         use_conformers=use_conformers,
   2634         strict_n_conformers=strict_n_conformers,
   2635         normalize_partial_charges=normalize_partial_charges,
   2636         raise_exception_types=[],
   2637         _cls=self.__class__,
   2638     )
   2639 elif isinstance(toolkit_registry, ToolkitWrapper):
   2640     toolkit_wrapper: ToolkitWrapper = toolkit_registry

File [~/Documents/openff/openff-docs/.soap/examples/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py:370](http://localhost:8888/home/joshmitchell/Documents/openff/openff-docs/.soap/examples/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py#line=369), in ToolkitRegistry.call(self, method_name, raise_exception_types, *args, **kwargs)
    368 for toolkit, error in errors:
    369     msg += " {} {} : {}\n".format(toolkit, type(error), error)
--> 370 raise ValueError(msg)

ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[H][O][C@@]1([H])[c]2[c]([c]([O][c]3[c]([H])[c]([F])[c]([H])[c]([C]#[N])[c]3[H])[c]([H])[c]([H])[c]2[S](=[O])(=[O])[C]([H])([H])[H])[C]([H])([H])[C]1([F])[F]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2023.03.3, ToolkitWrapper around AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around The RDKit version 2023.03.3 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are ['mmff94', 'gasteiger'] 
 ToolkitWrapper around AmberTools version 22.0 <class 'subprocess.CalledProcessError'> : Command '['antechamber', '-i', 'molecule.sdf', '-fi', 'sdf', '-o', 'charged.mol2', '-fo', 'mol2', '-pf', 'yes', '-dr', 'n', '-c', 'bcc', '-nc', '0.0']' returned non-zero exit status 1.
 ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1bcc"" is not supported by the Built-in toolkit. Available charge methods are ['zeros', 'formal_charge']

See also https://github.com/openforcefield/openff-docs/actions/runs/8342106212/job/22829552667#step:7:249

Computing environment (please complete the following information):

• Operating system: Arch Linux

Output of running `conda list`

List of packages in environment: "/home/joshmitchell/Documents/openff/openff-docs/.soap/examples"

  Name                           Version         Build                           Channel    
──────────────────────────────────────────────────────────────────────────────────────────────
  _libgcc_mutex                  0.1             conda_forge                     conda-forge
  _openmp_mutex                  4.5             2_gnu                           conda-forge
  absl-py                        2.1.0           pyhd8ed1ab_0                    conda-forge
  aiohttp                        3.9.3           py310h2372a71_1                 conda-forge
  aiosignal                      1.3.1           pyhd8ed1ab_0                    conda-forge
  ambertools                     22.5            py310hd182041_0                 conda-forge
  annotated-types                0.6.0           pyhd8ed1ab_0                    conda-forge
  anyio                          4.3.0           pyhd8ed1ab_0                    conda-forge
  argon2-cffi                    23.1.0          pyhd8ed1ab_0                    conda-forge
  argon2-cffi-bindings           21.2.0          py310h2372a71_4                 conda-forge
  arpack                         3.7.0           hdefa2d7_2                      conda-forge
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  ase                            3.22.1          pyhd8ed1ab_1                    conda-forge
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  dask-core                      2024.3.1        pyhd8ed1ab_0                    conda-forge
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  debugpy                        1.8.1           py310hc6cd4ac_0                 conda-forge
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  defusedxml                     0.7.1           pyhd8ed1ab_0                    conda-forge
  dgl                            2.0.0           py310hf4f05e9_0                 conda-forge
  distributed                    2024.3.1        pyhd8ed1ab_0                    conda-forge
  entrypoints                    0.4             pyhd8ed1ab_0                    conda-forge
  exceptiongroup                 1.2.0           pyhd8ed1ab_2                    conda-forge
  executing                      2.0.1           pyhd8ed1ab_0                    conda-forge
  expat                          2.6.2           h59595ed_0                      conda-forge
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  fonts-conda-forge              1               0                               conda-forge
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  gawk                           5.3.0           ha916aea_0                      conda-forge
  gcc_impl_linux-64              11.4.0          h7aa1c59_5                      conda-forge
  gcc_linux-64                   11.4.0          h0f0c6b6_3                      conda-forge
  gettext                        0.21.1          h27087fc_0                      conda-forge
  gflags                         2.2.2           he1b5a44_1004                   conda-forge
  gfortran_impl_linux-64         11.4.0          h86428dc_5                      conda-forge
  gfortran_linux-64              11.4.0          h8f970dc_3                      conda-forge
  giflib                         5.2.1           h0b41bf4_3                      conda-forge
  gitdb                          4.0.11          pyhd8ed1ab_0                    conda-forge
  gitpython                      3.1.42          pyhd8ed1ab_0                    conda-forge
  glog                           0.6.0           h6f12383_0                      conda-forge
  gmp                            6.3.0           h59595ed_1                      conda-forge
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  gsl                            2.7             he838d99_0                      conda-forge
  gxx_impl_linux-64              11.4.0          h7aa1c59_5                      conda-forge
  gxx_linux-64                   11.4.0          h2730b16_3                      conda-forge
  h11                            0.14.0          pyhd8ed1ab_0                    conda-forge
  h2                             4.1.0           pyhd8ed1ab_0                    conda-forge
  h5py                           3.10.0          nompi_py310h65828d5_101         conda-forge
  hdf4                           4.2.15          h2a13503_7                      conda-forge
  hdf5                           1.14.3          mpi_mpich_ha2c2bf8_0            conda-forge
  hpack                          4.0.0           pyh9f0ad1d_0                    conda-forge
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  icu                            73.2            h59595ed_0                      conda-forge
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  ipykernel                      6.29.3          pyhd33586a_0                    conda-forge
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  json5                          0.9.24          pyhd8ed1ab_0                    conda-forge
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  jsonschema-specifications      2023.12.1       pyhd8ed1ab_0                    conda-forge
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  jupyter_server_terminals       0.5.3           pyhd8ed1ab_0                    conda-forge
  jupyterlab                     4.1.5           pyhd8ed1ab_0                    conda-forge
  jupyterlab_pygments            0.3.0           pyhd8ed1ab_1                    conda-forge
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  jupyterlab_widgets             3.0.10          pyhd8ed1ab_0                    conda-forge
  keras                          2.15.0          pyhd8ed1ab_0                    conda-forge
  kernel-headers_linux-64        2.6.32          he073ed8_17                     conda-forge
  keyutils                       1.6.1           h166bdaf_0                      conda-forge
  kim-api                        2.3.0           h097297d_1                      conda-forge
  kiwisolver                     1.4.5           py310hd41b1e2_1                 conda-forge
  krb5                           1.21.2          h659d440_0                      conda-forge
  lammps                         2023.11.21      cpu_py310_h8f80a90_mpi_mpich_5  conda-forge
  lcms2                          2.16            hb7c19ff_0                      conda-forge
  ld_impl_linux-64               2.40            h41732ed_0                      conda-forge
  lerc                           4.0.0           h27087fc_0                      conda-forge
  libabseil                      20230802.1      cxx17_h59595ed_0                conda-forge
  libaec                         1.1.2           h59595ed_1                      conda-forge
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  libgcc-devel_linux-64          11.4.0          h922705a_105                    conda-forge
  libgcc-ng                      13.2.0          h807b86a_5                      conda-forge
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  libgfortran5                   13.2.0          ha4646dd_5                      conda-forge
  libglib                        2.80.0          hf2295e7_0                      conda-forge
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  libgoogle-cloud                2.12.0          h5206363_4                      conda-forge
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  libhwloc                       2.9.3           default_h554bfaf_1009           conda-forge
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  libllvm15                      15.0.7          hb3ce162_4                      conda-forge
  libnetcdf                      4.9.2           mpi_mpich_h60ccfc9_13           conda-forge
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  libnl                          3.9.0           hd590300_0                      conda-forge
  libnsl                         2.0.1           hd590300_0                      conda-forge
  libopenblas                    0.3.26          pthreads_h413a1c8_0             conda-forge
  libparquet                     15.0.0          h352af49_0_cpu                  conda-forge
  libpnetcdf                     1.12.3          mpi_mpich_h4ac58e2_101          conda-forge
  libpng                         1.6.43          h2797004_0                      conda-forge
  libprotobuf                    4.24.4          hf27288f_0                      conda-forge
  libre2-11                      2023.09.01      h7a70373_1                      conda-forge
  libsanitizer                   11.4.0          h4dcbe23_5                      conda-forge
  libsodium                      1.0.18          h36c2ea0_1                      conda-forge
  libsqlite                      3.45.2          h2797004_0                      conda-forge
  libssh2                        1.11.0          h0841786_0                      conda-forge
  libstdcxx-devel_linux-64       11.4.0          h922705a_105                    conda-forge
  libstdcxx-ng                   13.2.0          h7e041cc_5                      conda-forge
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Additional context This is probably an upstream issue but I'm documenting it here anyway.

[j-wags]

Seems to be re-emergence of #1767. Here @Yoshanuikabundi has identified that the issue only occurs when running with one core.

[Yoshanuikabundi]

Ok I systematically ran ten charge assignments under the conditions that I believed led to the crash. 9 of them failed and 1 succeeded. So I think there is a stochastic element to the problem.

I also experimented with changing atom ordering, and specifying the conformers used to calculate charges. I had an atom ordering that worked every time, and an atom ordering that failed 9 times out of 10, so I generated a conformer for each ordering and then tried each conformer on the opposite ordering with the use_conformers argument (after remapping the conformer). The conformers looked very similar and didn't have anything obviously wrong with them - the main difference was a 180 degree rotation of a hydroxyl group. Moreover, changing the conformer to one generated from the opposite ordering didn't change the results. I was really surprised to see this, but it seems to be the atom ordering itself and not the conformation.

[j-wags]

Thanks for looking deeper into this.

Decisive morning-jeff is looking at this and sees two options:

• Commit what might be a very large amount of time to dig into the root cause, which is very likely to be deep in RDKit/AmberTools, where both tools behave reasonably independently and this behavior only emerges when they're strung together in the particular way that we've strung them together, and so the problem is unlikely to be fixed by their devs even if we report it, requiring us to instead solve this with an unreliable kludge in our code.
• Rescope this issue away from "fix this problem with AmberToolsWrapper in general" (since we'll have nagl am1bcc charges soon anyway) and focus on a minimal kludge to get our examples rendering.

I'm strongly in favor of the latter. I'll change the issue name to reflect this. @Yoshanuikabundi could you push the good atom ordering to https://github.com/openforcefield/openff-toolkit/pull/1846