1104 gather check json files

[atravitz]

#1104

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• Added a news entry

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[mikemhenry]

@atravitz are we bumping this to 1.4?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.56%. Comparing base (a823546) to head (3de396a).
Report is 99 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1112      +/-   ##
==========================================
- Coverage   94.15%   92.56%   -1.59%     
==========================================
  Files         141      141              
  Lines       10588    10651      +63     
==========================================
- Hits         9969     9859     -110     
- Misses        619      792     +173     

Flag	Coverage Δ
fast-tests	92.56% <100.00%> (?)
slow-tests	?

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[atravitz]

It looks like the rbfe_results dataset has 4 simulations with exceptions in unit_results.

for example, in rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json

"exception": ["SimulationNaNError", ["Propagating replica 1 at state 1 resulted in a NaN!\nThe state of the system and integrator before the error were saved in results/rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent/shared_RelativeHybridTopologyProtocolUnit-60df96a488094f63978880d19487d299_attempt_0/nan-error-logs"]], "traceback": "Traceback (most recent call last):\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py\", line 1326, in _propagate_replica\n mcmc_move.apply(thermodynamic_state, sampler_state, context_cache=self.sampler_context_cache)\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/mcmc.py\", line 1151, in apply\n super(LangevinDynamicsMove, self).apply(thermodynamic_state, sampler_state,\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/mcmc.py\", line 755, in apply\n raise IntegratorMoveError(err_msg, self, context)\nopenmmtools.mcmc.IntegratorMoveError: Potential energy is NaN after 20 attempts of integration with move LangevinDynamicsMove\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/gufe/protocols/protocolunit.py\", line 308, in execute\n outputs = self._execute(context, **inputs)\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py\", line 674, in _execute\n outputs = self.run(scratch_basepath=ctx.scratch, shared_basepath=ctx.shared)\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py\", line 617, in run\n sampler.equilibrate(int(equil_steps / mc_steps)) # type: ignore\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py\", line 696, in equilibrate\n self._propagate_replicas()\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/utils/utils.py\", line 95, in _wrapper\n return func(*args, **kwargs)\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py\", line 1299, in _propagate_replicas\n propagated_states, replica_ids = mpiplus.distribute(self._propagate_replica, range(self.n_replicas),\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/mpiplus/mpiplus.py\", line 523, in distribute\n all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/mpiplus/mpiplus.py\", line 523, in <listcomp>\n all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]\n File \"/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py\", line 1337, in _propagate_replica\n raise SimulationNaNError(message)\nopenmmtools.multistate.utils.SimulationNaNError: Propagating replica 1 at state 1 resulted in a NaN!\nThe state of the system and integrator before the error were saved in results/rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent/

@mikemhenry @jthorton - Is it time for us to use a tidier dataset, like one from industry benchmarking?

[mikemhenry]

I can't remember the providence of that data set, but don't we want some data that has exceptions so can test handling exceptions in our tooling? Or is this dataset supposed to be clean?

[atravitz]

@mikemhenry @jthorton disregard- this is due to an oversight by me when creating the parallel test dataset. this is working as intended, and I just need to update the test dataset on zenodo!

[mikemhenry]

@atravitz can you fix the merge conflict? I have a guess on the right DOI but I don't want to be wrong

[github-actions]

No API break detected ✅