strange permission problem with Sams?

[RiesBen]

Hi @IAlibay ,
my SAMS runs did die after this error (seems to be in the finalization stage?):

PermissionError: [Errno 13] Permission denied: '/lig_p38a_3flw_lig_p38a_3fly_rep0_complex_real_time_analysis.yaml'
CRITICAL:mpiplus.mpiplus:MPI node 1/1 raised an exception and called Abort()! The exception traceback follows

Traceback (most recent call last):
File "path/Experiments/free_energies/src/scripts/run_system_sams.py", line 100, in
complex_transform.run(dry=False, verbose=True)
File "path/openfe/openfe/setup/methods/openmm/equil_rbfe_methods.py", line 945, in run
sampler.extend(int(prod_steps.m / mc_steps)) # type: ignore
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 821, in extend
self.run(n_iterations)
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 787, in run
self._update_analysis()
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 1661, in _update_analysis
self._last_err_free_energy = self._offline_analysis()
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper
return run_single_node(rank, task, *args, **kwargs)
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node
result = task(*args, **kwargs)
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 621, in _delayed_termination
return func(*args, **kwargs)
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/openmmtools/utils.py", line 94, in _wrapper
return func(*args, **kwargs)
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 1587, in _offline_analysis
self._reporter.write_current_statistics(data_dict)
File "path/miniconda3/envs/openfe/lib/python3.9/site-packages/openmmtools/multistate/multistatereporter.py", line 1341, in write_current_statistics
with open(output_filepath, "a") as out_file:
PermissionError: [Errno 13] Permission denied: '/lig_p38a_3flw_lig_p38a_3fly_rep0_complex_real_time_analysis.yaml'

[IAlibay]

@RiesBen can you re-run adding a "./" before the output and checkpoint file names?

[RiesBen]

Trying this. But this seems to me like behavior we might want to avoid?

[IAlibay]

yeah we'll need to push for change upstream

[mikemhenry]

Please open bug reports for openmmtools! I've got write access their so we can get things fixed

[RiesBen]

@mikemhenry Hi, I raised an issue, sorry was quite busy past weeks. Hope it helps? :)

[RiesBen]

I think next we can close this issue :)

[mikemhenry]

Fixed with choderalab/openmmtools#616