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CRITICAL logs show unusual exception
See original GitHub issueThe _CRITICAL.logs I see contain
2018-10-12 23:14:51,070 - CRITICAL - yank.mpi - MPI node 1/12 raised an exception and called Abort()! The exception traceback follows
Traceback (most recent call last):
File "run_yank.py", line 153, in <module>
main(args.yaml_script_path, args.job_id, args.n_jobs)
File "run_yank.py", line 141, in main
experiment_builder.run_experiments()
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/experiment.py", line 796, in run_experiments
send_results_to='all')
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/mpi.py", line 531, in distribute
*other_args, **kwargs)
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/mpi.py", line 386, in exec_tasks
raise error
AttributeError: Group 1/12 Node 1/1 received an exception from another MPI process. Original stack trace follow:
Traceback (most recent call last):
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/mpi.py", line 357, in exec_tasks
results.append(task(distributed_arg, *other_args, **kwargs))
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/experiment.py", line 3120, in _run_experiment
built_experiment.run(n_iterations=switch_experiment_interval)
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/experiment.py", line 460, in run
alchemical_phase = AlchemicalPhase.from_storage(phase)
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/yank.py", line 811, in from_storage
sampler = sampler_class.from_storage(storage)
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/multistate/multistatesampler.py", line 222, in from_storage
sampler = cls._instantiate_sampler_from_reporter(reporter)
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/multistate/multistatesampler.py", line 854, in _instantiate_sampler_from_reporter
options['mcmc_moves'] = reporter.read_mcmc_moves()
File "/home/chodera/miniconda/lib/python3.6/site-packages/yank/multistate/multistatereporter.py", line 748, in read_mcmc_moves
mcmc_moves.append(mmtools.utils.deserialize(serialized_move))
File "/home/chodera/miniconda/lib/python3.6/site-packages/openmmtools/utils.py", line 597, in deserialize
names.append(serialization.pop(_SERIALIZED_MANGLED_PREFIX + key))
AttributeError: 'NoneType' object has no attribute 'pop
I have installed
openmm 7.4.0 py36_cuda92_1 omnia/label/dev
openmmtools 0.15.0 py36_0 omnia
yank 0.23.7 py36_0 omnia
with openmm 7.3.0.dev-f8dcb72.
Issue Analytics
- State:
- Created 5 years ago
- Comments:5 (5 by maintainers)
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Great detective work! I wonder if there’s a way we can raise an exception if the NetCDF file is corrupted.
I’ll spend more time investigating the “safe termination” as discussed in https://github.com/choderalab/yank/issues/1081
Could we add error checking for empty strings being returned in this particular case? This seems to occur in multiple different NetCDF files for me.