yank-example-hydration-phenol-Analysis-error

[owenustc]

Hi, I run example of yank, run-explicit.sh, and meet the error as follow, and my Yank Version is 0.25.2. mbar is 3.0.5.dev-Unknown, openmm is 7.6.0.dev-ad113a0.
dcdplugin) Could not access file 'explicit/experiments/trailblaze/solvent1/coordinates.dcd'. dcdplugin) Could not access file 'explicit/experiments/trailblaze/solvent2/coordinates.dcd'. Traceback (most recent call last): File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistateanalyzer.py", line 403, in get value = instance._cache[self.name] KeyError: 'mbar'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/miniconda3/bin/yank", line 10, in sys.exit(main()) File "/root/miniconda3/lib/python3.9/site-packages/yank/cli.py", line 73, in main dispatched = getattr(commands, command).dispatch(command_args) File "/root/miniconda3/lib/python3.9/site-packages/yank/commands/script.py", line 155, in dispatch yaml_builder.run_experiments(write_status=write_status) File "/root/miniconda3/lib/python3.9/site-packages/yank/experiment.py", line 751, in run_experiments completed[exp_index] = self._run_experiment(exp, write_status=write_status) File "/root/miniconda3/lib/python3.9/site-packages/yank/experiment.py", line 3251, in _run_experiment built_experiment.run(n_iterations=switch_experiment_interval) File "/root/miniconda3/lib/python3.9/site-packages/yank/experiment.py", line 427, in run alchemical_phase.run(n_iterations=iterations_to_run) File "/root/miniconda3/lib/python3.9/site-packages/yank/yank.py", line 1207, in run self._sampler.run(n_iterations=n_iterations) File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 690, in run self._update_analysis() File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 1553, in _update_analysis self._last_err_free_energy = self._offline_analysis() File "/root/miniconda3/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper return run_single_node(rank, task, *args, **kwargs) File "/root/miniconda3/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node result = task(*args, **kwargs) File "/root/miniconda3/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 621, in _delayed_termination return func(*args, **kwargs) File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/utils.py", line 87, in _wrapper return func(*args, **kwargs) File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 1428, in _offline_analysis mbar = analysis.mbar File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistateanalyzer.py", line 405, in get value = self._get_default(instance) File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistateanalyzer.py", line 426, in _get_default value = self._default(self, instance) File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistateanalyzer.py", line 2130, in mbar return instance._create_mbar(instance._unbiased_decorrelated_u_ln, File "/root/miniconda3/lib/python3.9/site-packages/openmmtools/multistate/multistateanalyzer.py", line 1041, in _create_mbar self.mbar = MBAR(energy_matrix, samples_per_state, **self._extra_analysis_kwargs) File "/root/miniconda3/lib/python3.9/site-packages/pymbar/mbar.py", line 304, in init self.f_k = mbar_solvers.solve_mbar_for_all_states(self.u_kn, self.N_k, self.f_k, solver_protocol) File "/root/miniconda3/lib/python3.9/site-packages/pymbar/mbar_solvers.py", line 547, in solve_mbar_for_all_states f_k_nonzero, all_results = solve_mbar(u_kn[states_with_samples], N_k[states_with_samples], File "/root/miniconda3/lib/python3.9/site-packages/pymbar/mbar_solvers.py", line 515, in solve_mbar f_k_nonzero, results = solve_mbar_once(u_kn_nonzero, N_k_nonzero, f_k_nonzero, **options) File "/root/miniconda3/lib/python3.9/site-packages/pymbar/mbar_solvers.py", line 444, in solve_mbar_once results = adaptive(u_kn_nonzero, N_k_nonzero, f_k_nonzero, tol=tol, options=options) File "/root/miniconda3/lib/python3.9/site-packages/pymbar/mbar_solvers.py", line 293, in adaptive Hinvg = np.linalg.lstsq(H, g, rcond=-1)[0] File "<array_function internals>", line 5, in lstsq File "/root/miniconda3/lib/python3.9/site-packages/numpy/linalg/linalg.py", line 2306, in lstsq x, resids, rank, s = gufunc(a, b, rcond, signature=signature, extobj=extobj) ValueError: On entry to DLASCL parameter number 4 had an illegal value 2022-01-25 15:10:37,626: Single node: executing <bound method MultiStateReporter.close of <openmmtools.multistate.multistatereporter.MultiStateReporter object at 0x7fb598b10eb0>> 2022-01-25 15:10:37,640: Single node: executing <bound method MultiStateReporter.close of <openmmtools.multistate.multistatereporter.MultiStateReporter object at 0x7fb5348841c0>> Analyzing data... Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. Traceback (most recent call last): File "/root/miniconda3/bin/yank", line 10, in sys.exit(main()) File "/root/miniconda3/lib/python3.9/site-packages/yank/cli.py", line 73, in main dispatched = getattr(commands, command).dispatch(command_args) File "/root/miniconda3/lib/python3.9/site-packages/yank/commands/analyze.py", line 148, in dispatch single_run() File "/root/miniconda3/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper return run_single_node(rank, task, *args, **kwargs) File "/root/miniconda3/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node result = task(*args, **kwargs) File "/root/miniconda3/lib/python3.9/site-packages/yank/commands/analyze.py", line 143, in single_run output = analyze.analyze_directory(args['--store'], **analyzer_kwargs) File "/root/miniconda3/lib/python3.9/site-packages/yank/analyze.py", line 782, in analyze_directory auto_experiment_analyzer = ExperimentAnalyzer(source_directory, **analyzer_kwargs) File "/root/miniconda3/lib/python3.9/site-packages/yank/analyze.py", line 297, in init raise RuntimeError(err_msg) RuntimeError: Cannot find analysis.yaml script in experiments Exception ignored in: <function ExperimentAnalyzer.del at 0x7fa5ebca9ca0> Traceback (most recent call last): File "/root/miniconda3/lib/python3.9/site-packages/yank/analyze.py", line 336, in del for phase, analyzer in self.analyzers.items(): AttributeError: 'ExperimentAnalyzer' object has no attribute 'analyzers'

[lilyminium]

File "/root/miniconda3/lib/python3.9/site-packages/yank/analyze.py", line 297, in init raise RuntimeError(err_msg) RuntimeError: Cannot find analysis.yaml script in experiments

I think the underlying cause of this error might be the lack of an analysis.yaml script, not yaml version. @owenustc do you have one?