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35 """Test gromacs.mdrun operation.
37 Factory produces deferred execution operation.
39 TODO: Factory expects input for conformation, topology, simulation parameters, simulation state.
41 TODO: Factory accepts additional keyword input to indicate binding
42 to the "potential" interface.
52 # Configure the `logging` module before proceeding any further.
53 gmx.logger.setLevel(logging.WARNING)
56 from mpi4py import MPI
57 rank_number = MPI.COMM_WORLD.Get_rank()
63 rank_tag = 'rank{}:'.format(rank_number)
65 # Use this formatter to improve the caplog log records.
66 formatter = logging.Formatter(rank_tag + '%(name)s:%(levelname)s: %(message)s')
68 # For additional console logging, create and attach a stream handler.
70 # ch = logging.StreamHandler()
71 # ch.setFormatter(formatter)
72 # logging.getLogger().addHandler(ch)
75 @pytest.mark.usefixtures('cleandir')
76 def test_run_from_tpr(spc_water_box, mdrun_kwargs):
77 assert os.path.exists(spc_water_box)
79 md = gmx.mdrun(spc_water_box)
81 # TODO: better handling of output on unused MPI ranks.
84 @pytest.mark.withmpi_only
85 @pytest.mark.usefixtures('cleandir')
86 def test_run_trivial_ensemble(spc_water_box, caplog, mdrun_kwargs):
87 from mpi4py import MPI
88 current_rank = MPI.COMM_WORLD.Get_rank()
89 with caplog.at_level(logging.DEBUG):
90 caplog.handler.setFormatter(formatter)
91 with caplog.at_level(logging.WARNING, 'gmxapi'), \
92 caplog.at_level(logging.DEBUG, 'gmxapi.mdrun'), \
93 caplog.at_level(logging.DEBUG, 'gmxapi.modify_input'), \
94 caplog.at_level(logging.DEBUG, 'gmxapi.read_tpr'), \
95 caplog.at_level(logging.DEBUG, 'gmxapi.simulation'):
97 tpr_filename = spc_water_box
99 simulation_input = gmx.read_tpr([tpr_filename] * ensemble_width)
100 assert simulation_input.output.ensemble_width == ensemble_width
101 assert len(simulation_input.output._simulation_input.result()) == ensemble_width
102 md = gmx.mdrun(simulation_input)
103 assert md.output.ensemble_width == ensemble_width
106 output_directory = md.output._work_dir.result()
107 logging.info('output_directory result: {}'.format(str(output_directory)))
108 assert len(output_directory) == 2
110 # Note that the 'cleandir' test fixture will clean up the output directory on
111 # other ranks, so only check the current rank. Generally, our behavior
112 # is undefined if the client removes the working directory while the job
113 # is in progress. We can consider adding some sort of synchronization at
114 # the end of the job if running in temporary directories becomes an
115 # important use case outside of testing.
116 assert output_directory[0] != output_directory[1]
117 assert os.path.exists(output_directory[current_rank])
118 assert os.path.exists(md.output.trajectory.result()[current_rank])
121 @pytest.mark.usefixtures('cleandir')
122 def test_run_from_read_tpr_op(spc_water_box, caplog, mdrun_kwargs):
123 with caplog.at_level(logging.DEBUG):
124 caplog.handler.setFormatter(formatter)
125 with caplog.at_level(logging.DEBUG, 'gmxapi'):
126 simulation_input = gmx.read_tpr(spc_water_box)
127 md = gmx.mdrun(input=simulation_input)
131 assert os.path.exists(md.output.trajectory.result())
134 @pytest.mark.usefixtures('cleandir')
135 def test_run_from_modify_input_op(spc_water_box, caplog, mdrun_kwargs):
136 with caplog.at_level(logging.DEBUG):
138 simulation_input = gmx.read_tpr(spc_water_box)
139 modified_input = gmx.modify_input(input=simulation_input, parameters={'nsteps': 4})
140 md = gmx.mdrun(input=modified_input)