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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.
50 from gmxapi.testsupport import withmpi_only
52 # Configure the `logging` module before proceeding any further.
53 gmx.logger.setLevel(logging.DEBUG)
56 from mpi4py import MPI
57 rank_number = MPI.COMM_WORLD.Get_rank()
62 rank_tag = 'rank{}:'.format(rank_number)
64 # Use this formatter to improve the caplog log records.
65 formatter = logging.Formatter(rank_tag + '%(name)s:%(levelname)s: %(message)s')
67 # For additional console logging, create and attach a stream handler.
69 # ch = logging.StreamHandler()
70 # ch.setFormatter(formatter)
71 # logging.getLogger().addHandler(ch)
74 @pytest.mark.usefixtures('cleandir')
75 def test_run_from_tpr(spc_water_box):
76 assert os.path.exists(spc_water_box)
78 md = gmx.mdrun(spc_water_box)
80 # TODO: better handling of output on unused MPI ranks.
84 @pytest.mark.usefixtures('cleandir')
85 def test_run_trivial_ensemble(spc_water_box, caplog):
86 from mpi4py import MPI
87 current_rank = MPI.COMM_WORLD.Get_rank()
88 with caplog.at_level(logging.DEBUG):
89 caplog.handler.setFormatter(formatter)
90 with caplog.at_level(logging.WARNING, 'gmxapi'), \
91 caplog.at_level(logging.DEBUG, 'gmxapi.mdrun'), \
92 caplog.at_level(logging.DEBUG, 'gmxapi.modify_input'), \
93 caplog.at_level(logging.DEBUG, 'gmxapi.read_tpr'), \
94 caplog.at_level(logging.DEBUG, 'gmxapi.simulation'):
96 tpr_filename = spc_water_box
98 md = gmx.mdrun([tpr_filename] * ensemble_width)
99 assert md.output.ensemble_width == ensemble_width
102 output_directory = md.output._work_dir.result()
103 logging.info('output_directory result: {}'.format(str(output_directory)))
104 assert len(output_directory) == 2
106 # Note that the 'cleandir' test fixture will clean up the output directory on
107 # other ranks, so only check the current rank.
108 assert output_directory[0] != output_directory[1]
109 assert os.path.exists(output_directory[current_rank])