python_packaging/test/test_fr15.py

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  34
  35 """Test gmxapi functionality described in roadmap.rst."""
  36
  37 import logging
  38
  39 import pytest
  40
  41 import gmxapi as gmx
  42
  43 # Configure the `logging` module before proceeding any further.
  44 gmx.logger.setLevel(logging.WARNING)
  45
  46 try:
  47     from mpi4py import MPI
  48     rank_number = MPI.COMM_WORLD.Get_rank()
  49 except ImportError:
  50     rank_number = 0
  51     rank_tag = ''
  52     MPI = None
  53 else:
  54     rank_tag = 'rank{}:'.format(rank_number)
  55
  56 # Use this formatter to improve the caplog log records.
  57 formatter = logging.Formatter(rank_tag + '%(name)s:%(levelname)s: %(message)s')
  58
  59 @pytest.mark.usefixtures('cleandir')
  60 def test_fr15(spc_water_box, caplog):
  61     """FR15: Simulation input modification.
  62
  63     * *gmx.modify_input produces new (tpr) simulation input in data flow operation*
  64       (requires interaction with library development)
  65     """
  66     try:
  67         from mpi4py import MPI
  68         current_rank = MPI.COMM_WORLD.Get_rank()
  69         ensemble_size = MPI.COMM_WORLD.Get_size()
  70     except ImportError:
  71         current_rank = 0
  72         ensemble_size = 1
  73
  74     with caplog.at_level(logging.DEBUG):
  75         caplog.handler.setFormatter(formatter)
  76         with caplog.at_level(logging.WARNING, 'gmxapi'), \
  77                  caplog.at_level(logging.DEBUG, 'gmxapi.mdrun'), \
  78                  caplog.at_level(logging.DEBUG, 'gmxapi.modify_input'), \
  79                  caplog.at_level(logging.DEBUG, 'gmxapi.read_tpr'), \
  80                  caplog.at_level(logging.DEBUG, 'gmxapi.simulation'):
  81
  82             initial_input = gmx.read_tpr([spc_water_box for _ in range(ensemble_size)])
  83             parameters = list([{'ld-seed': i} for i in range(ensemble_size)])
  84             param_sweep = gmx.modify_input(input=initial_input,
  85                                            parameters=parameters
  86                                            )
  87             md = gmx.mdrun(param_sweep)
  88             # TODO: (#3179) Handle ensembles of size 1 more elegantly.
  89             if md.output.ensemble_width > 1:
  90                 result_list = md.output.parameters['ld-seed'].result()
  91             else:
  92                 result_list = [md.output.parameters['ld-seed'].result()]
  93             for expected, actual in zip(parameters, result_list):
  94                 assert expected['ld-seed'] == actual