def test__read_configuration_file():
pyposmat_app = PyposmatIterativeSampler(configuration_filename=config_fn)
pyposmat_app.read_configuration_file()
assert type(pyposmat_app.configuration_filename) is str
assert type(pyposmat_app.configuration) is PyposmatConfigurationFile
assert os.path.isabs(pyposmat_app.configuration_filename)
assert pyposmat_app.configuration_filename == os.path.abspath(config_fn)
def test__initialize_data_directory__with_relative_path_arg():
test_data_dir_path = 'test_dir'
pyposmat_app = PyposmatIterativeSampler(configuration_filename = config_fn)
pyposmat_app.read_configuration_file()
is_created,s = pyposmat_app.initialize_data_directory(data_directory=test_data_dir_path)
assert s == os.path.join(os.getcwd(),test_data_dir_path)
assert pyposmat_app.data_directory == os.path.join(os.getcwd(),test_data_dir_path)
shutil.rmtree(test_data_dir_path)
def test__determine_rv_seeds__seeds_do_not_change_when_run_again():
pyposmat_app = PyposmatIterativeSampler(configuration_filename=config_fn)
pyposmat_app.read_configuration_file()
pyposmat_app.setup_mpi_environment()
pyposmat_app.determine_rv_seeds()
# make sure the seed doesn't change when it's run again
old_seed = pyposmat_app.rv_seed
old_seeds = pyposmat_app.rv_seeds
pyposmat_app.determine_rv_seeds()
assert pyposmat_app.rv_seed == old_seed
assert np.array_equal(pyposmat_app.rv_seeds, old_seeds)
def dev__determine_rv_seeds():
pyposmat_app = PyposmatIterativeSampler(configuration_filename=config_fn)
pyposmat_app.read_configuration_file()
pyposmat_app.setup_mpi_environment()
pyposmat_app.determine_rv_seeds()
print('pyposmat_app.rv_seed:')
print('\ttype:{}.'.format(str(type(pyposmat_app.rv_seed))))
print('pyposmat_app.rv_seeds:')
print(pyposmat_app.rv_seeds.shape)
def test__initialize_rank_directory():
pyposmat_app = PyposmatIterativeSampler(configuration_filename = config_fn)
pyposmat_app.setup_mpi_environment()
pyposmat_app.initialize_rank_directory()
assert os.path.isabs(pyposmat_app.rank_directory)
assert pyposmat_app.rank_directory == os.path.abspath('rank_{}'.format(pyposmat_app.mpi_rank))
def dev__setup_mpi_environment():
pyposmat_app = PyposmatIterativeSampler(configuration_filename=config_fn)
pyposmat_app.read_configuration_file()
pyposmat_app.setup_mpi_environment()
print('pyposmat_app.mpi_rank:{}'.format(str(pyposmat_app.mpi_rank)))
print('pyposmat_app.mpi_size:{}'.format(str(pyposmat_app.mpi_size)))
def test__determine_rv_seeds__no_args__attribute_not_none():
pyposmat_app = PyposmatIterativeSampler(configuration_filename=config_fn)
pyposmat_app.read_configuration_file()
pyposmat_app.setup_mpi_environment()
pyposmat_app.rv_seed = 1
assert type(pyposmat_app.rv_seed) is int
assert type(pyposmat_app.rv_seeds) is type(None)
assert pyposmat_app.rv_seed == 1
pyposmat_app.determine_rv_seeds()
assert type(pyposmat_app.rv_seed) is int
assert type(pyposmat_app.rv_seeds) is np.ndarray
assert pyposmat_app.rv_seed == 1
assert pyposmat_app.rv_seeds.shape[0] == pyposmat_app.mpi_size
assert pyposmat_app.rv_seeds.shape[1] == pyposmat_app.n_iterations
def test__setup_mpi_environment():
pyposmat_app = PyposmatIterativeSampler(configuration_filename=config_fn)
pyposmat_app.read_configuration_file()
pyposmat_app.setup_mpi_environment()
assert type(pyposmat_app.mpi_comm) is MPI.Intracomm
assert type(pyposmat_app.mpi_rank) is int
assert type(pyposmat_app.mpi_size) is int
import os,shutil,sys
import numpy as np
from mpi4py import MPI
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.pyposmat.engines import PyposmatIterativeSampler
# set to true, if you want to restart the simulation, and recover from the last iteration
# which was completed.
is_restart = False
if __name__ == "__main__":
pyposmat_data_dir = 'data'
pyposmat_filename_in = os.path.join(
pyposmat_data_dir,'pyposmat.config.in')
#------------------------------------------------------------------------------
# RUN PYPOSMAT
#------------------------------------------------------------------------------
pyposmat_app = PyposmatIterativeSampler(
configuration_filename = pyposmat_filename_in,
is_restart=is_restart
)
pyposmat_app.data_dir = pyposmat_data_dir
pyposmat_app.read_configuration_file()
pyposmat_app.run_all()
import os,shutil,sys
import numpy as np
from mpi4py import MPI
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.pyposmat.engines import PyposmatIterativeSampler
from pypospack.pyposmat.data import PyposmatDataFile
import pandas as pd
class Dev__PyposmatIterativeSampler(PyposmatIterativeSampler):
pass
if __name__ == "__main__":
pyposmat_data_dir = 'data__Ni__eam__born_exp_fs_00'
pyposmat_filename_in = os.path.join(
'data__Ni__eam__born_exp_fs_00',
'pyposmat.config.in')
#------------------------------------------------------------------------------
# RUN PYPOSMAT
#------------------------------------------------------------------------------
pyposmat_app = PyposmatIterativeSampler(
configuration_filename = pyposmat_filename_in)
pyposmat_app.data_directory = 'data__Ni__eam__born_exp_fs_00'
pyposmat_app.read_configuration_file()
#pyposmat_app.run_restart()
#exit()
pyposmat_app.run_all()
import os,shutil,sys
import numpy as np
from mpi4py import MPI
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.pyposmat.engines import PyposmatIterativeSampler
if __name__ == "__main__":
import Ni__eam__born_exp_fs_0 as config
pyposmat_filename_in = 'pyposmat.config.in'
#------------------------------------------------------------------------------
# RUN PYPOSMAT
#------------------------------------------------------------------------------
pyposmat_app = PyposmatIterativeSampler(
configuration_filename = pyposmat_filename_in)
pyposmat_app.read_configuration_file()
#pyposmat_app.read_configuration_file(filename=pyposmat_configuration_filename)
pyposmat_app.run_all()
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.pyposmat.data import PyposmatDataFile
import os
import pypospack.utils
_pypospack_root = pypospack.utils.get_pypospack_root_directory()
_simulation_root = os.path.join(
_pypospack_root,
'examples','Ni__eam__born_exp_rose','01_preconditioning_3.5NN')
_pyposmat_configuration_fn = os.path.join(_simulation_root,'data','pyposmat.config.in')
_pyosmat_log_fn = 'pyposmat.log'
_i_iteration = 0
_last_datafile_fn = os.path.join(_simulation_root,'data','pyposmat.kde.1.out')
_new_datafile_fn = 'pyposmat.results.1.out'
engine = PyposmatIterativeSampler(
configuration_filename=_pyposmat_configuration_fn,
log_fn='pyposmat.log')
engine.read_configuration_file(
filename=_pyposmat_configuration_fn)
_data_fn = os.path.join(_simulation_root,'data','pyposmat.results.0.out')
engine.analyze_results(
i_iteration=0,
data_fn=_data_fn,
config_fn=_pyposmat_configuration_fn,
kde_fn='pyposmat.kde.1.out')
def dev__run_parametric_sampling():
o = PyposmatIterativeSampler(configuration_filename=config_fn)
o.data_dir = pyposmat_data_dir
o.read_configuration_file()
# ensure that the configuration is actually setup as parametric
assert o.configuration.sampling_type[i_iteration]['type'] == 'parametric'
#this setup happens in run_all()
o.setup_mpi_environment()
o.initialize_data_directory()
o.i_iteration = i_iteration
o.log_iteration_information(i_iteration=o.i_iteration)
#this setup happens in run_simulations()
o.initialize_rank_directory()
# ensure that the paths are absolute paths
assert os.path.isabs(o.rank_directory)
assert os.path.isabs(o.configuration_filename)
config_filename = o.configuration_filename
results_filename = os.path.join(o.rank_directory,
'pyposmat.results.{}.out')
bad_parameters_filename = os.path.join(o.rank_directory,
'pyposmat.bad_parameters.{}.out')
os.chdir(o.rank_directory)
o.determine_rv_seeds()
o.initialize_sampler(config_fn=config_filename,
results_fn=results_filename,
mpi_rank=o.mpi_rank,
mpi_size=o.mpi_size,
o_log=o.o_log)
o.run_parametric_sampling(i_iteration=i_iteration)
def test__read_configuration_files__no_args():
engine = PyposmatIterativeSampler(
configuration_filename=_pyposmat_configuration_fn,
log_fn='pyposmat.log')
engine.read_configuration_file()
assert type(engine.configuration) is PyposmatConfigurationFile
def test____init__():
engine = PyposmatIterativeSampler(
configuration_filename=_pyposmat_configuration_fn,
log_fn='pyposmat.log')