def test_loading_as_new(self):
filename = make_temp_dir('asnew.h5')
traj = Trajectory(name='TestPartial', filename=filename, add_time=True)
traj.f_add_parameter('x', 3)
traj.f_add_parameter('y', 2)
traj.f_explore({'x': [12,3,44], 'y':[1,23,4]})
traj.f_store()
traj = load_trajectory(name=traj.v_name, filename=filename)
with self.assertRaises(TypeError):
traj.f_shrink()
traj = load_trajectory(name=traj.v_name, filename=filename, as_new=True,
new_name='TestTraj', add_time=False)
self.assertTrue(traj.v_name == 'TestTraj')
self.assertEqual(len(traj), 3)
self.assertEqual(len(traj._explored_parameters), 2)
traj.f_shrink()
self.assertTrue(len(traj) == 1)
def test_loading_as_new(self):
filename = make_temp_dir('asnew.h5')
traj = Trajectory(name='TestPartial', filename=filename)
traj.f_add_parameter('x', 3)
traj.f_add_parameter('y', 2)
traj.f_explore({'x': [12,3,44], 'y':[1,23,4]})
traj.f_store()
traj = load_trajectory(name=traj.v_name, filename=filename)
with self.assertRaises(TypeError):
traj.f_shrink()
traj = load_trajectory(name=traj.v_name, filename=filename, as_new=True,
new_name='TestTraj', add_time=False)
self.assertTrue(traj.v_name == 'TestTraj')
self.assertTrue(len(traj) == 3)
traj.f_shrink()
self.assertTrue(len(traj) == 1)
def test_links_according_to_run(self):
traj = Trajectory()
traj.f_add_parameter('test.hi', 44)
traj.f_explore({'hi': [1, 2, 3]})
traj.f_add_parameter_group('test.test.test2')
traj.f_add_parameter_group('test2')
traj.test2.f_add_link('test', traj.test)
traj.v_idx = 1
def test_links_according_to_run(self):
traj = Trajectory()
traj.f_add_parameter('test.hi', 44)
traj.f_explore({'hi': [1,2,3]})
traj.f_add_parameter_group('test.test.test2')
traj.f_add_parameter_group('test2')
traj.test2.f_add_link('test', traj.test)
traj.v_idx = 1
def test_wildcard_search(self):
traj = Trajectory(name='Testwildcard',
filename=make_temp_dir('wilcard.hdf5'),
add_time=True)
traj.f_add_parameter('expl', 2)
traj.f_explore({'expl': [1, 2, 3, 4]})
traj.f_add_result('wc2test.$.hhh', 333)
traj.f_add_leaf('results.wctest.run_00000000.jjj', 42)
traj.f_add_result('results.wctest.run_00000001.jjj', 43)
traj.f_add_result('results.wctest.%s.jjj' % traj.f_wildcard('$', -1),
43)
traj.v_crun = 1
self.assertTrue(traj.results.wctest['$'].jjj == 43)
self.assertTrue(traj.results.wc2test.crun.hhh == 333)
traj.f_store()
get_root_logger().info('Removing child1')
traj.f_remove_child('results', recursive=True)
get_root_logger().info('Doing auto-load')
traj.v_auto_load = True
self.assertTrue(traj.results.wctest['$'].jjj == 43)
self.assertTrue(traj.results.wc2test.crun.hhh == 333)
get_root_logger().info('Removing child2')
traj.f_remove_child('results', recursive=True)
get_root_logger().info('auto-loading')
traj.v_auto_load = True
self.assertTrue(traj.results.wctest[-1].jjj == 43)
self.assertTrue(traj.results.wc2test[-1].hhh == 333)
get_root_logger().info('Removing child3')
traj.f_remove_child('results', recursive=True)
get_root_logger().info('auto-loading')
traj.v_auto_load = True
self.assertTrue(traj.results.wctest[1].jjj == 43)
self.assertTrue(traj.results.wc2test[-1].hhh == 333)
get_root_logger().info('Done with wildcard test')
def test_loading_explored_parameters(self):
filename = make_temp_dir('load_explored.hdf5')
traj = Trajectory(filename=filename, overwrite_file=True, add_time=False)
traj.par.x = Parameter('x', 42, comment='answer')
traj.f_explore({'x':[1,2,3,4]})
traj.f_store()
name = traj.v_name
traj = Trajectory(filename=filename, add_time=False)
traj.f_load()
x = traj.f_get('x')
self.assertIs(x, traj._explored_parameters['parameters.x'])
def test_file_renaming(self):
traj_name = 'test'
traj = Trajectory('test', add_time=False)
traj.f_add_parameter('x', 42)
traj.f_explore({'x': [1,2,3]})
rename_string = '$traj_$set_$run'
solution_1 = 'test_run_set_ALL_run_ALL'
solution_2 = 'test_run_set_00000_run_00000000'
renaming_1 = rename_log_file(rename_string, traj)
self.assertEqual(renaming_1, solution_1)
traj.v_idx = 0
renaming_2 = rename_log_file(rename_string, traj)
self.assertEqual(renaming_2, solution_2)
def test_loading_explored_parameters(self):
filename = make_temp_dir('load_explored.hdf5')
traj = Trajectory(filename=filename, overwrite_file=True, add_time=False)
traj.par.x = Parameter('x', 42, comment='answer')
traj.f_explore({'x':[1,2,3,4]})
traj.f_store()
name = traj.v_name
traj = Trajectory(filename=filename, add_time=False)
traj.f_load()
x = traj.f_get('x')
self.assertIs(x, traj._explored_parameters['parameters.x'])
def test_file_renaming(self):
traj_name = 'test'
traj = Trajectory('test', add_time=False)
traj.f_add_parameter('x', 42)
traj.f_explore({'x': [1,2,3]})
rename_string = '$traj_$set_$run'
solution_1 = 'test_run_set_ALL_run_ALL'
solution_2 = 'test_run_set_00000_run_00000000'
renaming_1 = rename_log_file(rename_string, traj)
self.assertEqual(renaming_1, solution_1)
traj.v_idx = 0
renaming_2 = rename_log_file(rename_string, traj)
self.assertEqual(renaming_2, solution_2)
def test_find_in_all_runs_with_links(self):
traj = Trajectory()
traj.f_add_parameter('FloatParam')
traj.par.FloatParam = 4.0
self.explore_dict = {'FloatParam': [1.0, 1.1, 1.2, 1.3]}
traj.f_explore(self.explore_dict)
self.assertTrue(len(traj) == 4)
traj.f_add_result('results.runs.run_00000000.sub.resulttest', 42)
traj.f_add_result('results.runs.run_00000001.sub.resulttest', 43)
traj.f_add_result('results.runs.run_00000002.sub.resulttest', 44)
traj.f_add_result('results.runs.run_00000002.sub.resulttest2', 42)
traj.f_add_result('results.runs.run_00000003.sub.resulttest2', 43)
traj.f_add_derived_parameter(
'derived_parameters.runs.run_00000002.testing', 44)
res_dict = traj.f_get_from_runs('resulttest', fast_access=True)
self.assertTrue(len(res_dict) == 3)
self.assertTrue(res_dict['run_00000001'] == 43)
self.assertTrue('run_00000003' not in res_dict)
res_dict = traj.f_get_from_runs(name='sub.resulttest2',
use_indices=True)
self.assertTrue(len(res_dict) == 2)
self.assertTrue(res_dict[3] is traj.f_get('run_00000003.resulttest2'))
self.assertTrue(1 not in res_dict)
traj.res.runs.r_0.f_add_link('resulttest2',
traj.r_1.f_get('resulttest'))
res_dict = traj.f_get_from_runs(name='resulttest2', use_indices=True)
self.assertTrue(len(res_dict) == 3)
self.assertTrue(res_dict[0] is traj.f_get('run_00000001.resulttest'))
self.assertTrue(1 not in res_dict)
res_dict = traj.f_get_from_runs(name='resulttest2',
use_indices=True,
with_links=False)
self.assertTrue(len(res_dict) == 2)
self.assertTrue(0 not in res_dict)
self.assertTrue(1 not in res_dict)
def test_wildcard_search(self):
traj = Trajectory(name='Testwildcard', filename=make_temp_dir('wilcard.hdf5'),
add_time=True)
traj.f_add_parameter('expl', 2)
traj.f_explore({'expl':[1,2,3,4]})
traj.f_add_result('wc2test.$.hhh', 333)
traj.f_add_leaf('results.wctest.run_00000000.jjj', 42)
traj.f_add_result('results.wctest.run_00000001.jjj', 43)
traj.f_add_result('results.wctest.%s.jjj' % traj.f_wildcard('$', -1), 43)
traj.v_crun = 1
self.assertTrue(traj.results.wctest['$'].jjj==43)
self.assertTrue(traj.results.wc2test.crun.hhh==333)
traj.f_store()
get_root_logger().info('Removing child1')
traj.f_remove_child('results', recursive=True)
get_root_logger().info('Doing auto-load')
traj.v_auto_load = True
self.assertTrue(traj.results.wctest['$'].jjj==43)
self.assertTrue(traj.results.wc2test.crun.hhh==333)
get_root_logger().info('Removing child2')
traj.f_remove_child('results', recursive=True)
get_root_logger().info('auto-loading')
traj.v_auto_load = True
self.assertTrue(traj.results.wctest[-1].jjj==43)
self.assertTrue(traj.results.wc2test[-1].hhh==333)
get_root_logger().info('Removing child3')
traj.f_remove_child('results', recursive=True)
get_root_logger().info('auto-loading')
traj.v_auto_load = True
self.assertTrue(traj.results.wctest[1].jjj==43)
self.assertTrue(traj.results.wc2test[-1].hhh==333)
get_root_logger().info('Done with wildcard test')
def test_no_run_information_loading(self):
filename = make_temp_dir('testnoruninfo.hdf5')
traj = Trajectory(name='TestDelete',
filename=filename,
add_time=True)
length = 100000
traj.par.x = Parameter('', 42)
traj.f_explore({'x': range(length)})
traj.f_store()
traj = load_trajectory(index=-1, filename=filename, with_run_information=False)
self.assertEqual(len(traj), length)
self.assertEqual(len(traj._run_information), 1)
def test_no_run_information_loading(self):
filename = make_temp_dir('testnoruninfo.hdf5')
traj = Trajectory(name='TestDelete',
filename=filename)
length = 100000
traj.v_lazy_adding = True
traj.par.x = 42
traj.f_explore({'x': range(length)})
traj.f_store()
traj = load_trajectory(index=-1, filename=filename, with_run_information=False)
self.assertEqual(len(traj), length)
self.assertEqual(len(traj._run_information), 1)
def test_find_in_all_runs_with_links(self):
traj = Trajectory()
traj.f_add_parameter('FloatParam')
traj.par.FloatParam=4.0
self.explore_dict = {'FloatParam':[1.0,1.1,1.2,1.3]}
traj.f_explore(self.explore_dict)
self.assertTrue(len(traj) == 4)
traj.f_add_result('results.runs.run_00000000.sub.resulttest', 42)
traj.f_add_result('results.runs.run_00000001.sub.resulttest', 43)
traj.f_add_result('results.runs.run_00000002.sub.resulttest', 44)
traj.f_add_result('results.runs.run_00000002.sub.resulttest2', 42)
traj.f_add_result('results.runs.run_00000003.sub.resulttest2', 43)
traj.f_add_derived_parameter('derived_parameters.runs.run_00000002.testing', 44)
res_dict = traj.f_get_from_runs('resulttest', fast_access=True)
self.assertTrue(len(res_dict)==3)
self.assertTrue(res_dict['run_00000001']==43)
self.assertTrue('run_00000003' not in res_dict)
res_dict = traj.f_get_from_runs(name='sub.resulttest2', use_indices=True)
self.assertTrue(len(res_dict)==2)
self.assertTrue(res_dict[3] is traj.f_get('run_00000003.resulttest2'))
self.assertTrue(1 not in res_dict)
traj.res.runs.r_0.f_add_link('resulttest2', traj.r_1.f_get('resulttest'))
res_dict = traj.f_get_from_runs(name='resulttest2', use_indices=True)
self.assertTrue(len(res_dict)==3)
self.assertTrue(res_dict[0] is traj.f_get('run_00000001.resulttest'))
self.assertTrue(1 not in res_dict)
res_dict = traj.f_get_from_runs(name='resulttest2', use_indices=True, with_links=False)
self.assertTrue(len(res_dict)==2)
self.assertTrue(0 not in res_dict)
self.assertTrue(1 not in res_dict)
def test_get_all_not_links(self):
traj = Trajectory()
traj.f_add_parameter('test.hi', 44)
traj.f_explore({'hi': [1, 2, 3]})
traj.f_add_parameter_group('test.test.test2')
traj.f_add_parameter_group('test2')
traj.test2.f_add_link('test', traj.test)
nodes = traj.f_get_all('par.test')
self.assertTrue(len(nodes) == 2)
nodes = traj.f_get_all('par.test', shortcuts=False)
self.assertTrue(len(nodes) == 1)
traj.f_set_crun(0)
traj.f_add_group('f.$.h')
traj.f_add_group('f.$.g.h')
traj.f_add_group('f.$.i')
traj.crun.i.f_add_link('h', traj.crun.h)
nodes = traj.f_get_all('$.h')
self.assertTrue(len(nodes) == 2)
nodes = traj.f_get_all('h')
self.assertTrue(len(nodes) == 2)
traj.v_idx = -1
nodes = traj.f_get_all('h')
self.assertTrue(len(nodes) == 2)
def test_get_all_not_links(self):
traj = Trajectory()
traj.f_add_parameter('test.hi', 44)
traj.f_explore({'hi': [1,2,3]})
traj.f_add_parameter_group('test.test.test2')
traj.f_add_parameter_group('test2')
traj.test2.f_add_link('test', traj.test)
nodes = traj.f_get_all('par.test')
self.assertTrue(len(nodes) == 2)
nodes = traj.f_get_all('par.test', shortcuts=False)
self.assertTrue(len(nodes) == 1)
traj.f_set_crun(0)
traj.f_add_group('f.$.h')
traj.f_add_group('f.$.g.h')
traj.f_add_group('f.$.i')
traj.crun.i.f_add_link('h', traj.crun.h)
nodes = traj.f_get_all('$.h')
self.assertTrue(len(nodes)==2)
nodes = traj.f_get_all('h')
self.assertTrue(len(nodes)==2)
traj.v_idx = -1
nodes = traj.f_get_all('h')
self.assertTrue(len(nodes)==2)
def main():
"""Main function to protect the *entry point* of the program."""
# Load settings from file
settings_file = 'pypet_settings.pkl'
settings = load_obj(settings_file)
# Print settings dictionary
print('\nSettings dictionary:')
for key, value in settings.items():
print(key, ' : ', value)
print('\nParameters to explore:')
for key, value in settings.items():
if isinstance(value, list):
print(key, ' : ', value)
# Create new folder to store results
traj_dir = os.getcwd()
# Read output path (if provided)
if len(sys.argv) > 1:
# Add trailing slash if missing
dir_provided = os.path.join(sys.argv[1], '')
# Check if provided directory exists
if os.path.isdir(dir_provided):
# Convert to full path
traj_dir = os.path.abspath(dir_provided)
else:
print(
'WARNING: Output path not found, current directory will be used instead'
)
else:
print(
'WARNING: Output path not provided, current directory will be used instead'
)
# Add time stamp (the final '' is to make sure there is a trailing slash)
traj_dir = os.path.join(traj_dir,
datetime.now().strftime("%Y_%m_%d_%Hh%Mm%Ss"), '')
# Create directory with time stamp
os.makedirs(traj_dir)
# Change current directory to the one containing the trajectory files
os.chdir(traj_dir)
print('Trajectory and results will be stored in: {0}'.format(traj_dir))
# Create new pypet Trajectory object
traj_filename = 'traj.hdf5'
traj_fullpath = os.path.join(traj_dir, traj_filename)
traj = Trajectory(filename=traj_fullpath)
# -------------------------------------------------------------------
# Add config parameters (those that DO NOT influence the final result of the experiment)
traj.f_add_config('debug', False, comment='Activate debug mode')
# #traj.f_add_config('max_mem_frac', 0.7, comment='Fraction of global GPU memory to use')
# Set up trajectory parameters
param_to_explore = {}
for key, val in settings.items():
if isinstance(val, list):
param_to_explore[key] = val
traj.f_add_parameter(key, val[0])
else:
traj.f_add_parameter(key, val)
# Define parameter combinations to explore (a trajectory in
# the parameter space). The second argument, the tuple, specifies the order
# of the cartesian product.
# The variable on the right most side changes fastest and defines the
# 'inner for-loop' of the cartesian product
explore_dict = cartesian_product(param_to_explore,
tuple(param_to_explore.keys()))
print(explore_dict)
traj.f_explore(explore_dict)
# Store trajectory parameters to disk
pypet_utils.print_traj_leaves(traj,
'parameters',
file=os.path.join(traj_dir,
'traj_parameters.txt'))
# Store trajectory
traj.f_store()
# Define PBS script
bash_lines = '\n'.join([
'#! /bin/bash',
'#PBS -P InfoDynFuncStruct',
'#PBS -l select=1:ncpus=1:mem=1GB',
#'#PBS -l select=1:ncpus=1:ngpus=1:mem=1GB',
'#PBS -M [email protected]',
'#PBS -m abe',
'module load java',
'module load python/3.5.1',
'module load cuda/8.0.44',
'source /project/RDS-FEI-InfoDynFuncStruct-RW/Leo/idtxl_env/bin/activate',
'cd ${traj_dir}',
'python ${python_script_path} ${traj_dir} ${traj_filename} ${file_prefix} $PBS_ARRAY_INDEX'
])
# Save PBS script file (automatically generated)
bash_script_name = 'run_python_script.pbs'
job_script_path = os.path.join(traj_dir, bash_script_name)
with open(job_script_path, 'w', newline='\n') as bash_file:
bash_file.writelines(bash_lines)
# Run job array
job_walltime_hours = 0
job_walltime_minutes = 5
#after_job_array_ends = 1573895
job_settings = {
'N': 'run_traj',
'l': 'walltime={0}:{1}:00'.format(job_walltime_hours,
job_walltime_minutes),
#'W': 'depend=afteranyarray:{0}[]'.format(after_job_array_ends),
'q': 'defaultQ'
}
if len(traj.f_get_run_names()) > 1:
job_settings['J'] = '{0}-{1}'.format(0,
len(traj.f_get_run_names()) - 1)
job_args = {
'python_script_path':
'/project/RDS-FEI-InfoDynFuncStruct-RW/Leo/inference/hpc_pypet_single_run.py',
'traj_dir': traj_dir,
'traj_filename': traj_filename,
'file_prefix': 'none'
}
run_job_array(job_script_path, job_settings, job_args)
def test_delete_whole_subtrees(self):
filename = make_temp_dir('testdeltree.hdf5')
traj = Trajectory(name='TestDelete',
filename=filename, large_overview_tables=True,
add_time=True)
res = traj.f_add_result('mytest.yourtest.test', a='b', c='d')
dpar = traj.f_add_derived_parameter('mmm.gr.dpdp', 666)
res = traj.f_add_result('hhh.ll', a='b', c='d')
res = traj.f_add_derived_parameter('hhh.gg', 555)
traj.f_store()
with pt.open_file(filename) as fh:
daroot = fh.root._f_get_child(traj.v_name)
dpar_table = daroot.overview.derived_parameters_overview
self.assertTrue(len(dpar_table) == 2)
res_table = daroot.overview.results_overview
self.assertTrue((len(res_table)) == 2)
with self.assertRaises(TypeError):
traj.f_remove_item(traj.yourtest)
with self.assertRaises(TypeError):
traj.f_delete_item(traj.yourtest)
traj.f_remove_item(traj.yourtest, recursive=True)
self.assertTrue('mytest' in traj)
self.assertTrue('yourtest' not in traj)
traj.f_load(load_data=2)
self.assertTrue('yourtest.test' in traj)
traj.f_delete_item(traj.yourtest, recursive=True, remove_from_trajectory=True)
traj.f_delete_item(traj.mmm, recursive=True, remove_from_trajectory=True)
traj.f_load(load_data=2)
self.assertTrue('yourtest.test' not in traj)
self.assertTrue('yourtest' not in traj)
with pt.open_file(filename) as fh:
daroot = fh.root._f_get_child(traj.v_name)
dpar_table = daroot.overview.derived_parameters_overview
self.assertTrue(len(dpar_table) == 2)
res_table = daroot.overview.results_overview
self.assertTrue((len(res_table)) == 2)
traj.f_add_parameter('ggg', 43)
traj.f_add_parameter('hhh.mmm', 45)
traj.f_add_parameter('jjj', 55)
traj.f_add_parameter('hhh.nnn', 55555)
traj.f_explore({'ggg':[1,2,3]})
traj.f_store()
with pt.open_file(filename) as fh:
daroot = fh.root._f_get_child(traj.v_name)
par_table = daroot.overview.parameters_overview
self.assertTrue(len(par_table) == 4)
traj.f_delete_item('par.hhh', recursive=True, remove_from_trajectory=True)
traj.f_add_parameter('saddsdfdsfd', 111)
traj.f_store()
with pt.open_file(filename) as fh:
daroot = fh.root._f_get_child(traj.v_name)
par_table = daroot.overview.parameters_overview
self.assertTrue(len(par_table) == 5)
def test_delete_whole_subtrees(self):
filename = make_temp_dir('testdeltree.hdf5')
traj = Trajectory(name='TestDelete',
filename=filename, large_overview_tables=True)
res = traj.f_add_result('mytest.yourtest.test', a='b', c='d')
dpar = traj.f_add_derived_parameter('mmm.gr.dpdp', 666)
res = traj.f_add_result('hhh.ll', a='b', c='d')
res = traj.f_add_derived_parameter('hhh.gg', 555)
traj.f_store()
with ptcompat.open_file(filename) as fh:
daroot = ptcompat.get_child(fh.root, traj.v_name)
dpar_table = daroot.overview.derived_parameters_overview
self.assertTrue(len(dpar_table) == 2)
res_table = daroot.overview.results_overview
self.assertTrue((len(res_table)) == 2)
with self.assertRaises(TypeError):
traj.f_remove_item(traj.yourtest)
with self.assertRaises(TypeError):
traj.f_delete_item(traj.yourtest)
traj.f_remove_item(traj.yourtest, recursive=True)
self.assertTrue('mytest' in traj)
self.assertTrue('yourtest' not in traj)
traj.f_load(load_data=2)
self.assertTrue('yourtest.test' in traj)
traj.f_delete_item(traj.yourtest, recursive=True, remove_from_trajectory=True)
traj.f_delete_item(traj.mmm, recursive=True, remove_from_trajectory=True)
traj.f_load(load_data=2)
self.assertTrue('yourtest.test' not in traj)
self.assertTrue('yourtest' not in traj)
with ptcompat.open_file(filename) as fh:
daroot = ptcompat.get_child(fh.root, traj.v_name)
dpar_table = daroot.overview.derived_parameters_overview
self.assertTrue(len(dpar_table) == 2)
res_table = daroot.overview.results_overview
self.assertTrue((len(res_table)) == 2)
traj.f_add_parameter('ggg', 43)
traj.f_add_parameter('hhh.mmm', 45)
traj.f_add_parameter('jjj', 55)
traj.f_add_parameter('hhh.nnn', 55555)
traj.f_explore({'ggg':[1,2,3]})
traj.f_store()
with ptcompat.open_file(filename) as fh:
daroot = ptcompat.get_child(fh.root, traj.v_name)
par_table = daroot.overview.parameters_overview
self.assertTrue(len(par_table) == 4)
traj.f_delete_item('par.hhh', recursive=True, remove_from_trajectory=True)
traj.f_add_parameter('saddsdfdsfd', 111)
traj.f_store()
with ptcompat.open_file(filename) as fh:
daroot = ptcompat.get_child(fh.root, traj.v_name)
par_table = daroot.overview.parameters_overview
self.assertTrue(len(par_table) == 5)
# with self.assertRaises(TypeError):
# # We cannot delete something containing an explored parameter
# traj.f_delete_item('par', recursive=True)
with self.assertRaises(TypeError):
traj.f_delete_item('ggg')
