def test_columns_type_mismatch(self):
numgen_spec = copy.deepcopy(self.numgen_spec)
numproc_spec = copy.deepcopy(self.numproc_spec)
numgen_spec[TaskSpecSchema.conf] = {'columns_option': 'listnotnums'}
tspec_list = [numgen_spec, numproc_spec]
tgraph_invalid = TaskGraph(tspec_list)
with self.assertRaises(LookupError) as cm:
tgraph_invalid.run(['numproc.sum'])
outerr_msg = '{}'.format(cm.exception)
errmsg = 'Task "numproc" column "list" expected type "numbers" got '\
'type "notnumbers" instead.'
self.assertIn(errmsg, outerr_msg)
def test_columns_name_mismatch(self):
numgen_spec = copy.deepcopy(self.numgen_spec)
numproc_spec = copy.deepcopy(self.numproc_spec)
numgen_spec[TaskSpecSchema.conf] = {'columns_option': 'rangenums'}
tspec_list = [numgen_spec, numproc_spec]
tgraph_invalid = TaskGraph(tspec_list)
with self.assertRaises(LookupError) as cm:
tgraph_invalid.run(['numproc.sum'])
outerr_msg = '{}'.format(cm.exception)
errmsg = 'Task "numproc" missing required column "list" from '\
'"numgen.numlist".'
self.assertIn(errmsg, outerr_msg)
def mortgage_greenflow_run(run_params_dict):
'''Using dataframe-flow runs the tasks/workflow specified in the
run_params_dict. Expected run_params_dict ex:
run_params_dict = {
'replace_spec': replace_spec,
'task_spec_list': greenflow_task_spec_list,
'out_list': out_list
}
greenflow_task_spec_list - Mortgage ETL workflow list of task-specs. Refer to
module mortgage_common function mortgage_etl_workflow_def.
out_list - Expected to specify one output which should be the final
dataframe produced by the mortgage ETL workflow.
:param run_params_dict: Dictionary with parameters and greenflow task list to
run mortgage workflow.
'''
from greenflow.dataframe_flow import TaskGraph
task_spec_list = run_params_dict['task_spec_list']
out_list = run_params_dict['out_list']
replace_spec = run_params_dict['replace_spec']
task_graph = TaskGraph(task_spec_list)
(final_perf_acq_df, ) = task_graph.run(out_list, replace_spec)
return final_perf_acq_df
def test_ports_connection_subclass_type_mismatch(self):
numgen_spec = copy.deepcopy(self.numgen_spec)
numproc_spec = copy.deepcopy(self.numproc_spec)
numgen_spec[TaskSpecSchema.conf] = {'columns_option': 'listnums'}
numproc_spec[TaskSpecSchema.conf] = {'port_type': MyList}
tspec_list = [numgen_spec, numproc_spec]
tgraph_invalid = TaskGraph(tspec_list)
with self.assertRaises(TypeError) as cm:
tgraph_invalid.run(['numproc.sum'])
outerr_msg = '{}'.format(cm.exception)
errmsg = 'Connected nodes do not have matching port types. '\
'Fix port types.'
self.assertIn(errmsg, outerr_msg)
def test_ports_output_type_mismatch(self):
numgen_spec = copy.deepcopy(self.numgen_spec)
numproc_spec = copy.deepcopy(self.numproc_spec)
numgen_spec[TaskSpecSchema.conf] = {
'columns_option': 'listnums',
'out_type': 'rangenums'
}
tspec_list = [numgen_spec, numproc_spec]
tgraph_invalid = TaskGraph(tspec_list)
with self.assertRaises(TypeError) as cm:
tgraph_invalid.run(['numproc.sum'])
outerr_msg = '{}'.format(cm.exception)
errmsg = 'Node "numgen" output port "numlist" produced wrong type '\
'"<class \'range\'>". Expected type "[<class \'list\'>]"'
self.assertEqual(errmsg, outerr_msg)
def test_columns_and_ports_types_match(self):
numgen_spec = copy.deepcopy(self.numgen_spec)
numproc_spec = copy.deepcopy(self.numproc_spec)
numgen_spec[TaskSpecSchema.conf] = {'columns_option': 'listnums'}
tspec_list = [numgen_spec, numproc_spec]
tgraph_valid = TaskGraph(tspec_list)
sumout, = tgraph_valid.run(['numproc.sum'])
self.assertEqual(sumout, 45)
def test_ports_connection_subclass_type_match(self):
numgen_spec = copy.deepcopy(self.numgen_spec)
numproc_spec = copy.deepcopy(self.numproc_spec)
numgen_spec[TaskSpecSchema.conf] = {
'port_type': MyList,
'columns_option': 'mylistnums'
}
numproc_spec[TaskSpecSchema.conf] = {'port_type': list}
tspec_list = [numgen_spec, numproc_spec]
tgraph_valid = TaskGraph(tspec_list)
sumout, = tgraph_valid.run(['numproc.sum'])
self.assertEqual(sumout, 45)
class TestTaskGraphAPI(unittest.TestCase):
def setUp(self):
import gc # python garbage collector
# warmup
s = pd.Series([1, 2, 3, None, 4])
del (s)
gc.collect()
os.environ['GREENFLOW_PLUGIN_MODULE'] = 'tests.unit.custom_port_nodes'
points_task_spec = {
TaskSpecSchema.task_id: 'points_task',
TaskSpecSchema.node_type: 'PointNode',
TaskSpecSchema.conf: {
'npts': 1000
},
TaskSpecSchema.inputs: []
}
distance_task_spec = {
TaskSpecSchema.task_id: 'distance_by_df',
TaskSpecSchema.node_type: 'DistanceNode',
TaskSpecSchema.conf: {},
TaskSpecSchema.inputs: {
'points_df_in': 'points_task.points_df_out'
}
}
tspec_list = [points_task_spec, distance_task_spec]
self.tgraph = TaskGraph(tspec_list)
# Create a temporary directory
self._test_dir = tempfile.mkdtemp()
os.environ['GREENFLOW_CACHE_DIR'] = os.path.join(
self._test_dir, '.cache')
def tearDown(self):
global DEFAULT_MODULE
os.environ['GREENFLOW_PLUGIN_MODULE'] = DEFAULT_MODULE
os.environ['GREENFLOW_CACHE_DIR'] = Node.cache_dir
shutil.rmtree(self._test_dir)
@ordered
def test_viz_graph(self):
'''Test taskgraph to networkx graph conversion for graph visualization.
'''
nx_graph = self.tgraph.viz_graph(show_ports=True)
nx_nodes = [
'points_task', 'points_task.points_df_out', 'distance_by_df',
'distance_by_df.distance_df', 'distance_by_df.distance_abs_df'
]
nx_edges = [('points_task', 'points_task.points_df_out'),
('points_task.points_df_out', 'distance_by_df'),
('distance_by_df', 'distance_by_df.distance_df'),
('distance_by_df', 'distance_by_df.distance_abs_df')]
self.assertEqual(list(nx_graph.nodes), nx_nodes)
self.assertEqual(list(nx_graph.edges), nx_edges)
@ordered
def test_build(self):
'''Test build of a taskgraph and that all inputs and outputs are set
for the tasks withink a taskgraph.
'''
self.tgraph.build()
points_node = self.tgraph['points_task']
distance_node = self.tgraph['distance_by_df']
onode_info = {
'to_node': distance_node,
'to_port': 'points_df_in',
'from_port': 'points_df_out'
}
self.assertIn(onode_info, points_node.outputs)
onode_cols = {
'points_df_out': {
'x': 'float64',
'y': 'float64'
},
'points_ddf_out': {
'x': 'float64',
'y': 'float64'
}
}
self.assertEqual(onode_cols, points_node.meta_setup().outports)
inode_info = {
'from_node': points_node,
'from_port': 'points_df_out',
'to_port': 'points_df_in'
}
self.assertIn(inode_info, distance_node.inputs)
inode_in_cols = {'points_df_in': {'x': 'float64', 'y': 'float64'}}
self.assertEqual(inode_in_cols, distance_node.get_input_meta())
inode_out_cols = {
'distance_df': {
'distance_df': 'float64',
'x': 'float64',
'y': 'float64'
},
'distance_abs_df': {
'distance_abs_df': 'float64',
'x': 'float64',
'y': 'float64'
}
}
self.assertEqual(inode_out_cols, distance_node.meta_setup().outports)
@ordered
def test_run(self):
'''Test that a taskgraph can run successfully.
'''
outlist = ['distance_by_df.distance_df']
# Using numpy random seed to get repeatable and deterministic results.
# For seed 2335 should get something around 761.062831178.
replace_spec = {
'points_task': {
TaskSpecSchema.conf: {
'npts': 1000,
'nseed': 2335
}
}
}
(dist_df_w_df, ) = self.tgraph.run(outputs=outlist,
replace=replace_spec)
dist_sum = dist_df_w_df['distance_df'].sum()
# self.assertAlmostEqual(dist_sum, 0.0, places, msg, delta)
self.assertAlmostEqual(dist_sum, 761.062831178) # match to 7 places
@ordered
def test_save(self):
'''Test that a taskgraph can be save to a yaml file.
'''
workflow_file = os.path.join(self._test_dir,
'test_save_taskgraph.yaml')
self.tgraph.save_taskgraph(workflow_file)
with open(workflow_file) as wf:
workflow_str = wf.read()
# verify the workflow contentst same as expected. Empty list if same.
global TASKGRAPH_YAML
cdiff = list(context_diff(TASKGRAPH_YAML, workflow_str))
cdiff_empty = cdiff == []
err_msg = 'Taskgraph yaml contents do not match expected results.\n'\
'SHOULD HAVE SAVED:\n\n'\
'{wyaml}\n\n'\
'INSTEAD FILE CONTAINS:\n\n'\
'{fcont}\n\n'\
'DIFF:\n\n'\
'{diff}'.format(wyaml=TASKGRAPH_YAML, fcont=workflow_str,
diff=''.join(cdiff))
self.assertTrue(cdiff_empty, err_msg)
@ordered
def test_load(self):
'''Test that a taskgraph can be loaded from a yaml file.
'''
workflow_file = os.path.join(self._test_dir,
'test_load_taskgraph.yaml')
global TASKGRAPH_YAML
with open(workflow_file, 'w') as wf:
wf.write(TASKGRAPH_YAML)
tspec_list = [task._task_spec for task in self.tgraph]
tgraph = TaskGraph.load_taskgraph(workflow_file)
all_tasks_exist = True
for task in tgraph:
if task._task_spec not in tspec_list:
all_tasks_exist = False
break
with StringIO() as yf:
yaml.dump(tspec_list,
yf,
default_flow_style=False,
sort_keys=False)
yf.seek(0)
err_msg = 'Load taskgraph failed. Missing expected task items.\n'\
'EXPECTED TASKGRAPH YAML:\n\n'\
'{wyaml}\n\n'\
'GOT TASKS FORMATTED AS YAML:\n\n'\
'{tlist}\n\n'.format(wyaml=TASKGRAPH_YAML, tlist=yf.read())
self.assertTrue(all_tasks_exist, err_msg)
@ordered
def test_save_load_cache(self):
'''Test caching of tasks outputs within a taskgraph.
1. Save points_task output to cache when running the taskgraph.
2. Load points_task df from cache when running the taskgraph.
'''
replace_spec = {'points_task': {TaskSpecSchema.save: True}}
outlist = ['distance_by_df.distance_df']
with warnings.catch_warnings():
# ignore UserWarning: Using CPU via Pandas to write HDF dataset
warnings.filterwarnings(
'ignore',
message='Using CPU via Pandas to write HDF dataset',
category=UserWarning,
)
# ignore RuntimeWarning: numpy.ufunc size changed
warnings.filterwarnings('ignore',
category=RuntimeWarning,
message='numpy.ufunc size changed')
(_, ) = self.tgraph.run(outputs=outlist, replace=replace_spec)
cache_dir = os.path.join(self._test_dir, '.cache', 'points_task.hdf5')
self.assertTrue(os.path.exists(cache_dir))
replace_spec = {'points_task': {TaskSpecSchema.load: True}}
with warnings.catch_warnings():
# ignore UserWarning: Using CPU via Pandas to read HDF dataset
warnings.filterwarnings(
'ignore',
message='Using CPU via Pandas to read HDF dataset',
category=UserWarning)
(_, ) = self.tgraph.run(outputs=outlist, replace=replace_spec)
def main():
_basedir = os.path.dirname(__file__)
# mortgage_data_path = '/datasets/rapids_data/mortgage'
mortgage_data_path = os.path.join(_basedir, 'mortgage_data')
# Using some default csv files for testing.
# csvfile_names = os.path.join(mortgage_data_path, 'names.csv')
# acq_data_path = os.path.join(mortgage_data_path, 'acq')
# perf_data_path = os.path.join(mortgage_data_path, 'perf')
# csvfile_acqdata = os.path.join(acq_data_path, 'Acquisition_2000Q1.txt')
# csvfile_perfdata = \
# os.path.join(perf_data_path, 'Performance_2000Q1.txt_0')
# mortgage_etl_workflow_def(
# csvfile_names, csvfile_acqdata, csvfile_perfdata)
greenflow_task_spec_list = mortgage_etl_workflow_def()
start_year = 2000
end_year = 2001 # end_year is inclusive
# end_year = 2016 # end_year is inclusive
# part_count = 16 # the number of data files to train against
part_count = 12 # the number of data files to train against
# part_count = 4 # the number of data files to train against
mortgage_run_params_dict_list = generate_mortgage_greenflow_run_params_list(
mortgage_data_path, start_year, end_year, part_count,
greenflow_task_spec_list)
_basedir = os.path.dirname(__file__)
mortgage_lib_module = os.path.join(_basedir, 'mortgage_greenflow_plugins.py')
mortgage_workflow_runner_task = {
TaskSpecSchema.task_id:
MortgageTaskNames.mortgage_workflow_runner_task_name,
TaskSpecSchema.node_type: 'MortgageWorkflowRunner',
TaskSpecSchema.conf: {
'mortgage_run_params_dict_list': mortgage_run_params_dict_list
},
TaskSpecSchema.inputs: [],
TaskSpecSchema.filepath: mortgage_lib_module
}
# Can be multi-gpu. Set ngpus > 1. This is different than dask xgboost
# which is distributed multi-gpu i.e. dask-xgboost could distribute on one
# node or multiple nodes. In distributed mode the dmatrix is disributed.
ngpus = 1
xgb_gpu_params = {
'nround': 100,
'max_depth': 8,
'max_leaves': 2 ** 8,
'alpha': 0.9,
'eta': 0.1,
'gamma': 0.1,
'learning_rate': 0.1,
'subsample': 1,
'reg_lambda': 1,
'scale_pos_weight': 2,
'min_child_weight': 30,
'tree_method': 'gpu_hist',
'n_gpus': ngpus,
# 'distributed_dask': True,
'loss': 'ls',
# 'objective': 'gpu:reg:linear',
'objective': 'reg:squarederror',
'max_features': 'auto',
'criterion': 'friedman_mse',
'grow_policy': 'lossguide',
'verbose': True
}
xgb_trainer_task = {
TaskSpecSchema.task_id: MortgageTaskNames.xgb_trainer_task_name,
TaskSpecSchema.node_type: 'XgbMortgageTrainer',
TaskSpecSchema.conf: {
'delete_dataframes': False,
'xgb_gpu_params': xgb_gpu_params
},
TaskSpecSchema.inputs: [
MortgageTaskNames.mortgage_workflow_runner_task_name
],
TaskSpecSchema.filepath: mortgage_lib_module
}
task_spec_list = [mortgage_workflow_runner_task, xgb_trainer_task]
task_graph = TaskGraph(task_spec_list)
# out_list = [MortgageTaskNames.mortgage_workflow_runner_task_name]
# ((mortgage_feat_df_pandas, delinq_df_pandas),) = task_graph.run(out_list)
out_list = [MortgageTaskNames.xgb_trainer_task_name]
(bst,) = task_graph.run(out_list)
print('XGBOOST BOOSTER:\n', bst)
def main():
memory_limit = 128e9
threads_per_worker = 4
cluster = LocalCUDACluster(memory_limit=memory_limit,
threads_per_worker=threads_per_worker)
client = Client(cluster)
sched_info = client.scheduler_info()
print('CLIENT: {}'.format(client))
print('SCHEDULER INFO:\n{}'.format(json.dumps(sched_info, indent=2)))
# Importing here in case RMM is used later on. Must start client prior
# to importing cudf stuff if using RMM.
from greenflow.dataframe_flow import (TaskSpecSchema, TaskGraph)
# workers_names = \
# [iw['name'] for iw in client.scheduler_info()['workers'].values()]
# nworkers = len(workers_names)
_basedir = os.path.dirname(__file__)
# mortgage_data_path = '/datasets/rapids_data/mortgage'
mortgage_data_path = os.path.join(_basedir, 'mortgage_data')
# Using some default csv files for testing.
# csvfile_names = os.path.join(mortgage_data_path, 'names.csv')
# acq_data_path = os.path.join(mortgage_data_path, 'acq')
# perf_data_path = os.path.join(mortgage_data_path, 'perf')
# csvfile_acqdata = os.path.join(acq_data_path, 'Acquisition_2000Q1.txt')
# csvfile_perfdata = \
# os.path.join(perf_data_path, 'Performance_2000Q1.txt_0')
# mortgage_etl_workflow_def(
# csvfile_names, csvfile_acqdata, csvfile_perfdata)
greenflow_task_spec_list = mortgage_etl_workflow_def()
start_year = 2000
end_year = 2001 # end_year is inclusive
# end_year = 2016 # end_year is inclusive
# part_count = 16 # the number of data files to train against
# create_dmatrix_serially - When False on same node if not enough host RAM
# then it's a race condition when creating the dmatrix. Make sure enough
# host RAM otherwise set to True.
# create_dmatrix_serially = False
# able to do 18 with create_dmatrix_serially set to True
part_count = 18 # the number of data files to train against
create_dmatrix_serially = True
# part_count = 4 # the number of data files to train against
# Use RAPIDS Memory Manager. Seems to work fine without it.
use_rmm = False
# Clean up intermediate dataframes in the xgboost training task.
delete_dataframes = True
mortgage_run_params_dict_list = generate_mortgage_greenflow_run_params_list(
mortgage_data_path, start_year, end_year, part_count,
greenflow_task_spec_list)
_basedir = os.path.dirname(__file__)
mortgage_lib_module = os.path.join(_basedir,
'mortgage_greenflow_plugins.py')
filter_dask_logger = False
mortgage_workflow_runner_task = {
TaskSpecSchema.task_id:
MortgageTaskNames.dask_mortgage_workflow_runner_task_name,
TaskSpecSchema.node_type: 'DaskMortgageWorkflowRunner',
TaskSpecSchema.conf: {
'mortgage_run_params_dict_list': mortgage_run_params_dict_list,
'client': client,
'use_rmm': use_rmm,
'filter_dask_logger': filter_dask_logger,
},
TaskSpecSchema.inputs: [],
TaskSpecSchema.filepath: mortgage_lib_module
}
dxgb_gpu_params = {
'nround': 100,
'max_depth': 8,
'max_leaves': 2**8,
'alpha': 0.9,
'eta': 0.1,
'gamma': 0.1,
'learning_rate': 0.1,
'subsample': 1,
'reg_lambda': 1,
'scale_pos_weight': 2,
'min_child_weight': 30,
'tree_method': 'gpu_hist',
'n_gpus': 1,
'distributed_dask': True,
'loss': 'ls',
# 'objective': 'gpu:reg:linear',
'objective': 'reg:squarederror',
'max_features': 'auto',
'criterion': 'friedman_mse',
'grow_policy': 'lossguide',
'verbose': True
}
dxgb_trainer_task = {
TaskSpecSchema.task_id:
MortgageTaskNames.dask_xgb_trainer_task_name,
TaskSpecSchema.node_type:
'DaskXgbMortgageTrainer',
TaskSpecSchema.conf: {
'create_dmatrix_serially': create_dmatrix_serially,
'delete_dataframes': delete_dataframes,
'dxgb_gpu_params': dxgb_gpu_params,
'client': client,
'filter_dask_logger': filter_dask_logger
},
TaskSpecSchema.inputs:
[MortgageTaskNames.dask_mortgage_workflow_runner_task_name],
TaskSpecSchema.filepath:
mortgage_lib_module
}
task_spec_list = [mortgage_workflow_runner_task, dxgb_trainer_task]
out_list = [MortgageTaskNames.dask_xgb_trainer_task_name]
task_graph = TaskGraph(task_spec_list)
(bst, ) = task_graph.run(out_list)
print('XGBOOST BOOSTER:\n', bst)