Added start method to parallelization

main_package/classes/estimators/structure_constraint_based_estimator.py

@@ -24,6 +24,7 @@ from utility.decorators import timing,timing_write
 import multiprocessing
 from multiprocessing import Pool
 
+from multiprocessing import get_context
 
 class StructureConstraintBasedEstimator(se.StructureEstimator):
     """
@@ -241,7 +242,9 @@ class StructureConstraintBasedEstimator(se.StructureEstimator):
         self.sample_path.structure.clean_structure_edges()
 
         'Estimate the best parents for each node'
-        with multiprocessing.Pool(processes=cpu_count) as pool:
+        #with multiprocessing.Pool(processes=cpu_count) as pool:
+        with get_context("spawn").Pool(processes=cpu_count) as pool:
+        
             list_edges_partial = pool.starmap(ctpc_algo, zip(
                                                                  self.nodes,
                                                                  total_vars_numb_array))

main_package/classes/estimators/structure_score_based_estimator.py

@@ -24,6 +24,7 @@ import optimizers.tabu_search as tabu
 
 from utility.decorators import timing,timing_write
 
+from multiprocessing import get_context
 
 
 #from numba import njit
@@ -92,7 +93,8 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
             cpu_count = 1
 
         'Estimate the best parents for each node'
-        with multiprocessing.Pool(processes=cpu_count) as pool:
+        with get_context("spawn").Pool(processes=cpu_count) as pool:
+        #with multiprocessing.Pool(processes=cpu_count) as pool:
             list_edges_partial = pool.starmap(estimate_parents, zip(
                                                                 self.nodes,
                                                                 l_max_parents,

main_package/tests/estimators/test_structure_constraint_based_estimator.py

@@ -15,6 +15,8 @@ import structure_graph.sample_path as sp
 import estimators.structure_constraint_based_estimator as se
 import utility.json_importer as ji
 
+from multiprocessing import set_start_method
+
 import copy
 
 
@@ -22,7 +24,7 @@ class TestStructureConstraintBasedEstimator(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         #cls.read_files = glob.glob(os.path.join('../../data', "*.json"))
-        cls.importer = ji.JsonImporter("../../data/networks_and_trajectories_ternary_data_15.json", 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        cls.importer = ji.JsonImporter("../../data/networks_and_trajectories_ternary_data_15.json", 'samples', 'dyn.str', 'variables', 'Time', 'Name',1)
         cls.s1 = sp.SamplePath(cls.importer)
         cls.s1.build_trajectories()
         cls.s1.build_structure()
@@ -31,6 +33,7 @@ class TestStructureConstraintBasedEstimator(unittest.TestCase):
         true_edges = copy.deepcopy(self.s1.structure.edges)
         true_edges = set(map(tuple, true_edges))
 
+        set_start_method("spawn")
         se1 = se.StructureConstraintBasedEstimator(self.s1,0.1,0.1)
         edges = se1.estimate_structure(disable_multiprocessing=False)
         

main_package/tests/estimators/test_structure_score_based_estimator.py

@@ -16,6 +16,9 @@ import structure_graph.sample_path as sp
 import estimators.structure_score_based_estimator as se
 import utility.json_importer as ji
 
+from multiprocessing import set_start_method
+
+
 
 
 class TestStructureScoreBasedEstimator(unittest.TestCase):
@@ -23,7 +26,7 @@ class TestStructureScoreBasedEstimator(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         #cls.read_files = glob.glob(os.path.join('../../data', "*.json"))
-        cls.importer = ji.JsonImporter("../../data/networks_and_trajectories_binary_data_01_3.json", 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        cls.importer = ji.JsonImporter("../../data/networks_and_trajectories_ternary_data_15.json", 'samples', 'dyn.str', 'variables', 'Time', 'Name')
         cls.s1 = sp.SamplePath(cls.importer)
         cls.s1.build_trajectories()
         cls.s1.build_structure()
@@ -34,12 +37,17 @@ class TestStructureScoreBasedEstimator(unittest.TestCase):
         true_edges = copy.deepcopy(self.s1.structure.edges)
         true_edges = set(map(tuple, true_edges))
 
+        set_start_method("spawn")
         se1 = se.StructureScoreBasedEstimator(self.s1)
         edges = se1.estimate_structure(
-                            max_parents = None,
-                            iterations_number = 100,
-                            patience = None
-                            )
+                                    max_parents = None,
+                                    iterations_number = 100,
+                                    patience = 35,
+                                    tabu_length = 15,
+                                    tabu_rules_duration = 15,
+                                    optimizer = 'tabu',
+                                    disable_multiprocessing=False
+                                    )
         
 
         self.assertEqual(edges, true_edges)

main_package/tests/optimizers/test_tabu_search.py

@@ -42,7 +42,8 @@ class TestTabuSearch(unittest.TestCase):
                             patience = None,
                             tabu_length = 15,
                             tabu_rules_duration = 15,
-                            optimizer = 'tabu'
+                            optimizer = 'tabu',
+                            disable_multiprocessing=True
                             )