skip benchmark with GNU error

benchmarks/benchmark_base.py

@@ -394,3 +394,22 @@ def geometry(self):
             v_inner=np.array([-1, -1], dtype=np.float64),
             v_outer=np.array([-1, -1], dtype=np.float64),
         )
+
+
+    @property
+    def estimators(self):
+        return radfield_mc_estimators.RadiationFieldMCEstimators(
+            j_estimator=np.array([0.0, 0.0], dtype=np.float64),
+            nu_bar_estimator=np.array([0.0, 0.0], dtype=np.float64),
+            j_blue_estimator=np.array(
+                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], dtype=np.float64
+            ),
+            Edotlu_estimator=np.array(
+                [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0]], dtype=np.float64
+            ),
+            photo_ion_estimator=np.empty((0, 0), dtype=np.float64),
+            stim_recomb_estimator=np.empty((0, 0), dtype=np.float64),
+            bf_heating_estimator=np.empty((0, 0), dtype=np.float64),
+            stim_recomb_cooling_estimator=np.empty((0, 0), dtype=np.float64),
+            photo_ion_estimator_statistics=np.empty((0, 0), dtype=np.int64),
+        )

benchmarks/run_tardis.py

@@ -4,8 +4,6 @@
 
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis import run_tardis
-from tardis.io.configuration.config_reader import Configuration
-
 
 class BenchmarkRunTardis(BenchmarkBase):
     """
@@ -14,12 +12,8 @@ class BenchmarkRunTardis(BenchmarkBase):
 
     def __init__(self):
         super().__init__()
-        self.config = None
-
-    def setup(self):
         filename = "data/tardis_configv1_benchmark.yml"
-        path = self.get_relative_path(filename)
-        self.config = Configuration.from_yaml(path)
+        self.path = self.get_relative_path(filename)
 
     def time_run_tardis(self):
-        run_tardis(self.config, log_level="ERROR", show_progress_bars=False)
+        run_tardis(self.path, log_level="ERROR", show_progress_bars=False)

benchmarks/transport_geometry_calculate_distances.py

@@ -14,18 +14,9 @@ class BenchmarkTransportGeometryCalculateDistances(BenchmarkBase):
     def model(self):
         return 5.2e7
 
-    @parameterize(
-        {
-            "Packet params": [
-                {"mu": 0.3, "r": 7.5e14},
-                {"mu": -0.3, "r": 7.5e13},
-                {"mu": -0.3, "r": 7.5e14},
-            ]
-        }
-    )
-    def time_calculate_distance_boundary(self, packet_params):
-        mu = packet_params["mu"]
-        r = packet_params["r"]
+    def time_calculate_distance_boundary(self):
+        mu = 0.3
+        r = 7.5e14
 
         calculate_distances.calculate_distance_boundary(
             r, mu, self.geometry.r_inner[0], self.geometry.r_outer[0]

benchmarks/transport_montecarlo_numba_formal_integral_p.py

@@ -12,7 +12,8 @@
 from tardis.io.configuration.config_reader import Configuration
 from tardis.model.geometry.radial1d import NumbaRadial1DGeometry
 
-
+# Error in all functions: Terminating: fork() called from a process already using GNU OpenMP, this is unsafe. 
+@skip_benchmark
 class BenchmarkMontecarloMontecarloNumbaNumbaFormalIntegral(BenchmarkBase):
     """
     Class to benchmark the numba formal integral function.
@@ -53,16 +54,14 @@ def __init__(self):
     def time_intensity_black_body(self, parameters):
         nu = parameters["nu"]
         temperature = parameters["temperature"]
-        func = formal_integral.intensity_black_body
-        func(nu, temperature)
+        formal_integral.intensity_black_body(nu, temperature)
 
     @parameterize({"N": (1e2, 1e3, 1e4, 1e5)})
     def time_trapezoid_integration(self, n):
-        func = formal_integral.trapezoid_integration
         h = 1.0
         data = np.random.random(int(n))
 
-        func(data, h)
+        formal_integral.trapezoid_integration(data, h)
 
     @staticmethod
     def calculate_z(r, p):
@@ -106,6 +105,8 @@ def time_explosion(self):
         # time taken for a photon to move 1 cm
         return 1 / c.c.cgs.value
 
+    # Error: Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
+    @skip_benchmark
     @parameterize({"p": [0.0, 0.5, 1.0], "Test data": TESTDATA})
     def time_calculate_z(self, p, test_data):
         func = formal_integral.calculate_z
@@ -121,15 +122,14 @@ def time_populate_z_photosphere(self, p, test_data):
         formal_integral.FormalIntegrator(
             self.formal_integral_geometry(test_data), None, None
         )
-        func = formal_integral.populate_z
         r_inner = self.formal_integral_geometry(test_data).r_inner
         self.formal_integral_geometry(test_data).r_outer
 
         p = r_inner[0] * p
         oz = np.zeros_like(r_inner)
         oshell_id = np.zeros_like(oz, dtype=np.int64)
 
-        func(
+        formal_integral.populate_z(
             self.formal_integral_geometry(test_data),
             self.formal_integral_geometry(test_data),
             p,
@@ -159,6 +159,8 @@ def time_populate_z_shells(self, p, test_data) -> None:
             oshell_id,
         )
 
+    # Error: Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
+    @skip_benchmark
     @parameterize(
         {
             "Parameters": [
@@ -174,13 +176,15 @@ def time_calculate_p_values(self, Parameters):
 
     # Benchmark for functions in FormalIntegrator class
 
+    # Error: Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
+    @skip_benchmark  
     def time_FormalIntegrator_functions(self):
         self.FormalIntegrator.calculate_spectrum(
             self.Simulation.transport.transport_state.spectrum.frequency
         )
         self.FormalIntegrator.make_source_function()
         self.FormalIntegrator.generate_numba_objects()
         self.FormalIntegrator.formal_integral(
-            self.Simulation.transport.transport_state.spectrum.frequency, 
+            self.Simulation.transport.transport_state.spectrum.frequency,
             1000
         )

benchmarks/transport_montecarlo_numba_interface.py

@@ -23,72 +23,4 @@ def time_opacity_state_initialize(self, input_params):
             line_interaction_type,
             self.verysimple_disable_line_scattering,
             self.verysimple_continuum_processes_enabled,
-        )
-
-
-    @parameterize(
-        {
-            "parameters": [
-                {
-                    "nus": [3.0e15, 0.0, 1e15, 1e5],
-                    "energies": [0.4, 0.1, 0.6, 1e10],
-                    "initial_mus": [0.1, 0, 1, 0.9],
-                    "initial_rs": [3e42, 4.5e45, 0, 9.0e40],
-                    "last_interaction_in_nus": np.array(
-                        [3.0e15, 0.0, 1e15, 1e5], dtype=np.float64
-                    ),
-                    "last_interaction_types": np.array([1, 1, 3, 2], dtype=np.int64),
-                    "last_interaction_in_ids": np.array([100, 0, 1, 1000], dtype=np.int64),
-                    "last_interaction_out_ids": np.array(
-                        [1201, 123, 545, 1232], dtype=np.int64
-                    ),
-                    "last_interaction_shell_ids": np.array([2, -1, 6, 0], dtype=np.int64)
-                }
-            ]
-        }
-    )
-    def time_VPacketCollection_add_packet(self, parameters):
-        verysimple_3vpacket_collection = self.verysimple_3vpacket_collection
-
-        nus = parameters["nus"]
-        energies = parameters["energies"]
-        initial_mus = parameters["initial_mus"]
-        initial_rs = parameters["initial_rs"]
-        last_interaction_in_nus = parameters["last_interaction_in_nus"]
-        last_interaction_types = parameters["last_interaction_types"]
-        last_interaction_in_ids = parameters["last_interaction_in_ids"]
-        last_interaction_out_ids = parameters["last_interaction_out_ids"]
-        last_interaction_shell_ids = parameters["last_interaction_shell_ids"]
-
-        for (
-            nu,
-            energy,
-            initial_mu,
-            initial_r,
-            last_interaction_in_nu,
-            last_interaction_type,
-            last_interaction_in_id,
-            last_interaction_out_id,
-            last_interaction_shell_id,
-        ) in zip(
-            nus,
-            energies,
-            initial_mus,
-            initial_rs,
-            last_interaction_in_nus,
-            last_interaction_types,
-            last_interaction_in_ids,
-            last_interaction_out_ids,
-            last_interaction_shell_ids,
-        ):
-            verysimple_3vpacket_collection.add_packet(
-                nu,
-                energy,
-                initial_mu,
-                initial_r,
-                last_interaction_in_nu,
-                last_interaction_type,
-                last_interaction_in_id,
-                last_interaction_out_id,
-                last_interaction_shell_id,
-            )
+        )

benchmarks/transport_montecarlo_opacities.py

@@ -89,16 +89,3 @@ def time_pair_creation_opacity_calculation(
         calculate_opacity.pair_creation_opacity_calculation(
             energy, ejecta_density, iron_group_fraction
         )
-
-    @parameterize(
-        {
-            "Energy": [
-                511.0, 
-                255.5, 
-                0.0, 
-                511.0e7,
-            ]
-        }
-    )
-    def time_kappa_calculation(self, energy):
-        calculate_opacity.kappa_calculation(energy)

benchmarks/transport_montecarlo_packet.py

@@ -23,24 +23,6 @@ class BenchmarkMontecarloMontecarloNumbaPacket(BenchmarkBase):
     Class to benchmark the numba packet function.
     """
 
-    @property
-    def estimators(self):
-        return radfield_mc_estimators.RadiationFieldMCEstimators(
-            j_estimator=np.array([0.0, 0.0], dtype=np.float64),
-            nu_bar_estimator=np.array([0.0, 0.0], dtype=np.float64),
-            j_blue_estimator=np.array(
-                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], dtype=np.float64
-            ),
-            Edotlu_estimator=np.array(
-                [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0]], dtype=np.float64
-            ),
-            photo_ion_estimator=np.empty((0, 0), dtype=np.float64),
-            stim_recomb_estimator=np.empty((0, 0), dtype=np.float64),
-            bf_heating_estimator=np.empty((0, 0), dtype=np.float64),
-            stim_recomb_cooling_estimator=np.empty((0, 0), dtype=np.float64),
-            photo_ion_estimator_statistics=np.empty((0, 0), dtype=np.int64),
-        )
-
     @parameterize(
         {
             "Parameters": [

benchmarks/transport_montecarlo_single_packet_loop.py

@@ -4,20 +4,22 @@
 
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.transport.montecarlo import single_packet_loop
+from asv_runner.benchmarks.mark import skip_benchmark
 
 
 class BenchmarkMontecarloMontecarloNumbaVpacket(BenchmarkBase):
     """
     Class to benchmark the single packet loop function.
     """
 
+    @skip_benchmark
     def time_single_packet_loop(self):
         single_packet_loop.single_packet_loop(
             self.packet,
             self.verysimple_numba_radial_1d_geometry,
             self.verysimple_time_explosion,
             self.verysimple_opacity_state,
-            self.verysimple_radfield_mc_estimators,
+            self.estimators,
             self.verysimple_packet_collection,
             self.rpacket_tracker,
             self.montecarlo_configuration

benchmarks/transport_montecarlo_vpacket.py

@@ -3,7 +3,7 @@
 """
 
 import numpy as np
-from asv_runner.benchmarks.mark import parameterize
+from asv_runner.benchmarks.mark import parameterize, skip_benchmark
 
 import tardis.transport.montecarlo.vpacket as vpacket
 from benchmarks.benchmark_base import BenchmarkBase
@@ -144,6 +144,7 @@ def time_trace_bad_vpacket(self):
             continuum_processes_enabled,
         )
 
+    @skip_benchmark
     @parameterize(
         {
             "Paramters": [