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_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.
@@ -106,6 +107,8 @@ 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
@@ -159,6 +162,8 @@ 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 +179,15 @@ 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_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": [