Fix t8code ocassionally segfaults (#2043)

* Adding explicit finalizing calls in elixirs. * Wrapping forest commit call in disabled GC. * Applying formater. --------- Co-authored-by: Johannes Markert <[email protected]> Co-authored-by: Andrew Winters <[email protected]>
trixi-framework · Aug 23, 2024 · 90eebb0 · 90eebb0
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diff --git a/examples/t8code_2d_dgsem/elixir_advection_amr_solution_independent.jl b/examples/t8code_2d_dgsem/elixir_advection_amr_solution_independent.jl
@@ -139,3 +139,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl
@@ -78,3 +78,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             save_everystep = false, callback = callbacks);
 
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_advection_basic.jl b/examples/t8code_2d_dgsem/elixir_advection_basic.jl
@@ -55,3 +55,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
 
 # Print the timer summary
 summary_callback()
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_advection_nonconforming_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_nonconforming_flag.jl
@@ -85,3 +85,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
 
 # Print the timer summary
 summary_callback()
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl
@@ -71,3 +71,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
 
 # Print the timer summary.
 summary_callback()
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl b/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl
@@ -85,3 +85,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_euler_sedov.jl b/examples/t8code_2d_dgsem/elixir_euler_sedov.jl
@@ -93,3 +93,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_euler_shockcapturing_ec.jl b/examples/t8code_2d_dgsem/elixir_euler_shockcapturing_ec.jl
@@ -64,3 +64,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl
@@ -85,3 +85,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl b/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl
@@ -72,3 +72,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
 println("Number of gravity subcycles: ", semi.gravity_counter.ncalls_since_readout)
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/t8code_2d_dgsem/elixir_mhd_alfven_wave.jl
@@ -57,3 +57,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl b/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl
@@ -124,3 +124,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_2d_dgsem/elixir_shallowwater_source_terms.jl b/examples/t8code_2d_dgsem/elixir_shallowwater_source_terms.jl
@@ -55,3 +55,7 @@ callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback)
 sol = solve(ode, RDPK3SpFSAL49(); abstol = 1.0e-8, reltol = 1.0e-8,
             ode_default_options()..., callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_advection_amr.jl b/examples/t8code_3d_dgsem/elixir_advection_amr.jl
@@ -64,3 +64,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl b/examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl
@@ -95,3 +95,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_advection_basic.jl b/examples/t8code_3d_dgsem/elixir_advection_basic.jl
@@ -57,3 +57,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
 
 # Print the timer summary
 summary_callback()
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_advection_nonconforming.jl b/examples/t8code_3d_dgsem/elixir_advection_nonconforming.jl
@@ -83,3 +83,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
 
 # Print the timer summary
 summary_callback()
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl b/examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl
@@ -88,3 +88,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
 
 # Print the timer summary
 summary_callback()
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_euler_ec.jl b/examples/t8code_3d_dgsem/elixir_euler_ec.jl
@@ -82,3 +82,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_euler_free_stream.jl b/examples/t8code_3d_dgsem/elixir_euler_free_stream.jl
@@ -108,3 +108,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_euler_free_stream_extruded.jl b/examples/t8code_3d_dgsem/elixir_euler_free_stream_extruded.jl
@@ -96,3 +96,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), #maxiters=1
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_euler_sedov.jl b/examples/t8code_3d_dgsem/elixir_euler_sedov.jl
@@ -95,3 +95,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl b/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl
@@ -110,3 +110,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonperiodic.jl b/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonperiodic.jl
@@ -60,3 +60,7 @@ sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
+
+# Finalize `T8codeMesh` to make sure MPI related objects in t8code are
+# released before `MPI` finalizes.
+!isinteractive() && finalize(mesh)
diff --git a/src/meshes/t8code_mesh.jl b/src/meshes/t8code_mesh.jl
@@ -731,9 +731,14 @@ function adapt!(mesh::T8codeMesh, adapt_callback; recursive = true, balance = tr
 
         t8_forest_set_ghost(new_forest, ghost, T8_GHOST_FACES) # Note: MPI support not available yet so it is a dummy call.
 
+        # Julias's GC leads to random segfaults here. Temporarily switch it off.
+        GC.enable(false)
+
         # The old forest is destroyed here.
         # Call `t8_forest_ref(Ref(mesh.forest))` to keep it.
         t8_forest_commit(new_forest)
+
+        GC.enable(true)
     end
 
     mesh.forest = new_forest