Invalid Memory Access for 'fsils' Assembly Type in Trilinos Linear Algebra (addresses SimVascular#470) (SimVascular#471)

dcodoni · web-flow · commit 3e2e2bab88c2 · 2025-11-10T17:14:29.000-08:00
* Fixed the segmentation fault on the fsils assembly type in the trilinos implementation.
* nnzPerRow variables was used in assembly but was not created before
* correctly creating nnzPerRow using unsorted order

* Added integration test case ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos to test 'fsils' assembly type when using trilinos library

* Adding default for krylov space dimension for CG adn BICGS linear solver types
diff --git a/Code/Source/liner_solver/ls.cpp b/Code/Source/liner_solver/ls.cpp
@@ -34,18 +34,20 @@ void fsils_ls_create(FSILS_lsType& ls, LinearSolverType LS_type, double relTol,
 
     case LinearSolverType::LS_TYPE_GMRES:
       ls.RI.relTol = 0.1;
-      ls.RI.mItr   = 4;
+      ls.RI.mItr   = 1000;
       ls.RI.sD     = 250;
     break;
 
     case LinearSolverType::LS_TYPE_CG:
       ls.RI.relTol = 1.E-2;
       ls.RI.mItr   = 1000;
+      ls.RI.sD     = 250;
     break;
 
     case LinearSolverType::LS_TYPE_BICGS:
       ls.RI.relTol = 1.E-2;
-      ls.RI.mItr   = 500;
+      ls.RI.mItr   = 1000;
+      ls.RI.sD     = 250;
     break;
 
     default:
diff --git a/Code/Source/solver/trilinos_impl.cpp b/Code/Source/solver/trilinos_impl.cpp
@@ -159,6 +159,9 @@ void trilinos_lhs_create(const Teuchos::RCP<Trilinos> &trilinos_, const int numG
   globalDofGIDs.reserve(numGhostAndLocalNodes * dof);
   globalGhostDofGIDs.reserve(numGhostAndLocalNodes * dof); 
 
+  nnzPerRow.clear (); // for fsils assembly
+  nnzPerRow.reserve(numGhostAndLocalNodes);
+
   // Define localtoglobal to be used for unqiue partition map
   //only take ltgSorted(1:numLocalNodes) since those are owned by the processor
   //
@@ -179,6 +182,7 @@ void trilinos_lhs_create(const Teuchos::RCP<Trilinos> &trilinos_, const int numG
     {
       globalGhostDofGIDs.emplace_back(ltgSorted[i] * dof + d);
     }
+    nnzPerRow.emplace_back(rowPtr[i+1] - rowPtr[i]);
   }
 
   /*
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/endo_pressure.dat b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/endo_pressure.dat
@@ -0,0 +1,3 @@
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+size 20865
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/fibersLongCells.vtu b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/fibersLongCells.vtu
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diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/fibersSheetCells.vtu b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/fibersSheetCells.vtu
@@ -0,0 +1,3 @@
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+size 99744
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-complete.exterior.vtp b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-complete.exterior.vtp
@@ -0,0 +1,3 @@
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+size 19832
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-complete.mesh.vtu b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-complete.mesh.vtu
@@ -0,0 +1,3 @@
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+size 27192
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-surfaces/endo.vtp b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-surfaces/endo.vtp
@@ -0,0 +1,3 @@
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+size 10038
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-surfaces/epi.vtp b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-surfaces/epi.vtp
@@ -0,0 +1,3 @@
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+size 11982
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-surfaces/top.vtp b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/mesh/mesh-surfaces/top.vtp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 3940
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/result_001.vtu b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/result_001.vtu
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fda0ce16348dd0d7e46f8fc3fd98dc68b71ec3d3c8363705656cfbfc7e8a1f71
+size 256530
diff --git a/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/solver.xml b/tests/cases/ustruct/LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos/solver.xml
@@ -0,0 +1,114 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<svMultiPhysicsFile version="0.1">
+
+<GeneralSimulationParameters>
+  <Continue_previous_simulation> 0 </Continue_previous_simulation>
+  <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions> 
+  <Number_of_time_steps> 1 </Number_of_time_steps> 
+  <Time_step_size> 1e-2 </Time_step_size> 
+  <Spectral_radius_of_infinite_time_step> 0.50 </Spectral_radius_of_infinite_time_step> 
+  <Searched_file_name_to_trigger_stop> STOP_SIM </Searched_file_name_to_trigger_stop> 
+
+  <Save_results_to_VTK_format> 1 </Save_results_to_VTK_format> 
+  <Name_prefix_of_saved_VTK_files> result </Name_prefix_of_saved_VTK_files> 
+  <!-- <Save_results_in_folder> results_svfsiplus </Save_results_in_folder> -->
+  <Increment_in_saving_VTK_files> 1 </Increment_in_saving_VTK_files> 
+  <Start_saving_after_time_step> 1 </Start_saving_after_time_step> 
+
+  <Increment_in_saving_restart_files> 50 </Increment_in_saving_restart_files> 
+  <Convert_BIN_to_VTK_format> 0 </Convert_BIN_to_VTK_format> 
+
+  <Verbose> 1 </Verbose> 
+  <Warning> 1 </Warning> 
+  <Debug> 1 </Debug> 
+
+</GeneralSimulationParameters>
+
+<Add_mesh name="msh" > 
+
+  <Mesh_file_path> mesh/mesh-complete.mesh.vtu </Mesh_file_path>
+
+  <Add_face name="endo">
+      <Face_file_path> mesh/mesh-surfaces/endo.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="epi">
+      <Face_file_path> mesh/mesh-surfaces/epi.vtp </Face_file_path>
+  </Add_face>
+
+  <Add_face name="top">
+      <Face_file_path> mesh/mesh-surfaces/top.vtp </Face_file_path>
+  </Add_face>
+
+  <Fiber_direction_file_path> mesh/fibersLongCells.vtu </Fiber_direction_file_path>
+  <Fiber_direction_file_path> mesh/fibersSheetCells.vtu </Fiber_direction_file_path>
+
+  <Mesh_scale_factor> 100.0 </Mesh_scale_factor> <!-- Convert from m to cm -->
+</Add_mesh>
+
+
+<Add_equation type="ustruct" > 
+   <Coupled> true </Coupled>
+   <Min_iterations> 3 </Min_iterations>  
+   <Max_iterations> 20 </Max_iterations> 
+   <Tolerance> 1e-10 </Tolerance> 
+
+   <Density> 1.0 </Density>                           <!-- g/cm^3 -->
+   <Elasticity_modulus> 1.0e6 </Elasticity_modulus>   <!-- dyne/cm^2 -->
+   <Poisson_ratio> 0.483333 </Poisson_ratio>
+   
+    <Constitutive_model type="HolzapfelOgden-ModifiedAnisotropy"> 
+     <a> 590.0 </a>                                   <!-- dyne/cm^2 -->
+     <b> 8.023 </b>                                   <!-- no units -->
+     <a4f> 184720.0 </a4f>
+     <b4f> 16.026 </b4f>
+     <a4s> 24810.0 </a4s>
+     <b4s> 11.12 </b4s>
+     <afs> 2160.0 </afs>
+     <bfs> 11.436 </bfs>
+     <k> 100.0 </k>
+   </Constitutive_model>
+
+   <Dilational_penalty_model> ST91 </Dilational_penalty_model>
+   <Penalty_parameter>1.0e7</Penalty_parameter>
+
+   <Output type="Spatial" >
+     <Pressure> true </Pressure>
+     <Displacement> true </Displacement>
+     <Velocity> true </Velocity>
+     <Jacobian> true </Jacobian>
+     <Stress> true </Stress>
+     <Strain> true </Strain>
+     <Cauchy_stress> true </Cauchy_stress>
+     <Def_grad> true </Def_grad>
+     <VonMises_stress> true </VonMises_stress>
+   </Output>
+
+   <LS type="GMRES" >
+      <Linear_algebra type="trilinos" >
+         <Preconditioner> trilinos-riluk0 </Preconditioner>
+         <Assembly> fsils </Assembly>
+      </Linear_algebra>
+      <Tolerance> 1e-14 </Tolerance>
+      <Max_iterations> 10000 </Max_iterations> 
+      <Krylov_space_dimension> 300 </Krylov_space_dimension>
+   </LS>
+
+   <Add_BC name="top" > 
+      <Type> Dirichlet </Type> 
+      <Value> 0.0 </Value>
+   </Add_BC> 
+
+   <Add_BC name="endo" > 
+      <Type> Neu </Type> 
+      <Time_dependence> Unsteady </Time_dependence> 
+      <Temporal_values_file_path> endo_pressure.dat </Temporal_values_file_path> 
+      <Ramp_function> false </Ramp_function> 
+      <Follower_pressure_load> true </Follower_pressure_load> 
+   </Add_BC> 
+
+</Add_equation>
+
+</svMultiPhysicsFile>
+
+
diff --git a/tests/test_ustruct.py b/tests/test_ustruct.py
@@ -46,6 +46,10 @@ def test_LV_HolzapfelOgdenModifiedAnisotropy_passive(n_proc):
     test_folder = "LV_HolzapfelOgdenModifiedAnisotropy_passive"
     run_with_reference(base_folder, test_folder, fields, n_proc)
 
+def test_LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos(n_proc):
+    test_folder = "LV_HolzapfelOgdenModifiedAnisotropy_passive_trilinos"
+    run_with_reference(base_folder, test_folder, fields, n_proc)
+
 def test_LV_NeoHookean_passive_genBC(n_proc):
     test_folder = "LV_NeoHookean_passive_genBC"
 

Original file line number	Diff line number	Diff line change
`@@ -159,6 +159,9 @@ void trilinos_lhs_create(const Teuchos::RCP<Trilinos> &trilinos_, const int numG`
`159`	`159`	`globalDofGIDs.reserve(numGhostAndLocalNodes * dof);`
`160`	`160`	`globalGhostDofGIDs.reserve(numGhostAndLocalNodes * dof);`
`161`	`161`
	`162`	`+ nnzPerRow.clear (); // for fsils assembly`
	`163`	`+ nnzPerRow.reserve(numGhostAndLocalNodes);`
	`164`	`+`
`162`	`165`	`// Define localtoglobal to be used for unqiue partition map`
`163`	`166`	`//only take ltgSorted(1:numLocalNodes) since those are owned by the processor`
`164`	`167`	`//`
`@@ -179,6 +182,7 @@ void trilinos_lhs_create(const Teuchos::RCP<Trilinos> &trilinos_, const int numG`
`179`	`182`	`{`
`180`	`183`	`globalGhostDofGIDs.emplace_back(ltgSorted[i] * dof + d);`
`181`	`184`	`}`
	`185`	`+ nnzPerRow.emplace_back(rowPtr[i+1] - rowPtr[i]);`
`182`	`186`	`}`
`183`	`187`
`184`	`188`	`/*`
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