File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47428ms, 87.13% of 54435ms total Dropped 864 nodes (cum <= 272.18ms) flat flat% sum% cum cum% 0 0% 0% 54367ms 99.88% __libc_start_call_main 0 0% 0% 54367ms 99.88% __libc_start_main_impl 0 0% 0% 54367ms 99.88% _start 0 0% 0% 54351ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54351ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54351ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54351ms 99.85% main 0 0% 0% 54310ms 99.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54310ms 99.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54310ms 99.77% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54060ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 45532ms 83.64% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45496ms 83.58% MeshBasedCellPopulation::Update 0 0% 0% 25098ms 46.11% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25098ms 46.11% MeshBasedCellPopulation::TessellateIfNeeded 179ms 0.33% 0.33% 22402ms 41.15% VertexMesh::VertexMesh 0 0% 0.33% 16705ms 30.69% MutableMesh::ReMesh 0 0% 0.33% 12624ms 23.19% tetgen::tetrahedralize 2ms 0.0037% 0.33% 12488ms 22.94% tetgen::tetgenmesh::delaunizevertices 16ms 0.029% 0.36% 12483ms 22.93% tetgen::tetgenmesh::incrflipdelaunay 537ms 0.99% 1.35% 11189ms 20.55% TetrahedralMesh::EdgeIterator::operator++ 547ms 1.00% 2.35% 11076ms 20.35% tetgen::tetgenmesh::lawson 28ms 0.051% 2.40% 9260ms 17.01% std::set::insert (inline) 199ms 0.37% 2.77% 8789ms 16.15% std::_Rb_tree::_M_insert_unique 3024ms 5.56% 8.33% 8635ms 15.86% std::_Rb_tree::_M_lower_bound (inline) 350ms 0.64% 8.97% 8634ms 15.86% VertexElement::AddFace 250ms 0.46% 9.43% 8115ms 14.91% std::_Rb_tree::find (partial-inline) 0 0% 9.43% 7532ms 13.84% std::set::count (inline) 119ms 0.22% 9.65% 5480ms 10.07% std::less::operator() (inline) 5422ms 9.96% 19.61% 5423ms 9.96% std::operator< (inline) 256ms 0.47% 20.08% 5262ms 9.67% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.08% 4995ms 9.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.08% 4876ms 8.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0055% 20.08% 4856ms 8.92% AbstractNumericalMethod::ComputeForcesIncludingDamping 164ms 0.3% 20.38% 4613ms 8.47% operator new 1055ms 1.94% 22.32% 4376ms 8.04% __GI___libc_malloc 4189ms 7.70% 30.02% 4189ms 7.70% std::_Rb_tree_increment 1ms 0.0018% 30.02% 4030ms 7.40% MeshBasedCellPopulation::UpdateNodePairs 42ms 0.077% 30.10% 4018ms 7.38% std::__new_allocator::allocate (inline) 6ms 0.011% 30.11% 3996ms 7.34% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 30.11% 3995ms 7.34% std::allocator_traits::allocate (inline) 5ms 0.0092% 30.12% 3887ms 7.14% std::_Rb_tree::~_Rb_tree (inline) 11ms 0.02% 30.14% 3883ms 7.13% MeshBasedCellPopulation::SpringIterator::operator++ 1476ms 2.71% 32.85% 3881ms 7.13% std::_Rb_tree::_M_erase 0 0% 32.85% 3856ms 7.08% std::set::~set (inline) 1225ms 2.25% 35.10% 3641ms 6.69% std::_Rb_tree::_M_get_insert_unique_pos 131ms 0.24% 35.34% 3482ms 6.40% tetgen::tetgenmesh::insphere_sos 0 0% 35.34% 3388ms 6.22% AbstractCellPopulation::WriteResultsToFiles 1009ms 1.85% 37.19% 3341ms 6.14% __GI___libc_free 3072ms 5.64% 42.84% 3337ms 6.13% tetgen::insphere 7ms 0.013% 42.85% 3314ms 6.09% TetrahedralMesh::ImportFromMesher 0 0% 42.85% 3282ms 6.03% std::_Rb_tree::_M_create_node (inline) 0 0% 42.85% 3249ms 5.97% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.85% 3244ms 5.96% std::_Rb_tree::_M_get_node (inline) 36ms 0.066% 42.92% 3220ms 5.92% Node::AddElement 2ms 0.0037% 42.92% 3046ms 5.60% std::set_intersection (inline) 210ms 0.39% 43.30% 3044ms 5.59% std::__set_intersection 2342ms 4.30% 47.61% 3004ms 5.52% _int_malloc 127ms 0.23% 47.84% 2950ms 5.42% std::__new_allocator::deallocate (inline) 0 0% 47.84% 2928ms 5.38% std::allocator_traits::deallocate (inline) 2814ms 5.17% 53.01% 2814ms 5.17% std::_Rb_tree::_S_right (inline) 0 0% 53.01% 2714ms 4.99% VertexMesh::~VertexMesh 183ms 0.34% 53.35% 2565ms 4.71% tetgen::tetgenmesh::flip23 187ms 0.34% 53.69% 2394ms 4.40% std::_Rb_tree_const_iterator::operator++ (inline) 95ms 0.17% 53.86% 2338ms 4.30% MutableElement::AddNode 1188ms 2.18% 56.05% 2329ms 4.28% _int_free 2ms 0.0037% 56.05% 2274ms 4.18% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 193ms 0.35% 56.40% 2266ms 4.16% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 146ms 0.27% 56.67% 2109ms 3.87% Node::~Node 3ms 0.0055% 56.68% 2080ms 3.82% std::_Rb_tree_iterator::operator++ (inline) 160ms 0.29% 56.97% 1872ms 3.44% VertexMesh::Clear 0 0% 56.97% 1840ms 3.38% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.97% 1821ms 3.35% std::_Rb_tree::_M_put_node (inline) 1819ms 3.34% 60.31% 1819ms 3.34% std::_Rb_tree_insert_and_rebalance 163ms 0.3% 60.61% 1778ms 3.27% tetgen::tetgenmesh::flip32 4ms 0.0073% 60.62% 1693ms 3.11% Element::Element 1378ms 2.53% 63.15% 1456ms 2.67% tetgen::orient3d 1ms 0.0018% 63.15% 1366ms 2.51% Element::RegisterWithNodes (inline) 139ms 0.26% 63.41% 1280ms 2.35% TetrahedralMesh::Clear 164ms 0.3% 63.71% 1268ms 2.33% tetgen::tetgenmesh::enqueueflipface 1204ms 2.21% 65.92% 1204ms 2.21% Node::GetIndex 34ms 0.062% 65.99% 1174ms 2.16% tetgen::tetgenmesh::locate 19ms 0.035% 66.02% 1126ms 2.07% std::_Vector_base::_M_deallocate (inline) 705ms 1.30% 67.32% 1103ms 2.03% malloc_consolidate 69ms 0.13% 67.44% 1096ms 2.01% std::map::operator[] 97ms 0.18% 67.62% 1087ms 2.00% tetgen::tetgenmesh::preciselocate 0 0% 67.62% 1070ms 1.97% std::vector::~vector (inline) 70ms 0.13% 67.75% 1000ms 1.84% std::vector::_M_realloc_insert 0 0% 67.75% 959ms 1.76% std::_Rb_tree::lower_bound (inline) 0 0% 67.75% 959ms 1.76% std::map::lower_bound (inline) 1ms 0.0018% 67.75% 958ms 1.76% std::_Vector_base::~_Vector_base (inline) 5ms 0.0092% 67.76% 939ms 1.72% _int_free_maybe_consolidate 3ms 0.0055% 67.77% 888ms 1.63% VoronoiDataWriter::Visit 827ms 1.52% 69.28% 827ms 1.52% tetgen::tetgenmesh::triface::triface 113ms 0.21% 69.49% 812ms 1.49% std::vector::push_back (inline) 807ms 1.48% 70.97% 807ms 1.48% unlink_chunk 636ms 1.17% 72.14% 781ms 1.43% AbstractElement::GetNodeGlobalIndex 3ms 0.0055% 72.15% 780ms 1.43% VertexMesh::GenerateVerticesFromElementCircumcentres 7ms 0.013% 72.16% 758ms 1.39% std::_Vector_base::_M_allocate (inline) 0 0% 72.16% 746ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 386ms 0.71% 72.87% 737ms 1.35% tetgen::tetgenmesh::fnextself 1ms 0.0018% 72.87% 702ms 1.29% AbstractTwoBodyInteractionForce::AddForceContribution 21ms 0.039% 72.91% 687ms 1.26% boost::numeric::ublas::vector_assign (inline) 4ms 0.0073% 72.92% 681ms 1.25% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.033% 72.95% 660ms 1.21% AbstractTetrahedralElement::CalculateJacobian 16ms 0.029% 72.98% 658ms 1.21% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 59ms 0.11% 73.09% 658ms 1.21% __atan2 10ms 0.018% 73.11% 649ms 1.19% boost::numeric::ublas::c_vector::c_vector (inline) 642ms 1.18% 74.29% 642ms 1.18% tetgen::tetgenmesh::oppo 629ms 1.16% 75.44% 629ms 1.16% [libchaste_mesh.so] 604ms 1.11% 76.55% 604ms 1.11% tetgen::tetgenmesh::triface::operator= 476ms 0.87% 77.43% 599ms 1.10% __ieee754_atan2_fma 0 0% 77.43% 580ms 1.07% std::set::find (inline) 221ms 0.41% 77.83% 544ms 1% AbstractElement::GetNodeLocation 507ms 0.93% 78.76% 507ms 0.93% std::vector::size (inline) 491ms 0.9% 79.67% 491ms 0.9% Node::rGetLocation 50ms 0.092% 79.76% 485ms 0.89% tetgen::tetgenmesh::enextfnext 0 0% 79.76% 466ms 0.86% std::insert_iterator::operator= (inline) 52ms 0.096% 79.85% 465ms 0.85% AbstractTetrahedralElement::RefreshJacobian 315ms 0.58% 80.43% 461ms 0.85% tetgen::tetgenmesh::sym 40ms 0.073% 80.51% 457ms 0.84% tetgen::tetgenmesh::enext2fnext 0 0% 80.51% 449ms 0.82% boost::numeric::ublas::inner_prod (inline) 3ms 0.0055% 80.51% 448ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.035% 80.55% 445ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 20ms 0.037% 80.58% 444ms 0.82% Element::CalculateCircumsphere 0 0% 80.58% 424ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 19ms 0.035% 80.62% 423ms 0.78% std::_Rb_tree_iterator::operator-- (inline) 110ms 0.2% 80.82% 417ms 0.77% boost::numeric::ublas::indexing_vector_assign 397ms 0.73% 81.55% 397ms 0.73% tetgen::tetgenmesh::org 221ms 0.41% 81.95% 393ms 0.72% AbstractTetrahedralMesh::GetElement 392ms 0.72% 82.67% 392ms 0.72% AbstractElement::IsDeleted 21ms 0.039% 82.71% 390ms 0.72% VertexMesh::CalculateUnitNormalToFaceWithArea 388ms 0.71% 83.43% 388ms 0.71% boost::numeric::ublas::c_vector::operator() 31ms 0.057% 83.48% 385ms 0.71% tetgen::tetgenmesh::queue::push 383ms 0.7% 84.19% 383ms 0.7% std::_Rb_tree_decrement 0 0% 84.19% 382ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 196ms 0.36% 84.55% 374ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0018% 84.55% 367ms 0.67% Cell::GetCellId 2ms 0.0037% 84.55% 365ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 78ms 0.14% 84.70% 356ms 0.65% __dynamic_cast 3ms 0.0055% 84.70% 355ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 255ms 0.47% 85.17% 352ms 0.65% tetgen::tetgenmesh::link::add 243ms 0.45% 85.62% 337ms 0.62% tetgen::tetgenmesh::bond 4ms 0.0073% 85.62% 324ms 0.6% AbstractTetrahedralElement::AbstractTetrahedralElement 11ms 0.02% 85.64% 322ms 0.59% std::vector::insert (inline) 313ms 0.57% 86.22% 313ms 0.57% tetgen::tetgenmesh::pointmark 139ms 0.26% 86.47% 306ms 0.56% Inverse 7ms 0.013% 86.49% 300ms 0.55% VertexElement::~VertexElement 0 0% 86.49% 290ms 0.53% AbstractCellProperty::IsSubType (inline) 0 0% 86.49% 289ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 58ms 0.11% 86.59% 287ms 0.53% tetgen::tetgenmesh::queue::pop 0 0% 86.59% 284ms 0.52% tcache_get (inline) 284ms 0.52% 87.11% 284ms 0.52% tcache_get_n (inline) 7ms 0.013% 87.13% 276ms 0.51% VertexMesh::GetVolumeOfElement