File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49758ms, 86.32% of 57643ms total Dropped 874 nodes (cum <= 288.21ms) flat flat% sum% cum cum% 0 0% 0% 57591ms 99.91% __libc_start_call_main 0 0% 0% 57591ms 99.91% __libc_start_main_impl 0 0% 0% 57591ms 99.91% _start 0 0% 0% 57577ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57577ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57577ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57577ms 99.89% main 0 0% 0% 57538ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57538ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57538ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57275ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 48499ms 84.14% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48463ms 84.07% MeshBasedCellPopulation::Update 0 0% 0% 27729ms 48.10% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27729ms 48.10% MeshBasedCellPopulation::TessellateIfNeeded 201ms 0.35% 0.35% 24477ms 42.46% VertexMesh::VertexMesh 0 0% 0.35% 17015ms 29.52% MutableMesh::ReMesh 0 0% 0.35% 12948ms 22.46% tetgen::tetrahedralize 7ms 0.012% 0.36% 12806ms 22.22% tetgen::tetgenmesh::delaunizevertices 5ms 0.0087% 0.37% 12793ms 22.19% tetgen::tetgenmesh::incrflipdelaunay 557ms 0.97% 1.34% 11468ms 19.89% TetrahedralMesh::EdgeIterator::operator++ 583ms 1.01% 2.35% 11384ms 19.75% tetgen::tetgenmesh::lawson 29ms 0.05% 2.40% 9862ms 17.11% std::set::insert (inline) 197ms 0.34% 2.74% 9327ms 16.18% std::_Rb_tree::_M_insert_unique 394ms 0.68% 3.42% 9170ms 15.91% VertexElement::AddFace 3124ms 5.42% 8.84% 8773ms 15.22% std::_Rb_tree::_M_lower_bound (inline) 240ms 0.42% 9.26% 8207ms 14.24% std::_Rb_tree::find (inline) 0 0% 9.26% 7623ms 13.22% std::set::count (inline) 267ms 0.46% 9.72% 5727ms 9.94% std::_Rb_tree::_M_insert_ (inline) 113ms 0.2% 9.92% 5449ms 9.45% std::less::operator() (inline) 5395ms 9.36% 19.28% 5395ms 9.36% std::operator< (inline) 251ms 0.44% 19.71% 5140ms 8.92% operator new 0 0% 19.71% 5095ms 8.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.71% 4973ms 8.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0052% 19.72% 4947ms 8.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 1086ms 1.88% 21.60% 4795ms 8.32% __GI___libc_malloc 4771ms 8.28% 29.88% 4771ms 8.28% std::_Rb_tree_increment 47ms 0.082% 29.96% 4389ms 7.61% std::__new_allocator::allocate (inline) 0 0% 29.96% 4368ms 7.58% std::allocator_traits::allocate (inline) 5ms 0.0087% 29.97% 4123ms 7.15% std::_Rb_tree::~_Rb_tree (inline) 1541ms 2.67% 32.64% 4115ms 7.14% std::_Rb_tree::_M_erase 0 0% 32.64% 4081ms 7.08% MeshBasedCellPopulation::UpdateNodePairs 0 0% 32.64% 4077ms 7.07% std::set::~set (inline) 4ms 0.0069% 32.65% 4069ms 7.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 5ms 0.0087% 32.66% 3939ms 6.83% MeshBasedCellPopulation::SpringIterator::operator++ 1097ms 1.90% 34.56% 3779ms 6.56% __GI___libc_free 1131ms 1.96% 36.52% 3746ms 6.50% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.012% 36.54% 3676ms 6.38% std::set_intersection (inline) 233ms 0.4% 36.94% 3669ms 6.37% std::__set_intersection 25ms 0.043% 36.98% 3574ms 6.20% Node::AddElement 0 0% 36.98% 3569ms 6.19% std::_Rb_tree::_M_create_node (inline) 0 0% 36.98% 3542ms 6.14% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.98% 3529ms 6.12% std::_Rb_tree::_M_get_node (inline) 120ms 0.21% 37.19% 3523ms 6.11% tetgen::tetgenmesh::insphere_sos 0 0% 37.19% 3511ms 6.09% AbstractCellPopulation::WriteResultsToFiles 3094ms 5.37% 42.56% 3385ms 5.87% tetgen::insphere 2483ms 4.31% 46.87% 3380ms 5.86% _int_malloc 141ms 0.24% 47.11% 3360ms 5.83% std::__new_allocator::deallocate (inline) 0 0% 47.11% 3340ms 5.79% std::allocator_traits::deallocate (inline) 0 0% 47.11% 3278ms 5.69% VertexMesh::~VertexMesh 6ms 0.01% 47.12% 3240ms 5.62% TetrahedralMesh::ImportFromMesher 3178ms 5.51% 52.63% 3178ms 5.51% std::_Rb_tree::_S_right (inline) 188ms 0.33% 52.96% 2954ms 5.12% std::_Rb_tree_const_iterator::operator++ (inline) 239ms 0.41% 53.38% 2760ms 4.79% tetgen::tetgenmesh::flip23 76ms 0.13% 53.51% 2742ms 4.76% MutableElement::AddNode 1202ms 2.09% 55.59% 2678ms 4.65% _int_free 0 0% 55.59% 2334ms 4.05% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 216ms 0.37% 55.97% 2318ms 4.02% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 113ms 0.2% 56.16% 2285ms 3.96% Node::~Node 2ms 0.0035% 56.17% 2110ms 3.66% std::_Rb_tree_iterator::operator++ (inline) 169ms 0.29% 56.46% 2109ms 3.66% VertexMesh::Clear 1988ms 3.45% 59.91% 1988ms 3.45% std::_Rb_tree_insert_and_rebalance 0 0% 59.91% 1916ms 3.32% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.91% 1906ms 3.31% std::_Rb_tree::_M_put_node (inline) 140ms 0.24% 60.15% 1804ms 3.13% tetgen::tetgenmesh::flip32 3ms 0.0052% 60.16% 1636ms 2.84% Element::Element 1525ms 2.65% 62.80% 1525ms 2.65% Node::GetIndex 973ms 1.69% 64.49% 1458ms 2.53% malloc_consolidate 10ms 0.017% 64.51% 1444ms 2.51% std::_Vector_base::_M_deallocate (inline) 1343ms 2.33% 66.84% 1430ms 2.48% tetgen::orient3d 0 0% 66.84% 1347ms 2.34% std::vector::~vector (inline) 2ms 0.0035% 66.84% 1301ms 2.26% Element::RegisterWithNodes (inline) 160ms 0.28% 67.12% 1294ms 2.24% tetgen::tetgenmesh::enqueueflipface 2ms 0.0035% 67.12% 1273ms 2.21% std::_Vector_base::~_Vector_base (inline) 5ms 0.0087% 67.13% 1262ms 2.19% _int_free_maybe_consolidate 163ms 0.28% 67.41% 1258ms 2.18% TetrahedralMesh::Clear 43ms 0.075% 67.49% 1181ms 2.05% tetgen::tetgenmesh::locate 1110ms 1.93% 69.41% 1110ms 1.93% unlink_chunk 61ms 0.11% 69.52% 1095ms 1.90% std::map::operator[] 105ms 0.18% 69.70% 1095ms 1.90% tetgen::tetgenmesh::preciselocate 67ms 0.12% 69.82% 1060ms 1.84% std::vector::_M_realloc_insert 0 0% 69.82% 962ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 69.82% 962ms 1.67% std::map::lower_bound (inline) 8ms 0.014% 69.83% 958ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 69.83% 942ms 1.63% VoronoiDataWriter::Visit 925ms 1.60% 71.44% 925ms 1.60% tetgen::tetgenmesh::triface::triface 107ms 0.19% 71.62% 863ms 1.50% std::vector::push_back (inline) 10ms 0.017% 71.64% 849ms 1.47% std::_Vector_base::_M_allocate (inline) 0 0% 71.64% 798ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 631ms 1.09% 72.73% 762ms 1.32% AbstractElement::GetNodeGlobalIndex 377ms 0.65% 73.39% 738ms 1.28% tetgen::tetgenmesh::fnextself 9ms 0.016% 73.40% 712ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 73.40% 712ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.016% 73.42% 675ms 1.17% AbstractTetrahedralElement::CalculateJacobian 670ms 1.16% 74.58% 670ms 1.16% [libchaste_mesh.so] 669ms 1.16% 75.74% 669ms 1.16% tetgen::tetgenmesh::oppo 12ms 0.021% 75.76% 666ms 1.16% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 303ms 0.53% 76.29% 662ms 1.15% AbstractElement::GetNodeLocation 11ms 0.019% 76.31% 644ms 1.12% boost::numeric::ublas::vector_assign (inline) 11ms 0.019% 76.33% 616ms 1.07% boost::numeric::ublas::c_vector::c_vector (inline) 615ms 1.07% 77.39% 615ms 1.07% tetgen::tetgenmesh::triface::operator= 43ms 0.075% 77.47% 607ms 1.05% __atan2 0 0% 77.47% 581ms 1.01% std::set::find (inline) 571ms 0.99% 78.46% 571ms 0.99% Node::rGetLocation 451ms 0.78% 79.24% 564ms 0.98% __ieee754_atan2_fma 0 0% 79.24% 515ms 0.89% std::insert_iterator::operator= (inline) 515ms 0.89% 80.13% 515ms 0.89% std::vector::size (inline) 0 0% 80.13% 500ms 0.87% boost::numeric::ublas::inner_prod (inline) 63ms 0.11% 80.24% 500ms 0.87% tetgen::tetgenmesh::enextfnext 45ms 0.078% 80.32% 498ms 0.86% AbstractTetrahedralElement::RefreshJacobian 5ms 0.0087% 80.33% 495ms 0.86% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.05% 80.38% 490ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 480ms 0.83% 81.21% 480ms 0.83% AbstractElement::IsDeleted 0 0% 81.21% 473ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 9ms 0.016% 81.23% 472ms 0.82% Element::CalculateCircumsphere 25ms 0.043% 81.27% 441ms 0.77% tetgen::tetgenmesh::queue::push 273ms 0.47% 81.75% 438ms 0.76% tetgen::tetgenmesh::sym 37ms 0.064% 81.81% 435ms 0.75% tetgen::tetgenmesh::enext2fnext 18ms 0.031% 81.84% 434ms 0.75% VertexMesh::CalculateUnitNormalToFaceWithArea 431ms 0.75% 82.59% 431ms 0.75% boost::numeric::ublas::c_vector::operator() 108ms 0.19% 82.78% 429ms 0.74% boost::numeric::ublas::indexing_vector_assign 230ms 0.4% 83.18% 419ms 0.73% AbstractTetrahedralMesh::GetElement 156ms 0.27% 83.45% 413ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 281ms 0.49% 83.93% 411ms 0.71% tetgen::tetgenmesh::link::add 19ms 0.033% 83.97% 394ms 0.68% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.97% 390ms 0.68% VertexMeshWriter::WriteVtkUsingMesh 10ms 0.017% 83.98% 390ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 8ms 0.014% 84.00% 385ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 379ms 0.66% 84.66% 379ms 0.66% tetgen::tetgenmesh::org 4ms 0.0069% 84.66% 371ms 0.64% Cell::GetCellId 369ms 0.64% 85.30% 369ms 0.64% std::_Rb_tree_decrement 76ms 0.13% 85.43% 366ms 0.63% __dynamic_cast 260ms 0.45% 85.89% 363ms 0.63% tetgen::tetgenmesh::bond 59ms 0.1% 85.99% 362ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 4ms 0.0069% 85.99% 331ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 12ms 0.021% 86.02% 324ms 0.56% std::vector::insert (inline) 10ms 0.017% 86.03% 322ms 0.56% VertexElement::~VertexElement 129ms 0.22% 86.26% 314ms 0.54% Inverse 2ms 0.0035% 86.26% 302ms 0.52% AbstractCellProperty::IsSubType (inline) 3ms 0.0052% 86.27% 300ms 0.52% VertexMesh::GetVolumeOfElement 0 0% 86.27% 297ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 32ms 0.056% 86.32% 291ms 0.5% tetgen::insphereadapt