File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53687ms, 86.68% of 61940ms total Dropped 850 nodes (cum <= 309.70ms) flat flat% sum% cum cum% 0 0% 0% 61884ms 99.91% __libc_start_call_main 0 0% 0% 61884ms 99.91% __libc_start_main_impl 0 0% 0% 61884ms 99.91% _start 0 0% 0% 61866ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61866ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61866ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61866ms 99.88% main 0 0% 0% 61832ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61832ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61832ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61557ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 52535ms 84.82% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52496ms 84.75% MeshBasedCellPopulation::Update 0 0% 0% 28374ms 45.81% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 28373ms 45.81% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 216ms 0.35% 0.35% 25363ms 40.95% VertexMesh::VertexMesh 0 0% 0.35% 20124ms 32.49% MutableMesh::ReMesh 0 0% 0.35% 16272ms 26.27% tetgen::tetrahedralize 3ms 0.0048% 0.35% 16123ms 26.03% tetgen::tetgenmesh::delaunizevertices 6ms 0.0097% 0.36% 16114ms 26.02% tetgen::tetgenmesh::incrflipdelaunay 520ms 0.84% 1.20% 14485ms 23.39% tetgen::tetgenmesh::lawson 659ms 1.06% 2.27% 12282ms 19.83% TetrahedralMesh::EdgeIterator::operator++ 31ms 0.05% 2.32% 9866ms 15.93% std::set::insert (inline) 357ms 0.58% 2.89% 9661ms 15.60% VertexElement::AddFace 225ms 0.36% 3.26% 9394ms 15.17% std::_Rb_tree::_M_insert_unique 3074ms 4.96% 8.22% 8920ms 14.40% std::_Rb_tree::_M_lower_bound (inline) 297ms 0.48% 8.70% 8422ms 13.60% std::_Rb_tree::find (inline) 0 0% 8.70% 7857ms 12.68% std::set::count (inline) 112ms 0.18% 8.88% 5743ms 9.27% std::less::operator() (inline) 5697ms 9.20% 18.08% 5697ms 9.20% std::operator< (inline) 330ms 0.53% 18.61% 5680ms 9.17% std::_Rb_tree::_M_insert_ (inline) 0 0% 18.61% 5402ms 8.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.61% 5269ms 8.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0048% 18.61% 5244ms 8.47% AbstractNumericalMethod::ComputeForcesIncludingDamping 177ms 0.29% 18.90% 5014ms 8.09% operator new 4958ms 8.00% 26.91% 4958ms 8.00% std::_Rb_tree_increment 1209ms 1.95% 28.86% 4754ms 7.68% __GI___libc_malloc 2ms 0.0032% 28.86% 4375ms 7.06% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0065% 28.87% 4367ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 27ms 0.044% 28.91% 4352ms 7.03% std::__new_allocator::allocate (inline) 0 0% 28.91% 4329ms 6.99% std::allocator_traits::allocate (inline) 19ms 0.031% 28.94% 4211ms 6.80% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.0097% 28.95% 4163ms 6.72% std::_Rb_tree::~_Rb_tree (inline) 1350ms 2.18% 31.13% 4152ms 6.70% std::_Rb_tree::_M_erase 0 0% 31.13% 4108ms 6.63% std::set::~set (inline) 1ms 0.0016% 31.13% 3957ms 6.39% std::set_intersection (inline) 244ms 0.39% 31.53% 3956ms 6.39% std::__set_intersection 1224ms 1.98% 33.50% 3904ms 6.30% __GI___libc_free 129ms 0.21% 33.71% 3844ms 6.21% tetgen::tetgenmesh::insphere_sos 1265ms 2.04% 35.75% 3764ms 6.08% std::_Rb_tree::_M_get_insert_unique_pos 3406ms 5.50% 41.25% 3699ms 5.97% tetgen::insphere 136ms 0.22% 41.47% 3528ms 5.70% tetgen::tetgenmesh::flip23 0 0% 41.47% 3517ms 5.68% std::_Rb_tree::_M_create_node (inline) 167ms 0.27% 41.74% 3509ms 5.67% std::__new_allocator::deallocate (inline) 0 0% 41.74% 3496ms 5.64% std::allocator_traits::deallocate (inline) 0 0% 41.74% 3481ms 5.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.74% 3481ms 5.62% std::_Rb_tree::_M_get_node (inline) 0 0% 41.74% 3452ms 5.57% AbstractCellPopulation::WriteResultsToFiles 196ms 0.32% 42.06% 3228ms 5.21% std::_Rb_tree_const_iterator::operator++ (inline) 2407ms 3.89% 45.94% 3223ms 5.20% _int_malloc 55ms 0.089% 46.03% 3203ms 5.17% Node::AddElement 24ms 0.039% 46.07% 3084ms 4.98% TetrahedralMesh::ImportFromMesher 0 0% 46.07% 3029ms 4.89% VertexMesh::~VertexMesh 2883ms 4.65% 50.72% 2883ms 4.65% std::_Rb_tree::_S_right (inline) 1333ms 2.15% 52.88% 2674ms 4.32% _int_free 167ms 0.27% 53.15% 2538ms 4.10% tetgen::tetgenmesh::flip32 58ms 0.094% 53.24% 2523ms 4.07% MutableElement::AddNode 4ms 0.0065% 53.25% 2331ms 3.76% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 229ms 0.37% 53.62% 2281ms 3.68% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 53.62% 2232ms 3.60% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.62% 2220ms 3.58% std::_Rb_tree::_M_put_node (inline) 155ms 0.25% 53.87% 2210ms 3.57% Node::~Node 1ms 0.0016% 53.87% 2066ms 3.34% std::_Rb_tree_iterator::operator++ (inline) 160ms 0.26% 54.13% 1988ms 3.21% VertexMesh::Clear 245ms 0.4% 54.52% 1949ms 3.15% tetgen::tetgenmesh::enqueueflipface 1914ms 3.09% 57.61% 1914ms 3.09% std::_Rb_tree_insert_and_rebalance 1588ms 2.56% 60.18% 1588ms 2.56% Node::GetIndex 1474ms 2.38% 62.56% 1565ms 2.53% tetgen::orient3d 5ms 0.0081% 62.56% 1495ms 2.41% Element::Element 48ms 0.077% 62.64% 1325ms 2.14% tetgen::tetgenmesh::locate 871ms 1.41% 64.05% 1319ms 2.13% malloc_consolidate 80ms 0.13% 64.18% 1303ms 2.10% TetrahedralMesh::Clear 20ms 0.032% 64.21% 1296ms 2.09% std::_Vector_base::_M_deallocate (inline) 84ms 0.14% 64.34% 1236ms 2.00% tetgen::tetgenmesh::preciselocate 0 0% 64.34% 1234ms 1.99% std::vector::~vector (inline) 6ms 0.0097% 64.35% 1162ms 1.88% Element::RegisterWithNodes (inline) 1ms 0.0016% 64.36% 1136ms 1.83% std::_Vector_base::~_Vector_base (inline) 4ms 0.0065% 64.36% 1123ms 1.81% _int_free_maybe_consolidate 69ms 0.11% 64.47% 1121ms 1.81% std::map::operator[] 1107ms 1.79% 66.26% 1107ms 1.79% tetgen::tetgenmesh::oppo 60ms 0.097% 66.36% 1085ms 1.75% std::vector::_M_realloc_insert 838ms 1.35% 67.71% 1029ms 1.66% AbstractElement::GetNodeGlobalIndex 1008ms 1.63% 69.34% 1008ms 1.63% tetgen::tetgenmesh::triface::triface 999ms 1.61% 70.95% 999ms 1.61% unlink_chunk 0 0% 70.95% 978ms 1.58% std::_Rb_tree::lower_bound (inline) 0 0% 70.95% 978ms 1.58% std::map::lower_bound (inline) 309ms 0.5% 71.45% 895ms 1.44% tetgen::tetgenmesh::sym 128ms 0.21% 71.66% 883ms 1.43% std::vector::push_back (inline) 0 0% 71.66% 882ms 1.42% VoronoiDataWriter::Visit 6ms 0.0097% 71.67% 858ms 1.39% VertexMesh::GenerateVerticesFromElementCircumcentres 5ms 0.0081% 71.67% 853ms 1.38% std::_Vector_base::_M_allocate (inline) 830ms 1.34% 73.01% 830ms 1.34% tetgen::tetgenmesh::triface::operator= 822ms 1.33% 74.34% 822ms 1.33% [libchaste_mesh.so] 0 0% 74.34% 748ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 0 0% 74.34% 713ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.023% 74.36% 677ms 1.09% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 17ms 0.027% 74.39% 674ms 1.09% boost::numeric::ublas::vector_assign (inline) 8ms 0.013% 74.40% 667ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 35ms 0.057% 74.46% 636ms 1.03% tetgen::tetgenmesh::queue::push 12ms 0.019% 74.48% 633ms 1.02% boost::numeric::ublas::c_vector::c_vector (inline) 239ms 0.39% 74.87% 618ms 1% tetgen::tetgenmesh::bond 382ms 0.62% 75.48% 601ms 0.97% tetgen::tetgenmesh::link::add 14ms 0.023% 75.51% 597ms 0.96% AbstractTetrahedralElement::CalculateJacobian 57ms 0.092% 75.60% 597ms 0.96% __atan2 358ms 0.58% 76.18% 596ms 0.96% tetgen::tetgenmesh::fnextself 590ms 0.95% 77.13% 590ms 0.95% tetgen::tetgenmesh::decode 53ms 0.086% 77.21% 579ms 0.93% tetgen::tetgenmesh::enext2fnext 0 0% 77.21% 563ms 0.91% std::set::find (inline) 553ms 0.89% 78.11% 553ms 0.89% AbstractElement::IsDeleted 56ms 0.09% 78.20% 547ms 0.88% tetgen::tetgenmesh::enextfnext 542ms 0.88% 79.07% 542ms 0.88% std::vector::size (inline) 426ms 0.69% 79.76% 538ms 0.87% __ieee754_atan2_fma 245ms 0.4% 80.15% 528ms 0.85% AbstractElement::GetNodeLocation 0 0% 80.15% 525ms 0.85% boost::numeric::ublas::inner_prod (inline) 1ms 0.0016% 80.16% 524ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 46ms 0.074% 80.23% 523ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 510ms 0.82% 81.05% 510ms 0.82% Node::rGetLocation 0 0% 81.05% 500ms 0.81% std::insert_iterator::operator= (inline) 18ms 0.029% 81.08% 436ms 0.7% Element::CalculateCircumsphere 0 0% 81.08% 434ms 0.7% std::_Rb_tree::_M_insert_unique_ (inline) 4ms 0.0065% 81.09% 432ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 199ms 0.32% 81.41% 431ms 0.7% AbstractTetrahedralMesh::GetElement 18ms 0.029% 81.44% 429ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 426ms 0.69% 82.13% 426ms 0.69% tetgen::tetgenmesh::org 193ms 0.31% 82.44% 421ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 110ms 0.18% 82.62% 419ms 0.68% boost::numeric::ublas::indexing_vector_assign 39ms 0.063% 82.68% 406ms 0.66% AbstractTetrahedralElement::RefreshJacobian 3ms 0.0048% 82.68% 406ms 0.66% Cell::GetCellId 1ms 0.0016% 82.69% 406ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 82ms 0.13% 82.82% 402ms 0.65% __dynamic_cast 26ms 0.042% 82.86% 400ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 399ms 0.64% 83.51% 399ms 0.64% boost::numeric::ublas::c_vector::operator() 0 0% 83.51% 383ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 366ms 0.59% 84.10% 366ms 0.59% tetgen::tetgenmesh::encode 12ms 0.019% 84.12% 352ms 0.57% std::vector::insert (inline) 351ms 0.57% 84.68% 351ms 0.57% tetgen::tetgenmesh::pointmark 1ms 0.0016% 84.68% 347ms 0.56% AbstractCellProperty::IsSubType (inline) 347ms 0.56% 85.24% 347ms 0.56% std::_Rb_tree_decrement 10ms 0.016% 85.26% 336ms 0.54% VertexElement::~VertexElement 84ms 0.14% 85.40% 333ms 0.54% tetgen::tetgenmesh::queue::pop 3ms 0.0048% 85.40% 328ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.40% 328ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 115ms 0.19% 85.59% 327ms 0.53% Inverse 324ms 0.52% 86.11% 324ms 0.52% tetgen::tetgenmesh::face::face 36ms 0.058% 86.17% 320ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 315ms 0.51% 86.68% 315ms 0.51% tetgen::tetgenmesh::dest