File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 82332ms, 88.32% of 93220ms total Dropped 1031 nodes (cum <= 466.10ms) flat flat% sum% cum cum% 0 0% 0% 92990ms 99.75% __libc_start_call_main 0 0% 0% 92990ms 99.75% __libc_start_main_impl 0 0% 0% 92990ms 99.75% _start 0 0% 0% 92972ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 92972ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 92972ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 92972ms 99.73% main 0 0% 0% 92940ms 99.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 92940ms 99.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 92940ms 99.70% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0011% 0.0011% 92933ms 99.69% AbstractCellBasedSimulation::Solve 11ms 0.012% 0.013% 49233ms 52.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.013% 0.026% 46100ms 49.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 51ms 0.055% 0.08% 45123ms 48.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 391ms 0.42% 0.5% 35295ms 37.86% NagaiHondaForce::AddForceContribution 0 0% 0.5% 32247ms 34.59% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.0064% 0.51% 19204ms 20.60% VertexBasedCellPopulation::Update 0 0% 0.51% 19078ms 20.47% MutableVertexMesh::ReMesh 8571ms 9.19% 9.70% 16301ms 17.49% Cylindrical2dVertexMesh::GetVectorFromAtoB 101ms 0.11% 9.81% 15519ms 16.65% Cell::ReadyToDivide 31ms 0.033% 9.84% 14612ms 15.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 79ms 0.085% 9.93% 14451ms 15.50% NagaiHondaForce::GetAdhesionParameter 68ms 0.073% 10.00% 12485ms 13.39% SimpleWntCellCycleModel::UpdateCellCyclePhase 343ms 0.37% 10.37% 12380ms 13.28% boost::numeric::ublas::c_vector::c_vector (partial-inline) 91ms 0.098% 10.47% 11606ms 12.45% CellPropertyCollection::GetPropertiesType (inline) 493ms 0.53% 10.99% 11585ms 12.43% std::__new_allocator::allocate (inline) 0 0% 10.99% 11063ms 11.87% std::allocator_traits::allocate (inline) 223ms 0.24% 11.23% 11043ms 11.85% boost::numeric::ublas::vector_assign (inline) 843ms 0.9% 12.14% 10979ms 11.78% operator new 0 0% 12.14% 10868ms 11.66% std::_Rb_tree::_M_create_node (inline) 0 0% 12.14% 10561ms 11.33% std::_Rb_tree::_M_get_node (inline) 3486ms 3.74% 15.88% 9823ms 10.54% __GI___libc_malloc 104ms 0.11% 15.99% 9514ms 10.21% VertexBasedCellPopulation::GetDampingConstant 75ms 0.08% 16.07% 9509ms 10.20% AbstractCellProperty::IsSubType (inline) 2526ms 2.71% 18.78% 9423ms 10.11% __dynamic_cast 0 0% 18.78% 9369ms 10.05% std::_Rb_tree::_Alloc_node::operator() (inline) 47ms 0.05% 18.83% 9360ms 10.04% AbstractTargetAreaModifier::UpdateTargetAreas 48ms 0.051% 18.88% 9268ms 9.94% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 8ms 0.0086% 18.89% 9150ms 9.82% AbstractCellBasedSimulation::DoCellBirth 127ms 0.14% 19.03% 8777ms 9.42% MutableVertexMesh::CheckForIntersections 877ms 0.94% 19.97% 8171ms 8.77% std::_Rb_tree::_M_erase 0 0% 19.97% 8165ms 8.76% std::_Rb_tree::_M_drop_node (inline) 2327ms 2.50% 22.46% 7929ms 8.51% boost::numeric::ublas::indexing_vector_assign 275ms 0.3% 22.76% 7669ms 8.23% std::_Rb_tree::~_Rb_tree (inline) 51ms 0.055% 22.81% 7511ms 8.06% Cell::GetMutationState 114ms 0.12% 22.93% 7421ms 7.96% std::__new_allocator::deallocate (inline) 0 0% 22.93% 7399ms 7.94% std::allocator_traits::deallocate (inline) 0 0% 22.93% 7334ms 7.87% std::_Rb_tree::_M_put_node (inline) 0 0% 22.93% 7317ms 7.85% std::set::~set (inline) 406ms 0.44% 23.37% 7162ms 7.68% VertexMesh::GetNextEdgeGradientOfElementAtNode 1874ms 2.01% 25.38% 7135ms 7.65% __GI___libc_free 47ms 0.05% 25.43% 7020ms 7.53% VertexBasedCellPopulation::GetLocationOfCellCentre 440ms 0.47% 25.90% 6889ms 7.39% std::map::operator[] (partial-inline) 0 0% 25.90% 6838ms 7.34% std::set::insert (inline) 499ms 0.54% 26.44% 6756ms 7.25% VertexMesh::GetCentroidOfElement 3ms 0.0032% 26.44% 6641ms 7.12% MutableVertexMesh::RemoveDeletedNodesAndElements 492ms 0.53% 26.97% 6508ms 6.98% VertexMesh::ElementIncludesPoint 750ms 0.8% 27.77% 6301ms 6.76% std::_Rb_tree::_M_insert_ (inline) 58ms 0.062% 27.84% 5912ms 6.34% std::set_intersection (inline) 283ms 0.3% 28.14% 5854ms 6.28% std::__set_intersection 108ms 0.12% 28.26% 5844ms 6.27% std::_Rb_tree::_Rb_tree (partial-inline) 5737ms 6.15% 34.41% 5737ms 6.15% boost::numeric::ublas::c_vector::operator() 908ms 0.97% 35.38% 5655ms 6.07% AbstractMesh::GetDistanceBetweenNodes 578ms 0.62% 36.00% 5565ms 5.97% std::_Rb_tree::_M_copy (inline) 14ms 0.015% 36.02% 5430ms 5.82% std::set::set (inline) 5404ms 5.80% 41.82% 5404ms 5.80% __strcmp_evex 150ms 0.16% 41.98% 5266ms 5.65% SimpleWntCellCycleModel::GetWntLevel 4504ms 4.83% 46.81% 5209ms 5.59% _int_free 123ms 0.13% 46.94% 4989ms 5.35% WntConcentration::GetWntLevel 572ms 0.61% 47.55% 4822ms 5.17% std::_Rb_tree::_M_clone_node (inline) 2159ms 2.32% 49.87% 4769ms 5.12% __cxxabiv1::__si_class_type_info::__do_dyncast 572ms 0.61% 50.48% 4761ms 5.11% boost::numeric::ublas::c_vector::operator[] (inline) 16ms 0.017% 50.50% 4710ms 5.05% MutableVertexMesh::RemoveDeletedNodes 3893ms 4.18% 54.68% 4649ms 4.99% _int_malloc 66ms 0.071% 54.75% 4603ms 4.94% EdgeHelper::RemoveDeletedEdges 1996ms 2.14% 56.89% 4567ms 4.90% std::_Rb_tree::_M_lower_bound (inline) 0 0% 56.89% 4476ms 4.80% std::insert_iterator::operator= (inline) 16ms 0.017% 56.91% 4331ms 4.65% EdgeHelper::UpdateEdgesMapKey 0 0% 56.91% 4162ms 4.46% std::_Rb_tree::_M_insert_unique_ (inline) 107ms 0.11% 57.02% 4054ms 4.35% MutableElement::ResetIndex 0 0% 57.02% 3975ms 4.26% std::_Rb_tree::lower_bound (inline) 0 0% 57.02% 3975ms 4.26% std::map::lower_bound (inline) 36ms 0.039% 57.06% 3970ms 4.26% Cell::GetCellProliferativeType 3950ms 4.24% 61.30% 3950ms 4.24% boost::numeric::ublas::same_impl_ex 0 0% 61.30% 3889ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 55ms 0.059% 61.36% 3549ms 3.81% AbstractCellPopulation::GetCellUsingLocationIndex 3128ms 3.36% 64.71% 3128ms 3.36% [libchaste_cell_based.so] 161ms 0.17% 64.88% 3082ms 3.31% AbstractCellProperty::IsType (inline) 43ms 0.046% 64.93% 3058ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 100ms 0.11% 65.04% 2872ms 3.08% Cell::SetCellProliferativeType 106ms 0.11% 65.15% 2726ms 2.92% boost::detail::shared_count::~shared_count (inline) 0 0% 65.15% 2726ms 2.92% boost::shared_ptr::~shared_ptr (inline) 0 0% 65.15% 2676ms 2.87% std::_Rb_tree::_M_insert_unique (inline) 725ms 0.78% 65.93% 2645ms 2.84% AbstractElement::GetNodeLocation 2565ms 2.75% 68.68% 2573ms 2.76% boost::detail::sp_counted_base::release 24ms 0.026% 68.71% 2431ms 2.61% std::_Rb_tree::_M_emplace_hint_unique 133ms 0.14% 68.85% 2374ms 2.55% boost::numeric::ublas::vector_binary::size (inline) 7ms 0.0075% 68.86% 2360ms 2.53% AbstractCellPopulation::Iterator::operator++ (inline) 204ms 0.22% 69.08% 2358ms 2.53% AbstractCellPopulation::Iterator::IsRealCell (inline) 351ms 0.38% 69.45% 2357ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 71ms 0.076% 69.53% 2318ms 2.49% std::_Rb_tree::erase 0 0% 69.53% 2242ms 2.41% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.53% 2201ms 2.36% boost::numeric::ublas::c_vector::operator-= (inline) 21ms 0.023% 69.55% 2165ms 2.32% Cell::GetCellData 2120ms 2.27% 71.82% 2120ms 2.27% std::_Rb_tree::_S_right (inline) 49ms 0.053% 71.88% 2079ms 2.23% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.88% 2072ms 2.22% AbstractCellPopulation::WriteResultsToFiles 2038ms 2.19% 74.06% 2038ms 2.19% [libchaste_mesh.so] 33ms 0.035% 74.10% 2000ms 2.15% CellPropertyCollection::HasProperty 265ms 0.28% 74.38% 1964ms 2.11% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 74.38% 1957ms 2.10% Cell::HasCellProperty (inline) 394ms 0.42% 74.81% 1939ms 2.08% AbstractCellProperty::IsSame 30ms 0.032% 74.84% 1794ms 1.92% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.84% 1714ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0032% 74.84% 1706ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 83ms 0.089% 74.93% 1622ms 1.74% VertexMesh::GetVolumeOfElement 293ms 0.31% 75.24% 1601ms 1.72% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 199ms 0.21% 75.46% 1545ms 1.66% std::type_info::operator== (inline) 1ms 0.0011% 75.46% 1539ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.46% 1539ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.46% 1537ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.46% 1499ms 1.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 59ms 0.063% 75.52% 1496ms 1.60% MutableVertexMesh::CheckForSwapsFromShortEdges 128ms 0.14% 75.66% 1465ms 1.57% CellPropertyCollection::AddProperty 1406ms 1.51% 77.17% 1406ms 1.51% std::_Rb_tree_increment 0 0% 77.17% 1370ms 1.47% boost::numeric::ublas::vector_binary::operator() (inline) 53ms 0.057% 77.22% 1356ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 57ms 0.061% 77.29% 1327ms 1.42% VertexMesh::GetSurfaceAreaOfElement 64ms 0.069% 77.35% 1313ms 1.41% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 77.35% 1300ms 1.39% tcache_get (inline) 1300ms 1.39% 78.75% 1300ms 1.39% tcache_get_n (inline) 3ms 0.0032% 78.75% 1296ms 1.39% OffLatticeSimulation::ApplyBoundaries 33ms 0.035% 78.79% 1136ms 1.22% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 37ms 0.04% 78.83% 1118ms 1.20% CellPropertyRegistry::Get 89ms 0.095% 78.92% 1117ms 1.20% boost::numeric::ublas::vector_reference::operator() (inline) 44ms 0.047% 78.97% 1087ms 1.17% Node::RemoveElement 655ms 0.7% 79.67% 1069ms 1.15% std::_Rb_tree::equal_range (inline) 1ms 0.0011% 79.67% 1044ms 1.12% std::set::erase (inline) 27ms 0.029% 79.70% 1014ms 1.09% boost::numeric::ublas::detail::expression_type_check (inline) 39ms 0.042% 79.74% 1009ms 1.08% Edge::AddElement 9ms 0.0097% 79.75% 1001ms 1.07% MutableElement::RegisterWithEdges (inline) 958ms 1.03% 80.78% 958ms 1.03% [libstdc++.so.6.0.33] 0 0% 80.78% 953ms 1.02% CellPropertyCollection::~CellPropertyCollection (inline) 145ms 0.16% 80.94% 949ms 1.02% boost::numeric::ublas::detail::equals 657ms 0.7% 81.64% 891ms 0.96% CellPropertyCollection::GetProperty 877ms 0.94% 82.58% 877ms 0.94% std::_Rb_tree_insert_and_rebalance 0 0% 82.58% 865ms 0.93% boost::numeric::ublas::norm_2 (inline) 321ms 0.34% 82.93% 836ms 0.9% boost::numeric::ublas::vector_norm_2::apply 0 0% 82.93% 832ms 0.89% std::__new_allocator::destroy (inline) 0 0% 82.93% 832ms 0.89% std::allocator_traits::destroy (inline) 0 0% 82.93% 831ms 0.89% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.93% 822ms 0.88% VertexMeshWriter::MakeVtkMesh 7ms 0.0075% 82.93% 809ms 0.87% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 790ms 0.85% 83.78% 790ms 0.85% Node::rGetLocation 0 0% 83.78% 780ms 0.84% std::_Rb_tree::clear (inline) 0 0% 83.78% 776ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0032% 83.79% 776ms 0.83% boost::numeric::ublas::c_vector::swap 119ms 0.13% 83.91% 773ms 0.83% std::swap_ranges (inline) 0 0% 83.91% 758ms 0.81% std::map::clear (inline) 745ms 0.8% 84.71% 745ms 0.8% tcache_put (inline) 65ms 0.07% 84.78% 727ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.78% 683ms 0.73% boost::numeric::ublas::norm_inf (inline) 243ms 0.26% 85.04% 683ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 87ms 0.093% 85.14% 668ms 0.72% std::_Rb_tree::find (inline) 0 0% 85.14% 654ms 0.7% std::iter_swap (inline) 654ms 0.7% 85.84% 654ms 0.7% std::swap (inline) 303ms 0.33% 86.16% 645ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 73ms 0.078% 86.24% 619ms 0.66% MutableElement::GetNodeLocalIndex 619ms 0.66% 86.91% 619ms 0.66% std::vector::size (inline) 52ms 0.056% 86.96% 611ms 0.66% std::less::operator() (inline) 0 0% 86.96% 600ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.029% 86.99% 600ms 0.64% std::_Rb_tree::_M_insert_node (inline) 1ms 0.0011% 86.99% 581ms 0.62% vtkPolygon::New 0 0% 86.99% 580ms 0.62% vtkPolygon::vtkPolygon 445ms 0.48% 87.47% 559ms 0.6% std::operator< (inline) 0 0% 87.47% 550ms 0.59% std::map::find (inline) 10ms 0.011% 87.48% 532ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.48% 532ms 0.57% boost::numeric::ublas::vector::vector (inline) 21ms 0.023% 87.50% 530ms 0.57% MutableElement::RegisterWithNodes (inline) 56ms 0.06% 87.56% 498ms 0.53% Node::AddElement 0 0% 87.56% 497ms 0.53% std::_Vector_base::_M_allocate (inline) 484ms 0.52% 88.08% 484ms 0.52% Node::GetIndex 0 0% 88.08% 479ms 0.51% std::map::map (inline) 223ms 0.24% 88.32% 467ms 0.5% Edge::GetMapIndex