File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95006ms, 87.87% of 108127ms total Dropped 1118 nodes (cum <= 540.63ms) flat flat% sum% cum cum% 0 0% 0% 107830ms 99.73% __libc_start_call_main 0 0% 0% 107830ms 99.73% __libc_start_main_impl 0 0% 0% 107830ms 99.73% _start 0 0% 0% 107808ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107808ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107808ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107808ms 99.70% main 0 0% 0% 107775ms 99.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107775ms 99.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107775ms 99.67% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00092% 0.00092% 107767ms 99.67% AbstractCellBasedSimulation::Solve 12ms 0.011% 0.012% 56952ms 52.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 10ms 0.0092% 0.021% 53138ms 49.14% ForwardEulerNumericalMethod::UpdateAllNodePositions 58ms 0.054% 0.075% 51649ms 47.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 372ms 0.34% 0.42% 40008ms 37.00% NagaiHondaForce::AddForceContribution 0 0% 0.42% 37208ms 34.41% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.42% 21939ms 20.29% VertexBasedCellPopulation::Update 3ms 0.0028% 0.42% 21811ms 20.17% MutableVertexMesh::ReMesh 80ms 0.074% 0.5% 18356ms 16.98% Cell::ReadyToDivide 9172ms 8.48% 8.98% 17770ms 16.43% Cylindrical2dVertexMesh::GetVectorFromAtoB 33ms 0.031% 9.01% 17268ms 15.97% AbstractPhaseBasedCellCycleModel::ReadyToDivide 103ms 0.095% 9.11% 17156ms 15.87% NagaiHondaForce::GetAdhesionParameter 98ms 0.091% 9.20% 14911ms 13.79% SimpleWntCellCycleModel::UpdateCellCyclePhase 883ms 0.82% 10.01% 14169ms 13.10% std::__new_allocator::allocate (inline) 395ms 0.37% 10.38% 13673ms 12.65% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.38% 13575ms 12.55% std::allocator_traits::allocate (inline) 73ms 0.068% 10.45% 13312ms 12.31% CellPropertyCollection::GetPropertiesType (inline) 0 0% 10.45% 13284ms 12.29% std::_Rb_tree::_M_create_node (inline) 1018ms 0.94% 11.39% 13202ms 12.21% operator new 0 0% 11.39% 12906ms 11.94% std::_Rb_tree::_M_get_node (inline) 280ms 0.26% 11.65% 12198ms 11.28% boost::numeric::ublas::vector_assign (inline) 4079ms 3.77% 15.42% 11812ms 10.92% __GI___libc_malloc 0 0% 15.42% 11480ms 10.62% std::_Rb_tree::_Alloc_node::operator() (inline) 94ms 0.087% 15.51% 11275ms 10.43% VertexBasedCellPopulation::GetDampingConstant 59ms 0.055% 15.56% 11147ms 10.31% AbstractTargetAreaModifier::UpdateTargetAreas 41ms 0.038% 15.60% 11040ms 10.21% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 6ms 0.0055% 15.60% 10840ms 10.03% AbstractCellBasedSimulation::DoCellBirth 107ms 0.099% 15.70% 10768ms 9.96% AbstractCellProperty::IsSubType (inline) 3132ms 2.90% 18.60% 10686ms 9.88% __dynamic_cast 130ms 0.12% 18.72% 9787ms 9.05% MutableVertexMesh::CheckForIntersections 1106ms 1.02% 19.74% 9681ms 8.95% std::_Rb_tree::_M_erase 0 0% 19.74% 9625ms 8.90% std::_Rb_tree::_M_drop_node (inline) 332ms 0.31% 20.05% 9029ms 8.35% std::_Rb_tree::~_Rb_tree (inline) 519ms 0.48% 20.53% 8858ms 8.19% std::map::operator[] (partial-inline) 2558ms 2.37% 22.90% 8812ms 8.15% boost::numeric::ublas::indexing_vector_assign 118ms 0.11% 23.00% 8774ms 8.11% std::__new_allocator::deallocate (inline) 0 0% 23.00% 8750ms 8.09% std::allocator_traits::deallocate (inline) 60ms 0.055% 23.06% 8663ms 8.01% Cell::GetMutationState 0 0% 23.06% 8650ms 8.00% std::_Rb_tree::_M_put_node (inline) 0 0% 23.06% 8576ms 7.93% std::set::~set (inline) 51ms 0.047% 23.11% 8552ms 7.91% VertexBasedCellPopulation::GetLocationOfCellCentre 2339ms 2.16% 25.27% 8531ms 7.89% __GI___libc_free 0 0% 25.27% 8143ms 7.53% std::set::insert (inline) 693ms 0.64% 25.91% 8023ms 7.42% VertexMesh::GetCentroidOfElement 7ms 0.0065% 25.92% 7842ms 7.25% MutableVertexMesh::RemoveDeletedNodesAndElements 439ms 0.41% 26.32% 7687ms 7.11% VertexMesh::GetNextEdgeGradientOfElementAtNode 120ms 0.11% 26.43% 7544ms 6.98% std::_Rb_tree::_Rb_tree (partial-inline) 877ms 0.81% 27.25% 7517ms 6.95% std::_Rb_tree::_M_insert_ (inline) 546ms 0.5% 27.75% 7287ms 6.74% VertexMesh::ElementIncludesPoint 759ms 0.7% 28.45% 7202ms 6.66% std::_Rb_tree::_M_copy (inline) 15ms 0.014% 28.47% 6970ms 6.45% std::set::set (inline) 194ms 0.18% 28.65% 6703ms 6.20% SimpleWntCellCycleModel::GetWntLevel 46ms 0.043% 28.69% 6641ms 6.14% std::set_intersection (inline) 258ms 0.24% 28.93% 6595ms 6.10% std::__set_intersection 6394ms 5.91% 34.84% 6394ms 5.91% boost::numeric::ublas::c_vector::operator() 121ms 0.11% 34.95% 6350ms 5.87% WntConcentration::GetWntLevel 2446ms 2.26% 37.21% 6271ms 5.80% std::_Rb_tree::_M_lower_bound (inline) 721ms 0.67% 37.88% 6179ms 5.71% std::_Rb_tree::_M_clone_node (inline) 5375ms 4.97% 42.85% 6117ms 5.66% _int_free 986ms 0.91% 43.76% 5995ms 5.54% AbstractMesh::GetDistanceBetweenNodes 5845ms 5.41% 49.17% 5845ms 5.41% __strcmp_evex 22ms 0.02% 49.19% 5586ms 5.17% MutableVertexMesh::RemoveDeletedNodes 4558ms 4.22% 53.41% 5560ms 5.14% _int_malloc 53ms 0.049% 53.45% 5444ms 5.03% EdgeHelper::RemoveDeletedEdges 0 0% 53.45% 5390ms 4.98% std::_Rb_tree::lower_bound (inline) 0 0% 53.45% 5390ms 4.98% std::map::lower_bound (inline) 612ms 0.57% 54.02% 5331ms 4.93% boost::numeric::ublas::c_vector::operator[] (inline) 12ms 0.011% 54.03% 5183ms 4.79% EdgeHelper::UpdateEdgesMapKey 0 0% 54.03% 5150ms 4.76% std::insert_iterator::operator= (inline) 2372ms 2.19% 56.23% 5102ms 4.72% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.23% 4821ms 4.46% std::_Rb_tree::_M_insert_unique_ (inline) 130ms 0.12% 56.35% 4750ms 4.39% MutableElement::ResetIndex 56ms 0.052% 56.40% 4643ms 4.29% AbstractCellPopulation::GetCellUsingLocationIndex 4513ms 4.17% 60.57% 4513ms 4.17% boost::numeric::ublas::same_impl_ex 0 0% 60.57% 4416ms 4.08% AbstractCellBasedSimulation::DoCellRemoval (inline) 28ms 0.026% 60.60% 4388ms 4.06% Cell::GetCellProliferativeType 166ms 0.15% 60.75% 3419ms 3.16% AbstractCellProperty::IsType (inline) 3388ms 3.13% 63.88% 3388ms 3.13% [libchaste_cell_based.so] 48ms 0.044% 63.93% 3380ms 3.13% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 63.93% 3322ms 3.07% std::_Rb_tree::_M_insert_unique 3259ms 3.01% 66.94% 3259ms 3.01% std::_Rb_tree::_S_right (inline) 98ms 0.091% 67.03% 3224ms 2.98% Cell::SetCellProliferativeType 802ms 0.74% 67.77% 3187ms 2.95% AbstractElement::GetNodeLocation 135ms 0.12% 67.90% 3091ms 2.86% boost::detail::shared_count::~shared_count (inline) 0 0% 67.90% 3091ms 2.86% boost::shared_ptr::~shared_ptr (inline) 5ms 0.0046% 67.90% 2969ms 2.75% AbstractCellPopulation::Iterator::operator++ (inline) 199ms 0.18% 68.09% 2962ms 2.74% AbstractCellPopulation::Iterator::IsRealCell (inline) 2875ms 2.66% 70.75% 2903ms 2.68% boost::detail::sp_counted_base::release 32ms 0.03% 70.78% 2887ms 2.67% std::_Rb_tree::_M_emplace_hint_unique 68ms 0.063% 70.84% 2753ms 2.55% std::_Rb_tree::erase 152ms 0.14% 70.98% 2641ms 2.44% boost::numeric::ublas::vector_binary::size (inline) 304ms 0.28% 71.26% 2641ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.26% 2571ms 2.38% boost::numeric::ublas::c_vector::assign (inline) 16ms 0.015% 71.28% 2490ms 2.30% Cell::GetCellData 0 0% 71.28% 2435ms 2.25% AbstractCellPopulation::WriteResultsToFiles 54ms 0.05% 71.33% 2392ms 2.21% CellPropertyCollection::HasProperty 0 0% 71.33% 2384ms 2.20% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 71.33% 2331ms 2.16% Cell::HasCellProperty (inline) 38ms 0.035% 71.36% 2304ms 2.13% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 55ms 0.051% 71.41% 2289ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2228ms 2.06% 73.47% 2228ms 2.06% [libchaste_mesh.so] 283ms 0.26% 73.73% 2165ms 2.00% VertexMesh::GetAreaGradientOfElementAtNode 488ms 0.45% 74.19% 2124ms 1.96% AbstractCellProperty::IsSame 330ms 0.31% 74.49% 2066ms 1.91% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.49% 2005ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 74.49% 1991ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 141ms 0.13% 74.62% 1873ms 1.73% CellPropertyCollection::AddProperty 0 0% 74.62% 1805ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 0 0% 74.62% 1804ms 1.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 92ms 0.085% 74.71% 1763ms 1.63% VertexMesh::GetVolumeOfElement 57ms 0.053% 74.76% 1750ms 1.62% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.0028% 74.76% 1719ms 1.59% tcache_get (inline) 1716ms 1.59% 76.35% 1716ms 1.59% tcache_get_n (inline) 1659ms 1.53% 77.89% 1659ms 1.53% std::_Rb_tree_increment 214ms 0.2% 78.08% 1636ms 1.51% std::type_info::operator== (inline) 63ms 0.058% 78.14% 1624ms 1.50% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 78.14% 1550ms 1.43% OffLatticeSimulation::ApplyBoundaries 3ms 0.0028% 78.15% 1526ms 1.41% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.15% 1526ms 1.41% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 62ms 0.057% 78.20% 1509ms 1.40% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.20% 1475ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 87ms 0.08% 78.28% 1406ms 1.30% VertexMesh::GetSurfaceAreaOfElement 45ms 0.042% 78.32% 1358ms 1.26% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 782ms 0.72% 79.05% 1323ms 1.22% std::_Rb_tree::equal_range (inline) 34ms 0.031% 79.08% 1287ms 1.19% Node::RemoveElement 0 0% 79.08% 1253ms 1.16% std::set::erase (inline) 22ms 0.02% 79.10% 1208ms 1.12% MutableElement::RegisterWithEdges (inline) 39ms 0.036% 79.14% 1200ms 1.11% Edge::AddElement 101ms 0.093% 79.23% 1188ms 1.10% boost::numeric::ublas::vector_reference::operator() (inline) 1181ms 1.09% 80.32% 1181ms 1.09% std::_Rb_tree_insert_and_rebalance 1154ms 1.07% 81.39% 1154ms 1.07% [libstdc++.so.6.0.33] 0 0% 81.39% 1138ms 1.05% CellPropertyCollection::~CellPropertyCollection (inline) 52ms 0.048% 81.44% 1091ms 1.01% CellPropertyRegistry::Get 29ms 0.027% 81.46% 1042ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 10ms 0.0092% 81.47% 1013ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 996ms 0.92% 82.39% 996ms 0.92% Node::rGetLocation 0 0% 82.39% 989ms 0.91% std::_Rb_tree::clear (inline) 0 0% 82.39% 979ms 0.91% std::__new_allocator::destroy (inline) 0 0% 82.39% 979ms 0.91% std::allocator_traits::destroy (inline) 0 0% 82.39% 976ms 0.9% std::_Rb_tree::_M_destroy_node (inline) 175ms 0.16% 82.56% 974ms 0.9% boost::numeric::ublas::detail::equals 125ms 0.12% 82.67% 961ms 0.89% std::_Rb_tree::find (inline) 0 0% 82.67% 958ms 0.89% std::map::clear (inline) 0 0% 82.67% 912ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.68% 912ms 0.84% boost::numeric::ublas::c_vector::swap 1ms 0.00092% 82.68% 911ms 0.84% VertexMeshWriter::MakeVtkMesh 141ms 0.13% 82.81% 908ms 0.84% std::swap_ranges (inline) 0 0% 82.81% 890ms 0.82% boost::numeric::ublas::norm_2 (inline) 646ms 0.6% 83.40% 882ms 0.82% CellPropertyCollection::GetProperty 335ms 0.31% 83.71% 864ms 0.8% boost::numeric::ublas::vector_norm_2::apply 60ms 0.055% 83.77% 861ms 0.8% std::less::operator() (inline) 82ms 0.076% 83.84% 853ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 834ms 0.77% 84.62% 834ms 0.77% tcache_put (inline) 1ms 0.00092% 84.62% 831ms 0.77% std::map::find (inline) 619ms 0.57% 85.19% 801ms 0.74% std::operator< (inline) 0 0% 85.19% 767ms 0.71% std::iter_swap (inline) 767ms 0.71% 85.90% 767ms 0.71% std::swap (inline) 12ms 0.011% 85.91% 738ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.91% 725ms 0.67% std::_Rb_tree::_Auto_node::_M_insert (inline) 18ms 0.017% 85.93% 725ms 0.67% std::_Rb_tree::_M_insert_node (inline) 348ms 0.32% 86.25% 695ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 2ms 0.0018% 86.25% 681ms 0.63% vtkPolygon::New 679ms 0.63% 86.88% 679ms 0.63% std::vector::size (inline) 0 0% 86.88% 678ms 0.63% vtkPolygon::vtkPolygon 60ms 0.055% 86.93% 677ms 0.63% MutableElement::GetNodeLocalIndex 120ms 0.11% 87.04% 669ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 2ms 0.0018% 87.05% 666ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 87.05% 649ms 0.6% std::map::map (inline) 0 0% 87.05% 645ms 0.6% boost::numeric::ublas::norm_inf (inline) 214ms 0.2% 87.24% 645ms 0.6% boost::numeric::ublas::vector_norm_inf::apply (inline) 7ms 0.0065% 87.25% 601ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.25% 601ms 0.56% boost::numeric::ublas::vector::vector (inline) 588ms 0.54% 87.79% 588ms 0.54% Node::GetIndex 17ms 0.016% 87.81% 576ms 0.53% MutableElement::RegisterWithNodes (inline) 46ms 0.043% 87.85% 554ms 0.51% Node::AddElement 13ms 0.012% 87.87% 547ms 0.51% std::vector::_M_default_append (inline)