File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96088ms, 87.58% of 109711ms total Dropped 1105 nodes (cum <= 548.55ms) flat flat% sum% cum cum% 0 0% 0% 109338ms 99.66% __libc_start_call_main 0 0% 0% 109338ms 99.66% __libc_start_main_impl 0 0% 0% 109338ms 99.66% _start 0 0% 0% 109317ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109317ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109317ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109317ms 99.64% main 0 0% 0% 109270ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109270ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109270ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 109262ms 99.59% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.019% 56732ms 51.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.029% 53380ms 48.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 137ms 0.12% 0.15% 52273ms 47.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 339ms 0.31% 0.46% 40194ms 36.64% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.46% 39407ms 35.92% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.46% 24258ms 22.11% VertexBasedCellPopulation::Update 3ms 0.0027% 0.47% 24092ms 21.96% MutableVertexMesh::ReMesh 14557ms 13.27% 13.74% 23165ms 21.11% Cylindrical2dVertexMesh::GetVectorFromAtoB 91ms 0.083% 13.82% 17685ms 16.12% Cell::ReadyToDivide 82ms 0.075% 13.89% 16426ms 14.97% AbstractPhaseBasedCellCycleModel::ReadyToDivide 341ms 0.31% 14.20% 14698ms 13.40% NagaiHondaForce::GetAdhesionParameter 169ms 0.15% 14.36% 14099ms 12.85% SimpleWntCellCycleModel::UpdateCellCyclePhase 121ms 0.11% 14.47% 13799ms 12.58% CellPropertyCollection::GetPropertiesType (inline) 482ms 0.44% 14.91% 13749ms 12.53% boost::numeric::ublas::c_vector::c_vector (partial-inline) 336ms 0.31% 15.21% 12301ms 11.21% boost::numeric::ublas::vector_assign (inline) 149ms 0.14% 15.35% 11886ms 10.83% MutableVertexMesh::CheckForIntersections 3523ms 3.21% 18.56% 11836ms 10.79% __dynamic_cast 74ms 0.067% 18.63% 11719ms 10.68% AbstractCellProperty::IsSubType (inline) 97ms 0.088% 18.72% 11491ms 10.47% VertexBasedCellPopulation::GetDampingConstant 68ms 0.062% 18.78% 10635ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 50ms 0.046% 18.82% 10544ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.026% 18.85% 10439ms 9.51% AbstractCellBasedSimulation::DoCellBirth 1472ms 1.34% 20.19% 10131ms 9.23% std::__new_allocator::allocate (inline) 0 0% 20.19% 9606ms 8.76% std::_Rb_tree::_M_create_node (inline) 0 0% 20.19% 9583ms 8.73% std::allocator_traits::allocate (inline) 2817ms 2.57% 22.76% 9438ms 8.60% boost::numeric::ublas::indexing_vector_assign 373ms 0.34% 23.10% 9327ms 8.50% VertexMesh::GetNextEdgeGradientOfElementAtNode 1270ms 1.16% 24.26% 9198ms 8.38% std::_Rb_tree::_M_erase 0 0% 24.26% 8899ms 8.11% std::_Rb_tree::_M_get_node (inline) 30ms 0.027% 24.29% 8812ms 8.03% VertexBasedCellPopulation::GetLocationOfCellCentre 754ms 0.69% 24.97% 8757ms 7.98% operator new 96ms 0.088% 25.06% 8754ms 7.98% Cell::GetMutationState 877ms 0.8% 25.86% 8733ms 7.96% VertexMesh::ElementIncludesPoint 0 0% 25.86% 8467ms 7.72% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.86% 8389ms 7.65% std::_Rb_tree::_M_drop_node (inline) 212ms 0.19% 26.05% 8260ms 7.53% std::_Rb_tree::~_Rb_tree (inline) 426ms 0.39% 26.44% 8241ms 7.51% VertexMesh::GetCentroidOfElement 266ms 0.24% 26.68% 8139ms 7.42% std::__new_allocator::deallocate (inline) 0 0% 26.68% 8130ms 7.41% std::allocator_traits::deallocate (inline) 0 0% 26.68% 8059ms 7.35% std::_Rb_tree::_M_put_node (inline) 17ms 0.015% 26.70% 7941ms 7.24% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.70% 7823ms 7.13% std::set::~set (inline) 450ms 0.41% 27.11% 7820ms 7.13% std::map::operator[] (partial-inline) 2913ms 2.66% 29.76% 7809ms 7.12% __GI___libc_malloc 2633ms 2.40% 32.16% 7600ms 6.93% __GI___libc_free 1434ms 1.31% 33.47% 7378ms 6.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 146ms 0.13% 33.60% 7358ms 6.71% std::_Rb_tree::_Rb_tree (partial-inline) 733ms 0.67% 34.27% 6968ms 6.35% std::_Rb_tree::_M_copy (inline) 29ms 0.026% 34.30% 6853ms 6.25% std::set::set (inline) 6569ms 5.99% 40.29% 6569ms 5.99% __strcmp_avx2 126ms 0.11% 40.40% 6405ms 5.84% SimpleWntCellCycleModel::GetWntLevel 2561ms 2.33% 42.74% 6255ms 5.70% std::_Rb_tree::_M_lower_bound (inline) 196ms 0.18% 42.91% 6191ms 5.64% WntConcentration::GetWntLevel 6108ms 5.57% 48.48% 6108ms 5.57% boost::numeric::ublas::c_vector::operator() 836ms 0.76% 49.24% 5962ms 5.43% std::_Rb_tree::_M_clone_node (inline) 2953ms 2.69% 51.94% 5631ms 5.13% __cxxabiv1::__si_class_type_info::__do_dyncast 27ms 0.025% 51.96% 5495ms 5.01% MutableVertexMesh::RemoveDeletedNodes 1944ms 1.77% 53.73% 5317ms 4.85% boost::numeric::ublas::c_vector::operator[] (inline) 30ms 0.027% 53.76% 5301ms 4.83% EdgeHelper::RemoveDeletedEdges 0 0% 53.76% 5240ms 4.78% std::set::insert (inline) 0 0% 53.76% 5143ms 4.69% std::_Rb_tree::lower_bound (inline) 0 0% 53.76% 5143ms 4.69% std::map::lower_bound (inline) 37ms 0.034% 53.79% 5000ms 4.56% EdgeHelper::UpdateEdgesMapKey 4519ms 4.12% 57.91% 4951ms 4.51% _int_free 172ms 0.16% 58.07% 4828ms 4.40% MutableElement::ResetIndex 2ms 0.0018% 58.07% 4696ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 123ms 0.11% 58.18% 4485ms 4.09% AbstractCellPopulation::GetCellUsingLocationIndex 497ms 0.45% 58.64% 4416ms 4.03% std::_Rb_tree::_M_insert_ (inline) 111ms 0.1% 58.74% 4344ms 3.96% std::set_intersection (inline) 231ms 0.21% 58.95% 4233ms 3.86% std::__set_intersection 42ms 0.038% 58.99% 3908ms 3.56% Cell::GetCellProliferativeType 3795ms 3.46% 62.44% 3795ms 3.46% boost::numeric::ublas::same_impl_ex 54ms 0.049% 62.49% 3744ms 3.41% AbstractCellProperty::IsType (inline) 16ms 0.015% 62.51% 3583ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2296ms 2.09% 64.60% 3285ms 2.99% _int_malloc 0 0% 64.60% 3274ms 2.98% std::insert_iterator::operator= (inline) 68ms 0.062% 64.66% 3167ms 2.89% std::_Rb_tree::erase 74ms 0.067% 64.73% 3149ms 2.87% Cell::SetCellProliferativeType 947ms 0.86% 65.59% 3148ms 2.87% AbstractElement::GetNodeLocation 3103ms 2.83% 68.42% 3103ms 2.83% std::_Rb_tree::_S_right (inline) 6ms 0.0055% 68.43% 2866ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.021% 68.45% 2681ms 2.44% CellPropertyCollection::HasProperty 776ms 0.71% 69.16% 2678ms 2.44% AbstractCellProperty::IsSame 0 0% 69.16% 2651ms 2.42% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.16% 2573ms 2.35% Cell::HasCellProperty (inline) 549ms 0.5% 69.66% 2546ms 2.32% boost::numeric::ublas::vector_binary::size (inline) 235ms 0.21% 69.87% 2529ms 2.31% std::_Rb_tree_const_iterator::operator++ (inline) 236ms 0.22% 70.09% 2523ms 2.30% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.09% 2498ms 2.28% boost::numeric::ublas::c_vector::assign (inline) 21ms 0.019% 70.11% 2467ms 2.25% Cell::GetCellData 0 0% 70.11% 2460ms 2.24% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0018% 70.11% 2374ms 2.16% std::_Rb_tree::_M_insert_unique (inline) 89ms 0.081% 70.19% 2313ms 2.11% VertexMesh::GetVolumeOfElement 9ms 0.0082% 70.20% 2296ms 2.09% AbstractCellPopulation::Iterator::operator++ (inline) 174ms 0.16% 70.35% 2275ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 40ms 0.036% 70.39% 2231ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 35ms 0.032% 70.42% 2185ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 1362ms 1.24% 71.66% 2047ms 1.87% std::_Rb_tree::equal_range (inline) 2033ms 1.85% 73.52% 2033ms 1.85% std::_Rb_tree_increment 1ms 0.00091% 73.52% 2012ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.52% 2000ms 1.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.52% 2000ms 1.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0018% 73.52% 1994ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 451ms 0.41% 73.93% 1902ms 1.73% std::type_info::operator== (inline) 77ms 0.07% 74.00% 1811ms 1.65% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.00% 1795ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 74.02% 1771ms 1.61% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 40ms 0.036% 74.06% 1616ms 1.47% VertexMesh::GetSurfaceAreaOfElement 37ms 0.034% 74.09% 1584ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 52ms 0.047% 74.14% 1568ms 1.43% Node::RemoveElement 89ms 0.081% 74.22% 1544ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 6ms 0.0055% 74.23% 1520ms 1.39% std::set::erase (inline) 1ms 0.00091% 74.23% 1431ms 1.30% tcache_get (inline) 1430ms 1.30% 75.53% 1430ms 1.30% tcache_get_n (inline) 3ms 0.0027% 75.53% 1360ms 1.24% OffLatticeSimulation::ApplyBoundaries 147ms 0.13% 75.67% 1353ms 1.23% CellPropertyCollection::AddProperty 0 0% 75.67% 1332ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.67% 1317ms 1.20% boost::numeric::ublas::norm_2 (inline) 58ms 0.053% 75.72% 1317ms 1.20% boost::numeric::ublas::vector_reference::operator() (inline) 69ms 0.063% 75.78% 1311ms 1.19% std::less::operator() (inline) 613ms 0.56% 76.34% 1306ms 1.19% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1300ms 1.18% 77.53% 1300ms 1.18% [libchaste_cell_based.so] 91ms 0.083% 77.61% 1245ms 1.13% std::_Rb_tree::_M_erase_aux (partial-inline) 1035ms 0.94% 78.55% 1242ms 1.13% std::operator< (inline) 25ms 0.023% 78.57% 1173ms 1.07% CellPropertyRegistry::Get 1169ms 1.07% 79.64% 1169ms 1.07% std::_Rb_tree_insert_and_rebalance 110ms 0.1% 79.74% 1161ms 1.06% std::_Rb_tree::find (inline) 11ms 0.01% 79.75% 1159ms 1.06% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.75% 1156ms 1.05% std::_Rb_tree::clear (inline) 0 0% 79.75% 1139ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 79.75% 1135ms 1.03% std::map::clear (inline) 5ms 0.0046% 79.75% 1070ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.75% 1035ms 0.94% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0082% 79.76% 1035ms 0.94% boost::numeric::ublas::c_vector::swap (inline) 76ms 0.069% 79.83% 1026ms 0.94% std::swap_ranges (inline) 1008ms 0.92% 80.75% 1008ms 0.92% Node::rGetLocation 109ms 0.099% 80.85% 1001ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.85% 1001ms 0.91% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.85% 970ms 0.88% std::map::find (inline) 952ms 0.87% 81.72% 952ms 0.87% std::swap (inline) 0 0% 81.72% 950ms 0.87% std::iter_swap (inline) 2ms 0.0018% 81.72% 933ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 184ms 0.17% 81.89% 919ms 0.84% boost::numeric::ublas::detail::equals 0 0% 81.89% 858ms 0.78% VertexMeshWriter::MakeVtkMesh 851ms 0.78% 82.66% 851ms 0.78% std::vector::size (inline) 818ms 0.75% 83.41% 844ms 0.77% boost::detail::sp_counted_base::release 786ms 0.72% 84.13% 786ms 0.72% [libchaste_mesh.so] 113ms 0.1% 84.23% 784ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 19ms 0.017% 84.25% 782ms 0.71% MutableElement::RegisterWithEdges (inline) 373ms 0.34% 84.59% 776ms 0.71% Edge::GetMapIndex 32ms 0.029% 84.62% 772ms 0.7% Edge::AddElement 0 0% 84.62% 767ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 230ms 0.21% 84.82% 751ms 0.68% std::__new_allocator::construct (inline) 0 0% 84.82% 751ms 0.68% std::allocator_traits::construct (inline) 425ms 0.39% 85.21% 742ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.21% 707ms 0.64% std::_Rb_tree::_M_construct_node (inline) 118ms 0.11% 85.32% 694ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 85.32% 691ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 85.34% 691ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.34% 683ms 0.62% boost::numeric::ublas::norm_inf (inline) 389ms 0.35% 85.69% 683ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.00091% 85.70% 678ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 85.70% 673ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 175ms 0.16% 85.85% 662ms 0.6% boost::shared_ptr::shared_ptr (inline) 660ms 0.6% 86.46% 660ms 0.6% Node::GetIndex 1ms 0.00091% 86.46% 639ms 0.58% vtkPolygon::New 0 0% 86.46% 637ms 0.58% vtkPolygon::vtkPolygon 624ms 0.57% 87.03% 624ms 0.57% [libstdc++.so.6.0.33] 31ms 0.028% 87.05% 580ms 0.53% MutableElement::RegisterWithNodes (inline) 23ms 0.021% 87.08% 571ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.08% 571ms 0.52% boost::numeric::ublas::vector::vector (inline) 8ms 0.0073% 87.08% 570ms 0.52% std::vector::_M_default_append (inline) 549ms 0.5% 87.58% 549ms 0.5% boost::shared_ptr::operator-> (inline)