File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95261ms, 88.38% of 107780ms total Dropped 1133 nodes (cum <= 538.90ms) flat flat% sum% cum cum% 0 0% 0% 107317ms 99.57% __libc_start_call_main 0 0% 0% 107317ms 99.57% __libc_start_main_impl 0 0% 0% 107317ms 99.57% _start 0 0% 0% 107296ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107296ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107296ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107296ms 99.55% main 0 0% 0% 107259ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107259ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107259ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107252ms 99.51% AbstractCellBasedSimulation::Solve 11ms 0.01% 0.012% 55763ms 51.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 23ms 0.021% 0.033% 52626ms 48.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 148ms 0.14% 0.17% 51111ms 47.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 345ms 0.32% 0.49% 39650ms 36.79% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.49% 38599ms 35.81% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.49% 23849ms 22.13% VertexBasedCellPopulation::Update 2ms 0.0019% 0.5% 23720ms 22.01% MutableVertexMesh::ReMesh 14502ms 13.46% 13.95% 22828ms 21.18% Cylindrical2dVertexMesh::GetVectorFromAtoB 94ms 0.087% 14.04% 17394ms 16.14% Cell::ReadyToDivide 87ms 0.081% 14.12% 16132ms 14.97% AbstractPhaseBasedCellCycleModel::ReadyToDivide 352ms 0.33% 14.45% 14862ms 13.79% NagaiHondaForce::GetAdhesionParameter 443ms 0.41% 14.86% 14181ms 13.16% boost::numeric::ublas::c_vector::c_vector (partial-inline) 117ms 0.11% 14.97% 13809ms 12.81% SimpleWntCellCycleModel::UpdateCellCyclePhase 154ms 0.14% 15.11% 13477ms 12.50% CellPropertyCollection::GetPropertiesType (inline) 390ms 0.36% 15.47% 12617ms 11.71% boost::numeric::ublas::vector_assign (inline) 153ms 0.14% 15.61% 12050ms 11.18% MutableVertexMesh::CheckForIntersections 3125ms 2.90% 18.51% 11054ms 10.26% __dynamic_cast 71ms 0.066% 18.58% 10955ms 10.16% AbstractCellProperty::IsSubType (inline) 65ms 0.06% 18.64% 10951ms 10.16% VertexBasedCellPopulation::GetDampingConstant 88ms 0.082% 18.72% 10473ms 9.72% AbstractTargetAreaModifier::UpdateTargetAreas 61ms 0.057% 18.78% 10357ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 18.80% 10167ms 9.43% AbstractCellBasedSimulation::DoCellBirth 1320ms 1.22% 20.02% 10043ms 9.32% std::__new_allocator::allocate (inline) 0 0% 20.02% 9542ms 8.85% std::allocator_traits::allocate (inline) 0 0% 20.02% 9513ms 8.83% std::_Rb_tree::_M_create_node (inline) 2618ms 2.43% 22.45% 9314ms 8.64% boost::numeric::ublas::indexing_vector_assign 782ms 0.73% 23.18% 8902ms 8.26% VertexMesh::ElementIncludesPoint 0 0% 23.18% 8877ms 8.24% std::_Rb_tree::_M_get_node (inline) 1284ms 1.19% 24.37% 8869ms 8.23% std::_Rb_tree::_M_erase 823ms 0.76% 25.13% 8851ms 8.21% operator new 26ms 0.024% 25.16% 8845ms 8.21% VertexBasedCellPopulation::GetLocationOfCellCentre 353ms 0.33% 25.49% 8760ms 8.13% VertexMesh::GetNextEdgeGradientOfElementAtNode 79ms 0.073% 25.56% 8419ms 7.81% Cell::GetMutationState 0 0% 25.56% 8376ms 7.77% std::_Rb_tree::_Alloc_node::operator() (inline) 465ms 0.43% 25.99% 8364ms 7.76% VertexMesh::GetCentroidOfElement 219ms 0.2% 26.19% 8124ms 7.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.19% 7994ms 7.42% std::_Rb_tree::_M_drop_node (inline) 3162ms 2.93% 29.13% 7851ms 7.28% __GI___libc_malloc 242ms 0.22% 29.35% 7815ms 7.25% std::__new_allocator::deallocate (inline) 0 0% 29.35% 7765ms 7.20% std::allocator_traits::deallocate (inline) 2975ms 2.76% 32.11% 7736ms 7.18% __GI___libc_free 0 0% 32.11% 7696ms 7.14% std::_Rb_tree::_M_put_node (inline) 0 0% 32.11% 7671ms 7.12% std::set::~set (inline) 12ms 0.011% 32.12% 7315ms 6.79% MutableVertexMesh::RemoveDeletedNodesAndElements 452ms 0.42% 32.54% 7112ms 6.60% std::map::operator[] (partial-inline) 1422ms 1.32% 33.86% 7094ms 6.58% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 154ms 0.14% 34.00% 6923ms 6.42% std::_Rb_tree::_Rb_tree (partial-inline) 686ms 0.64% 34.64% 6511ms 6.04% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 34.65% 6510ms 6.04% std::set::set (inline) 97ms 0.09% 34.74% 6456ms 5.99% SimpleWntCellCycleModel::GetWntLevel 6355ms 5.90% 40.64% 6355ms 5.90% __strcmp_avx2 160ms 0.15% 40.79% 6278ms 5.82% WntConcentration::GetWntLevel 5894ms 5.47% 46.26% 5894ms 5.47% boost::numeric::ublas::c_vector::operator() 2405ms 2.23% 48.49% 5601ms 5.20% std::_Rb_tree::_M_lower_bound (inline) 706ms 0.66% 49.14% 5568ms 5.17% std::_Rb_tree::_M_clone_node (inline) 2690ms 2.50% 51.64% 5539ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.00093% 51.64% 5472ms 5.08% std::set::insert (inline) 28ms 0.026% 51.66% 5189ms 4.81% MutableVertexMesh::RemoveDeletedNodes 34ms 0.032% 51.70% 5030ms 4.67% EdgeHelper::RemoveDeletedEdges 1472ms 1.37% 53.06% 4783ms 4.44% boost::numeric::ublas::c_vector::operator[] (inline) 38ms 0.035% 53.10% 4756ms 4.41% EdgeHelper::UpdateEdgesMapKey 4434ms 4.11% 57.21% 4746ms 4.40% _int_free 62ms 0.058% 57.27% 4631ms 4.30% std::set_intersection (inline) 206ms 0.19% 57.46% 4599ms 4.27% MutableElement::ResetIndex 574ms 0.53% 57.99% 4598ms 4.27% std::_Rb_tree::_M_insert_ (inline) 306ms 0.28% 58.28% 4569ms 4.24% std::__set_intersection 1ms 0.00093% 58.28% 4564ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.28% 4482ms 4.16% std::_Rb_tree::lower_bound (inline) 0 0% 58.28% 4482ms 4.16% std::map::lower_bound (inline) 4056ms 3.76% 62.04% 4056ms 3.76% boost::numeric::ublas::same_impl_ex 124ms 0.12% 62.16% 3933ms 3.65% AbstractCellPopulation::GetCellUsingLocationIndex 37ms 0.034% 62.19% 3854ms 3.58% Cell::GetCellProliferativeType 63ms 0.058% 62.25% 3688ms 3.42% AbstractCellProperty::IsType (inline) 14ms 0.013% 62.26% 3502ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.26% 3259ms 3.02% std::insert_iterator::operator= (inline) 919ms 0.85% 63.11% 3232ms 3.00% AbstractElement::GetNodeLocation 2204ms 2.04% 65.16% 3128ms 2.90% _int_malloc 43ms 0.04% 65.20% 3092ms 2.87% Cell::SetCellProliferativeType 679ms 0.63% 65.83% 3037ms 2.82% boost::numeric::ublas::vector_binary::size (inline) 30ms 0.028% 65.86% 2892ms 2.68% std::_Rb_tree::erase 2ms 0.0019% 65.86% 2889ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 449ms 0.42% 66.27% 2816ms 2.61% std::_Rb_tree_const_iterator::operator++ (inline) 714ms 0.66% 66.94% 2657ms 2.47% AbstractCellProperty::IsSame 2615ms 2.43% 69.36% 2615ms 2.43% std::_Rb_tree::_S_right (inline) 39ms 0.036% 69.40% 2606ms 2.42% CellPropertyCollection::HasProperty 0 0% 69.40% 2582ms 2.40% std::_Rb_tree::_M_insert_unique 259ms 0.24% 69.64% 2525ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.64% 2507ms 2.33% Cell::HasCellProperty (inline) 0 0% 69.64% 2480ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 19ms 0.018% 69.66% 2445ms 2.27% Cell::GetCellData 0 0% 69.66% 2384ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.66% 2315ms 2.15% boost::numeric::ublas::c_vector::assign (inline) 89ms 0.083% 69.74% 2215ms 2.06% VertexMesh::GetVolumeOfElement 97ms 0.09% 69.83% 2212ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.00093% 69.83% 2209ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 254ms 0.24% 70.07% 2207ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 2185ms 2.03% 72.09% 2185ms 2.03% std::_Rb_tree_increment 31ms 0.029% 72.12% 2131ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00093% 72.12% 1963ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.12% 1953ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 433ms 0.4% 72.53% 1943ms 1.80% std::type_info::operator== (inline) 0 0% 72.53% 1895ms 1.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.53% 1895ms 1.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1266ms 1.17% 73.70% 1889ms 1.75% std::_Rb_tree::equal_range (inline) 70ms 0.065% 73.77% 1828ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.77% 1733ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.028% 73.79% 1687ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 20ms 0.019% 73.81% 1621ms 1.50% VertexMesh::GetSurfaceAreaOfElement 165ms 0.15% 73.96% 1597ms 1.48% CellPropertyCollection::AddProperty 57ms 0.053% 74.02% 1512ms 1.40% Node::RemoveElement 24ms 0.022% 74.04% 1480ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 83ms 0.077% 74.12% 1476ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 18ms 0.017% 74.13% 1466ms 1.36% std::set::erase (inline) 1ms 0.00093% 74.13% 1377ms 1.28% tcache_get (inline) 1376ms 1.28% 75.41% 1376ms 1.28% tcache_get_n (inline) 133ms 0.12% 75.53% 1360ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.53% 1287ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 75.53% 1250ms 1.16% boost::numeric::ublas::vector_binary::operator() (inline) 74ms 0.069% 75.60% 1205ms 1.12% std::less::operator() (inline) 0 0% 75.60% 1203ms 1.12% boost::numeric::ublas::norm_2 (inline) 531ms 0.49% 76.10% 1198ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1143ms 1.06% 77.16% 1143ms 1.06% [libchaste_cell_based.so] 69ms 0.064% 77.22% 1138ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 77.22% 1137ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 907ms 0.84% 78.06% 1131ms 1.05% std::operator< (inline) 110ms 0.1% 78.16% 1126ms 1.04% std::_Rb_tree::find (inline) 1120ms 1.04% 79.20% 1120ms 1.04% Node::rGetLocation 19ms 0.018% 79.22% 1091ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 31ms 0.029% 79.25% 1079ms 1.00% CellPropertyRegistry::Get 1079ms 1.00% 80.25% 1079ms 1.00% std::_Rb_tree_insert_and_rebalance 9ms 0.0084% 80.26% 1014ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00093% 80.26% 968ms 0.9% std::_Rb_tree::clear (inline) 22ms 0.02% 80.28% 959ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.28% 957ms 0.89% std::map::clear (inline) 942ms 0.87% 81.15% 942ms 0.87% std::vector::size (inline) 165ms 0.15% 81.31% 939ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 81.31% 939ms 0.87% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.31% 928ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0084% 81.32% 928ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 0 0% 81.32% 923ms 0.86% std::map::find (inline) 180ms 0.17% 81.48% 922ms 0.86% boost::numeric::ublas::detail::equals 94ms 0.087% 81.57% 919ms 0.85% std::swap_ranges (inline) 373ms 0.35% 81.92% 896ms 0.83% Edge::GetMapIndex 876ms 0.81% 82.73% 876ms 0.81% [libchaste_mesh.so] 5ms 0.0046% 82.73% 840ms 0.78% VertexMeshWriter::MakeVtkMesh 826ms 0.77% 83.50% 826ms 0.77% std::swap (inline) 0 0% 83.50% 825ms 0.77% std::iter_swap (inline) 113ms 0.1% 83.60% 778ms 0.72% MutableElement::GetNodeLocalIndex 26ms 0.024% 83.63% 770ms 0.71% MutableElement::RegisterWithEdges (inline) 470ms 0.44% 84.06% 764ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 39ms 0.036% 84.10% 757ms 0.7% Edge::AddElement 733ms 0.68% 84.78% 738ms 0.68% boost::detail::sp_counted_base::release 12ms 0.011% 84.79% 730ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 101ms 0.094% 84.89% 727ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 127ms 0.12% 85.00% 726ms 0.67% boost::shared_ptr::shared_ptr (inline) 113ms 0.1% 85.11% 718ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 704ms 0.65% 85.76% 704ms 0.65% Node::GetIndex 0 0% 85.76% 692ms 0.64% boost::numeric::ublas::norm_inf (inline) 360ms 0.33% 86.10% 692ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 117ms 0.11% 86.20% 684ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.20% 684ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.20% 665ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.20% 664ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.20% 653ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 86.22% 653ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.22% 636ms 0.59% std::_Rb_tree::_M_construct_node (inline) 559ms 0.52% 86.74% 599ms 0.56% boost::detail::shared_count::shared_count (inline) 1ms 0.00093% 86.74% 595ms 0.55% vtkPolygon::New 2ms 0.0019% 86.75% 593ms 0.55% vtkPolygon::vtkPolygon 0 0% 86.75% 588ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 579ms 0.54% 87.28% 579ms 0.54% boost::shared_ptr::operator-> (inline) 576ms 0.53% 87.82% 576ms 0.53% [libstdc++.so.6.0.33] 13ms 0.012% 87.83% 575ms 0.53% std::vector::_M_default_append (inline) 571ms 0.53% 88.36% 571ms 0.53% operator delete 27ms 0.025% 88.38% 569ms 0.53% MutableElement::RegisterWithNodes (inline)