File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96041ms, 88.74% of 108222ms total Dropped 1088 nodes (cum <= 541.11ms) flat flat% sum% cum cum% 0 0% 0% 107778ms 99.59% __libc_start_call_main 0 0% 0% 107778ms 99.59% __libc_start_main_impl 0 0% 0% 107778ms 99.59% _start 0 0% 0% 107759ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107759ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107759ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107759ms 99.57% main 0 0% 0% 107722ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107722ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107722ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107715ms 99.53% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.016% 55808ms 51.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.032% 52666ms 48.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 125ms 0.12% 0.15% 51581ms 47.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 399ms 0.37% 0.52% 40001ms 36.96% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.52% 39054ms 36.09% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.52% 24230ms 22.39% VertexBasedCellPopulation::Update 1ms 0.00092% 0.52% 24121ms 22.29% MutableVertexMesh::ReMesh 14442ms 13.34% 13.87% 23001ms 21.25% Cylindrical2dVertexMesh::GetVectorFromAtoB 73ms 0.067% 13.93% 17404ms 16.08% Cell::ReadyToDivide 110ms 0.1% 14.03% 16223ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 344ms 0.32% 14.35% 14798ms 13.67% NagaiHondaForce::GetAdhesionParameter 435ms 0.4% 14.75% 14489ms 13.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 133ms 0.12% 14.88% 13764ms 12.72% SimpleWntCellCycleModel::UpdateCellCyclePhase 129ms 0.12% 15.00% 13653ms 12.62% CellPropertyCollection::GetPropertiesType (inline) 387ms 0.36% 15.35% 12903ms 11.92% boost::numeric::ublas::vector_assign (inline) 108ms 0.1% 15.45% 12033ms 11.12% MutableVertexMesh::CheckForIntersections 3254ms 3.01% 18.46% 11355ms 10.49% __dynamic_cast 70ms 0.065% 18.52% 11218ms 10.37% AbstractCellProperty::IsSubType (inline) 60ms 0.055% 18.58% 11084ms 10.24% VertexBasedCellPopulation::GetDampingConstant 90ms 0.083% 18.66% 10405ms 9.61% AbstractTargetAreaModifier::UpdateTargetAreas 58ms 0.054% 18.72% 10283ms 9.50% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 17ms 0.016% 18.73% 10225ms 9.45% AbstractCellBasedSimulation::DoCellBirth 1328ms 1.23% 19.96% 10115ms 9.35% std::__new_allocator::allocate (inline) 2665ms 2.46% 22.42% 9640ms 8.91% boost::numeric::ublas::indexing_vector_assign 0 0% 22.42% 9538ms 8.81% std::allocator_traits::allocate (inline) 0 0% 22.42% 9481ms 8.76% std::_Rb_tree::_M_create_node (inline) 1432ms 1.32% 23.75% 9216ms 8.52% std::_Rb_tree::_M_erase 758ms 0.7% 24.45% 8929ms 8.25% VertexMesh::ElementIncludesPoint 844ms 0.78% 25.23% 8918ms 8.24% operator new 352ms 0.33% 25.55% 8889ms 8.21% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.55% 8823ms 8.15% std::_Rb_tree::_M_get_node (inline) 25ms 0.023% 25.57% 8755ms 8.09% VertexBasedCellPopulation::GetLocationOfCellCentre 75ms 0.069% 25.64% 8653ms 8.00% Cell::GetMutationState 224ms 0.21% 25.85% 8373ms 7.74% std::_Rb_tree::~_Rb_tree (inline) 502ms 0.46% 26.31% 8348ms 7.71% VertexMesh::GetCentroidOfElement 0 0% 26.31% 8196ms 7.57% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.31% 8054ms 7.44% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.31% 7930ms 7.33% std::set::~set (inline) 3129ms 2.89% 29.21% 7870ms 7.27% __GI___libc_malloc 247ms 0.23% 29.43% 7786ms 7.19% std::__new_allocator::deallocate (inline) 0 0% 29.43% 7762ms 7.17% std::allocator_traits::deallocate (inline) 0 0% 29.43% 7709ms 7.12% std::_Rb_tree::_M_put_node (inline) 2957ms 2.73% 32.17% 7626ms 7.05% __GI___libc_free 22ms 0.02% 32.19% 7418ms 6.85% MutableVertexMesh::RemoveDeletedNodesAndElements 466ms 0.43% 32.62% 7306ms 6.75% std::map::operator[] (partial-inline) 1384ms 1.28% 33.90% 7221ms 6.67% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 151ms 0.14% 34.04% 6758ms 6.24% std::_Rb_tree::_Rb_tree (partial-inline) 6396ms 5.91% 39.95% 6396ms 5.91% boost::numeric::ublas::c_vector::operator() 115ms 0.11% 40.05% 6384ms 5.90% SimpleWntCellCycleModel::GetWntLevel 650ms 0.6% 40.65% 6374ms 5.89% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 40.66% 6330ms 5.85% std::set::set (inline) 6246ms 5.77% 46.44% 6246ms 5.77% __strcmp_avx2 133ms 0.12% 46.56% 6162ms 5.69% WntConcentration::GetWntLevel 2828ms 2.61% 49.17% 5577ms 5.15% __cxxabiv1::__si_class_type_info::__do_dyncast 2338ms 2.16% 51.33% 5557ms 5.13% std::_Rb_tree::_M_lower_bound (inline) 29ms 0.027% 51.36% 5473ms 5.06% MutableVertexMesh::RemoveDeletedNodes 736ms 0.68% 52.04% 5446ms 5.03% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.04% 5371ms 4.96% std::set::insert (inline) 44ms 0.041% 52.08% 5303ms 4.90% EdgeHelper::RemoveDeletedEdges 34ms 0.031% 52.11% 5021ms 4.64% EdgeHelper::UpdateEdgesMapKey 1526ms 1.41% 53.52% 4920ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 4347ms 4.02% 57.54% 4663ms 4.31% _int_free 1ms 0.00092% 57.54% 4587ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 209ms 0.19% 57.73% 4544ms 4.20% MutableElement::ResetIndex 515ms 0.48% 58.21% 4536ms 4.19% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.21% 4522ms 4.18% std::_Rb_tree::lower_bound (inline) 0 0% 58.21% 4522ms 4.18% std::map::lower_bound (inline) 55ms 0.051% 58.26% 4500ms 4.16% std::set_intersection (inline) 261ms 0.24% 58.50% 4445ms 4.11% std::__set_intersection 4031ms 3.72% 62.22% 4031ms 3.72% boost::numeric::ublas::same_impl_ex 49ms 0.045% 62.27% 4010ms 3.71% Cell::GetCellProliferativeType 115ms 0.11% 62.38% 3993ms 3.69% AbstractCellPopulation::GetCellUsingLocationIndex 64ms 0.059% 62.43% 3522ms 3.25% AbstractCellProperty::IsType (inline) 8ms 0.0074% 62.44% 3479ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 852ms 0.79% 63.23% 3315ms 3.06% AbstractElement::GetNodeLocation 0 0% 63.23% 3245ms 3.00% std::insert_iterator::operator= (inline) 60ms 0.055% 63.28% 3146ms 2.91% Cell::SetCellProliferativeType 2207ms 2.04% 65.32% 3142ms 2.90% _int_malloc 645ms 0.6% 65.92% 2956ms 2.73% boost::numeric::ublas::vector_binary::size (inline) 29ms 0.027% 65.95% 2899ms 2.68% std::_Rb_tree::erase 3ms 0.0028% 65.95% 2884ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 459ms 0.42% 66.37% 2733ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 2713ms 2.51% 68.88% 2713ms 2.51% std::_Rb_tree::_S_right (inline) 223ms 0.21% 69.09% 2528ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 57ms 0.053% 69.14% 2514ms 2.32% CellPropertyCollection::HasProperty 709ms 0.66% 69.79% 2501ms 2.31% AbstractCellProperty::IsSame 1ms 0.00092% 69.80% 2487ms 2.30% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.80% 2436ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.80% 2429ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.80% 2420ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.80% 2402ms 2.22% Cell::HasCellProperty (inline) 32ms 0.03% 69.82% 2383ms 2.20% Cell::GetCellData 103ms 0.095% 69.92% 2337ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 88ms 0.081% 70.00% 2298ms 2.12% VertexMesh::GetVolumeOfElement 40ms 0.037% 70.04% 2276ms 2.10% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0028% 70.04% 2253ms 2.08% AbstractCellPopulation::Iterator::operator++ (inline) 252ms 0.23% 70.27% 2229ms 2.06% AbstractCellPopulation::Iterator::IsRealCell 2101ms 1.94% 72.22% 2101ms 1.94% std::_Rb_tree_increment 1ms 0.00092% 72.22% 2020ms 1.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.22% 2020ms 1.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 82ms 0.076% 72.29% 2009ms 1.86% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 72.29% 1992ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 72.29% 1975ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1350ms 1.25% 73.54% 1957ms 1.81% std::_Rb_tree::equal_range (inline) 428ms 0.4% 73.94% 1792ms 1.66% std::type_info::operator== (inline) 0 0% 73.94% 1773ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 37ms 0.034% 73.97% 1668ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 111ms 0.1% 74.07% 1624ms 1.50% boost::numeric::ublas::vector_reference::operator() (inline) 30ms 0.028% 74.10% 1595ms 1.47% VertexMesh::GetSurfaceAreaOfElement 162ms 0.15% 74.25% 1542ms 1.42% CellPropertyCollection::AddProperty 42ms 0.039% 74.29% 1489ms 1.38% Node::RemoveElement 21ms 0.019% 74.31% 1457ms 1.35% std::set::erase (inline) 0 0% 74.31% 1455ms 1.34% boost::numeric::ublas::vector_binary::operator() (inline) 97ms 0.09% 74.40% 1446ms 1.34% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 33ms 0.03% 74.43% 1445ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.43% 1417ms 1.31% tcache_get (inline) 1417ms 1.31% 75.74% 1417ms 1.31% tcache_get_n (inline) 0 0% 75.74% 1285ms 1.19% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.74% 1276ms 1.18% boost::numeric::ublas::norm_2 (inline) 522ms 0.48% 76.22% 1265ms 1.17% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.22% 1246ms 1.15% OffLatticeSimulation::ApplyBoundaries 1207ms 1.12% 77.34% 1207ms 1.12% Node::rGetLocation 81ms 0.075% 77.41% 1146ms 1.06% std::less::operator() (inline) 97ms 0.09% 77.50% 1116ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1103ms 1.02% 78.52% 1103ms 1.02% std::_Rb_tree_insert_and_rebalance 1097ms 1.01% 79.53% 1097ms 1.01% [libchaste_cell_based.so] 1ms 0.00092% 79.53% 1075ms 0.99% std::_Rb_tree::clear (inline) 25ms 0.023% 79.56% 1069ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 864ms 0.8% 80.36% 1065ms 0.98% std::operator< (inline) 8ms 0.0074% 80.36% 1063ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.36% 1062ms 0.98% std::map::clear (inline) 78ms 0.072% 80.44% 1003ms 0.93% std::_Rb_tree::find (inline) 155ms 0.14% 80.58% 997ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.58% 997ms 0.92% boost::shared_ptr::~shared_ptr (inline) 26ms 0.024% 80.60% 982ms 0.91% CellPropertyRegistry::Get 979ms 0.9% 81.51% 979ms 0.9% [libchaste_mesh.so] 393ms 0.36% 81.87% 975ms 0.9% Edge::GetMapIndex 15ms 0.014% 81.88% 972ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 953ms 0.88% 82.77% 953ms 0.88% std::vector::size (inline) 148ms 0.14% 82.90% 945ms 0.87% boost::numeric::ublas::detail::equals 108ms 0.1% 83.00% 870ms 0.8% MutableElement::GetNodeLocalIndex 2ms 0.0018% 83.00% 865ms 0.8% VertexMeshWriter::MakeVtkMesh 0 0% 83.00% 861ms 0.8% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0028% 83.01% 861ms 0.8% boost::numeric::ublas::c_vector::swap (inline) 78ms 0.072% 83.08% 858ms 0.79% std::swap_ranges (inline) 818ms 0.76% 83.83% 822ms 0.76% boost::detail::sp_counted_base::release 162ms 0.15% 83.98% 811ms 0.75% boost::shared_ptr::shared_ptr (inline) 0 0% 83.98% 800ms 0.74% std::map::find (inline) 797ms 0.74% 84.72% 797ms 0.74% Node::GetIndex 781ms 0.72% 85.44% 781ms 0.72% std::swap (inline) 0 0% 85.44% 780ms 0.72% std::iter_swap (inline) 119ms 0.11% 85.55% 759ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 457ms 0.42% 85.97% 747ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.97% 745ms 0.69% boost::numeric::ublas::norm_inf (inline) 367ms 0.34% 86.31% 745ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.31% 724ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 32ms 0.03% 86.34% 723ms 0.67% Edge::AddElement 110ms 0.1% 86.44% 716ms 0.66% std::__new_allocator::construct (inline) 0 0% 86.44% 716ms 0.66% std::allocator_traits::construct (inline) 20ms 0.018% 86.46% 711ms 0.66% MutableElement::RegisterWithEdges (inline) 0 0% 86.46% 709ms 0.66% std::_Vector_base::_M_allocate (inline) 0 0% 86.46% 658ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.46% 654ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 86.48% 654ms 0.6% std::_Rb_tree::_M_insert_node (inline) 620ms 0.57% 87.06% 649ms 0.6% boost::detail::shared_count::shared_count (inline) 0 0% 87.06% 631ms 0.58% vtkPolygon::New 1ms 0.00092% 87.06% 630ms 0.58% vtkPolygon::vtkPolygon 610ms 0.56% 87.62% 610ms 0.56% operator delete 12ms 0.011% 87.63% 603ms 0.56% std::vector::_M_default_append (inline) 17ms 0.016% 87.65% 594ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.65% 594ms 0.55% boost::numeric::ublas::vector::vector (inline) 0 0% 87.65% 592ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 32ms 0.03% 87.68% 580ms 0.54% MutableElement::RegisterWithNodes (inline) 579ms 0.54% 88.21% 579ms 0.54% [libstdc++.so.6.0.33] 552ms 0.51% 88.72% 552ms 0.51% boost::shared_ptr::operator-> (inline) 24ms 0.022% 88.74% 544ms 0.5% Node::AddElement