File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96807ms, 88.66% of 109195ms total Dropped 1084 nodes (cum <= 545.98ms) flat flat% sum% cum cum% 0 0% 0% 108741ms 99.58% __libc_start_call_main 0 0% 0% 108741ms 99.58% __libc_start_main_impl 0 0% 0% 108741ms 99.58% _start 0 0% 0% 108721ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108721ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108721ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108721ms 99.57% main 0 0% 0% 108684ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108684ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108684ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108675ms 99.52% AbstractCellBasedSimulation::Solve 17ms 0.016% 0.019% 56596ms 51.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.015% 0.034% 53364ms 48.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 131ms 0.12% 0.15% 52266ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 424ms 0.39% 0.54% 40320ms 36.92% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.54% 39263ms 35.96% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.54% 24330ms 22.28% VertexBasedCellPopulation::Update 0 0% 0.54% 24206ms 22.17% MutableVertexMesh::ReMesh 14684ms 13.45% 13.99% 23257ms 21.30% Cylindrical2dVertexMesh::GetVectorFromAtoB 70ms 0.064% 14.05% 17377ms 15.91% Cell::ReadyToDivide 98ms 0.09% 14.14% 16161ms 14.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 338ms 0.31% 14.45% 14812ms 13.56% NagaiHondaForce::GetAdhesionParameter 417ms 0.38% 14.84% 14394ms 13.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 120ms 0.11% 14.95% 13771ms 12.61% SimpleWntCellCycleModel::UpdateCellCyclePhase 120ms 0.11% 15.06% 13435ms 12.30% CellPropertyCollection::GetPropertiesType (inline) 398ms 0.36% 15.42% 12806ms 11.73% boost::numeric::ublas::vector_assign (inline) 128ms 0.12% 15.54% 12094ms 11.08% MutableVertexMesh::CheckForIntersections 75ms 0.069% 15.61% 11411ms 10.45% VertexBasedCellPopulation::GetDampingConstant 3285ms 3.01% 18.61% 11046ms 10.12% __dynamic_cast 99ms 0.091% 18.71% 10996ms 10.07% AbstractCellProperty::IsSubType (inline) 97ms 0.089% 18.79% 10439ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 58ms 0.053% 18.85% 10294ms 9.43% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 18.87% 10246ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1376ms 1.26% 20.13% 10080ms 9.23% std::__new_allocator::allocate (inline) 2687ms 2.46% 22.59% 9613ms 8.80% boost::numeric::ublas::indexing_vector_assign 0 0% 22.59% 9558ms 8.75% std::allocator_traits::allocate (inline) 0 0% 22.59% 9532ms 8.73% std::_Rb_tree::_M_create_node (inline) 1392ms 1.27% 23.86% 9291ms 8.51% std::_Rb_tree::_M_erase 24ms 0.022% 23.88% 8994ms 8.24% VertexBasedCellPopulation::GetLocationOfCellCentre 385ms 0.35% 24.24% 8952ms 8.20% VertexMesh::GetNextEdgeGradientOfElementAtNode 821ms 0.75% 24.99% 8937ms 8.18% VertexMesh::ElementIncludesPoint 0 0% 24.99% 8900ms 8.15% std::_Rb_tree::_M_get_node (inline) 808ms 0.74% 25.73% 8815ms 8.07% operator new 78ms 0.071% 25.80% 8544ms 7.82% Cell::GetMutationState 467ms 0.43% 26.23% 8500ms 7.78% VertexMesh::GetCentroidOfElement 222ms 0.2% 26.43% 8470ms 7.76% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.43% 8359ms 7.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.43% 8229ms 7.54% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.43% 8022ms 7.35% std::set::~set (inline) 249ms 0.23% 26.66% 7981ms 7.31% std::__new_allocator::deallocate (inline) 0 0% 26.66% 7951ms 7.28% std::allocator_traits::deallocate (inline) 0 0% 26.66% 7894ms 7.23% std::_Rb_tree::_M_put_node (inline) 2965ms 2.72% 29.37% 7815ms 7.16% __GI___libc_malloc 479ms 0.44% 29.81% 7745ms 7.09% std::map::operator[] (partial-inline) 2925ms 2.68% 32.49% 7719ms 7.07% __GI___libc_free 17ms 0.016% 32.51% 7633ms 6.99% MutableVertexMesh::RemoveDeletedNodesAndElements 1381ms 1.26% 33.77% 7153ms 6.55% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 166ms 0.15% 33.92% 6887ms 6.31% std::_Rb_tree::_Rb_tree (partial-inline) 123ms 0.11% 34.04% 6523ms 5.97% SimpleWntCellCycleModel::GetWntLevel 664ms 0.61% 34.65% 6521ms 5.97% std::_Rb_tree::_M_copy (inline) 13ms 0.012% 34.66% 6498ms 5.95% std::set::set (inline) 143ms 0.13% 34.79% 6288ms 5.76% WntConcentration::GetWntLevel 2379ms 2.18% 36.97% 6186ms 5.67% std::_Rb_tree::_M_lower_bound (inline) 6173ms 5.65% 42.62% 6173ms 5.65% boost::numeric::ublas::c_vector::operator() 6074ms 5.56% 48.18% 6074ms 5.56% __strcmp_avx2 731ms 0.67% 48.85% 5576ms 5.11% std::_Rb_tree::_M_clone_node (inline) 16ms 0.015% 48.87% 5440ms 4.98% MutableVertexMesh::RemoveDeletedNodes 2727ms 2.50% 51.36% 5374ms 4.92% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.36% 5367ms 4.92% std::set::insert (inline) 28ms 0.026% 51.39% 5287ms 4.84% EdgeHelper::RemoveDeletedEdges 0 0% 51.39% 5038ms 4.61% std::_Rb_tree::lower_bound (inline) 0 0% 51.39% 5038ms 4.61% std::map::lower_bound (inline) 29ms 0.027% 51.42% 5029ms 4.61% EdgeHelper::UpdateEdgesMapKey 1560ms 1.43% 52.84% 4933ms 4.52% boost::numeric::ublas::c_vector::operator[] (inline) 4452ms 4.08% 56.92% 4784ms 4.38% _int_free 219ms 0.2% 57.12% 4764ms 4.36% MutableElement::ResetIndex 2ms 0.0018% 57.12% 4682ms 4.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 557ms 0.51% 57.63% 4598ms 4.21% std::_Rb_tree::_M_insert_ (inline) 56ms 0.051% 57.69% 4466ms 4.09% std::set_intersection (inline) 250ms 0.23% 57.91% 4410ms 4.04% std::__set_intersection 87ms 0.08% 57.99% 4348ms 3.98% AbstractCellPopulation::GetCellUsingLocationIndex 4199ms 3.85% 61.84% 4199ms 3.85% boost::numeric::ublas::same_impl_ex 43ms 0.039% 61.88% 3900ms 3.57% Cell::GetCellProliferativeType 63ms 0.058% 61.94% 3620ms 3.32% AbstractCellProperty::IsType (inline) 8ms 0.0073% 61.94% 3607ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 797ms 0.73% 62.67% 3258ms 2.98% AbstractElement::GetNodeLocation 0 0% 62.67% 3208ms 2.94% std::insert_iterator::operator= (inline) 2304ms 2.11% 64.78% 3162ms 2.90% _int_malloc 3153ms 2.89% 67.67% 3153ms 2.89% std::_Rb_tree::_S_right (inline) 52ms 0.048% 67.72% 3065ms 2.81% Cell::SetCellProliferativeType 38ms 0.035% 67.75% 3017ms 2.76% std::_Rb_tree::erase 3ms 0.0027% 67.76% 2854ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 584ms 0.53% 68.29% 2849ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 473ms 0.43% 68.72% 2819ms 2.58% std::_Rb_tree_const_iterator::operator++ (inline) 34ms 0.031% 68.76% 2563ms 2.35% CellPropertyCollection::HasProperty 710ms 0.65% 69.41% 2550ms 2.34% AbstractCellProperty::IsSame 1ms 0.00092% 69.41% 2513ms 2.30% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.41% 2474ms 2.27% Cell::HasCellProperty (inline) 0 0% 69.41% 2472ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.41% 2410ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 223ms 0.2% 69.61% 2408ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.61% 2359ms 2.16% AbstractCellPopulation::WriteResultsToFiles 23ms 0.021% 69.63% 2355ms 2.16% Cell::GetCellData 103ms 0.094% 69.73% 2347ms 2.15% VertexMesh::GetVolumeOfElement 120ms 0.11% 69.84% 2272ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.0037% 69.84% 2240ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 184ms 0.17% 70.01% 2220ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 41ms 0.038% 70.05% 2183ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 2176ms 1.99% 72.04% 2176ms 1.99% std::_Rb_tree_increment 1406ms 1.29% 73.33% 2070ms 1.90% std::_Rb_tree::equal_range (inline) 0 0% 73.33% 1936ms 1.77% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.33% 1926ms 1.76% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0027% 73.33% 1876ms 1.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.33% 1876ms 1.72% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 72ms 0.066% 73.40% 1852ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 439ms 0.4% 73.80% 1840ms 1.69% std::type_info::operator== (inline) 25ms 0.023% 73.82% 1744ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.82% 1737ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 47ms 0.043% 73.86% 1628ms 1.49% Node::RemoveElement 15ms 0.014% 73.88% 1603ms 1.47% VertexMesh::GetSurfaceAreaOfElement 23ms 0.021% 73.90% 1598ms 1.46% std::set::erase (inline) 30ms 0.027% 73.93% 1559ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 67ms 0.061% 73.99% 1519ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.99% 1519ms 1.39% tcache_get (inline) 1519ms 1.39% 75.38% 1519ms 1.39% tcache_get_n (inline) 163ms 0.15% 75.53% 1481ms 1.36% CellPropertyCollection::AddProperty 127ms 0.12% 75.64% 1444ms 1.32% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00092% 75.64% 1390ms 1.27% OffLatticeSimulation::ApplyBoundaries 0 0% 75.64% 1339ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 71ms 0.065% 75.71% 1280ms 1.17% std::less::operator() (inline) 1212ms 1.11% 76.82% 1212ms 1.11% Node::rGetLocation 973ms 0.89% 77.71% 1209ms 1.11% std::operator< (inline) 0 0% 77.71% 1174ms 1.08% boost::numeric::ublas::norm_2 (inline) 0 0% 77.71% 1173ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 491ms 0.45% 78.16% 1162ms 1.06% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 65ms 0.06% 78.22% 1126ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1122ms 1.03% 79.25% 1122ms 1.03% std::_Rb_tree_insert_and_rebalance 101ms 0.092% 79.34% 1120ms 1.03% std::_Rb_tree::find (inline) 1092ms 1.00% 80.34% 1092ms 1.00% [libchaste_cell_based.so] 30ms 0.027% 80.37% 1051ms 0.96% CellPropertyRegistry::Get 0 0% 80.37% 1045ms 0.96% std::_Rb_tree::clear (inline) 22ms 0.02% 80.39% 1038ms 0.95% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 147ms 0.13% 80.52% 1036ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 80.52% 1036ms 0.95% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.52% 1033ms 0.95% std::map::clear (inline) 1020ms 0.93% 81.46% 1020ms 0.93% std::vector::size (inline) 4ms 0.0037% 81.46% 1018ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 413ms 0.38% 81.84% 985ms 0.9% Edge::GetMapIndex 943ms 0.86% 82.70% 943ms 0.86% [libchaste_mesh.so] 0 0% 82.70% 940ms 0.86% std::map::find (inline) 25ms 0.023% 82.72% 937ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.72% 897ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 82.73% 897ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 151ms 0.14% 82.87% 897ms 0.82% boost::numeric::ublas::detail::equals 76ms 0.07% 82.94% 892ms 0.82% std::swap_ranges (inline) 856ms 0.78% 83.72% 866ms 0.79% boost::detail::sp_counted_base::release 88ms 0.081% 83.80% 841ms 0.77% MutableElement::GetNodeLocalIndex 0 0% 83.80% 835ms 0.76% VertexMeshWriter::MakeVtkMesh 817ms 0.75% 84.55% 817ms 0.75% std::swap (inline) 0 0% 84.55% 816ms 0.75% std::iter_swap (inline) 97ms 0.089% 84.64% 788ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 23ms 0.021% 84.66% 780ms 0.71% MutableElement::RegisterWithEdges (inline) 202ms 0.18% 84.84% 771ms 0.71% boost::shared_ptr::shared_ptr (inline) 770ms 0.71% 85.55% 770ms 0.71% Node::GetIndex 32ms 0.029% 85.58% 764ms 0.7% Edge::AddElement 432ms 0.4% 85.97% 720ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.97% 705ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.97% 702ms 0.64% boost::numeric::ublas::norm_inf (inline) 391ms 0.36% 86.33% 702ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 119ms 0.11% 86.44% 684ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.44% 684ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.44% 682ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.47% 682ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.47% 657ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.47% 632ms 0.58% std::_Rb_tree::_M_construct_node (inline) 625ms 0.57% 87.04% 625ms 0.57% operator delete 0 0% 87.04% 605ms 0.55% vtkPolygon::New 0 0% 87.04% 605ms 0.55% vtkPolygon::vtkPolygon 25ms 0.023% 87.06% 593ms 0.54% MutableElement::RegisterWithNodes (inline) 576ms 0.53% 87.59% 576ms 0.53% [libstdc++.so.6.0.33] 552ms 0.51% 88.09% 569ms 0.52% boost::detail::shared_count::shared_count (inline) 32ms 0.029% 88.12% 563ms 0.52% Node::AddElement 552ms 0.51% 88.63% 552ms 0.51% boost::shared_ptr::operator-> (inline) 28ms 0.026% 88.66% 550ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.66% 550ms 0.5% boost::numeric::ublas::vector::vector (inline) 0 0% 88.66% 546ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)