File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98902ms, 89.98% of 109919ms total Dropped 1055 nodes (cum <= 549.60ms) flat flat% sum% cum cum% 0 0% 0% 109424ms 99.55% __libc_start_call_main 0 0% 0% 109424ms 99.55% __libc_start_main_impl 0 0% 0% 109424ms 99.55% _start 0 0% 0% 109406ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109406ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109406ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109406ms 99.53% main 0 0% 0% 109370ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109370ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109370ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 109362ms 99.49% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.019% 57443ms 52.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.03% 54231ms 49.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 114ms 0.1% 0.13% 53165ms 48.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 347ms 0.32% 0.45% 39996ms 36.39% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.45% 38903ms 35.39% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.45% 24098ms 21.92% VertexBasedCellPopulation::Update 1ms 0.00091% 0.45% 23972ms 21.81% MutableVertexMesh::ReMesh 14541ms 13.23% 13.68% 22996ms 20.92% Cylindrical2dVertexMesh::GetVectorFromAtoB 132ms 0.12% 13.80% 17606ms 16.02% CellPropertyCollection::GetPropertiesType (inline) 74ms 0.067% 13.87% 17563ms 15.98% Cell::ReadyToDivide 61ms 0.055% 13.92% 16600ms 15.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3592ms 3.27% 17.19% 15055ms 13.70% __dynamic_cast 73ms 0.066% 17.26% 14956ms 13.61% AbstractCellProperty::IsSubType (inline) 347ms 0.32% 17.57% 14783ms 13.45% NagaiHondaForce::GetAdhesionParameter 388ms 0.35% 17.93% 14319ms 13.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 110ms 0.1% 18.03% 13802ms 12.56% SimpleWntCellCycleModel::UpdateCellCyclePhase 351ms 0.32% 18.35% 12744ms 11.59% boost::numeric::ublas::vector_assign (inline) 66ms 0.06% 18.41% 12722ms 11.57% VertexBasedCellPopulation::GetDampingConstant 161ms 0.15% 18.55% 12076ms 10.99% MutableVertexMesh::CheckForIntersections 75ms 0.068% 18.62% 11062ms 10.06% Cell::GetMutationState 79ms 0.072% 18.69% 10552ms 9.60% AbstractTargetAreaModifier::UpdateTargetAreas 38ms 0.035% 18.73% 10450ms 9.51% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.025% 18.75% 10266ms 9.34% AbstractCellBasedSimulation::DoCellBirth 1226ms 1.12% 19.87% 10160ms 9.24% std::__new_allocator::allocate (inline) 0 0% 19.87% 9728ms 8.85% std::_Rb_tree::_M_create_node (inline) 0 0% 19.87% 9643ms 8.77% std::allocator_traits::allocate (inline) 2780ms 2.53% 22.40% 9602ms 8.74% boost::numeric::ublas::indexing_vector_assign 1362ms 1.24% 23.64% 9333ms 8.49% std::_Rb_tree::_M_erase 860ms 0.78% 24.42% 9033ms 8.22% operator new 0 0% 24.42% 9007ms 8.19% std::_Rb_tree::_M_get_node (inline) 411ms 0.37% 24.79% 8939ms 8.13% VertexMesh::GetNextEdgeGradientOfElementAtNode 739ms 0.67% 25.47% 8936ms 8.13% VertexMesh::ElementIncludesPoint 4030ms 3.67% 29.13% 8917ms 8.11% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.025% 29.16% 8721ms 7.93% VertexBasedCellPopulation::GetLocationOfCellCentre 207ms 0.19% 29.35% 8534ms 7.76% std::_Rb_tree::~_Rb_tree (inline) 0 0% 29.35% 8524ms 7.75% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 29.35% 8329ms 7.58% std::_Rb_tree::_M_drop_node (inline) 533ms 0.48% 29.83% 8268ms 7.52% VertexMesh::GetCentroidOfElement 0 0% 29.83% 8079ms 7.35% std::set::~set (inline) 252ms 0.23% 30.06% 8060ms 7.33% std::__new_allocator::deallocate (inline) 0 0% 30.06% 8033ms 7.31% std::allocator_traits::deallocate (inline) 3190ms 2.90% 32.96% 7980ms 7.26% __GI___libc_malloc 0 0% 32.96% 7969ms 7.25% std::_Rb_tree::_M_put_node (inline) 3054ms 2.78% 35.74% 7926ms 7.21% __GI___libc_free 18ms 0.016% 35.76% 7475ms 6.80% MutableVertexMesh::RemoveDeletedNodesAndElements 461ms 0.42% 36.18% 7265ms 6.61% std::map::operator[] (partial-inline) 7170ms 6.52% 42.70% 7170ms 6.52% __strcmp_avx2 1361ms 1.24% 43.94% 7168ms 6.52% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 213ms 0.19% 44.13% 6970ms 6.34% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.019% 44.15% 6547ms 5.96% std::set::set (inline) 674ms 0.61% 44.76% 6494ms 5.91% std::_Rb_tree::_M_copy (inline) 113ms 0.1% 44.87% 6341ms 5.77% SimpleWntCellCycleModel::GetWntLevel 6185ms 5.63% 50.49% 6185ms 5.63% boost::numeric::ublas::c_vector::operator() 133ms 0.12% 50.61% 6086ms 5.54% WntConcentration::GetWntLevel 2373ms 2.16% 52.77% 5577ms 5.07% std::_Rb_tree::_M_lower_bound (inline) 691ms 0.63% 53.40% 5561ms 5.06% std::_Rb_tree::_M_clone_node (inline) 0 0% 53.40% 5484ms 4.99% std::set::insert (inline) 24ms 0.022% 53.42% 5292ms 4.81% MutableVertexMesh::RemoveDeletedNodes 46ms 0.042% 53.46% 5223ms 4.75% Cell::GetCellProliferativeType 34ms 0.031% 53.50% 5135ms 4.67% EdgeHelper::RemoveDeletedEdges 37ms 0.034% 53.53% 4871ms 4.43% EdgeHelper::UpdateEdgesMapKey 4541ms 4.13% 57.66% 4868ms 4.43% _int_free 1501ms 1.37% 59.03% 4841ms 4.40% boost::numeric::ublas::c_vector::operator[] (inline) 186ms 0.17% 59.20% 4669ms 4.25% MutableElement::ResetIndex 465ms 0.42% 59.62% 4653ms 4.23% std::_Rb_tree::_M_insert_ (inline) 0 0% 59.62% 4527ms 4.12% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 59.62% 4500ms 4.09% std::_Rb_tree::lower_bound (inline) 0 0% 59.62% 4500ms 4.09% std::map::lower_bound (inline) 61ms 0.055% 59.67% 4405ms 4.01% std::set_intersection (inline) 220ms 0.2% 59.87% 4344ms 3.95% std::__set_intersection 77ms 0.07% 59.94% 4006ms 3.64% AbstractCellPopulation::GetCellUsingLocationIndex 4003ms 3.64% 63.59% 4003ms 3.64% boost::numeric::ublas::same_impl_ex 46ms 0.042% 63.63% 3710ms 3.38% Cell::SetCellProliferativeType 6ms 0.0055% 63.63% 3532ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 63.63% 3266ms 2.97% std::insert_iterator::operator= (inline) 789ms 0.72% 64.35% 3166ms 2.88% AbstractElement::GetNodeLocation 2270ms 2.07% 66.42% 3121ms 2.84% _int_malloc 16ms 0.015% 66.43% 3035ms 2.76% Cell::GetCellData 387ms 0.35% 66.78% 2978ms 2.71% std::_Rb_tree_const_iterator::operator++ (inline) 48ms 0.044% 66.83% 2935ms 2.67% std::_Rb_tree::erase 6ms 0.0055% 66.83% 2842ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 669ms 0.61% 67.44% 2836ms 2.58% boost::numeric::ublas::vector_binary::size (inline) 2731ms 2.48% 69.93% 2731ms 2.48% std::_Rb_tree::_S_right (inline) 66ms 0.06% 69.99% 2720ms 2.47% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0018% 69.99% 2642ms 2.40% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.99% 2465ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.99% 2448ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.99% 2439ms 2.22% AbstractCellPopulation::WriteResultsToFiles 2420ms 2.20% 72.19% 2420ms 2.20% std::_Rb_tree_increment 216ms 0.2% 72.39% 2403ms 2.19% VertexMesh::GetAreaGradientOfElementAtNode 38ms 0.035% 72.42% 2259ms 2.06% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0036% 72.42% 2173ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 83ms 0.076% 72.50% 2168ms 1.97% VertexMesh::GetVolumeOfElement 234ms 0.21% 72.71% 2162ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 72.71% 2002ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.71% 1995ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1308ms 1.19% 73.90% 1945ms 1.77% std::_Rb_tree::equal_range (inline) 113ms 0.1% 74.00% 1913ms 1.74% CellPropertyCollection::HasProperty 4ms 0.0036% 74.01% 1873ms 1.70% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.01% 1873ms 1.70% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 68ms 0.062% 74.07% 1866ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.07% 1795ms 1.63% Cell::HasCellProperty (inline) 0 0% 74.07% 1768ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 19ms 0.017% 74.09% 1684ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 189ms 0.17% 74.26% 1633ms 1.49% CellPropertyCollection::AddProperty 24ms 0.022% 74.28% 1607ms 1.46% VertexMesh::GetSurfaceAreaOfElement 51ms 0.046% 74.33% 1594ms 1.45% Node::RemoveElement 25ms 0.023% 74.35% 1559ms 1.42% std::set::erase (inline) 131ms 0.12% 74.47% 1511ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 71ms 0.065% 74.53% 1484ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 22ms 0.02% 74.55% 1482ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.55% 1475ms 1.34% tcache_get (inline) 1475ms 1.34% 75.90% 1475ms 1.34% tcache_get_n (inline) 828ms 0.75% 76.65% 1443ms 1.31% AbstractCellProperty::IsType (inline) 0 0% 76.65% 1432ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00091% 76.65% 1297ms 1.18% OffLatticeSimulation::ApplyBoundaries 0 0% 76.65% 1204ms 1.10% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.65% 1190ms 1.08% boost::numeric::ublas::norm_2 (inline) 518ms 0.47% 77.12% 1181ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1165ms 1.06% 78.18% 1165ms 1.06% Node::rGetLocation 63ms 0.057% 78.24% 1133ms 1.03% std::less::operator() (inline) 75ms 0.068% 78.31% 1120ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1114ms 1.01% 79.32% 1114ms 1.01% std::_Rb_tree_insert_and_rebalance 879ms 0.8% 80.12% 1070ms 0.97% std::operator< (inline) 106ms 0.096% 80.22% 1057ms 0.96% std::_Rb_tree::find (inline) 21ms 0.019% 80.24% 1049ms 0.95% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 156ms 0.14% 80.38% 1018ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.38% 1018ms 0.93% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0018% 80.38% 1011ms 0.92% std::_Rb_tree::clear (inline) 0 0% 80.38% 994ms 0.9% std::map::clear (inline) 10ms 0.0091% 80.39% 943ms 0.86% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 927ms 0.84% 81.23% 927ms 0.84% std::vector::size (inline) 924ms 0.84% 82.07% 924ms 0.84% [libchaste_mesh.so] 19ms 0.017% 82.09% 921ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 383ms 0.35% 82.44% 892ms 0.81% Edge::GetMapIndex 165ms 0.15% 82.59% 891ms 0.81% boost::numeric::ublas::detail::equals 0 0% 82.59% 861ms 0.78% VertexMeshWriter::MakeVtkMesh 164ms 0.15% 82.74% 857ms 0.78% boost::shared_ptr::shared_ptr (inline) 853ms 0.78% 83.51% 853ms 0.78% [libchaste_cell_based.so] 0 0% 83.51% 850ms 0.77% std::map::find (inline) 0 0% 83.51% 846ms 0.77% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 83.51% 834ms 0.76% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 83.52% 834ms 0.76% boost::numeric::ublas::c_vector::swap (inline) 825ms 0.75% 84.27% 831ms 0.76% boost::detail::sp_counted_base::release 66ms 0.06% 84.33% 828ms 0.75% std::swap_ranges (inline) 91ms 0.083% 84.41% 774ms 0.7% MutableElement::GetNodeLocalIndex 114ms 0.1% 84.52% 769ms 0.7% std::__new_allocator::construct (inline) 0 0% 84.52% 769ms 0.7% std::allocator_traits::construct (inline) 29ms 0.026% 84.54% 765ms 0.7% Edge::AddElement 764ms 0.7% 85.24% 764ms 0.7% std::swap (inline) 0 0% 85.24% 762ms 0.69% std::iter_swap (inline) 455ms 0.41% 85.65% 759ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 14ms 0.013% 85.66% 757ms 0.69% MutableElement::RegisterWithEdges (inline) 115ms 0.1% 85.77% 733ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.77% 721ms 0.66% std::_Rb_tree::_M_construct_node (inline) 469ms 0.43% 86.20% 701ms 0.64% CellPropertyCollection::GetProperty 654ms 0.59% 86.79% 693ms 0.63% boost::detail::shared_count::shared_count (inline) 685ms 0.62% 87.41% 685ms 0.62% Node::GetIndex 0 0% 87.41% 683ms 0.62% boost::numeric::ublas::norm_inf (inline) 334ms 0.3% 87.72% 683ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 87.72% 669ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 87.74% 669ms 0.61% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00091% 87.74% 636ms 0.58% std::_Vector_base::_M_allocate (inline) 1ms 0.00091% 87.74% 629ms 0.57% vtkPolygon::New 38ms 0.035% 87.78% 626ms 0.57% MutableElement::RegisterWithNodes (inline) 0 0% 87.78% 626ms 0.57% vtkPolygon::vtkPolygon 616ms 0.56% 88.34% 616ms 0.56% [libstdc++.so.6.0.33] 615ms 0.56% 88.90% 615ms 0.56% CellProperty::GetTypeId 29ms 0.026% 88.92% 587ms 0.53% Node::AddElement 586ms 0.53% 89.45% 586ms 0.53% operator delete 574ms 0.52% 89.98% 574ms 0.52% boost::shared_ptr::operator-> (inline) 0 0% 89.98% 560ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)