File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 93348ms, 87.00% of 107301ms total Dropped 1105 nodes (cum <= 536.50ms) flat flat% sum% cum cum% 0 0% 0% 106909ms 99.63% __libc_start_call_main 0 0% 0% 106909ms 99.63% __libc_start_main_impl 0 0% 0% 106909ms 99.63% _start 0 0% 0% 106887ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106887ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106887ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106887ms 99.61% main 0 0% 0% 106847ms 99.58% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106847ms 99.58% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106847ms 99.58% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 106838ms 99.57% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.017% 55383ms 51.61% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.016% 0.033% 52146ms 48.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 115ms 0.11% 0.14% 50996ms 47.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 330ms 0.31% 0.45% 39579ms 36.89% NagaiHondaForce::AddForceContribution 0 0% 0.45% 38633ms 36.00% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.45% 23756ms 22.14% VertexBasedCellPopulation::Update 0 0% 0.45% 23609ms 22.00% MutableVertexMesh::ReMesh 14688ms 13.69% 14.14% 23197ms 21.62% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.075% 14.21% 17409ms 16.22% Cell::ReadyToDivide 41ms 0.038% 14.25% 16219ms 15.12% AbstractPhaseBasedCellCycleModel::ReadyToDivide 352ms 0.33% 14.58% 14432ms 13.45% NagaiHondaForce::GetAdhesionParameter 398ms 0.37% 14.95% 14000ms 13.05% boost::numeric::ublas::c_vector::c_vector (partial-inline) 159ms 0.15% 15.10% 13829ms 12.89% SimpleWntCellCycleModel::UpdateCellCyclePhase 112ms 0.1% 15.20% 13090ms 12.20% CellPropertyCollection::GetPropertiesType (inline) 343ms 0.32% 15.52% 12604ms 11.75% boost::numeric::ublas::vector_assign (inline) 133ms 0.12% 15.65% 11849ms 11.04% MutableVertexMesh::CheckForIntersections 3274ms 3.05% 18.70% 11212ms 10.45% __dynamic_cast 83ms 0.077% 18.78% 11086ms 10.33% AbstractCellProperty::IsSubType (inline) 79ms 0.074% 18.85% 10897ms 10.16% VertexBasedCellPopulation::GetDampingConstant 67ms 0.062% 18.91% 10403ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 26ms 0.024% 18.94% 10312ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.029% 18.97% 10189ms 9.50% AbstractCellBasedSimulation::DoCellBirth 1167ms 1.09% 20.05% 9529ms 8.88% std::__new_allocator::allocate (inline) 2800ms 2.61% 22.66% 9448ms 8.81% boost::numeric::ublas::indexing_vector_assign 387ms 0.36% 23.02% 9215ms 8.59% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.02% 9045ms 8.43% std::_Rb_tree::_M_create_node (inline) 0 0% 23.02% 8965ms 8.36% std::allocator_traits::allocate (inline) 1204ms 1.12% 24.15% 8906ms 8.30% std::_Rb_tree::_M_erase 21ms 0.02% 24.16% 8841ms 8.24% VertexBasedCellPopulation::GetLocationOfCellCentre 878ms 0.82% 24.98% 8655ms 8.07% VertexMesh::ElementIncludesPoint 488ms 0.45% 25.44% 8417ms 7.84% VertexMesh::GetCentroidOfElement 735ms 0.68% 26.12% 8358ms 7.79% operator new 0 0% 26.12% 8322ms 7.76% std::_Rb_tree::_M_get_node (inline) 85ms 0.079% 26.20% 8268ms 7.71% Cell::GetMutationState 208ms 0.19% 26.40% 8084ms 7.53% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.40% 8075ms 7.53% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.40% 7919ms 7.38% std::_Rb_tree::_Alloc_node::operator() (inline) 244ms 0.23% 26.62% 7809ms 7.28% std::__new_allocator::deallocate (inline) 0 0% 26.62% 7807ms 7.28% std::allocator_traits::deallocate (inline) 0 0% 26.62% 7741ms 7.21% std::_Rb_tree::_M_put_node (inline) 0 0% 26.62% 7701ms 7.18% std::set::~set (inline) 22ms 0.021% 26.64% 7541ms 7.03% MutableVertexMesh::RemoveDeletedNodesAndElements 2791ms 2.60% 29.24% 7445ms 6.94% __GI___libc_malloc 1328ms 1.24% 30.48% 7402ms 6.90% AbstractMesh::GetDistanceBetweenNodes 2349ms 2.19% 32.67% 7326ms 6.83% __GI___libc_free 486ms 0.45% 33.12% 7303ms 6.81% std::map::operator[] (partial-inline) 182ms 0.17% 33.29% 6949ms 6.48% std::_Rb_tree::_Rb_tree (partial-inline) 28ms 0.026% 33.32% 6498ms 6.06% std::set::set (inline) 747ms 0.7% 34.02% 6495ms 6.05% std::_Rb_tree::_M_copy (inline) 154ms 0.14% 34.16% 6309ms 5.88% SimpleWntCellCycleModel::GetWntLevel 6200ms 5.78% 39.94% 6200ms 5.78% boost::numeric::ublas::c_vector::operator() 6191ms 5.77% 45.71% 6191ms 5.77% __strcmp_avx2 149ms 0.14% 45.85% 6069ms 5.66% WntConcentration::GetWntLevel 2449ms 2.28% 48.13% 5557ms 5.18% std::_Rb_tree::_M_lower_bound (inline) 2884ms 2.69% 50.82% 5528ms 5.15% __cxxabiv1::__si_class_type_info::__do_dyncast 821ms 0.77% 51.58% 5428ms 5.06% std::_Rb_tree::_M_clone_node (inline) 1907ms 1.78% 53.36% 5275ms 4.92% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.36% 5214ms 4.86% std::set::insert (inline) 22ms 0.021% 53.38% 5193ms 4.84% MutableVertexMesh::RemoveDeletedNodes 41ms 0.038% 53.42% 4991ms 4.65% EdgeHelper::RemoveDeletedEdges 4525ms 4.22% 57.64% 4960ms 4.62% _int_free 26ms 0.024% 57.66% 4674ms 4.36% EdgeHelper::UpdateEdgesMapKey 1ms 0.00093% 57.66% 4671ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 181ms 0.17% 57.83% 4626ms 4.31% MutableElement::ResetIndex 0 0% 57.83% 4589ms 4.28% std::_Rb_tree::lower_bound (inline) 0 0% 57.83% 4589ms 4.28% std::map::lower_bound (inline) 516ms 0.48% 58.31% 4369ms 4.07% std::_Rb_tree::_M_insert_ (inline) 126ms 0.12% 58.43% 4323ms 4.03% std::set_intersection (inline) 234ms 0.22% 58.65% 4197ms 3.91% std::__set_intersection 125ms 0.12% 58.76% 4070ms 3.79% AbstractCellPopulation::GetCellUsingLocationIndex 38ms 0.035% 58.80% 3958ms 3.69% Cell::GetCellProliferativeType 3794ms 3.54% 62.33% 3794ms 3.54% boost::numeric::ublas::same_impl_ex 11ms 0.01% 62.34% 3633ms 3.39% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 51ms 0.048% 62.39% 3567ms 3.32% AbstractCellProperty::IsType (inline) 0 0% 62.39% 3192ms 2.97% std::insert_iterator::operator= (inline) 64ms 0.06% 62.45% 3187ms 2.97% Cell::SetCellProliferativeType 2173ms 2.03% 64.48% 3060ms 2.85% _int_malloc 910ms 0.85% 65.32% 3013ms 2.81% AbstractElement::GetNodeLocation 80ms 0.075% 65.40% 2951ms 2.75% std::_Rb_tree::erase 7ms 0.0065% 65.40% 2799ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 258ms 0.24% 65.65% 2642ms 2.46% VertexMesh::GetAreaGradientOfElementAtNode 633ms 0.59% 66.24% 2624ms 2.45% boost::numeric::ublas::vector_binary::size (inline) 0 0% 66.24% 2595ms 2.42% boost::numeric::ublas::c_vector::operator-= (inline) 2564ms 2.39% 68.62% 2564ms 2.39% std::_Rb_tree::_S_right (inline) 0 0% 68.62% 2526ms 2.35% boost::numeric::ublas::c_vector::assign (inline) 35ms 0.033% 68.66% 2474ms 2.31% CellPropertyCollection::HasProperty 278ms 0.26% 68.92% 2460ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 610ms 0.57% 69.48% 2450ms 2.28% AbstractCellProperty::IsSame 1ms 0.00093% 69.49% 2415ms 2.25% std::_Rb_tree::_M_insert_unique 0 0% 69.49% 2385ms 2.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.49% 2382ms 2.22% Cell::HasCellProperty (inline) 63ms 0.059% 69.54% 2326ms 2.17% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 75ms 0.07% 69.61% 2313ms 2.16% VertexMesh::GetVolumeOfElement 28ms 0.026% 69.64% 2255ms 2.10% Cell::GetCellData 38ms 0.035% 69.68% 2183ms 2.03% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0019% 69.68% 2111ms 1.97% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.68% 2111ms 1.97% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.0028% 69.68% 2097ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 172ms 0.16% 69.84% 2080ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.84% 1959ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 69.84% 1948ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1946ms 1.81% 71.66% 1946ms 1.81% std::_Rb_tree_increment 62ms 0.058% 71.71% 1866ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 428ms 0.4% 72.11% 1840ms 1.71% std::type_info::operator== (inline) 1183ms 1.10% 73.22% 1831ms 1.71% std::_Rb_tree::equal_range (inline) 0 0% 73.22% 1752ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 28ms 0.026% 73.24% 1612ms 1.50% VertexMesh::GetSurfaceAreaOfElement 34ms 0.032% 73.27% 1591ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 56ms 0.052% 73.33% 1492ms 1.39% Node::RemoveElement 7ms 0.0065% 73.33% 1438ms 1.34% std::set::erase (inline) 66ms 0.062% 73.39% 1410ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 31ms 0.029% 73.42% 1408ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.42% 1400ms 1.30% tcache_get (inline) 1400ms 1.30% 74.73% 1400ms 1.30% tcache_get_n (inline) 93ms 0.087% 74.81% 1398ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 130ms 0.12% 74.93% 1370ms 1.28% CellPropertyCollection::AddProperty 0 0% 74.93% 1357ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 1334ms 1.24% 76.18% 1334ms 1.24% [libchaste_cell_based.so] 4ms 0.0037% 76.18% 1330ms 1.24% OffLatticeSimulation::ApplyBoundaries 0 0% 76.18% 1303ms 1.21% boost::numeric::ublas::norm_2 (inline) 562ms 0.52% 76.71% 1288ms 1.20% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 95ms 0.089% 76.79% 1246ms 1.16% std::_Rb_tree::_M_erase_aux (partial-inline) 66ms 0.062% 76.86% 1213ms 1.13% std::less::operator() (inline) 923ms 0.86% 77.72% 1147ms 1.07% std::operator< (inline) 1143ms 1.07% 78.78% 1143ms 1.07% std::_Rb_tree_insert_and_rebalance 24ms 0.022% 78.80% 1137ms 1.06% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 78.80% 1126ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 17ms 0.016% 78.82% 1107ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 228ms 0.21% 79.03% 1101ms 1.03% boost::numeric::ublas::detail::equals 28ms 0.026% 79.06% 1097ms 1.02% CellPropertyRegistry::Get 139ms 0.13% 79.19% 1092ms 1.02% boost::detail::shared_count::~shared_count (inline) 0 0% 79.19% 1092ms 1.02% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.19% 1058ms 0.99% boost::numeric::ublas::c_vector::assign_temporary (inline) 18ms 0.017% 79.20% 1058ms 0.99% boost::numeric::ublas::c_vector::swap (inline) 81ms 0.075% 79.28% 1040ms 0.97% std::swap_ranges (inline) 0 0% 79.28% 1037ms 0.97% std::_Rb_tree::clear (inline) 0 0% 79.28% 1015ms 0.95% std::map::clear (inline) 1ms 0.00093% 79.28% 1000ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 80ms 0.075% 79.36% 980ms 0.91% std::_Rb_tree::find (inline) 962ms 0.9% 80.25% 962ms 0.9% std::swap (inline) 0 0% 80.25% 959ms 0.89% std::iter_swap (inline) 957ms 0.89% 81.14% 957ms 0.89% Node::rGetLocation 886ms 0.83% 81.97% 910ms 0.85% boost::detail::sp_counted_base::release 848ms 0.79% 82.76% 848ms 0.79% std::vector::size (inline) 2ms 0.0019% 82.76% 846ms 0.79% VertexMeshWriter::MakeVtkMesh 0 0% 82.76% 816ms 0.76% std::map::find (inline) 107ms 0.1% 82.86% 810ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 82.86% 808ms 0.75% boost::numeric::ublas::norm_inf (inline) 432ms 0.4% 83.26% 808ms 0.75% boost::numeric::ublas::vector_norm_inf::apply (inline) 438ms 0.41% 83.67% 798ms 0.74% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 792ms 0.74% 84.41% 792ms 0.74% [libchaste_mesh.so] 249ms 0.23% 84.64% 773ms 0.72% std::__new_allocator::construct (inline) 0 0% 84.64% 773ms 0.72% std::allocator_traits::construct (inline) 23ms 0.021% 84.66% 767ms 0.71% MutableElement::RegisterWithEdges (inline) 17ms 0.016% 84.68% 764ms 0.71% Edge::AddElement 0 0% 84.68% 744ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.68% 723ms 0.67% std::_Rb_tree::_M_construct_node (inline) 158ms 0.15% 84.83% 714ms 0.67% boost::shared_ptr::shared_ptr (inline) 0 0% 84.83% 685ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 84.85% 685ms 0.64% std::_Rb_tree::_M_insert_node (inline) 0 0% 84.85% 682ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 333ms 0.31% 85.16% 655ms 0.61% Edge::GetMapIndex 149ms 0.14% 85.30% 649ms 0.6% MutableElement::GetNodeLocalIndex 0 0% 85.30% 640ms 0.6% std::_Vector_base::_M_allocate (inline) 639ms 0.6% 85.89% 639ms 0.6% [libstdc++.so.6.0.33] 0 0% 85.89% 603ms 0.56% vtkPolygon::New 2ms 0.0019% 85.90% 603ms 0.56% vtkPolygon::vtkPolygon 36ms 0.034% 85.93% 594ms 0.55% MutableElement::RegisterWithNodes (inline) 25ms 0.023% 85.95% 589ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.95% 589ms 0.55% boost::numeric::ublas::vector::vector (inline) 518ms 0.48% 86.44% 556ms 0.52% boost::detail::shared_count::shared_count (inline) 552ms 0.51% 86.95% 552ms 0.51% Node::GetIndex 27ms 0.025% 86.97% 548ms 0.51% Node::AddElement 23ms 0.021% 87.00% 547ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate