File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97254ms, 88.55% of 109825ms total Dropped 1118 nodes (cum <= 549.12ms) flat flat% sum% cum cum% 0 0% 0% 109302ms 99.52% __libc_start_call_main 0 0% 0% 109302ms 99.52% __libc_start_main_impl 0 0% 0% 109302ms 99.52% _start 0 0% 0% 109282ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109282ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109282ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109282ms 99.51% main 0 0% 0% 109242ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109242ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109242ms 99.47% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109235ms 99.46% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.014% 56583ms 51.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.026% 53189ms 48.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 141ms 0.13% 0.15% 51707ms 47.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 340ms 0.31% 0.46% 39843ms 36.28% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.47% 39404ms 35.88% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.47% 24467ms 22.28% VertexBasedCellPopulation::Update 1ms 0.00091% 0.47% 24328ms 22.15% MutableVertexMesh::ReMesh 14334ms 13.05% 13.52% 22626ms 20.60% Cylindrical2dVertexMesh::GetVectorFromAtoB 125ms 0.11% 13.63% 17704ms 16.12% Cell::ReadyToDivide 69ms 0.063% 13.70% 16399ms 14.93% AbstractPhaseBasedCellCycleModel::ReadyToDivide 379ms 0.35% 14.04% 14877ms 13.55% NagaiHondaForce::GetAdhesionParameter 420ms 0.38% 14.42% 14432ms 13.14% boost::numeric::ublas::c_vector::c_vector (partial-inline) 126ms 0.11% 14.54% 14022ms 12.77% SimpleWntCellCycleModel::UpdateCellCyclePhase 161ms 0.15% 14.69% 13871ms 12.63% CellPropertyCollection::GetPropertiesType (inline) 396ms 0.36% 15.05% 12928ms 11.77% boost::numeric::ublas::vector_assign (inline) 121ms 0.11% 15.16% 12029ms 10.95% MutableVertexMesh::CheckForIntersections 3473ms 3.16% 18.32% 11392ms 10.37% __dynamic_cast 80ms 0.073% 18.39% 11355ms 10.34% VertexBasedCellPopulation::GetDampingConstant 58ms 0.053% 18.44% 11273ms 10.26% AbstractCellProperty::IsSubType (inline) 90ms 0.082% 18.53% 10709ms 9.75% AbstractTargetAreaModifier::UpdateTargetAreas 81ms 0.074% 18.60% 10592ms 9.64% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1310ms 1.19% 19.79% 10475ms 9.54% std::__new_allocator::allocate (inline) 21ms 0.019% 19.81% 10287ms 9.37% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.81% 10124ms 9.22% std::_Rb_tree::_M_create_node (inline) 0 0% 19.81% 9879ms 9.00% std::allocator_traits::allocate (inline) 2787ms 2.54% 22.35% 9484ms 8.64% boost::numeric::ublas::indexing_vector_assign 1114ms 1.01% 23.36% 9325ms 8.49% operator new 0 0% 23.36% 9151ms 8.33% std::_Rb_tree::_M_get_node (inline) 1517ms 1.38% 24.75% 9060ms 8.25% std::_Rb_tree::_M_erase 377ms 0.34% 25.09% 8941ms 8.14% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.09% 8922ms 8.12% std::_Rb_tree::_Alloc_node::operator() (inline) 773ms 0.7% 25.79% 8918ms 8.12% VertexMesh::ElementIncludesPoint 27ms 0.025% 25.82% 8774ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 80ms 0.073% 25.89% 8747ms 7.96% Cell::GetMutationState 434ms 0.4% 26.29% 8326ms 7.58% VertexMesh::GetCentroidOfElement 213ms 0.19% 26.48% 8167ms 7.44% std::_Rb_tree::~_Rb_tree (inline) 3046ms 2.77% 29.25% 8032ms 7.31% __GI___libc_malloc 0 0% 29.25% 7948ms 7.24% std::_Rb_tree::_M_drop_node (inline) 17ms 0.015% 29.27% 7784ms 7.09% MutableVertexMesh::RemoveDeletedNodesAndElements 266ms 0.24% 29.51% 7759ms 7.06% std::__new_allocator::deallocate (inline) 0 0% 29.51% 7735ms 7.04% std::allocator_traits::deallocate (inline) 0 0% 29.51% 7660ms 6.97% std::set::~set (inline) 2918ms 2.66% 32.17% 7656ms 6.97% __GI___libc_free 0 0% 32.17% 7652ms 6.97% std::_Rb_tree::_M_put_node (inline) 412ms 0.38% 32.54% 7337ms 6.68% std::map::operator[] (partial-inline) 108ms 0.098% 32.64% 7288ms 6.64% std::_Rb_tree::_Rb_tree (partial-inline) 1394ms 1.27% 33.91% 6984ms 6.36% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 690ms 0.63% 34.54% 6942ms 6.32% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 34.55% 6793ms 6.19% std::set::set (inline) 112ms 0.1% 34.66% 6419ms 5.84% SimpleWntCellCycleModel::GetWntLevel 6379ms 5.81% 40.46% 6379ms 5.81% __strcmp_avx2 150ms 0.14% 40.60% 6220ms 5.66% WntConcentration::GetWntLevel 6151ms 5.60% 46.20% 6151ms 5.60% boost::numeric::ublas::c_vector::operator() 782ms 0.71% 46.91% 6088ms 5.54% std::_Rb_tree::_M_clone_node (inline) 2542ms 2.31% 49.23% 5883ms 5.36% std::_Rb_tree::_M_lower_bound (inline) 0 0% 49.23% 5510ms 5.02% std::set::insert (inline) 26ms 0.024% 49.25% 5500ms 5.01% MutableVertexMesh::RemoveDeletedNodes 29ms 0.026% 49.28% 5315ms 4.84% EdgeHelper::RemoveDeletedEdges 2607ms 2.37% 51.65% 5259ms 4.79% __cxxabiv1::__si_class_type_info::__do_dyncast 33ms 0.03% 51.68% 5043ms 4.59% EdgeHelper::UpdateEdgesMapKey 1519ms 1.38% 53.06% 4888ms 4.45% boost::numeric::ublas::c_vector::operator[] (inline) 228ms 0.21% 53.27% 4879ms 4.44% MutableElement::ResetIndex 0 0% 53.27% 4732ms 4.31% std::_Rb_tree::lower_bound (inline) 0 0% 53.27% 4732ms 4.31% std::map::lower_bound (inline) 4409ms 4.01% 57.29% 4731ms 4.31% _int_free 1ms 0.00091% 57.29% 4635ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 483ms 0.44% 57.73% 4578ms 4.17% std::_Rb_tree::_M_insert_ (inline) 41ms 0.037% 57.76% 4442ms 4.04% std::set_intersection (inline) 259ms 0.24% 58.00% 4401ms 4.01% std::__set_intersection 123ms 0.11% 58.11% 4067ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 3883ms 3.54% 61.65% 3883ms 3.54% boost::numeric::ublas::same_impl_ex 37ms 0.034% 61.68% 3865ms 3.52% Cell::GetCellProliferativeType 74ms 0.067% 61.75% 3846ms 3.50% AbstractCellProperty::IsType (inline) 10ms 0.0091% 61.76% 3506ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 841ms 0.77% 62.52% 3295ms 3.00% AbstractElement::GetNodeLocation 2306ms 2.10% 64.62% 3281ms 2.99% _int_malloc 0 0% 64.62% 3168ms 2.88% std::insert_iterator::operator= (inline) 55ms 0.05% 64.67% 3118ms 2.84% Cell::SetCellProliferativeType 43ms 0.039% 64.71% 3036ms 2.76% std::_Rb_tree::erase 2864ms 2.61% 67.32% 2864ms 2.61% std::_Rb_tree::_S_right (inline) 3ms 0.0027% 67.32% 2819ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 420ms 0.38% 67.71% 2783ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 820ms 0.75% 68.45% 2777ms 2.53% AbstractCellProperty::IsSame 592ms 0.54% 68.99% 2714ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.0046% 69.00% 2691ms 2.45% std::_Rb_tree::_M_insert_unique (inline) 37ms 0.034% 69.03% 2670ms 2.43% CellPropertyCollection::HasProperty 0 0% 69.03% 2585ms 2.35% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.03% 2569ms 2.34% Cell::HasCellProperty (inline) 0 0% 69.03% 2512ms 2.29% AbstractCellPopulation::WriteResultsToFiles 28ms 0.025% 69.06% 2473ms 2.25% Cell::GetCellData 213ms 0.19% 69.25% 2444ms 2.23% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.25% 2387ms 2.17% boost::numeric::ublas::c_vector::operator-= (inline) 234ms 0.21% 69.46% 2308ms 2.10% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.0036% 69.47% 2305ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 153ms 0.14% 69.61% 2287ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2202ms 2.01% 71.61% 2202ms 2.01% std::_Rb_tree_increment 87ms 0.079% 71.69% 2194ms 2.00% VertexMesh::GetVolumeOfElement 31ms 0.028% 71.72% 2154ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 1403ms 1.28% 73.00% 2077ms 1.89% std::_Rb_tree::equal_range (inline) 0 0% 73.00% 2057ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 73.00% 2044ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 501ms 0.46% 73.45% 1957ms 1.78% std::type_info::operator== (inline) 3ms 0.0027% 73.46% 1940ms 1.77% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.46% 1940ms 1.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 70ms 0.064% 73.52% 1838ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.52% 1830ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 41ms 0.037% 73.56% 1798ms 1.64% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 17ms 0.015% 73.57% 1630ms 1.48% VertexMesh::GetSurfaceAreaOfElement 170ms 0.15% 73.73% 1593ms 1.45% CellPropertyCollection::AddProperty 28ms 0.025% 73.75% 1590ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 48ms 0.044% 73.80% 1583ms 1.44% Node::RemoveElement 91ms 0.083% 73.88% 1583ms 1.44% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 21ms 0.019% 73.90% 1544ms 1.41% std::set::erase (inline) 136ms 0.12% 74.02% 1538ms 1.40% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.02% 1527ms 1.39% tcache_get (inline) 1527ms 1.39% 75.41% 1527ms 1.39% tcache_get_n (inline) 0 0% 75.41% 1411ms 1.28% boost::numeric::ublas::vector_binary::operator() (inline) 3ms 0.0027% 75.42% 1375ms 1.25% OffLatticeSimulation::ApplyBoundaries 0 0% 75.42% 1257ms 1.14% boost::numeric::ublas::norm_2 (inline) 523ms 0.48% 75.89% 1248ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 75.89% 1202ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 75ms 0.068% 75.96% 1184ms 1.08% std::less::operator() (inline) 1175ms 1.07% 77.03% 1175ms 1.07% Node::rGetLocation 29ms 0.026% 77.06% 1159ms 1.06% CellPropertyRegistry::Get 115ms 0.1% 77.16% 1159ms 1.06% std::_Rb_tree::find (inline) 20ms 0.018% 77.18% 1144ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 65ms 0.059% 77.24% 1118ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1ms 0.00091% 77.24% 1114ms 1.01% std::_Rb_tree::clear (inline) 908ms 0.83% 78.07% 1109ms 1.01% std::operator< (inline) 0 0% 78.07% 1102ms 1.00% std::map::clear (inline) 13ms 0.012% 78.08% 1077ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1056ms 0.96% 79.04% 1056ms 0.96% std::_Rb_tree_insert_and_rebalance 430ms 0.39% 79.43% 1030ms 0.94% std::__new_allocator::construct (inline) 0 0% 79.43% 1030ms 0.94% std::allocator_traits::construct (inline) 1018ms 0.93% 80.36% 1018ms 0.93% [libchaste_cell_based.so] 422ms 0.38% 80.74% 993ms 0.9% Edge::GetMapIndex 981ms 0.89% 81.64% 981ms 0.89% std::vector::size (inline) 0 0% 81.64% 973ms 0.89% std::_Rb_tree::_M_construct_node (inline) 0 0% 81.64% 967ms 0.88% std::map::find (inline) 126ms 0.11% 81.75% 964ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.75% 964ms 0.88% boost::shared_ptr::~shared_ptr (inline) 950ms 0.87% 82.62% 950ms 0.87% [libchaste_mesh.so] 24ms 0.022% 82.64% 927ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.64% 908ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0036% 82.64% 908ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 90ms 0.082% 82.72% 904ms 0.82% std::swap_ranges (inline) 177ms 0.16% 82.88% 893ms 0.81% boost::numeric::ublas::detail::equals 0 0% 82.88% 878ms 0.8% VertexMeshWriter::MakeVtkMesh 15ms 0.014% 82.90% 843ms 0.77% MutableElement::RegisterWithEdges (inline) 29ms 0.026% 82.92% 832ms 0.76% Edge::AddElement 0 0% 82.92% 814ms 0.74% std::iter_swap (inline) 814ms 0.74% 83.66% 814ms 0.74% std::swap (inline) 810ms 0.74% 84.40% 813ms 0.74% boost::detail::sp_counted_base::release 102ms 0.093% 84.50% 754ms 0.69% MutableElement::GetNodeLocalIndex 746ms 0.68% 85.17% 746ms 0.68% Node::GetIndex 452ms 0.41% 85.59% 744ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 14ms 0.013% 85.60% 729ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 112ms 0.1% 85.70% 729ms 0.66% boost::shared_ptr::shared_ptr (inline) 0 0% 85.70% 722ms 0.66% std::_Vector_base::_M_allocate (inline) 91ms 0.083% 85.78% 721ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 102ms 0.093% 85.88% 715ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 88ms 0.08% 85.96% 684ms 0.62% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.96% 684ms 0.62% boost::numeric::ublas::vector::vector (inline) 0 0% 85.96% 683ms 0.62% boost::numeric::ublas::norm_inf (inline) 391ms 0.36% 86.31% 683ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.31% 643ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 86.33% 643ms 0.59% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00091% 86.34% 643ms 0.59% vtkPolygon::New 0 0% 86.34% 642ms 0.58% vtkPolygon::vtkPolygon 0 0% 86.34% 630ms 0.57% CellPropertyCollection::~CellPropertyCollection (inline) 34ms 0.031% 86.37% 629ms 0.57% MutableElement::RegisterWithNodes (inline) 592ms 0.54% 86.91% 617ms 0.56% boost::detail::shared_count::shared_count (inline) 11ms 0.01% 86.92% 613ms 0.56% std::vector::_M_default_append (inline) 37ms 0.034% 86.95% 595ms 0.54% Node::AddElement 0 0% 86.95% 593ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 590ms 0.54% 87.49% 590ms 0.54% operator delete 586ms 0.53% 88.02% 586ms 0.53% [libstdc++.so.6.0.33] 586ms 0.53% 88.55% 586ms 0.53% boost::shared_ptr::operator-> (inline)