File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98103ms, 88.07% of 111396ms total Dropped 1119 nodes (cum <= 556.98ms) flat flat% sum% cum cum% 0 0% 0% 111046ms 99.69% __libc_start_call_main 0 0% 0% 111046ms 99.69% __libc_start_main_impl 0 0% 0% 111046ms 99.69% _start 0 0% 0% 111025ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 111025ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 111025ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 111025ms 99.67% main 0 0% 0% 110982ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110982ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110982ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0054% 0.0054% 110974ms 99.62% AbstractCellBasedSimulation::Solve 24ms 0.022% 0.027% 57607ms 51.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.039% 54029ms 48.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 152ms 0.14% 0.18% 52793ms 47.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 319ms 0.29% 0.46% 40516ms 36.37% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.46% 40318ms 36.19% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.46% 25127ms 22.56% VertexBasedCellPopulation::Update 5ms 0.0045% 0.47% 24966ms 22.41% MutableVertexMesh::ReMesh 14743ms 13.23% 13.70% 23421ms 21.02% Cylindrical2dVertexMesh::GetVectorFromAtoB 82ms 0.074% 13.78% 17355ms 15.58% Cell::ReadyToDivide 77ms 0.069% 13.85% 16046ms 14.40% AbstractPhaseBasedCellCycleModel::ReadyToDivide 367ms 0.33% 14.17% 14706ms 13.20% NagaiHondaForce::GetAdhesionParameter 520ms 0.47% 14.64% 14123ms 12.68% boost::numeric::ublas::c_vector::c_vector (partial-inline) 140ms 0.13% 14.77% 13833ms 12.42% CellPropertyCollection::GetPropertiesType (inline) 129ms 0.12% 14.88% 13711ms 12.31% SimpleWntCellCycleModel::UpdateCellCyclePhase 314ms 0.28% 15.16% 12584ms 11.30% boost::numeric::ublas::vector_assign (inline) 151ms 0.14% 15.30% 12004ms 10.78% MutableVertexMesh::CheckForIntersections 3282ms 2.95% 18.25% 11679ms 10.48% __dynamic_cast 72ms 0.065% 18.31% 11611ms 10.42% VertexBasedCellPopulation::GetDampingConstant 82ms 0.074% 18.38% 11595ms 10.41% AbstractCellProperty::IsSubType (inline) 53ms 0.048% 18.43% 10479ms 9.41% AbstractTargetAreaModifier::UpdateTargetAreas 46ms 0.041% 18.47% 10409ms 9.34% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1507ms 1.35% 19.83% 10289ms 9.24% std::__new_allocator::allocate (inline) 31ms 0.028% 19.85% 10157ms 9.12% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.85% 9723ms 8.73% std::_Rb_tree::_M_create_node (inline) 0 0% 19.85% 9688ms 8.70% std::allocator_traits::allocate (inline) 2863ms 2.57% 22.42% 9530ms 8.56% boost::numeric::ublas::indexing_vector_assign 380ms 0.34% 22.77% 9398ms 8.44% VertexMesh::GetNextEdgeGradientOfElementAtNode 1379ms 1.24% 24.00% 9097ms 8.17% std::_Rb_tree::_M_erase 0 0% 24.00% 8867ms 7.96% std::_Rb_tree::_M_get_node (inline) 893ms 0.8% 24.81% 8808ms 7.91% VertexMesh::ElementIncludesPoint 765ms 0.69% 25.49% 8798ms 7.90% operator new 23ms 0.021% 25.51% 8786ms 7.89% VertexBasedCellPopulation::GetLocationOfCellCentre 28ms 0.025% 25.54% 8747ms 7.85% MutableVertexMesh::RemoveDeletedNodesAndElements 90ms 0.081% 25.62% 8687ms 7.80% Cell::GetMutationState 0 0% 25.62% 8556ms 7.68% std::_Rb_tree::_Alloc_node::operator() (inline) 448ms 0.4% 26.02% 8377ms 7.52% VertexMesh::GetCentroidOfElement 0 0% 26.02% 8224ms 7.38% std::_Rb_tree::_M_drop_node (inline) 279ms 0.25% 26.27% 8117ms 7.29% std::_Rb_tree::~_Rb_tree (inline) 241ms 0.22% 26.49% 7965ms 7.15% std::__new_allocator::deallocate (inline) 0 0% 26.49% 7957ms 7.14% std::allocator_traits::deallocate (inline) 0 0% 26.49% 7879ms 7.07% std::_Rb_tree::_M_put_node (inline) 2985ms 2.68% 29.17% 7814ms 7.01% __GI___libc_malloc 225ms 0.2% 29.37% 7759ms 6.97% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.37% 7682ms 6.90% std::set::~set (inline) 461ms 0.41% 29.78% 7577ms 6.80% std::map::operator[] (partial-inline) 2565ms 2.30% 32.09% 7514ms 6.75% __GI___libc_free 1469ms 1.32% 33.40% 7407ms 6.65% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 773ms 0.69% 34.10% 7242ms 6.50% std::_Rb_tree::_M_copy (inline) 27ms 0.024% 34.12% 7197ms 6.46% std::set::set (inline) 6635ms 5.96% 40.08% 6635ms 5.96% __strcmp_avx2 891ms 0.8% 40.88% 6198ms 5.56% std::_Rb_tree::_M_clone_node (inline) 6171ms 5.54% 46.42% 6171ms 5.54% boost::numeric::ublas::c_vector::operator() 122ms 0.11% 46.53% 6158ms 5.53% SimpleWntCellCycleModel::GetWntLevel 2479ms 2.23% 48.75% 6008ms 5.39% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.14% 48.89% 5960ms 5.35% WntConcentration::GetWntLevel 2940ms 2.64% 51.53% 5623ms 5.05% __cxxabiv1::__si_class_type_info::__do_dyncast 264ms 0.24% 51.77% 5581ms 5.01% MutableElement::ResetIndex 20ms 0.018% 51.79% 5474ms 4.91% MutableVertexMesh::RemoveDeletedNodes 1968ms 1.77% 53.56% 5375ms 4.83% boost::numeric::ublas::c_vector::operator[] (inline) 28ms 0.025% 53.58% 5266ms 4.73% EdgeHelper::RemoveDeletedEdges 0 0% 53.58% 5132ms 4.61% std::set::insert (inline) 1ms 0.0009% 53.58% 5015ms 4.50% AbstractCellBasedSimulation::DoCellRemoval (inline) 4540ms 4.08% 57.66% 4934ms 4.43% _int_free 41ms 0.037% 57.69% 4932ms 4.43% EdgeHelper::UpdateEdgesMapKey 0 0% 57.69% 4889ms 4.39% std::_Rb_tree::lower_bound (inline) 0 0% 57.69% 4889ms 4.39% std::map::lower_bound (inline) 126ms 0.11% 57.81% 4597ms 4.13% AbstractCellPopulation::GetCellUsingLocationIndex 520ms 0.47% 58.27% 4304ms 3.86% std::_Rb_tree::_M_insert_ (inline) 151ms 0.14% 58.41% 4204ms 3.77% std::set_intersection (inline) 249ms 0.22% 58.63% 4053ms 3.64% std::__set_intersection 54ms 0.048% 58.68% 3954ms 3.55% Cell::GetCellProliferativeType 3781ms 3.39% 62.08% 3781ms 3.39% boost::numeric::ublas::same_impl_ex 46ms 0.041% 62.12% 3757ms 3.37% std::_Rb_tree::erase 7ms 0.0063% 62.12% 3725ms 3.34% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 50ms 0.045% 62.17% 3714ms 3.33% AbstractCellProperty::IsType (inline) 2147ms 1.93% 64.10% 3240ms 2.91% _int_malloc 69ms 0.062% 64.16% 3219ms 2.89% Cell::SetCellProliferativeType 3076ms 2.76% 66.92% 3076ms 2.76% std::_Rb_tree::_S_right (inline) 0 0% 66.92% 3058ms 2.75% std::insert_iterator::operator= (inline) 870ms 0.78% 67.70% 3049ms 2.74% AbstractElement::GetNodeLocation 26ms 0.023% 67.72% 2684ms 2.41% CellPropertyCollection::HasProperty 0 0% 67.72% 2646ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 67.72% 2633ms 2.36% boost::numeric::ublas::c_vector::assign (inline) 10ms 0.009% 67.73% 2633ms 2.36% std::_Rb_tree::_M_insert_unique_ (inline) 261ms 0.23% 67.97% 2624ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 218ms 0.2% 68.16% 2623ms 2.35% VertexMesh::GetAreaGradientOfElementAtNode 699ms 0.63% 68.79% 2604ms 2.34% AbstractCellProperty::IsSame 629ms 0.56% 69.35% 2600ms 2.33% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.35% 2584ms 2.32% Cell::HasCellProperty (inline) 1700ms 1.53% 70.88% 2541ms 2.28% std::_Rb_tree::equal_range (inline) 18ms 0.016% 70.90% 2520ms 2.26% Cell::GetCellData 0 0% 70.90% 2516ms 2.26% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.90% 2499ms 2.24% std::_Rb_tree::_M_insert_unique 92ms 0.083% 70.98% 2308ms 2.07% VertexMesh::GetVolumeOfElement 5ms 0.0045% 70.98% 2263ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 193ms 0.17% 71.16% 2245ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 67ms 0.06% 71.22% 2238ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 36ms 0.032% 71.25% 2171ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 2131ms 1.91% 73.16% 2131ms 1.91% std::_Rb_tree_increment 0 0% 73.16% 2065ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0009% 73.16% 2053ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 7ms 0.0063% 73.17% 2053ms 1.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.17% 2053ms 1.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 446ms 0.4% 73.57% 1905ms 1.71% std::type_info::operator== (inline) 0 0% 73.57% 1839ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 56ms 0.05% 73.62% 1812ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 61ms 0.055% 73.67% 1757ms 1.58% Node::RemoveElement 27ms 0.024% 73.70% 1741ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 15ms 0.013% 73.71% 1700ms 1.53% std::set::erase (inline) 33ms 0.03% 73.74% 1617ms 1.45% VertexMesh::GetSurfaceAreaOfElement 41ms 0.037% 73.78% 1583ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 86ms 0.077% 73.86% 1554ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.86% 1510ms 1.36% OffLatticeSimulation::ApplyBoundaries 142ms 0.13% 73.98% 1413ms 1.27% CellPropertyCollection::AddProperty 0 0% 73.98% 1379ms 1.24% tcache_get (inline) 1379ms 1.24% 75.22% 1379ms 1.24% tcache_get_n (inline) 1366ms 1.23% 76.45% 1366ms 1.23% [libchaste_cell_based.so] 103ms 0.092% 76.54% 1357ms 1.22% std::_Rb_tree::_M_erase_aux (partial-inline) 67ms 0.06% 76.60% 1348ms 1.21% std::less::operator() (inline) 0 0% 76.60% 1346ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 66ms 0.059% 76.66% 1319ms 1.18% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.66% 1310ms 1.18% boost::numeric::ublas::norm_2 (inline) 582ms 0.52% 77.18% 1297ms 1.16% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 26ms 0.023% 77.21% 1281ms 1.15% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 993ms 0.89% 78.10% 1281ms 1.15% std::operator< (inline) 0 0% 78.10% 1266ms 1.14% std::_Rb_tree::clear (inline) 0 0% 78.10% 1251ms 1.12% std::map::clear (inline) 5ms 0.0045% 78.10% 1248ms 1.12% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 78.10% 1167ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 103ms 0.092% 78.19% 1166ms 1.05% std::_Rb_tree::find (inline) 0 0% 78.19% 1121ms 1.01% boost::numeric::ublas::c_vector::assign_temporary (inline) 14ms 0.013% 78.21% 1121ms 1.01% boost::numeric::ublas::c_vector::swap (inline) 96ms 0.086% 78.29% 1107ms 0.99% std::swap_ranges (inline) 1061ms 0.95% 79.25% 1061ms 0.95% std::_Rb_tree_insert_and_rebalance 30ms 0.027% 79.27% 1059ms 0.95% CellPropertyRegistry::Get 113ms 0.1% 79.37% 1052ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 79.37% 1052ms 0.94% boost::shared_ptr::~shared_ptr (inline) 15ms 0.013% 79.39% 1017ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.39% 1011ms 0.91% std::iter_swap (inline) 1011ms 0.91% 80.29% 1011ms 0.91% std::swap (inline) 166ms 0.15% 80.44% 991ms 0.89% boost::numeric::ublas::detail::equals 0 0% 80.44% 990ms 0.89% std::map::find (inline) 983ms 0.88% 81.33% 983ms 0.88% Node::rGetLocation 277ms 0.25% 81.57% 945ms 0.85% std::__new_allocator::construct (inline) 0 0% 81.57% 945ms 0.85% std::allocator_traits::construct (inline) 854ms 0.77% 82.34% 892ms 0.8% boost::detail::sp_counted_base::release 858ms 0.77% 83.11% 858ms 0.77% std::vector::size (inline) 0 0% 83.11% 856ms 0.77% std::_Rb_tree::_M_construct_node (inline) 3ms 0.0027% 83.11% 848ms 0.76% VertexMeshWriter::MakeVtkMesh 101ms 0.091% 83.20% 839ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 2ms 0.0018% 83.21% 818ms 0.73% std::_Vector_base::_M_allocate (inline) 798ms 0.72% 83.92% 798ms 0.72% [libchaste_mesh.so] 19ms 0.017% 83.94% 758ms 0.68% MutableElement::RegisterWithEdges (inline) 18ms 0.016% 83.96% 756ms 0.68% Edge::AddElement 173ms 0.16% 84.11% 754ms 0.68% boost::shared_ptr::shared_ptr (inline) 461ms 0.41% 84.53% 744ms 0.67% Edge::GetMapIndex 0 0% 84.53% 743ms 0.67% boost::numeric::ublas::norm_inf (inline) 395ms 0.35% 84.88% 743ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 416ms 0.37% 85.25% 727ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.25% 723ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 7ms 0.0063% 85.26% 687ms 0.62% std::vector::_M_default_append (inline) 93ms 0.083% 85.34% 681ms 0.61% std::_Rb_tree::_M_upper_bound (inline) 138ms 0.12% 85.47% 674ms 0.61% MutableElement::GetNodeLocalIndex 0 0% 85.47% 672ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 37ms 0.033% 85.50% 641ms 0.58% MutableElement::RegisterWithNodes (inline) 487ms 0.44% 85.94% 625ms 0.56% malloc_consolidate 0 0% 85.94% 622ms 0.56% std::_Rb_tree::_Auto_node::_M_insert (inline) 14ms 0.013% 85.95% 622ms 0.56% std::_Rb_tree::_M_insert_node (inline) 20ms 0.018% 85.97% 621ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.97% 621ms 0.56% boost::numeric::ublas::vector::vector (inline) 3ms 0.0027% 85.97% 611ms 0.55% VertexElementMap::VertexElementMap 31ms 0.028% 86.00% 610ms 0.55% Node::AddElement 0 0% 86.00% 608ms 0.55% std::vector::resize (inline) 604ms 0.54% 86.54% 604ms 0.54% [libstdc++.so.6.0.33] 0 0% 86.54% 602ms 0.54% std::map::map (inline) 0 0% 86.54% 601ms 0.54% vtkPolygon::New 2ms 0.0018% 86.54% 601ms 0.54% vtkPolygon::vtkPolygon 543ms 0.49% 87.03% 581ms 0.52% boost::detail::shared_count::shared_count (inline) 573ms 0.51% 87.54% 573ms 0.51% Node::GetIndex 24ms 0.022% 87.57% 567ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 558ms 0.5% 88.07% 558ms 0.5% boost::shared_ptr::operator-> (inline)