File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98611ms, 88.02% of 112038ms total Dropped 1125 nodes (cum <= 560.19ms) flat flat% sum% cum cum% 0 0% 0% 111663ms 99.67% __libc_start_call_main 0 0% 0% 111663ms 99.67% __libc_start_main_impl 0 0% 0% 111663ms 99.67% _start 0 0% 0% 111642ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 111642ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 111642ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 111642ms 99.65% main 0 0% 0% 111599ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 111599ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 111599ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 111591ms 99.60% AbstractCellBasedSimulation::Solve 22ms 0.02% 0.022% 58196ms 51.94% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.018% 0.04% 54896ms 49.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 153ms 0.14% 0.18% 53768ms 47.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 330ms 0.29% 0.47% 40920ms 36.52% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.47% 39821ms 35.54% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.47% 24361ms 21.74% VertexBasedCellPopulation::Update 0 0% 0.47% 24235ms 21.63% MutableVertexMesh::ReMesh 14480ms 12.92% 13.40% 23065ms 20.59% Cylindrical2dVertexMesh::GetVectorFromAtoB 104ms 0.093% 13.49% 18330ms 16.36% Cell::ReadyToDivide 79ms 0.071% 13.56% 16966ms 15.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 140ms 0.12% 13.69% 14573ms 13.01% CellPropertyCollection::GetPropertiesType (inline) 313ms 0.28% 13.97% 14571ms 13.01% NagaiHondaForce::GetAdhesionParameter 139ms 0.12% 14.09% 14482ms 12.93% SimpleWntCellCycleModel::UpdateCellCyclePhase 497ms 0.44% 14.53% 13792ms 12.31% boost::numeric::ublas::c_vector::c_vector (partial-inline) 356ms 0.32% 14.85% 12316ms 10.99% boost::numeric::ublas::vector_assign (inline) 4124ms 3.68% 18.53% 12265ms 10.95% __dynamic_cast 81ms 0.072% 18.60% 12259ms 10.94% VertexBasedCellPopulation::GetDampingConstant 69ms 0.062% 18.67% 12176ms 10.87% AbstractCellProperty::IsSubType (inline) 145ms 0.13% 18.80% 11867ms 10.59% MutableVertexMesh::CheckForIntersections 68ms 0.061% 18.86% 10992ms 9.81% AbstractTargetAreaModifier::UpdateTargetAreas 49ms 0.044% 18.90% 10908ms 9.74% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.028% 18.93% 10713ms 9.56% AbstractCellBasedSimulation::DoCellBirth 1373ms 1.23% 20.15% 10162ms 9.07% std::__new_allocator::allocate (inline) 0 0% 20.15% 9653ms 8.62% std::_Rb_tree::_M_create_node (inline) 0 0% 20.15% 9568ms 8.54% std::allocator_traits::allocate (inline) 423ms 0.38% 20.53% 9427ms 8.41% VertexMesh::GetNextEdgeGradientOfElementAtNode 90ms 0.08% 20.61% 9219ms 8.23% Cell::GetMutationState 1294ms 1.15% 21.77% 9212ms 8.22% std::_Rb_tree::_M_erase 2768ms 2.47% 24.24% 9027ms 8.06% boost::numeric::ublas::indexing_vector_assign 34ms 0.03% 24.27% 8929ms 7.97% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.27% 8889ms 7.93% std::_Rb_tree::_M_get_node (inline) 736ms 0.66% 24.92% 8853ms 7.90% operator new 819ms 0.73% 25.65% 8607ms 7.68% VertexMesh::ElementIncludesPoint 0 0% 25.65% 8557ms 7.64% std::_Rb_tree::_Alloc_node::operator() (inline) 492ms 0.44% 26.09% 8546ms 7.63% std::_Rb_tree::~_Rb_tree (inline) 459ms 0.41% 26.50% 8412ms 7.51% VertexMesh::GetCentroidOfElement 0 0% 26.50% 8272ms 7.38% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.50% 8114ms 7.24% std::set::~set (inline) 9ms 0.008% 26.51% 7999ms 7.14% MutableVertexMesh::RemoveDeletedNodesAndElements 237ms 0.21% 26.72% 7974ms 7.12% std::__new_allocator::deallocate (inline) 0 0% 26.72% 7964ms 7.11% std::allocator_traits::deallocate (inline) 0 0% 26.72% 7908ms 7.06% std::_Rb_tree::_M_put_node (inline) 3107ms 2.77% 29.50% 7894ms 7.05% __GI___libc_malloc 407ms 0.36% 29.86% 7871ms 7.03% std::map::operator[] (partial-inline) 2616ms 2.33% 32.19% 7517ms 6.71% __GI___libc_free 209ms 0.19% 32.38% 7401ms 6.61% std::_Rb_tree::_Rb_tree (partial-inline) 1375ms 1.23% 33.61% 7352ms 6.56% AbstractMesh::GetDistanceBetweenNodes 14ms 0.012% 33.62% 6916ms 6.17% std::set::set (inline) 805ms 0.72% 34.34% 6900ms 6.16% std::_Rb_tree::_M_copy (inline) 6539ms 5.84% 40.18% 6539ms 5.84% __strcmp_avx2 165ms 0.15% 40.32% 6513ms 5.81% SimpleWntCellCycleModel::GetWntLevel 2488ms 2.22% 42.54% 6427ms 5.74% std::_Rb_tree::_M_lower_bound (inline) 167ms 0.15% 42.69% 6276ms 5.60% WntConcentration::GetWntLevel 806ms 0.72% 43.41% 5866ms 5.24% std::_Rb_tree::_M_clone_node (inline) 5790ms 5.17% 48.58% 5790ms 5.17% boost::numeric::ublas::c_vector::operator() 31ms 0.028% 48.61% 5546ms 4.95% MutableVertexMesh::RemoveDeletedNodes 2928ms 2.61% 51.22% 5408ms 4.83% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.22% 5370ms 4.79% std::set::insert (inline) 35ms 0.031% 51.25% 5339ms 4.77% EdgeHelper::RemoveDeletedEdges 0 0% 51.25% 5322ms 4.75% std::_Rb_tree::lower_bound (inline) 0 0% 51.25% 5322ms 4.75% std::map::lower_bound (inline) 1962ms 1.75% 53.00% 5222ms 4.66% boost::numeric::ublas::c_vector::operator[] (inline) 38ms 0.034% 53.04% 4993ms 4.46% EdgeHelper::UpdateEdgesMapKey 207ms 0.18% 53.22% 4897ms 4.37% MutableElement::ResetIndex 4537ms 4.05% 57.27% 4886ms 4.36% _int_free 145ms 0.13% 57.40% 4880ms 4.36% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0018% 57.40% 4729ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 537ms 0.48% 57.88% 4536ms 4.05% std::_Rb_tree::_M_insert_ (inline) 42ms 0.037% 57.92% 4311ms 3.85% Cell::GetCellProliferativeType 127ms 0.11% 58.03% 4227ms 3.77% std::set_intersection (inline) 249ms 0.22% 58.26% 4100ms 3.66% std::__set_intersection 57ms 0.051% 58.31% 3964ms 3.54% AbstractCellProperty::IsType (inline) 3720ms 3.32% 61.63% 3720ms 3.32% boost::numeric::ublas::same_impl_ex 11ms 0.0098% 61.64% 3580ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3319ms 2.96% 64.60% 3319ms 2.96% std::_Rb_tree::_S_right (inline) 50ms 0.045% 64.64% 3243ms 2.89% Cell::SetCellProliferativeType 2181ms 1.95% 66.59% 3133ms 2.80% _int_malloc 58ms 0.052% 66.64% 3113ms 2.78% std::_Rb_tree::erase 0 0% 66.64% 3094ms 2.76% std::insert_iterator::operator= (inline) 924ms 0.82% 67.47% 3086ms 2.75% AbstractElement::GetNodeLocation 85ms 0.076% 67.54% 3000ms 2.68% VertexMesh::GetVolumeOfElement 72ms 0.064% 67.61% 2958ms 2.64% CellPropertyCollection::HasProperty 744ms 0.66% 68.27% 2879ms 2.57% AbstractCellProperty::IsSame 0 0% 68.27% 2850ms 2.54% Cell::HasCellProperty (inline) 21ms 0.019% 68.29% 2731ms 2.44% Cell::GetCellData 5ms 0.0045% 68.29% 2706ms 2.42% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0018% 68.30% 2664ms 2.38% std::_Rb_tree::_M_insert_unique 599ms 0.53% 68.83% 2602ms 2.32% boost::numeric::ublas::vector_binary::size (inline) 183ms 0.16% 68.99% 2586ms 2.31% VertexMesh::GetAreaGradientOfElementAtNode 256ms 0.23% 69.22% 2544ms 2.27% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.22% 2541ms 2.27% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.22% 2452ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 37ms 0.033% 69.26% 2388ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.26% 2382ms 2.13% boost::numeric::ublas::c_vector::operator-= (inline) 7ms 0.0062% 69.26% 2214ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.15% 69.41% 2211ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 561ms 0.5% 69.91% 2135ms 1.91% std::type_info::operator== (inline) 1ms 0.00089% 69.91% 2101ms 1.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.91% 2101ms 1.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 47ms 0.042% 69.96% 2101ms 1.88% std::_Rb_tree::_M_emplace_hint_unique 1379ms 1.23% 71.19% 2088ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 71.19% 2067ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.19% 2055ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2041ms 1.82% 73.01% 2041ms 1.82% std::_Rb_tree_increment 68ms 0.061% 73.07% 1858ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.07% 1841ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 38ms 0.034% 73.10% 1739ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 105ms 0.094% 73.20% 1669ms 1.49% boost::numeric::ublas::c_vector::operator= (inline) 147ms 0.13% 73.33% 1591ms 1.42% CellPropertyCollection::AddProperty 46ms 0.041% 73.37% 1562ms 1.39% VertexMesh::GetSurfaceAreaOfElement 62ms 0.055% 73.42% 1544ms 1.38% Node::RemoveElement 82ms 0.073% 73.50% 1526ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 30ms 0.027% 73.52% 1518ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.0071% 73.53% 1486ms 1.33% std::set::erase (inline) 0 0% 73.53% 1451ms 1.30% tcache_get (inline) 1451ms 1.30% 74.83% 1451ms 1.30% tcache_get_n (inline) 16ms 0.014% 74.84% 1415ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00089% 74.84% 1384ms 1.24% OffLatticeSimulation::ApplyBoundaries 0 0% 74.84% 1347ms 1.20% boost::numeric::ublas::norm_2 (inline) 85ms 0.076% 74.92% 1347ms 1.20% std::less::operator() (inline) 612ms 0.55% 75.46% 1331ms 1.19% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 75.46% 1292ms 1.15% boost::numeric::ublas::vector_binary::operator() (inline) 1291ms 1.15% 76.62% 1291ms 1.15% [libchaste_cell_based.so] 1054ms 0.94% 77.56% 1262ms 1.13% std::operator< (inline) 1190ms 1.06% 78.62% 1190ms 1.06% __memcpy_avx_unaligned_erms 27ms 0.024% 78.64% 1185ms 1.06% CellPropertyRegistry::Get 24ms 0.021% 78.66% 1179ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.66% 1164ms 1.04% std::_Rb_tree::clear (inline) 0 0% 78.66% 1147ms 1.02% std::map::clear (inline) 54ms 0.048% 78.71% 1127ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 33ms 0.029% 78.74% 1127ms 1.01% std::__copy_move::__copy_m (inline) 0 0% 78.74% 1127ms 1.01% std::__copy_move_a (inline) 0 0% 78.74% 1127ms 1.01% std::__copy_move_a1 (inline) 0 0% 78.74% 1127ms 1.01% std::__copy_move_a2 (inline) 0 0% 78.74% 1127ms 1.01% std::copy (inline) 91ms 0.081% 78.82% 1116ms 1% std::_Rb_tree::find (inline) 4ms 0.0036% 78.83% 1097ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 151ms 0.13% 78.96% 1096ms 0.98% boost::detail::shared_count::~shared_count (inline) 0 0% 78.96% 1096ms 0.98% boost::shared_ptr::~shared_ptr (inline) 0 0% 78.96% 1096ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.96% 1067ms 0.95% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0018% 78.96% 1067ms 0.95% boost::numeric::ublas::c_vector::swap (inline) 79ms 0.071% 79.03% 1065ms 0.95% std::swap_ranges (inline) 1029ms 0.92% 79.95% 1029ms 0.92% std::_Rb_tree_insert_and_rebalance 11ms 0.0098% 79.96% 1015ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 177ms 0.16% 80.12% 992ms 0.89% boost::numeric::ublas::detail::equals 0 0% 80.12% 986ms 0.88% std::iter_swap (inline) 986ms 0.88% 81.00% 986ms 0.88% std::swap (inline) 985ms 0.88% 81.88% 985ms 0.88% Node::rGetLocation 0 0% 81.88% 965ms 0.86% std::map::find (inline) 0 0% 81.88% 928ms 0.83% CellPropertyCollection::~CellPropertyCollection (inline) 914ms 0.82% 82.70% 914ms 0.82% std::vector::size (inline) 882ms 0.79% 83.48% 907ms 0.81% boost::detail::sp_counted_base::release 0 0% 83.48% 877ms 0.78% VertexMeshWriter::MakeVtkMesh 244ms 0.22% 83.70% 821ms 0.73% std::__new_allocator::construct (inline) 0 0% 83.70% 821ms 0.73% std::allocator_traits::construct (inline) 819ms 0.73% 84.43% 819ms 0.73% [libchaste_mesh.so] 169ms 0.15% 84.58% 788ms 0.7% boost::shared_ptr::shared_ptr (inline) 23ms 0.021% 84.60% 787ms 0.7% MutableElement::RegisterWithEdges (inline) 33ms 0.029% 84.63% 779ms 0.7% Edge::AddElement 423ms 0.38% 85.01% 765ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.01% 764ms 0.68% std::_Rb_tree::_M_construct_node (inline) 397ms 0.35% 85.36% 758ms 0.68% Edge::GetMapIndex 0 0% 85.36% 755ms 0.67% boost::numeric::ublas::norm_inf (inline) 383ms 0.34% 85.71% 755ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 121ms 0.11% 85.81% 721ms 0.64% MutableElement::GetNodeLocalIndex 0 0% 85.81% 712ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 685ms 0.61% 86.43% 685ms 0.61% [libstdc++.so.6.0.33] 1ms 0.00089% 86.43% 674ms 0.6% std::_Vector_base::_M_allocate (inline) 661ms 0.59% 87.02% 661ms 0.59% Node::GetIndex 38ms 0.034% 87.05% 638ms 0.57% MutableElement::RegisterWithNodes (inline) 31ms 0.028% 87.08% 625ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.08% 625ms 0.56% boost::numeric::ublas::vector::vector (inline) 1ms 0.00089% 87.08% 621ms 0.55% vtkPolygon::New 1ms 0.00089% 87.08% 619ms 0.55% vtkPolygon::vtkPolygon 579ms 0.52% 87.60% 618ms 0.55% boost::detail::shared_count::shared_count (inline) 0 0% 87.60% 608ms 0.54% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.021% 87.62% 608ms 0.54% std::_Rb_tree::_M_insert_node (inline) 22ms 0.02% 87.64% 593ms 0.53% Node::AddElement 417ms 0.37% 88.01% 577ms 0.52% CellPropertyCollection::GetProperty 8ms 0.0071% 88.02% 563ms 0.5% std::vector::_M_default_append (inline)