File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96059ms, 87.48% of 109813ms total Dropped 1123 nodes (cum <= 549.07ms) flat flat% sum% cum cum% 0 0% 0% 109438ms 99.66% __libc_start_call_main 0 0% 0% 109438ms 99.66% __libc_start_main_impl 0 0% 0% 109438ms 99.66% _start 0 0% 0% 109416ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109416ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109416ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109416ms 99.64% main 0 0% 0% 109377ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109377ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109377ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 109370ms 99.60% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.022% 56664ms 51.60% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.032% 53438ms 48.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 155ms 0.14% 0.17% 52355ms 47.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 316ms 0.29% 0.46% 40056ms 36.48% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.46% 39234ms 35.73% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.46% 23989ms 21.85% VertexBasedCellPopulation::Update 0 0% 0.46% 23839ms 21.71% MutableVertexMesh::ReMesh 14715ms 13.40% 13.86% 23238ms 21.16% Cylindrical2dVertexMesh::GetVectorFromAtoB 111ms 0.1% 13.96% 18292ms 16.66% Cell::ReadyToDivide 79ms 0.072% 14.04% 16856ms 15.35% AbstractPhaseBasedCellCycleModel::ReadyToDivide 168ms 0.15% 14.19% 14410ms 13.12% SimpleWntCellCycleModel::UpdateCellCyclePhase 362ms 0.33% 14.52% 14361ms 13.08% NagaiHondaForce::GetAdhesionParameter 106ms 0.097% 14.61% 14032ms 12.78% CellPropertyCollection::GetPropertiesType (inline) 458ms 0.42% 15.03% 13719ms 12.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 287ms 0.26% 15.29% 12228ms 11.14% boost::numeric::ublas::vector_assign (inline) 3488ms 3.18% 18.47% 11905ms 10.84% __dynamic_cast 157ms 0.14% 18.61% 11824ms 10.77% MutableVertexMesh::CheckForIntersections 48ms 0.044% 18.66% 11813ms 10.76% AbstractCellProperty::IsSubType (inline) 91ms 0.083% 18.74% 11687ms 10.64% VertexBasedCellPopulation::GetDampingConstant 82ms 0.075% 18.81% 10990ms 10.01% AbstractTargetAreaModifier::UpdateTargetAreas 36ms 0.033% 18.85% 10887ms 9.91% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.025% 18.87% 10565ms 9.62% AbstractCellBasedSimulation::DoCellBirth 1375ms 1.25% 20.12% 9984ms 9.09% std::__new_allocator::allocate (inline) 0 0% 20.12% 9506ms 8.66% std::_Rb_tree::_M_create_node (inline) 0 0% 20.12% 9453ms 8.61% std::allocator_traits::allocate (inline) 2772ms 2.52% 22.65% 9389ms 8.55% boost::numeric::ublas::indexing_vector_assign 349ms 0.32% 22.97% 9317ms 8.48% VertexMesh::GetNextEdgeGradientOfElementAtNode 1254ms 1.14% 24.11% 8880ms 8.09% std::_Rb_tree::_M_erase 105ms 0.096% 24.20% 8810ms 8.02% Cell::GetMutationState 0 0% 24.20% 8720ms 7.94% std::_Rb_tree::_M_get_node (inline) 40ms 0.036% 24.24% 8624ms 7.85% VertexBasedCellPopulation::GetLocationOfCellCentre 813ms 0.74% 24.98% 8608ms 7.84% operator new 798ms 0.73% 25.71% 8568ms 7.80% VertexMesh::ElementIncludesPoint 0 0% 25.71% 8426ms 7.67% std::_Rb_tree::_Alloc_node::operator() (inline) 442ms 0.4% 26.11% 8164ms 7.43% VertexMesh::GetCentroidOfElement 0 0% 26.11% 8016ms 7.30% std::_Rb_tree::_M_drop_node (inline) 215ms 0.2% 26.31% 7991ms 7.28% std::_Rb_tree::~_Rb_tree (inline) 466ms 0.42% 26.73% 7820ms 7.12% std::map::operator[] (partial-inline) 240ms 0.22% 26.95% 7716ms 7.03% std::__new_allocator::deallocate (inline) 0 0% 26.95% 7713ms 7.02% std::allocator_traits::deallocate (inline) 23ms 0.021% 26.97% 7698ms 7.01% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.97% 7644ms 6.96% std::_Rb_tree::_M_put_node (inline) 0 0% 26.97% 7562ms 6.89% std::set::~set (inline) 2826ms 2.57% 29.54% 7557ms 6.88% __GI___libc_malloc 1494ms 1.36% 30.90% 7449ms 6.78% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 190ms 0.17% 31.08% 7339ms 6.68% std::_Rb_tree::_Rb_tree (partial-inline) 2249ms 2.05% 33.12% 7165ms 6.52% __GI___libc_free 6932ms 6.31% 39.44% 6932ms 6.31% __strcmp_avx2 793ms 0.72% 40.16% 6869ms 6.26% std::_Rb_tree::_M_copy (inline) 24ms 0.022% 40.18% 6852ms 6.24% std::set::set (inline) 2595ms 2.36% 42.54% 6291ms 5.73% std::_Rb_tree::_M_lower_bound (inline) 140ms 0.13% 42.67% 6247ms 5.69% SimpleWntCellCycleModel::GetWntLevel 6069ms 5.53% 48.20% 6069ms 5.53% boost::numeric::ublas::c_vector::operator() 168ms 0.15% 48.35% 6017ms 5.48% WntConcentration::GetWntLevel 852ms 0.78% 49.13% 5777ms 5.26% std::_Rb_tree::_M_clone_node (inline) 2837ms 2.58% 51.71% 5744ms 5.23% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.02% 51.73% 5440ms 4.95% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.73% 5362ms 4.88% std::set::insert (inline) 1958ms 1.78% 53.51% 5291ms 4.82% boost::numeric::ublas::c_vector::operator[] (inline) 30ms 0.027% 53.54% 5256ms 4.79% EdgeHelper::RemoveDeletedEdges 0 0% 53.54% 5179ms 4.72% std::_Rb_tree::lower_bound (inline) 0 0% 53.54% 5179ms 4.72% std::map::lower_bound (inline) 40ms 0.036% 53.58% 4940ms 4.50% EdgeHelper::UpdateEdgesMapKey 4477ms 4.08% 57.65% 4899ms 4.46% _int_free 1ms 0.00091% 57.66% 4672ms 4.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 170ms 0.15% 57.81% 4662ms 4.25% MutableElement::ResetIndex 128ms 0.12% 57.93% 4638ms 4.22% AbstractCellPopulation::GetCellUsingLocationIndex 496ms 0.45% 58.38% 4578ms 4.17% std::_Rb_tree::_M_insert_ (inline) 144ms 0.13% 58.51% 4196ms 3.82% std::set_intersection (inline) 46ms 0.042% 58.55% 4153ms 3.78% Cell::GetCellProliferativeType 58ms 0.053% 58.60% 4111ms 3.74% AbstractCellProperty::IsType (inline) 192ms 0.17% 58.78% 4052ms 3.69% std::__set_intersection 3771ms 3.43% 62.21% 3771ms 3.43% boost::numeric::ublas::same_impl_ex 12ms 0.011% 62.22% 3538ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 56ms 0.051% 62.27% 3340ms 3.04% Cell::SetCellProliferativeType 0 0% 62.27% 3185ms 2.90% std::insert_iterator::operator= (inline) 2212ms 2.01% 64.29% 3138ms 2.86% _int_malloc 3081ms 2.81% 67.09% 3081ms 2.81% std::_Rb_tree::_S_right (inline) 55ms 0.05% 67.15% 3046ms 2.77% std::_Rb_tree::erase 853ms 0.78% 67.92% 3024ms 2.75% AbstractElement::GetNodeLocation 830ms 0.76% 68.68% 2988ms 2.72% AbstractCellProperty::IsSame 37ms 0.034% 68.71% 2975ms 2.71% CellPropertyCollection::HasProperty 0 0% 68.71% 2871ms 2.61% Cell::HasCellProperty (inline) 14ms 0.013% 68.72% 2753ms 2.51% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.72% 2634ms 2.40% boost::numeric::ublas::c_vector::operator-= (inline) 646ms 0.59% 69.31% 2621ms 2.39% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 69.31% 2609ms 2.38% std::_Rb_tree::_M_insert_unique 210ms 0.19% 69.51% 2592ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 237ms 0.22% 69.72% 2530ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 24ms 0.022% 69.74% 2528ms 2.30% Cell::GetCellData 0 0% 69.74% 2527ms 2.30% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.74% 2441ms 2.22% AbstractCellPopulation::WriteResultsToFiles 33ms 0.03% 69.77% 2353ms 2.14% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 81ms 0.074% 69.85% 2344ms 2.13% VertexMesh::GetVolumeOfElement 526ms 0.48% 70.33% 2158ms 1.97% std::type_info::operator== (inline) 43ms 0.039% 70.37% 2136ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.0091% 70.37% 2112ms 1.92% AbstractCellPopulation::Iterator::operator++ (inline) 163ms 0.15% 70.52% 2100ms 1.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0027% 70.53% 2085ms 1.90% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.53% 2085ms 1.90% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2031ms 1.85% 72.37% 2031ms 1.85% std::_Rb_tree_increment 1332ms 1.21% 73.59% 1993ms 1.81% std::_Rb_tree::equal_range (inline) 0 0% 73.59% 1985ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.59% 1968ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 74ms 0.067% 73.66% 1825ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00091% 73.66% 1766ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.03% 73.69% 1696ms 1.54% VertexMesh::GetSurfaceAreaOfElement 16ms 0.015% 73.70% 1629ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 144ms 0.13% 73.83% 1599ms 1.46% CellPropertyCollection::AddProperty 44ms 0.04% 73.87% 1553ms 1.41% Node::RemoveElement 5ms 0.0046% 73.88% 1510ms 1.38% std::set::erase (inline) 33ms 0.03% 73.91% 1509ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.068% 73.97% 1463ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.97% 1387ms 1.26% tcache_get (inline) 1387ms 1.26% 75.24% 1387ms 1.26% tcache_get_n (inline) 0 0% 75.24% 1369ms 1.25% boost::numeric::ublas::norm_2 (inline) 57ms 0.052% 75.29% 1369ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.29% 1365ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 613ms 0.56% 75.85% 1353ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 71ms 0.065% 75.91% 1333ms 1.21% std::less::operator() (inline) 1278ms 1.16% 77.08% 1278ms 1.16% [libchaste_cell_based.so] 1029ms 0.94% 78.01% 1262ms 1.15% std::operator< (inline) 2ms 0.0018% 78.02% 1253ms 1.14% OffLatticeSimulation::ApplyBoundaries 33ms 0.03% 78.05% 1241ms 1.13% CellPropertyRegistry::Get 84ms 0.076% 78.12% 1216ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 1168ms 1.06% 79.19% 1168ms 1.06% std::_Rb_tree_insert_and_rebalance 0 0% 79.19% 1148ms 1.05% boost::numeric::ublas::c_vector::assign_temporary (inline) 17ms 0.015% 79.20% 1148ms 1.05% boost::numeric::ublas::c_vector::swap (inline) 80ms 0.073% 79.27% 1131ms 1.03% std::swap_ranges (inline) 105ms 0.096% 79.37% 1123ms 1.02% std::_Rb_tree::find (inline) 0 0% 79.37% 1108ms 1.01% std::_Rb_tree::clear (inline) 0 0% 79.37% 1094ms 1% std::map::clear (inline) 4ms 0.0036% 79.37% 1084ms 0.99% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.37% 1080ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 13ms 0.012% 79.38% 1068ms 0.97% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 134ms 0.12% 79.51% 1057ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.51% 1057ms 0.96% boost::shared_ptr::~shared_ptr (inline) 1052ms 0.96% 80.46% 1052ms 0.96% std::swap (inline) 0 0% 80.46% 1051ms 0.96% std::iter_swap (inline) 1010ms 0.92% 81.38% 1010ms 0.92% Node::rGetLocation 0 0% 81.38% 949ms 0.86% std::map::find (inline) 13ms 0.012% 81.40% 946ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 166ms 0.15% 81.55% 923ms 0.84% boost::numeric::ublas::detail::equals 872ms 0.79% 82.34% 899ms 0.82% boost::detail::sp_counted_base::release 865ms 0.79% 83.13% 865ms 0.79% std::vector::size (inline) 1ms 0.00091% 83.13% 854ms 0.78% VertexMeshWriter::MakeVtkMesh 238ms 0.22% 83.35% 854ms 0.78% std::__new_allocator::construct (inline) 0 0% 83.35% 854ms 0.78% std::allocator_traits::construct (inline) 110ms 0.1% 83.45% 852ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 806ms 0.73% 84.18% 806ms 0.73% [libchaste_mesh.so] 173ms 0.16% 84.34% 797ms 0.73% boost::shared_ptr::shared_ptr (inline) 0 0% 84.34% 787ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.34% 786ms 0.72% std::_Rb_tree::_M_construct_node (inline) 393ms 0.36% 84.70% 774ms 0.7% Edge::GetMapIndex 134ms 0.12% 84.82% 755ms 0.69% MutableElement::GetNodeLocalIndex 24ms 0.022% 84.84% 736ms 0.67% Edge::AddElement 17ms 0.015% 84.86% 736ms 0.67% MutableElement::RegisterWithEdges (inline) 1ms 0.00091% 84.86% 729ms 0.66% std::_Vector_base::_M_allocate (inline) 0 0% 84.86% 723ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 719ms 0.65% 85.51% 719ms 0.65% [libstdc++.so.6.0.33] 0 0% 85.51% 717ms 0.65% boost::numeric::ublas::norm_inf (inline) 368ms 0.34% 85.85% 717ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 368ms 0.34% 86.18% 690ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 687ms 0.63% 86.81% 687ms 0.63% Node::GetIndex 0 0% 86.81% 673ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.83% 673ms 0.61% std::_Rb_tree::_M_insert_node (inline) 601ms 0.55% 87.37% 624ms 0.57% boost::detail::shared_count::shared_count (inline) 9ms 0.0082% 87.38% 608ms 0.55% std::vector::_M_default_append (inline) 39ms 0.036% 87.42% 603ms 0.55% MutableElement::RegisterWithNodes (inline) 0 0% 87.42% 595ms 0.54% vtkPolygon::New 0 0% 87.42% 595ms 0.54% vtkPolygon::vtkPolygon 33ms 0.03% 87.45% 564ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.45% 564ms 0.51% boost::numeric::ublas::vector::vector (inline) 30ms 0.027% 87.48% 560ms 0.51% Node::AddElement