File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94190ms, 88.70% of 106188ms total Dropped 1111 nodes (cum <= 530.94ms) flat flat% sum% cum cum% 0 0% 0% 105914ms 99.74% __libc_start_call_main 0 0% 0% 105914ms 99.74% __libc_start_main_impl 0 0% 0% 105914ms 99.74% _start 0 0% 0% 105890ms 99.72% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 105890ms 99.72% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 105890ms 99.72% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 105890ms 99.72% main 0 0% 0% 105856ms 99.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 105856ms 99.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 105856ms 99.69% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0038% 0.0038% 105849ms 99.68% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.016% 55412ms 52.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.029% 51781ms 48.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 55ms 0.052% 0.081% 50269ms 47.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 388ms 0.37% 0.45% 38938ms 36.67% NagaiHondaForce::AddForceContribution 0 0% 0.45% 36921ms 34.77% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.45% 21828ms 20.56% VertexBasedCellPopulation::Update 1ms 0.00094% 0.45% 21713ms 20.45% MutableVertexMesh::ReMesh 106ms 0.1% 0.55% 18124ms 17.07% Cell::ReadyToDivide 9094ms 8.56% 9.11% 17628ms 16.60% Cylindrical2dVertexMesh::GetVectorFromAtoB 42ms 0.04% 9.15% 16935ms 15.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 91ms 0.086% 9.24% 15965ms 15.03% NagaiHondaForce::GetAdhesionParameter 100ms 0.094% 9.33% 14494ms 13.65% SimpleWntCellCycleModel::UpdateCellCyclePhase 401ms 0.38% 9.71% 13608ms 12.82% boost::numeric::ublas::c_vector::c_vector (partial-inline) 76ms 0.072% 9.78% 13454ms 12.67% CellPropertyCollection::GetPropertiesType (inline) 759ms 0.71% 10.50% 13374ms 12.59% std::__new_allocator::allocate (inline) 0 0% 10.50% 12867ms 12.12% std::allocator_traits::allocate (inline) 0 0% 10.50% 12604ms 11.87% std::_Rb_tree::_M_create_node (inline) 922ms 0.87% 11.37% 12574ms 11.84% operator new 0 0% 11.37% 12243ms 11.53% std::_Rb_tree::_M_get_node (inline) 304ms 0.29% 11.65% 12141ms 11.43% boost::numeric::ublas::vector_assign (inline) 3999ms 3.77% 15.42% 11337ms 10.68% __GI___libc_malloc 93ms 0.088% 15.51% 11075ms 10.43% AbstractCellProperty::IsSubType (inline) 36ms 0.034% 15.54% 11057ms 10.41% AbstractTargetAreaModifier::UpdateTargetAreas 96ms 0.09% 15.63% 10986ms 10.35% VertexBasedCellPopulation::GetDampingConstant 53ms 0.05% 15.68% 10969ms 10.33% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 2854ms 2.69% 18.37% 10950ms 10.31% __dynamic_cast 0 0% 18.37% 10900ms 10.26% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.0066% 18.37% 10686ms 10.06% AbstractCellBasedSimulation::DoCellBirth 160ms 0.15% 18.52% 9836ms 9.26% MutableVertexMesh::CheckForIntersections 1081ms 1.02% 19.54% 9121ms 8.59% std::_Rb_tree::_M_erase 0 0% 19.54% 9041ms 8.51% std::_Rb_tree::_M_drop_node (inline) 2599ms 2.45% 21.99% 8857ms 8.34% boost::numeric::ublas::indexing_vector_assign 466ms 0.44% 22.43% 8636ms 8.13% std::map::operator[] (partial-inline) 336ms 0.32% 22.75% 8575ms 8.08% std::_Rb_tree::~_Rb_tree (inline) 56ms 0.053% 22.80% 8264ms 7.78% Cell::GetMutationState 107ms 0.1% 22.90% 8228ms 7.75% std::__new_allocator::deallocate (inline) 0 0% 22.90% 8210ms 7.73% std::allocator_traits::deallocate (inline) 0 0% 22.90% 8160ms 7.68% std::set::~set (inline) 0 0% 22.90% 8133ms 7.66% std::_Rb_tree::_M_put_node (inline) 70ms 0.066% 22.96% 8074ms 7.60% VertexBasedCellPopulation::GetLocationOfCellCentre 2073ms 1.95% 24.92% 8057ms 7.59% __GI___libc_free 0 0% 24.92% 7927ms 7.47% std::set::insert (inline) 12ms 0.011% 24.93% 7698ms 7.25% MutableVertexMesh::RemoveDeletedNodesAndElements 413ms 0.39% 25.32% 7623ms 7.18% VertexMesh::GetNextEdgeGradientOfElementAtNode 545ms 0.51% 25.83% 7546ms 7.11% VertexMesh::GetCentroidOfElement 878ms 0.83% 26.66% 7295ms 6.87% std::_Rb_tree::_M_insert_ (inline) 546ms 0.51% 27.17% 7230ms 6.81% VertexMesh::ElementIncludesPoint 125ms 0.12% 27.29% 7008ms 6.60% std::_Rb_tree::_Rb_tree (partial-inline) 702ms 0.66% 27.95% 6673ms 6.28% std::_Rb_tree::_M_copy (inline) 6588ms 6.20% 34.15% 6588ms 6.20% boost::numeric::ublas::c_vector::operator() 6499ms 6.12% 40.27% 6499ms 6.12% __strcmp_evex 5ms 0.0047% 40.28% 6476ms 6.10% std::set::set (inline) 62ms 0.058% 40.34% 6338ms 5.97% std::set_intersection (inline) 252ms 0.24% 40.58% 6276ms 5.91% std::__set_intersection 2412ms 2.27% 42.85% 6232ms 5.87% std::_Rb_tree::_M_lower_bound (inline) 136ms 0.13% 42.97% 6164ms 5.80% SimpleWntCellCycleModel::GetWntLevel 5144ms 4.84% 47.82% 5921ms 5.58% _int_free 878ms 0.83% 48.65% 5912ms 5.57% AbstractMesh::GetDistanceBetweenNodes 132ms 0.12% 48.77% 5901ms 5.56% WntConcentration::GetWntLevel 786ms 0.74% 49.51% 5800ms 5.46% std::_Rb_tree::_M_clone_node (inline) 28ms 0.026% 49.54% 5581ms 5.26% MutableVertexMesh::RemoveDeletedNodes 57ms 0.054% 49.59% 5436ms 5.12% EdgeHelper::RemoveDeletedEdges 4492ms 4.23% 53.82% 5415ms 5.10% _int_malloc 599ms 0.56% 54.38% 5398ms 5.08% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 54.38% 5298ms 4.99% std::_Rb_tree::lower_bound (inline) 0 0% 54.38% 5298ms 4.99% std::map::lower_bound (inline) 2431ms 2.29% 56.67% 5256ms 4.95% __cxxabiv1::__si_class_type_info::__do_dyncast 20ms 0.019% 56.69% 5151ms 4.85% EdgeHelper::UpdateEdgesMapKey 0 0% 56.69% 4919ms 4.63% std::insert_iterator::operator= (inline) 61ms 0.057% 56.75% 4687ms 4.41% AbstractCellPopulation::GetCellUsingLocationIndex 29ms 0.027% 56.78% 4647ms 4.38% Cell::GetCellProliferativeType 129ms 0.12% 56.90% 4647ms 4.38% MutableElement::ResetIndex 0 0% 56.90% 4610ms 4.34% std::_Rb_tree::_M_insert_unique_ (inline) 1ms 0.00094% 56.90% 4391ms 4.14% AbstractCellBasedSimulation::DoCellRemoval (inline) 4380ms 4.12% 61.02% 4380ms 4.12% boost::numeric::ublas::same_impl_ex 158ms 0.15% 61.17% 3569ms 3.36% AbstractCellProperty::IsType (inline) 3466ms 3.26% 64.44% 3466ms 3.26% [libchaste_cell_based.so] 120ms 0.11% 64.55% 3456ms 3.25% Cell::SetCellProliferativeType 46ms 0.043% 64.59% 3384ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00094% 64.59% 3317ms 3.12% std::_Rb_tree::_M_insert_unique 3312ms 3.12% 67.71% 3312ms 3.12% std::_Rb_tree::_S_right (inline) 823ms 0.78% 68.49% 3052ms 2.87% AbstractElement::GetNodeLocation 136ms 0.13% 68.62% 2966ms 2.79% boost::detail::shared_count::~shared_count (inline) 0 0% 68.62% 2966ms 2.79% boost::shared_ptr::~shared_ptr (inline) 237ms 0.22% 68.84% 2887ms 2.72% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.0047% 68.84% 2881ms 2.71% AbstractCellPopulation::Iterator::operator++ (inline) 47ms 0.044% 68.89% 2813ms 2.65% std::_Rb_tree::_M_emplace_hint_unique 2738ms 2.58% 71.47% 2765ms 2.60% boost::detail::sp_counted_base::release 14ms 0.013% 71.48% 2686ms 2.53% Cell::GetCellData 71ms 0.067% 71.55% 2664ms 2.51% std::_Rb_tree::erase 142ms 0.13% 71.68% 2559ms 2.41% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.68% 2535ms 2.39% boost::numeric::ublas::c_vector::assign (inline) 45ms 0.042% 71.72% 2432ms 2.29% CellPropertyCollection::HasProperty 1ms 0.00094% 71.72% 2422ms 2.28% AbstractCellPopulation::WriteResultsToFiles 314ms 0.3% 72.02% 2415ms 2.27% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.02% 2380ms 2.24% Cell::HasCellProperty (inline) 50ms 0.047% 72.07% 2375ms 2.24% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 72.07% 2368ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 515ms 0.48% 72.55% 2319ms 2.18% AbstractCellProperty::IsSame 25ms 0.024% 72.58% 2203ms 2.07% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2175ms 2.05% 74.62% 2175ms 2.05% [libchaste_mesh.so] 255ms 0.24% 74.86% 2172ms 2.05% VertexMesh::GetAreaGradientOfElementAtNode 333ms 0.31% 75.18% 2013ms 1.90% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.18% 1996ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 75.18% 1987ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 135ms 0.13% 75.31% 1845ms 1.74% CellPropertyCollection::AddProperty 197ms 0.19% 75.49% 1804ms 1.70% std::type_info::operator== (inline) 2ms 0.0019% 75.50% 1794ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 92ms 0.087% 75.58% 1772ms 1.67% VertexMesh::GetVolumeOfElement 7ms 0.0066% 75.59% 1748ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.59% 1748ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 75ms 0.071% 75.66% 1732ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.66% 1704ms 1.60% std::_Rb_tree::_Auto_node::_Auto_node (inline) 52ms 0.049% 75.71% 1590ms 1.50% MutableVertexMesh::CheckForSwapsFromShortEdges 5ms 0.0047% 75.71% 1547ms 1.46% OffLatticeSimulation::ApplyBoundaries 0 0% 75.71% 1531ms 1.44% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.71% 1527ms 1.44% tcache_get (inline) 1527ms 1.44% 77.15% 1527ms 1.44% tcache_get_n (inline) 94ms 0.089% 77.24% 1502ms 1.41% VertexMesh::GetSurfaceAreaOfElement 74ms 0.07% 77.31% 1489ms 1.40% std::_Rb_tree::_M_erase_aux (partial-inline) 1464ms 1.38% 78.69% 1464ms 1.38% std::_Rb_tree_increment 48ms 0.045% 78.73% 1355ms 1.28% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 39ms 0.037% 78.77% 1297ms 1.22% Node::RemoveElement 797ms 0.75% 79.52% 1290ms 1.21% std::_Rb_tree::equal_range (inline) 120ms 0.11% 79.63% 1282ms 1.21% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00094% 79.63% 1259ms 1.19% std::set::erase (inline) 60ms 0.057% 79.69% 1229ms 1.16% CellPropertyRegistry::Get 39ms 0.037% 79.73% 1189ms 1.12% Edge::AddElement 12ms 0.011% 79.74% 1181ms 1.11% MutableElement::RegisterWithEdges (inline) 8ms 0.0075% 79.75% 1104ms 1.04% boost::numeric::ublas::detail::expression_type_check (inline) 1093ms 1.03% 80.78% 1093ms 1.03% [libstdc++.so.6.0.33] 0 0% 80.78% 1077ms 1.01% CellPropertyCollection::~CellPropertyCollection (inline) 1073ms 1.01% 81.79% 1073ms 1.01% std::_Rb_tree_insert_and_rebalance 200ms 0.19% 81.97% 1065ms 1.00% boost::numeric::ublas::detail::equals 1037ms 0.98% 82.95% 1037ms 0.98% Node::rGetLocation 0 0% 82.95% 1029ms 0.97% boost::numeric::ublas::norm_2 (inline) 116ms 0.11% 83.06% 1024ms 0.96% std::_Rb_tree::find (inline) 533ms 0.5% 83.56% 989ms 0.93% boost::numeric::ublas::vector_norm_2::apply 15ms 0.014% 83.58% 981ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.58% 914ms 0.86% std::__new_allocator::destroy (inline) 0 0% 83.58% 914ms 0.86% std::allocator_traits::destroy (inline) 0 0% 83.58% 909ms 0.86% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.00094% 83.58% 902ms 0.85% VertexMeshWriter::MakeVtkMesh 1ms 0.00094% 83.58% 890ms 0.84% std::_Rb_tree::clear (inline) 0 0% 83.58% 865ms 0.81% std::map::clear (inline) 0 0% 83.58% 861ms 0.81% std::map::find (inline) 656ms 0.62% 84.20% 849ms 0.8% CellPropertyCollection::GetProperty 846ms 0.8% 84.99% 846ms 0.8% tcache_put (inline) 0 0% 84.99% 835ms 0.79% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0047% 85.00% 835ms 0.79% boost::numeric::ublas::c_vector::swap 147ms 0.14% 85.14% 830ms 0.78% std::swap_ranges (inline) 65ms 0.061% 85.20% 819ms 0.77% std::less::operator() (inline) 57ms 0.054% 85.25% 788ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 581ms 0.55% 85.80% 754ms 0.71% std::operator< (inline) 0 0% 85.80% 733ms 0.69% std::_Rb_tree::_Auto_node::_M_insert (inline) 31ms 0.029% 85.83% 733ms 0.69% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.83% 730ms 0.69% boost::numeric::ublas::norm_inf (inline) 252ms 0.24% 86.06% 730ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 30ms 0.028% 86.09% 723ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 102ms 0.096% 86.19% 693ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 63ms 0.059% 86.25% 690ms 0.65% MutableElement::GetNodeLocalIndex 323ms 0.3% 86.55% 688ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.55% 683ms 0.64% std::iter_swap (inline) 683ms 0.64% 87.20% 683ms 0.64% std::swap (inline) 653ms 0.61% 87.81% 653ms 0.61% std::vector::size (inline) 0 0% 87.81% 645ms 0.61% vtkPolygon::New 0 0% 87.81% 645ms 0.61% vtkPolygon::vtkPolygon 1ms 0.00094% 87.81% 623ms 0.59% std::_Vector_base::_M_allocate (inline) 0 0% 87.81% 618ms 0.58% std::map::map (inline) 604ms 0.57% 88.38% 604ms 0.57% Node::GetIndex 15ms 0.014% 88.39% 602ms 0.57% MutableElement::RegisterWithNodes (inline) 42ms 0.04% 88.43% 582ms 0.55% Node::AddElement 284ms 0.27% 88.70% 551ms 0.52% Edge::GetMapIndex