File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 79520ms, 87.94% of 90421ms total Dropped 1069 nodes (cum <= 452.11ms) flat flat% sum% cum cum% 0 0% 0% 90173ms 99.73% __libc_start_call_main 0 0% 0% 90173ms 99.73% __libc_start_main_impl 0 0% 0% 90173ms 99.73% _start 0 0% 0% 90155ms 99.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 90155ms 99.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 90155ms 99.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 90155ms 99.71% main 0 0% 0% 90118ms 99.66% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 90118ms 99.66% CxxTest::TestRunner::runTest (inline) 0 0% 0% 90118ms 99.66% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0033% 0.0033% 90111ms 99.66% AbstractCellBasedSimulation::Solve 14ms 0.015% 0.019% 47532ms 52.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.012% 0.031% 44386ms 49.09% ForwardEulerNumericalMethod::UpdateAllNodePositions 66ms 0.073% 0.1% 43404ms 48.00% AbstractNumericalMethod::ComputeForcesIncludingDamping 417ms 0.46% 0.57% 33585ms 37.14% NagaiHondaForce::AddForceContribution 0 0% 0.57% 31534ms 34.87% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.57% 18845ms 20.84% VertexBasedCellPopulation::Update 0 0% 0.57% 18726ms 20.71% MutableVertexMesh::ReMesh 7810ms 8.64% 9.20% 15113ms 16.71% Cylindrical2dVertexMesh::GetVectorFromAtoB 71ms 0.079% 9.28% 14908ms 16.49% Cell::ReadyToDivide 19ms 0.021% 9.30% 14058ms 15.55% AbstractPhaseBasedCellCycleModel::ReadyToDivide 93ms 0.1% 9.40% 14051ms 15.54% NagaiHondaForce::GetAdhesionParameter 63ms 0.07% 9.47% 12019ms 13.29% SimpleWntCellCycleModel::UpdateCellCyclePhase 355ms 0.39% 9.87% 11432ms 12.64% boost::numeric::ublas::c_vector::c_vector (partial-inline) 664ms 0.73% 10.60% 11428ms 12.64% std::__new_allocator::allocate (inline) 67ms 0.074% 10.68% 11165ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 0 0% 10.68% 11005ms 12.17% std::allocator_traits::allocate (inline) 0 0% 10.68% 10813ms 11.96% std::_Rb_tree::_M_create_node (inline) 807ms 0.89% 11.57% 10695ms 11.83% operator new 0 0% 11.57% 10452ms 11.56% std::_Rb_tree::_M_get_node (inline) 209ms 0.23% 11.80% 10178ms 11.26% boost::numeric::ublas::vector_assign (inline) 3293ms 3.64% 15.44% 9608ms 10.63% __GI___libc_malloc 98ms 0.11% 15.55% 9485ms 10.49% VertexBasedCellPopulation::GetDampingConstant 0 0% 15.55% 9227ms 10.20% std::_Rb_tree::_Alloc_node::operator() (inline) 81ms 0.09% 15.64% 9067ms 10.03% AbstractCellProperty::IsSubType (inline) 2632ms 2.91% 18.55% 8990ms 9.94% __dynamic_cast 47ms 0.052% 18.60% 8985ms 9.94% AbstractTargetAreaModifier::UpdateTargetAreas 10ms 0.011% 18.61% 8929ms 9.87% AbstractCellBasedSimulation::DoCellBirth 39ms 0.043% 18.66% 8904ms 9.85% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 113ms 0.12% 18.78% 8320ms 9.20% MutableVertexMesh::CheckForIntersections 929ms 1.03% 19.81% 8003ms 8.85% std::_Rb_tree::_M_erase 0 0% 19.81% 7901ms 8.74% std::_Rb_tree::_M_drop_node (inline) 461ms 0.51% 20.32% 7773ms 8.60% std::map::operator[] (partial-inline) 2208ms 2.44% 22.76% 7477ms 8.27% boost::numeric::ublas::indexing_vector_assign 265ms 0.29% 23.05% 7476ms 8.27% std::_Rb_tree::~_Rb_tree (inline) 63ms 0.07% 23.12% 7200ms 7.96% Cell::GetMutationState 101ms 0.11% 23.23% 7189ms 7.95% std::__new_allocator::deallocate (inline) 0 0% 23.23% 7171ms 7.93% std::allocator_traits::deallocate (inline) 0 0% 23.23% 7127ms 7.88% std::_Rb_tree::_M_put_node (inline) 0 0% 23.23% 7123ms 7.88% std::set::~set (inline) 1802ms 1.99% 25.23% 6865ms 7.59% __GI___libc_free 384ms 0.42% 25.65% 6839ms 7.56% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.65% 6804ms 7.52% std::set::insert (inline) 30ms 0.033% 25.69% 6785ms 7.50% VertexBasedCellPopulation::GetLocationOfCellCentre 7ms 0.0077% 25.69% 6713ms 7.42% MutableVertexMesh::RemoveDeletedNodesAndElements 481ms 0.53% 26.23% 6332ms 7.00% VertexMesh::GetCentroidOfElement 810ms 0.9% 27.12% 6311ms 6.98% std::_Rb_tree::_M_insert_ (inline) 453ms 0.5% 27.62% 6101ms 6.75% VertexMesh::ElementIncludesPoint 110ms 0.12% 27.74% 5891ms 6.52% std::_Rb_tree::_Rb_tree (partial-inline) 609ms 0.67% 28.42% 5624ms 6.22% std::_Rb_tree::_M_copy (inline) 48ms 0.053% 28.47% 5614ms 6.21% std::set_intersection (inline) 227ms 0.25% 28.72% 5566ms 6.16% std::__set_intersection 12ms 0.013% 28.73% 5492ms 6.07% std::set::set (inline) 5471ms 6.05% 34.79% 5471ms 6.05% boost::numeric::ublas::c_vector::operator() 2115ms 2.34% 37.12% 5462ms 6.04% std::_Rb_tree::_M_lower_bound (inline) 851ms 0.94% 38.07% 5294ms 5.85% AbstractMesh::GetDistanceBetweenNodes 141ms 0.16% 38.22% 5153ms 5.70% SimpleWntCellCycleModel::GetWntLevel 4357ms 4.82% 43.04% 5020ms 5.55% _int_free 14ms 0.015% 43.06% 4963ms 5.49% MutableVertexMesh::RemoveDeletedNodes 104ms 0.12% 43.17% 4896ms 5.41% WntConcentration::GetWntLevel 674ms 0.75% 43.92% 4844ms 5.36% std::_Rb_tree::_M_clone_node (inline) 4843ms 5.36% 49.27% 4843ms 5.36% __strcmp_evex 42ms 0.046% 49.32% 4835ms 5.35% EdgeHelper::RemoveDeletedEdges 3912ms 4.33% 53.64% 4733ms 5.23% _int_malloc 0 0% 53.64% 4699ms 5.20% std::_Rb_tree::lower_bound (inline) 0 0% 53.64% 4699ms 5.20% std::map::lower_bound (inline) 10ms 0.011% 53.66% 4616ms 5.11% EdgeHelper::UpdateEdgesMapKey 516ms 0.57% 54.23% 4417ms 4.88% boost::numeric::ublas::c_vector::operator[] (inline) 2036ms 2.25% 56.48% 4342ms 4.80% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.48% 4264ms 4.72% std::insert_iterator::operator= (inline) 105ms 0.12% 56.59% 4003ms 4.43% MutableElement::ResetIndex 0 0% 56.59% 3984ms 4.41% std::_Rb_tree::_M_insert_unique_ (inline) 68ms 0.075% 56.67% 3981ms 4.40% AbstractCellPopulation::GetCellUsingLocationIndex 21ms 0.023% 56.69% 3758ms 4.16% Cell::GetCellProliferativeType 2ms 0.0022% 56.69% 3750ms 4.15% AbstractCellBasedSimulation::DoCellRemoval (inline) 3600ms 3.98% 60.68% 3600ms 3.98% boost::numeric::ublas::same_impl_ex 2993ms 3.31% 63.99% 2993ms 3.31% [libchaste_cell_based.so] 2910ms 3.22% 67.20% 2910ms 3.22% std::_Rb_tree::_S_right (inline) 46ms 0.051% 67.26% 2909ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 140ms 0.15% 67.41% 2835ms 3.14% AbstractCellProperty::IsType (inline) 0 0% 67.41% 2820ms 3.12% std::_Rb_tree::_M_insert_unique (inline) 94ms 0.1% 67.51% 2728ms 3.02% Cell::SetCellProliferativeType 30ms 0.033% 67.55% 2571ms 2.84% std::_Rb_tree::_M_emplace_hint_unique 647ms 0.72% 68.26% 2527ms 2.79% AbstractElement::GetNodeLocation 6ms 0.0066% 68.27% 2517ms 2.78% AbstractCellPopulation::Iterator::operator++ (inline) 226ms 0.25% 68.52% 2515ms 2.78% AbstractCellPopulation::Iterator::IsRealCell (inline) 103ms 0.11% 68.63% 2486ms 2.75% boost::detail::shared_count::~shared_count (inline) 0 0% 68.63% 2486ms 2.75% boost::shared_ptr::~shared_ptr (inline) 2321ms 2.57% 71.20% 2329ms 2.58% boost::detail::sp_counted_base::release 57ms 0.063% 71.26% 2283ms 2.52% std::_Rb_tree::erase 306ms 0.34% 71.60% 2251ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 131ms 0.14% 71.75% 2202ms 2.44% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.75% 2163ms 2.39% boost::numeric::ublas::c_vector::assign (inline) 22ms 0.024% 71.77% 2102ms 2.32% Cell::GetCellData 0 0% 71.77% 2039ms 2.26% AbstractCellPopulation::WriteResultsToFiles 44ms 0.049% 71.82% 1992ms 2.20% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.82% 1948ms 2.15% boost::numeric::ublas::c_vector::operator-= (inline) 1927ms 2.13% 73.95% 1927ms 2.13% [libchaste_mesh.so] 25ms 0.028% 73.98% 1888ms 2.09% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 38ms 0.042% 74.02% 1789ms 1.98% CellPropertyCollection::HasProperty 428ms 0.47% 74.49% 1761ms 1.95% AbstractCellProperty::IsSame 185ms 0.2% 74.70% 1751ms 1.94% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 74.70% 1744ms 1.93% Cell::HasCellProperty (inline) 248ms 0.27% 74.97% 1718ms 1.90% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.97% 1672ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.97% 1667ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 74.97% 1586ms 1.75% std::_Rb_tree::_Auto_node::_Auto_node (inline) 112ms 0.12% 75.10% 1539ms 1.70% CellPropertyCollection::AddProperty 60ms 0.066% 75.16% 1524ms 1.69% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.16% 1501ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0011% 75.16% 1496ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.16% 1496ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 80ms 0.088% 75.25% 1490ms 1.65% VertexMesh::GetVolumeOfElement 42ms 0.046% 75.30% 1391ms 1.54% MutableVertexMesh::CheckForSwapsFromShortEdges 165ms 0.18% 75.48% 1333ms 1.47% std::type_info::operator== (inline) 1ms 0.0011% 75.48% 1329ms 1.47% OffLatticeSimulation::ApplyBoundaries 1329ms 1.47% 76.95% 1329ms 1.47% std::_Rb_tree_increment 0 0% 76.95% 1297ms 1.43% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 76.95% 1241ms 1.37% tcache_get (inline) 1241ms 1.37% 78.32% 1241ms 1.37% tcache_get_n (inline) 57ms 0.063% 78.39% 1228ms 1.36% std::_Rb_tree::_M_erase_aux (partial-inline) 72ms 0.08% 78.47% 1199ms 1.33% VertexMesh::GetSurfaceAreaOfElement 50ms 0.055% 78.52% 1193ms 1.32% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 735ms 0.81% 79.34% 1129ms 1.25% std::_Rb_tree::equal_range (inline) 27ms 0.03% 79.37% 1125ms 1.24% Node::RemoveElement 0 0% 79.37% 1098ms 1.21% std::set::erase (inline) 49ms 0.054% 79.42% 1050ms 1.16% CellPropertyRegistry::Get 79ms 0.087% 79.51% 1050ms 1.16% boost::numeric::ublas::vector_reference::operator() (inline) 41ms 0.045% 79.55% 1026ms 1.13% Edge::AddElement 8ms 0.0088% 79.56% 1024ms 1.13% MutableElement::RegisterWithEdges (inline) 936ms 1.04% 80.60% 936ms 1.04% std::_Rb_tree_insert_and_rebalance 0 0% 80.60% 913ms 1.01% CellPropertyCollection::~CellPropertyCollection (inline) 912ms 1.01% 81.60% 912ms 1.01% [libstdc++.so.6.0.33] 23ms 0.025% 81.63% 912ms 1.01% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 81.63% 863ms 0.95% boost::numeric::ublas::norm_2 (inline) 148ms 0.16% 81.79% 857ms 0.95% boost::numeric::ublas::detail::equals 849ms 0.94% 82.73% 849ms 0.94% Node::rGetLocation 432ms 0.48% 83.21% 840ms 0.93% boost::numeric::ublas::vector_norm_2::apply 90ms 0.1% 83.31% 837ms 0.93% std::_Rb_tree::find (inline) 5ms 0.0055% 83.32% 817ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.32% 799ms 0.88% std::_Rb_tree::clear (inline) 1ms 0.0011% 83.32% 783ms 0.87% VertexMeshWriter::MakeVtkMesh 0 0% 83.32% 778ms 0.86% std::__new_allocator::destroy (inline) 0 0% 83.32% 778ms 0.86% std::allocator_traits::destroy (inline) 0 0% 83.32% 778ms 0.86% std::map::clear (inline) 0 0% 83.32% 776ms 0.86% std::_Rb_tree::_M_destroy_node (inline) 585ms 0.65% 83.96% 771ms 0.85% CellPropertyCollection::GetProperty 0 0% 83.96% 768ms 0.85% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 83.96% 768ms 0.85% boost::numeric::ublas::c_vector::swap (inline) 154ms 0.17% 84.13% 768ms 0.85% std::swap_ranges (inline) 728ms 0.81% 84.94% 728ms 0.81% tcache_put (inline) 0 0% 84.94% 711ms 0.79% std::map::find (inline) 58ms 0.064% 85.00% 682ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 42ms 0.046% 85.05% 646ms 0.71% std::less::operator() (inline) 0 0% 85.05% 645ms 0.71% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.025% 85.08% 645ms 0.71% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.08% 639ms 0.71% boost::numeric::ublas::norm_inf (inline) 233ms 0.26% 85.33% 639ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 629ms 0.7% 86.03% 629ms 0.7% std::vector::size (inline) 0 0% 86.03% 614ms 0.68% std::iter_swap (inline) 614ms 0.68% 86.71% 614ms 0.68% std::swap (inline) 279ms 0.31% 87.02% 610ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 483ms 0.53% 87.55% 604ms 0.67% std::operator< (inline) 1ms 0.0011% 87.55% 570ms 0.63% vtkPolygon::New 1ms 0.0011% 87.55% 569ms 0.63% vtkPolygon::vtkPolygon 1ms 0.0011% 87.55% 554ms 0.61% std::_Vector_base::_M_allocate (inline) 7ms 0.0077% 87.56% 531ms 0.59% MutableElement::RegisterWithNodes (inline) 51ms 0.056% 87.62% 523ms 0.58% MutableElement::GetNodeLocalIndex 41ms 0.045% 87.66% 509ms 0.56% Node::AddElement 254ms 0.28% 87.94% 485ms 0.54% Edge::GetMapIndex 0 0% 87.94% 456ms 0.5% std::map::map (inline)