File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95242ms, 88.78% of 107279ms total Dropped 1078 nodes (cum <= 536.39ms) flat flat% sum% cum cum% 0 0% 0% 106771ms 99.53% __libc_start_call_main 0 0% 0% 106771ms 99.53% __libc_start_main_impl 0 0% 0% 106771ms 99.53% _start 0 0% 0% 106749ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106749ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106749ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106749ms 99.51% main 0 0% 0% 106707ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106707ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106707ms 99.47% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 106700ms 99.46% AbstractCellBasedSimulation::Solve 10ms 0.0093% 0.011% 55458ms 51.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.028% 52333ms 48.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 124ms 0.12% 0.14% 51349ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 343ms 0.32% 0.46% 39715ms 37.02% NagaiHondaForce::AddForceContribution 2ms 0.0019% 0.47% 38342ms 35.74% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.47% 23684ms 22.08% VertexBasedCellPopulation::Update 1ms 0.00093% 0.47% 23551ms 21.95% MutableVertexMesh::ReMesh 14686ms 13.69% 14.16% 23046ms 21.48% Cylindrical2dVertexMesh::GetVectorFromAtoB 68ms 0.063% 14.22% 17625ms 16.43% Cell::ReadyToDivide 57ms 0.053% 14.28% 16425ms 15.31% AbstractPhaseBasedCellCycleModel::ReadyToDivide 345ms 0.32% 14.60% 14778ms 13.78% NagaiHondaForce::GetAdhesionParameter 370ms 0.34% 14.94% 14182ms 13.22% boost::numeric::ublas::c_vector::c_vector (partial-inline) 143ms 0.13% 15.08% 14134ms 13.17% SimpleWntCellCycleModel::UpdateCellCyclePhase 161ms 0.15% 15.23% 13489ms 12.57% CellPropertyCollection::GetPropertiesType (inline) 375ms 0.35% 15.58% 12723ms 11.86% boost::numeric::ublas::vector_assign (inline) 142ms 0.13% 15.71% 12061ms 11.24% MutableVertexMesh::CheckForIntersections 3096ms 2.89% 18.59% 11215ms 10.45% __dynamic_cast 136ms 0.13% 18.72% 11145ms 10.39% VertexBasedCellPopulation::GetDampingConstant 82ms 0.076% 18.80% 11143ms 10.39% AbstractCellProperty::IsSubType (inline) 85ms 0.079% 18.88% 10537ms 9.82% AbstractTargetAreaModifier::UpdateTargetAreas 60ms 0.056% 18.93% 10427ms 9.72% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 16ms 0.015% 18.95% 10220ms 9.53% AbstractCellBasedSimulation::DoCellBirth 1221ms 1.14% 20.09% 9789ms 9.12% std::__new_allocator::allocate (inline) 2635ms 2.46% 22.54% 9542ms 8.89% boost::numeric::ublas::indexing_vector_assign 0 0% 22.54% 9283ms 8.65% std::_Rb_tree::_M_create_node (inline) 0 0% 22.54% 9267ms 8.64% std::allocator_traits::allocate (inline) 1285ms 1.20% 23.74% 9048ms 8.43% std::_Rb_tree::_M_erase 794ms 0.74% 24.48% 8911ms 8.31% VertexMesh::ElementIncludesPoint 432ms 0.4% 24.88% 8884ms 8.28% VertexMesh::GetNextEdgeGradientOfElementAtNode 101ms 0.094% 24.98% 8746ms 8.15% Cell::GetMutationState 19ms 0.018% 24.99% 8645ms 8.06% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.99% 8641ms 8.05% std::_Rb_tree::_M_get_node (inline) 828ms 0.77% 25.77% 8635ms 8.05% operator new 213ms 0.2% 25.96% 8302ms 7.74% std::_Rb_tree::~_Rb_tree (inline) 463ms 0.43% 26.40% 8293ms 7.73% VertexMesh::GetCentroidOfElement 0 0% 26.40% 8183ms 7.63% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.40% 8140ms 7.59% std::_Rb_tree::_M_drop_node (inline) 236ms 0.22% 26.62% 7924ms 7.39% std::__new_allocator::deallocate (inline) 0 0% 26.62% 7885ms 7.35% std::allocator_traits::deallocate (inline) 0 0% 26.62% 7839ms 7.31% std::set::~set (inline) 3219ms 3.00% 29.62% 7816ms 7.29% __GI___libc_free 0 0% 29.62% 7815ms 7.28% std::_Rb_tree::_M_put_node (inline) 3142ms 2.93% 32.55% 7607ms 7.09% __GI___libc_malloc 10ms 0.0093% 32.55% 7180ms 6.69% MutableVertexMesh::RemoveDeletedNodesAndElements 1367ms 1.27% 33.83% 7134ms 6.65% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 465ms 0.43% 34.26% 6884ms 6.42% std::map::operator[] (partial-inline) 165ms 0.15% 34.42% 6810ms 6.35% std::_Rb_tree::_Rb_tree (partial-inline) 6600ms 6.15% 40.57% 6600ms 6.15% __strcmp_avx2 640ms 0.6% 41.16% 6402ms 5.97% std::_Rb_tree::_M_copy (inline) 17ms 0.016% 41.18% 6372ms 5.94% std::set::set (inline) 123ms 0.11% 41.30% 6368ms 5.94% SimpleWntCellCycleModel::GetWntLevel 143ms 0.13% 41.43% 6148ms 5.73% WntConcentration::GetWntLevel 6140ms 5.72% 47.15% 6140ms 5.72% boost::numeric::ublas::c_vector::operator() 2655ms 2.47% 49.63% 5816ms 5.42% __cxxabiv1::__si_class_type_info::__do_dyncast 715ms 0.67% 50.29% 5447ms 5.08% std::_Rb_tree::_M_clone_node (inline) 2277ms 2.12% 52.42% 5313ms 4.95% std::_Rb_tree::_M_lower_bound (inline) 0 0% 52.42% 5282ms 4.92% std::set::insert (inline) 23ms 0.021% 52.44% 5079ms 4.73% MutableVertexMesh::RemoveDeletedNodes 32ms 0.03% 52.47% 4923ms 4.59% EdgeHelper::RemoveDeletedEdges 1493ms 1.39% 53.86% 4761ms 4.44% boost::numeric::ublas::c_vector::operator[] (inline) 29ms 0.027% 53.89% 4652ms 4.34% EdgeHelper::UpdateEdgesMapKey 4263ms 3.97% 57.86% 4589ms 4.28% _int_free 194ms 0.18% 58.04% 4458ms 4.16% MutableElement::ResetIndex 56ms 0.052% 58.09% 4445ms 4.14% std::set_intersection (inline) 1ms 0.00093% 58.09% 4429ms 4.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 506ms 0.47% 58.57% 4415ms 4.12% std::_Rb_tree::_M_insert_ (inline) 267ms 0.25% 58.81% 4389ms 4.09% std::__set_intersection 0 0% 58.81% 4219ms 3.93% std::_Rb_tree::lower_bound (inline) 0 0% 58.81% 4219ms 3.93% std::map::lower_bound (inline) 4029ms 3.76% 62.57% 4029ms 3.76% boost::numeric::ublas::same_impl_ex 95ms 0.089% 62.66% 3872ms 3.61% AbstractCellProperty::IsType (inline) 48ms 0.045% 62.70% 3836ms 3.58% Cell::GetCellProliferativeType 113ms 0.11% 62.81% 3802ms 3.54% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.0037% 62.81% 3413ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 51ms 0.048% 62.86% 3226ms 3.01% Cell::SetCellProliferativeType 0 0% 62.86% 3209ms 2.99% std::insert_iterator::operator= (inline) 814ms 0.76% 63.62% 3146ms 2.93% AbstractElement::GetNodeLocation 2142ms 2.00% 65.61% 2991ms 2.79% _int_malloc 605ms 0.56% 66.18% 2814ms 2.62% boost::numeric::ublas::vector_binary::size (inline) 0 0% 66.18% 2796ms 2.61% boost::numeric::ublas::c_vector::operator-= (inline) 35ms 0.033% 66.21% 2780ms 2.59% std::_Rb_tree::erase 4ms 0.0037% 66.22% 2779ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 682ms 0.64% 66.85% 2723ms 2.54% AbstractCellProperty::IsSame 417ms 0.39% 67.24% 2723ms 2.54% std::_Rb_tree_const_iterator::operator++ (inline) 44ms 0.041% 67.28% 2630ms 2.45% CellPropertyCollection::HasProperty 2561ms 2.39% 69.67% 2561ms 2.39% std::_Rb_tree::_S_right (inline) 260ms 0.24% 69.91% 2540ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.91% 2524ms 2.35% Cell::HasCellProperty (inline) 2ms 0.0019% 69.91% 2503ms 2.33% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.91% 2388ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.91% 2328ms 2.17% AbstractCellPopulation::WriteResultsToFiles 26ms 0.024% 69.94% 2320ms 2.16% Cell::GetCellData 95ms 0.089% 70.02% 2212ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 44ms 0.041% 70.07% 2142ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00093% 70.07% 2139ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 212ms 0.2% 70.26% 2131ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 89ms 0.083% 70.35% 2128ms 1.98% VertexMesh::GetVolumeOfElement 2105ms 1.96% 72.31% 2105ms 1.96% std::_Rb_tree_increment 502ms 0.47% 72.78% 2041ms 1.90% std::type_info::operator== (inline) 6ms 0.0056% 72.78% 1936ms 1.80% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.78% 1936ms 1.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.78% 1897ms 1.77% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 72.79% 1888ms 1.76% VertexBasedCellPopulation::WriteCellVtkResultsToFile 79ms 0.074% 72.86% 1887ms 1.76% MutableVertexMesh::CheckForSwapsFromShortEdges 1240ms 1.16% 74.02% 1856ms 1.73% std::_Rb_tree::equal_range (inline) 0 0% 74.02% 1710ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.017% 74.03% 1648ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 19ms 0.018% 74.05% 1635ms 1.52% VertexMesh::GetSurfaceAreaOfElement 133ms 0.12% 74.17% 1571ms 1.46% boost::numeric::ublas::vector_reference::operator() (inline) 170ms 0.16% 74.33% 1527ms 1.42% CellPropertyCollection::AddProperty 0 0% 74.33% 1481ms 1.38% boost::numeric::ublas::vector_binary::operator() (inline) 50ms 0.047% 74.38% 1457ms 1.36% Node::RemoveElement 33ms 0.031% 74.41% 1447ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 88ms 0.082% 74.49% 1426ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 14ms 0.013% 74.50% 1416ms 1.32% std::set::erase (inline) 0 0% 74.50% 1337ms 1.25% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 74.50% 1337ms 1.25% boost::numeric::ublas::c_vector::swap 372ms 0.35% 74.85% 1337ms 1.25% std::swap_ranges (inline) 0 0% 74.85% 1294ms 1.21% tcache_get (inline) 1294ms 1.21% 76.06% 1294ms 1.21% tcache_get_n (inline) 0 0% 76.06% 1223ms 1.14% boost::numeric::ublas::norm_2 (inline) 1ms 0.00093% 76.06% 1212ms 1.13% OffLatticeSimulation::ApplyBoundaries 511ms 0.48% 76.54% 1211ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 42ms 0.039% 76.57% 1140ms 1.06% CellPropertyRegistry::Get 1140ms 1.06% 77.64% 1140ms 1.06% [libchaste_cell_based.so] 1114ms 1.04% 78.68% 1114ms 1.04% Node::rGetLocation 93ms 0.087% 78.76% 1111ms 1.04% std::less::operator() (inline) 0 0% 78.76% 1100ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 69ms 0.064% 78.83% 1092ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1063ms 0.99% 79.82% 1063ms 0.99% std::_Rb_tree_insert_and_rebalance 83ms 0.077% 79.89% 1055ms 0.98% std::_Rb_tree::find (inline) 14ms 0.013% 79.91% 1032ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 833ms 0.78% 80.68% 1018ms 0.95% std::operator< (inline) 191ms 0.18% 80.86% 1005ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 80.86% 1005ms 0.94% boost::shared_ptr::~shared_ptr (inline) 5ms 0.0047% 80.87% 967ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 966ms 0.9% 81.77% 966ms 0.9% std::swap (inline) 0 0% 81.77% 965ms 0.9% std::iter_swap (inline) 0 0% 81.77% 961ms 0.9% std::_Rb_tree::clear (inline) 956ms 0.89% 82.66% 956ms 0.89% std::vector::size (inline) 0 0% 82.66% 949ms 0.88% std::map::clear (inline) 16ms 0.015% 82.67% 943ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 119ms 0.11% 82.78% 926ms 0.86% boost::numeric::ublas::c_vector::operator= (inline) 146ms 0.14% 82.92% 914ms 0.85% boost::numeric::ublas::detail::equals 908ms 0.85% 83.77% 908ms 0.85% [libchaste_mesh.so] 0 0% 83.77% 874ms 0.81% std::map::find (inline) 343ms 0.32% 84.09% 872ms 0.81% Edge::GetMapIndex 1ms 0.00093% 84.09% 834ms 0.78% VertexMeshWriter::MakeVtkMesh 160ms 0.15% 84.24% 791ms 0.74% boost::shared_ptr::shared_ptr (inline) 779ms 0.73% 84.96% 783ms 0.73% boost::detail::sp_counted_base::release 463ms 0.43% 85.39% 776ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 119ms 0.11% 85.51% 733ms 0.68% MutableElement::GetNodeLocalIndex 0 0% 85.51% 724ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 30ms 0.028% 85.53% 724ms 0.67% Edge::AddElement 14ms 0.013% 85.55% 724ms 0.67% MutableElement::RegisterWithEdges (inline) 0 0% 85.55% 713ms 0.66% boost::numeric::ublas::norm_inf (inline) 361ms 0.34% 85.88% 713ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 109ms 0.1% 85.98% 695ms 0.65% std::__new_allocator::construct (inline) 0 0% 85.98% 695ms 0.65% std::allocator_traits::construct (inline) 0 0% 85.98% 694ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.01% 694ms 0.65% std::_Rb_tree::_M_insert_node (inline) 652ms 0.61% 86.62% 652ms 0.61% Node::GetIndex 0 0% 86.62% 642ms 0.6% std::_Rb_tree::_M_construct_node (inline) 601ms 0.56% 87.18% 631ms 0.59% boost::detail::shared_count::shared_count (inline) 2ms 0.0019% 87.18% 626ms 0.58% std::_Vector_base::_M_allocate (inline) 32ms 0.03% 87.21% 619ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 87.21% 614ms 0.57% vtkPolygon::New 1ms 0.00093% 87.21% 614ms 0.57% vtkPolygon::vtkPolygon 35ms 0.033% 87.24% 577ms 0.54% Node::AddElement 0 0% 87.24% 570ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 561ms 0.52% 87.77% 561ms 0.52% [libstdc++.so.6.0.33] 549ms 0.51% 88.28% 549ms 0.51% operator delete 539ms 0.5% 88.78% 539ms 0.5% boost::shared_ptr::operator-> (inline)