File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97106ms, 88.60% of 109606ms total Dropped 1085 nodes (cum <= 548.03ms) flat flat% sum% cum cum% 0 0% 0% 109132ms 99.57% __libc_start_call_main 0 0% 0% 109132ms 99.57% __libc_start_main_impl 0 0% 0% 109132ms 99.57% _start 0 0% 0% 109111ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109111ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109111ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109111ms 99.55% main 0 0% 0% 109069ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109069ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109069ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0055% 0.0055% 109060ms 99.50% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.024% 56098ms 51.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.044% 52828ms 48.20% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.17% 51741ms 47.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 386ms 0.35% 0.52% 39871ms 36.38% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.52% 39622ms 36.15% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.53% 24659ms 22.50% VertexBasedCellPopulation::Update 1ms 0.00091% 0.53% 24534ms 22.38% MutableVertexMesh::ReMesh 14463ms 13.20% 13.72% 23169ms 21.14% Cylindrical2dVertexMesh::GetVectorFromAtoB 86ms 0.078% 13.80% 17911ms 16.34% Cell::ReadyToDivide 72ms 0.066% 13.87% 16658ms 15.20% AbstractPhaseBasedCellCycleModel::ReadyToDivide 365ms 0.33% 14.20% 14867ms 13.56% NagaiHondaForce::GetAdhesionParameter 474ms 0.43% 14.63% 14470ms 13.20% boost::numeric::ublas::c_vector::c_vector (partial-inline) 128ms 0.12% 14.75% 14263ms 13.01% SimpleWntCellCycleModel::UpdateCellCyclePhase 156ms 0.14% 14.89% 13965ms 12.74% CellPropertyCollection::GetPropertiesType (inline) 363ms 0.33% 15.22% 12836ms 11.71% boost::numeric::ublas::vector_assign (inline) 126ms 0.11% 15.34% 12142ms 11.08% MutableVertexMesh::CheckForIntersections 81ms 0.074% 15.41% 11376ms 10.38% VertexBasedCellPopulation::GetDampingConstant 3139ms 2.86% 18.27% 11267ms 10.28% __dynamic_cast 75ms 0.068% 18.34% 11173ms 10.19% AbstractCellProperty::IsSubType (inline) 61ms 0.056% 18.40% 10788ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 71ms 0.065% 18.46% 10702ms 9.76% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1317ms 1.20% 19.66% 10476ms 9.56% std::__new_allocator::allocate (inline) 33ms 0.03% 19.70% 10357ms 9.45% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.70% 9962ms 9.09% std::_Rb_tree::_M_create_node (inline) 0 0% 19.70% 9952ms 9.08% std::allocator_traits::allocate (inline) 2736ms 2.50% 22.19% 9555ms 8.72% boost::numeric::ublas::indexing_vector_assign 1438ms 1.31% 23.50% 9319ms 8.50% std::_Rb_tree::_M_erase 773ms 0.71% 24.21% 9263ms 8.45% operator new 0 0% 24.21% 9246ms 8.44% std::_Rb_tree::_M_get_node (inline) 764ms 0.7% 24.91% 9011ms 8.22% VertexMesh::ElementIncludesPoint 74ms 0.068% 24.97% 8938ms 8.15% Cell::GetMutationState 0 0% 24.97% 8858ms 8.08% std::_Rb_tree::_Alloc_node::operator() (inline) 36ms 0.033% 25.01% 8837ms 8.06% VertexBasedCellPopulation::GetLocationOfCellCentre 334ms 0.3% 25.31% 8687ms 7.93% VertexMesh::GetNextEdgeGradientOfElementAtNode 228ms 0.21% 25.52% 8390ms 7.65% std::_Rb_tree::~_Rb_tree (inline) 471ms 0.43% 25.95% 8369ms 7.64% VertexMesh::GetCentroidOfElement 3249ms 2.96% 28.91% 8343ms 7.61% __GI___libc_malloc 0 0% 28.91% 8277ms 7.55% std::_Rb_tree::_M_drop_node (inline) 21ms 0.019% 28.93% 8079ms 7.37% MutableVertexMesh::RemoveDeletedNodesAndElements 246ms 0.22% 29.16% 8054ms 7.35% std::__new_allocator::deallocate (inline) 0 0% 29.16% 8013ms 7.31% std::allocator_traits::deallocate (inline) 2984ms 2.72% 31.88% 7958ms 7.26% __GI___libc_free 0 0% 31.88% 7941ms 7.25% std::_Rb_tree::_M_put_node (inline) 0 0% 31.88% 7910ms 7.22% std::set::~set (inline) 479ms 0.44% 32.32% 7192ms 6.56% std::map::operator[] (partial-inline) 150ms 0.14% 32.45% 7092ms 6.47% std::_Rb_tree::_Rb_tree (partial-inline) 1341ms 1.22% 33.68% 7021ms 6.41% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 6756ms 6.16% 39.84% 6756ms 6.16% __strcmp_avx2 693ms 0.63% 40.47% 6706ms 6.12% std::_Rb_tree::_M_copy (inline) 10ms 0.0091% 40.48% 6609ms 6.03% std::set::set (inline) 156ms 0.14% 40.62% 6459ms 5.89% SimpleWntCellCycleModel::GetWntLevel 143ms 0.13% 40.75% 6202ms 5.66% WntConcentration::GetWntLevel 6086ms 5.55% 46.31% 6086ms 5.55% boost::numeric::ublas::c_vector::operator() 0 0% 46.31% 5784ms 5.28% std::set::insert (inline) 746ms 0.68% 46.99% 5754ms 5.25% std::_Rb_tree::_M_clone_node (inline) 2436ms 2.22% 49.21% 5575ms 5.09% std::_Rb_tree::_M_lower_bound (inline) 2612ms 2.38% 51.59% 5544ms 5.06% __cxxabiv1::__si_class_type_info::__do_dyncast 30ms 0.027% 51.62% 5508ms 5.03% MutableVertexMesh::RemoveDeletedNodes 38ms 0.035% 51.66% 5330ms 4.86% EdgeHelper::RemoveDeletedEdges 260ms 0.24% 51.89% 5022ms 4.58% MutableElement::ResetIndex 33ms 0.03% 51.92% 5014ms 4.57% EdgeHelper::UpdateEdgesMapKey 1655ms 1.51% 53.43% 4975ms 4.54% boost::numeric::ublas::c_vector::operator[] (inline) 4508ms 4.11% 57.55% 4967ms 4.53% _int_free 542ms 0.49% 58.04% 4951ms 4.52% std::_Rb_tree::_M_insert_ (inline) 2ms 0.0018% 58.04% 4587ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.04% 4518ms 4.12% std::_Rb_tree::lower_bound (inline) 0 0% 58.04% 4518ms 4.12% std::map::lower_bound (inline) 47ms 0.043% 58.08% 4471ms 4.08% std::set_intersection (inline) 248ms 0.23% 58.31% 4424ms 4.04% std::__set_intersection 4115ms 3.75% 62.07% 4115ms 3.75% boost::numeric::ublas::same_impl_ex 106ms 0.097% 62.16% 3920ms 3.58% AbstractCellPopulation::GetCellUsingLocationIndex 75ms 0.068% 62.23% 3918ms 3.57% AbstractCellProperty::IsType (inline) 41ms 0.037% 62.27% 3875ms 3.54% Cell::GetCellProliferativeType 7ms 0.0064% 62.27% 3485ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.27% 3355ms 3.06% std::insert_iterator::operator= (inline) 47ms 0.043% 62.32% 3275ms 2.99% std::_Rb_tree::erase 755ms 0.69% 63.01% 3144ms 2.87% AbstractElement::GetNodeLocation 43ms 0.039% 63.04% 3125ms 2.85% Cell::SetCellProliferativeType 2137ms 1.95% 64.99% 3125ms 2.85% _int_malloc 654ms 0.6% 65.59% 2973ms 2.71% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.0027% 65.59% 2940ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0018% 65.60% 2844ms 2.59% std::_Rb_tree::_M_insert_unique 40ms 0.036% 65.63% 2802ms 2.56% CellPropertyCollection::HasProperty 689ms 0.63% 66.26% 2784ms 2.54% AbstractCellProperty::IsSame 2685ms 2.45% 68.71% 2685ms 2.45% std::_Rb_tree::_S_right (inline) 0 0% 68.71% 2684ms 2.45% Cell::HasCellProperty (inline) 388ms 0.35% 69.06% 2672ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.06% 2512ms 2.29% AbstractCellPopulation::WriteResultsToFiles 262ms 0.24% 69.30% 2488ms 2.27% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.30% 2472ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 38ms 0.035% 69.34% 2427ms 2.21% Cell::GetCellData 0 0% 69.34% 2410ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 108ms 0.099% 69.44% 2293ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 87ms 0.079% 69.52% 2225ms 2.03% VertexMesh::GetVolumeOfElement 1486ms 1.36% 70.87% 2207ms 2.01% std::_Rb_tree::equal_range (inline) 0 0% 70.87% 2138ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 39ms 0.036% 70.91% 2136ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 228ms 0.21% 71.12% 2123ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 2122ms 1.94% 73.05% 2122ms 1.94% std::_Rb_tree_increment 525ms 0.48% 73.53% 2095ms 1.91% std::type_info::operator== (inline) 0 0% 73.53% 2047ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.53% 2034ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 6ms 0.0055% 73.54% 1935ms 1.77% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.54% 1935ms 1.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 164ms 0.15% 73.69% 1920ms 1.75% CellPropertyCollection::AddProperty 0 0% 73.69% 1823ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 0 0% 73.69% 1793ms 1.64% tcache_get (inline) 1793ms 1.64% 75.32% 1793ms 1.64% tcache_get_n (inline) 66ms 0.06% 75.38% 1787ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 26ms 0.024% 75.41% 1689ms 1.54% VertexMesh::GetSurfaceAreaOfElement 35ms 0.032% 75.44% 1620ms 1.48% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 53ms 0.048% 75.49% 1588ms 1.45% Node::RemoveElement 20ms 0.018% 75.50% 1546ms 1.41% std::set::erase (inline) 122ms 0.11% 75.62% 1477ms 1.35% boost::numeric::ublas::vector_reference::operator() (inline) 23ms 0.021% 75.64% 1443ms 1.32% AbstractCellPopulation::GetLocationIndexUsingCell 61ms 0.056% 75.69% 1378ms 1.26% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.69% 1345ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 4ms 0.0036% 75.70% 1270ms 1.16% OffLatticeSimulation::ApplyBoundaries 79ms 0.072% 75.77% 1241ms 1.13% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 75.77% 1234ms 1.13% boost::numeric::ublas::norm_2 (inline) 564ms 0.51% 76.28% 1222ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 69ms 0.063% 76.35% 1190ms 1.09% std::less::operator() (inline) 26ms 0.024% 76.37% 1170ms 1.07% CellPropertyRegistry::Get 0 0% 76.37% 1161ms 1.06% std::_Rb_tree::clear (inline) 0 0% 76.37% 1146ms 1.05% std::map::clear (inline) 1136ms 1.04% 77.41% 1136ms 1.04% std::_Rb_tree_insert_and_rebalance 912ms 0.83% 78.24% 1121ms 1.02% std::operator< (inline) 1106ms 1.01% 79.25% 1106ms 1.01% [libchaste_cell_based.so] 0 0% 79.25% 1104ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1097ms 1.00% 80.25% 1097ms 1.00% Node::rGetLocation 17ms 0.016% 80.26% 1084ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 12ms 0.011% 80.27% 1049ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 91ms 0.083% 80.36% 1043ms 0.95% std::_Rb_tree::find (inline) 162ms 0.15% 80.51% 1016ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.51% 1016ms 0.93% boost::shared_ptr::~shared_ptr (inline) 1001ms 0.91% 81.42% 1001ms 0.91% [libchaste_mesh.so] 983ms 0.9% 82.32% 983ms 0.9% std::vector::size (inline) 458ms 0.42% 82.73% 960ms 0.88% Edge::GetMapIndex 0 0% 82.73% 956ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 82.74% 956ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 24ms 0.022% 82.76% 955ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 81ms 0.074% 82.84% 949ms 0.87% std::swap_ranges (inline) 187ms 0.17% 83.01% 917ms 0.84% boost::numeric::ublas::detail::equals 870ms 0.79% 83.80% 870ms 0.79% std::swap (inline) 0 0% 83.80% 868ms 0.79% std::iter_swap (inline) 0 0% 83.80% 859ms 0.78% VertexMeshWriter::MakeVtkMesh 109ms 0.099% 83.90% 830ms 0.76% MutableElement::GetNodeLocalIndex 821ms 0.75% 84.65% 827ms 0.75% boost::detail::sp_counted_base::release 2ms 0.0018% 84.65% 819ms 0.75% std::map::find (inline) 89ms 0.081% 84.73% 771ms 0.7% std::__new_allocator::construct (inline) 0 0% 84.73% 771ms 0.7% std::allocator_traits::construct (inline) 147ms 0.13% 84.87% 768ms 0.7% boost::shared_ptr::shared_ptr (inline) 96ms 0.088% 84.95% 762ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 416ms 0.38% 85.33% 751ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.33% 749ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 25ms 0.023% 85.36% 748ms 0.68% MutableElement::RegisterWithEdges (inline) 35ms 0.032% 85.39% 731ms 0.67% Edge::AddElement 0 0% 85.39% 716ms 0.65% std::_Rb_tree::_M_construct_node (inline) 2ms 0.0018% 85.39% 706ms 0.64% std::_Vector_base::_M_allocate (inline) 0 0% 85.39% 701ms 0.64% boost::numeric::ublas::norm_inf (inline) 341ms 0.31% 85.70% 701ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 700ms 0.64% 86.34% 700ms 0.64% Node::GetIndex 0 0% 86.34% 672ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.026% 86.36% 672ms 0.61% std::_Rb_tree::_M_insert_node (inline) 585ms 0.53% 86.90% 621ms 0.57% boost::detail::shared_count::shared_count (inline) 616ms 0.56% 87.46% 616ms 0.56% tcache_put (inline) 1ms 0.00091% 87.46% 611ms 0.56% vtkPolygon::New 1ms 0.00091% 87.46% 610ms 0.56% vtkPolygon::vtkPolygon 596ms 0.54% 88.01% 596ms 0.54% operator delete 0 0% 88.01% 591ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 573ms 0.52% 88.53% 573ms 0.52% boost::shared_ptr::operator-> (inline) 8ms 0.0073% 88.54% 573ms 0.52% std::vector::_M_default_append (inline) 35ms 0.032% 88.57% 566ms 0.52% MutableElement::RegisterWithNodes (inline) 30ms 0.027% 88.60% 554ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.60% 554ms 0.51% boost::numeric::ublas::vector::vector (inline)