File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 57849ms, 87.54% of 66080ms total Dropped 1070 nodes (cum <= 330.40ms) flat flat% sum% cum cum% 0 0% 0% 65811ms 99.59% __libc_start_call_main 0 0% 0% 65811ms 99.59% __libc_start_main_impl 0 0% 0% 65811ms 99.59% _start 0 0% 0% 65797ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65797ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65797ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65797ms 99.57% main 0 0% 0% 65758ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65758ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65758ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0015% 0.0015% 65753ms 99.51% AbstractCellBasedSimulation::Solve 10ms 0.015% 0.017% 34648ms 52.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.023% 0.039% 32350ms 48.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 51ms 0.077% 0.12% 31449ms 47.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 183ms 0.28% 0.39% 24320ms 36.80% NagaiHondaForce::AddForceContribution 0 0% 0.39% 22883ms 34.63% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.39% 14014ms 21.21% VertexBasedCellPopulation::Update 1ms 0.0015% 0.39% 13918ms 21.06% MutableVertexMesh::ReMesh 7000ms 10.59% 10.99% 12043ms 18.22% Cylindrical2dVertexMesh::GetVectorFromAtoB 45ms 0.068% 11.06% 10667ms 16.14% Cell::ReadyToDivide 71ms 0.11% 11.16% 10004ms 15.14% NagaiHondaForce::GetAdhesionParameter 38ms 0.058% 11.22% 9914ms 15.00% AbstractPhaseBasedCellCycleModel::ReadyToDivide 37ms 0.056% 11.28% 8498ms 12.86% SimpleWntCellCycleModel::UpdateCellCyclePhase 219ms 0.33% 11.61% 8341ms 12.62% boost::numeric::ublas::c_vector::c_vector (partial-inline) 64ms 0.097% 11.71% 7594ms 11.49% CellPropertyCollection::GetPropertiesType (inline) 231ms 0.35% 12.06% 7347ms 11.12% boost::numeric::ublas::vector_assign (inline) 472ms 0.71% 12.77% 7160ms 10.84% std::__new_allocator::allocate (inline) 46ms 0.07% 12.84% 6882ms 10.41% VertexBasedCellPopulation::GetDampingConstant 0 0% 12.84% 6879ms 10.41% std::allocator_traits::allocate (inline) 635ms 0.96% 13.80% 6732ms 10.19% operator new 0 0% 13.80% 6709ms 10.15% std::_Rb_tree::_M_create_node (inline) 683ms 1.03% 14.83% 6706ms 10.15% std::_Rb_tree::_M_erase 69ms 0.1% 14.94% 6558ms 9.92% MutableVertexMesh::CheckForIntersections 0 0% 14.94% 6526ms 9.88% std::_Rb_tree::_M_drop_node (inline) 30ms 0.045% 14.98% 6470ms 9.79% AbstractTargetAreaModifier::UpdateTargetAreas 0 0% 14.98% 6462ms 9.78% std::_Rb_tree::_M_get_node (inline) 340ms 0.51% 15.50% 6424ms 9.72% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.026% 15.52% 6402ms 9.69% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1404ms 2.12% 17.65% 6266ms 9.48% __dynamic_cast 47ms 0.071% 17.72% 6255ms 9.47% AbstractCellProperty::IsSubType (inline) 6ms 0.0091% 17.73% 6251ms 9.46% AbstractCellBasedSimulation::DoCellBirth 0 0% 17.73% 6110ms 9.25% std::set::~set (inline) 2606ms 3.94% 21.67% 5976ms 9.04% __GI___libc_malloc 0 0% 21.67% 5796ms 8.77% std::_Rb_tree::_Alloc_node::operator() (inline) 94ms 0.14% 21.81% 5769ms 8.73% std::__new_allocator::deallocate (inline) 0 0% 21.81% 5765ms 8.72% std::allocator_traits::deallocate (inline) 0 0% 21.81% 5710ms 8.64% std::_Rb_tree::_M_put_node (inline) 1705ms 2.58% 24.39% 5483ms 8.30% boost::numeric::ublas::indexing_vector_assign 1094ms 1.66% 26.05% 5373ms 8.13% __GI___libc_free 183ms 0.28% 26.33% 5067ms 7.67% VertexMesh::GetNextEdgeGradientOfElementAtNode 41ms 0.062% 26.39% 4942ms 7.48% Cell::GetMutationState 8ms 0.012% 26.40% 4861ms 7.36% MutableVertexMesh::RemoveDeletedNodesAndElements 470ms 0.71% 27.11% 4773ms 7.22% VertexMesh::ElementIncludesPoint 275ms 0.42% 27.53% 4716ms 7.14% std::map::operator[] (partial-inline) 26ms 0.039% 27.57% 4635ms 7.01% VertexBasedCellPopulation::GetLocationOfCellCentre 371ms 0.56% 28.13% 4399ms 6.66% VertexMesh::GetCentroidOfElement 0 0% 28.13% 4304ms 6.51% std::set::insert (inline) 834ms 1.26% 29.39% 4271ms 6.46% AbstractMesh::GetDistanceBetweenNodes 4036ms 6.11% 35.50% 4247ms 6.43% _int_free 118ms 0.18% 35.68% 4104ms 6.21% std::_Rb_tree::_Rb_tree (partial-inline) 441ms 0.67% 36.35% 3867ms 5.85% std::_Rb_tree::_M_copy (inline) 3ms 0.0045% 36.35% 3798ms 5.75% std::set::set (inline) 622ms 0.94% 37.29% 3780ms 5.72% std::_Rb_tree::_M_insert_ (inline) 3689ms 5.58% 42.87% 3689ms 5.58% boost::numeric::ublas::c_vector::operator() 3672ms 5.56% 48.43% 3672ms 5.56% __strcmp_evex 89ms 0.13% 48.57% 3531ms 5.34% SimpleWntCellCycleModel::GetWntLevel 74ms 0.11% 48.68% 3489ms 5.28% std::set_intersection (inline) 154ms 0.23% 48.91% 3415ms 5.17% std::__set_intersection 102ms 0.15% 49.06% 3361ms 5.09% WntConcentration::GetWntLevel 1958ms 2.96% 52.03% 3303ms 5.00% __cxxabiv1::__si_class_type_info::__do_dyncast 1607ms 2.43% 54.46% 3301ms 5.00% std::_Rb_tree::_M_lower_bound (inline) 412ms 0.62% 55.08% 3283ms 4.97% std::_Rb_tree::_M_clone_node (inline) 16ms 0.024% 55.11% 3248ms 4.92% MutableVertexMesh::RemoveDeletedNodes 21ms 0.032% 55.14% 3138ms 4.75% EdgeHelper::RemoveDeletedEdges 34ms 0.051% 55.19% 3002ms 4.54% EdgeHelper::UpdateEdgesMapKey 113ms 0.17% 55.36% 2966ms 4.49% MutableElement::ResetIndex 867ms 1.31% 56.67% 2962ms 4.48% boost::numeric::ublas::c_vector::operator[] (inline) 74ms 0.11% 56.79% 2852ms 4.32% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.79% 2833ms 4.29% std::_Rb_tree::lower_bound (inline) 0 0% 56.79% 2833ms 4.29% std::map::lower_bound (inline) 0 0% 56.79% 2668ms 4.04% std::insert_iterator::operator= (inline) 55ms 0.083% 56.87% 2647ms 4.01% Cell::GetCellProliferativeType 2629ms 3.98% 60.85% 2629ms 3.98% boost::numeric::ublas::same_impl_ex 0 0% 60.85% 2613ms 3.95% AbstractCellBasedSimulation::DoCellRemoval (inline) 1980ms 3.00% 63.84% 2556ms 3.87% _int_malloc 6ms 0.0091% 63.85% 2432ms 3.68% std::_Rb_tree::_M_insert_unique_ (inline) 101ms 0.15% 64.01% 2404ms 3.64% boost::detail::shared_count::~shared_count (inline) 0 0% 64.01% 2404ms 3.64% boost::shared_ptr::~shared_ptr (inline) 2267ms 3.43% 67.44% 2277ms 3.45% boost::detail::sp_counted_base::release 55ms 0.083% 67.52% 2239ms 3.39% AbstractCellProperty::IsType (inline) 76ms 0.12% 67.63% 2125ms 3.22% Cell::SetCellProliferativeType 30ms 0.045% 67.68% 1989ms 3.01% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 67.68% 1872ms 2.83% std::_Rb_tree::_M_insert_unique 28ms 0.042% 67.72% 1822ms 2.76% std::_Rb_tree::erase 471ms 0.71% 68.44% 1785ms 2.70% AbstractElement::GetNodeLocation 0 0% 68.44% 1769ms 2.68% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.44% 1735ms 2.63% AbstractCellPopulation::WriteResultsToFiles 292ms 0.44% 68.88% 1707ms 2.58% boost::numeric::ublas::vector_binary::size (inline) 21ms 0.032% 68.91% 1674ms 2.53% CellPropertyCollection::HasProperty 0 0% 68.91% 1633ms 2.47% Cell::HasCellProperty (inline) 144ms 0.22% 69.13% 1598ms 2.42% VertexMesh::GetAreaGradientOfElementAtNode 18ms 0.027% 69.15% 1586ms 2.40% std::_Rb_tree::_M_emplace_hint_unique 338ms 0.51% 69.67% 1570ms 2.38% AbstractCellProperty::IsSame 7ms 0.011% 69.68% 1553ms 2.35% AbstractCellPopulation::Iterator::operator++ (inline) 123ms 0.19% 69.86% 1545ms 2.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 15ms 0.023% 69.88% 1491ms 2.26% Cell::GetCellData 226ms 0.34% 70.23% 1488ms 2.25% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.23% 1437ms 2.17% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0015% 70.23% 1423ms 2.15% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.23% 1423ms 2.15% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0015% 70.23% 1420ms 2.15% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1365ms 2.07% 72.30% 1365ms 2.07% std::_Rb_tree::_S_right (inline) 17ms 0.026% 72.32% 1364ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 72.32% 1289ms 1.95% VertexMeshWriter::WriteVtkUsingMesh 0 0% 72.32% 1285ms 1.94% boost::numeric::ublas::c_vector::operator-= (inline) 129ms 0.2% 72.52% 1232ms 1.86% std::type_info::operator== (inline) 55ms 0.083% 72.60% 1184ms 1.79% VertexMesh::GetVolumeOfElement 8ms 0.012% 72.61% 1150ms 1.74% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 37ms 0.056% 72.67% 1107ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 95ms 0.14% 72.81% 1100ms 1.66% CellPropertyCollection::AddProperty 1092ms 1.65% 74.46% 1092ms 1.65% std::_Rb_tree_increment 47ms 0.071% 74.54% 1031ms 1.56% boost::numeric::ublas::vector_reference::operator() (inline) 199ms 0.3% 74.84% 1005ms 1.52% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 72ms 0.11% 74.95% 990ms 1.50% std::_Rb_tree::_M_erase_aux (partial-inline) 948ms 1.43% 76.38% 948ms 1.43% [libchaste_cell_based.so] 523ms 0.79% 77.17% 917ms 1.39% std::_Rb_tree::equal_range (inline) 0 0% 77.17% 913ms 1.38% std::_Rb_tree::_Auto_node::_Auto_node (inline) 23ms 0.035% 77.21% 905ms 1.37% VertexMesh::GetSurfaceAreaOfElement 1ms 0.0015% 77.21% 884ms 1.34% OffLatticeSimulation::ApplyBoundaries 0 0% 77.21% 882ms 1.33% boost::numeric::ublas::norm_2 (inline) 352ms 0.53% 77.74% 880ms 1.33% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 37ms 0.056% 77.80% 844ms 1.28% Node::RemoveElement 0 0% 77.80% 821ms 1.24% std::__new_allocator::destroy (inline) 0 0% 77.80% 821ms 1.24% std::allocator_traits::destroy (inline) 0 0% 77.80% 818ms 1.24% std::_Rb_tree::_M_destroy_node (inline) 6ms 0.0091% 77.81% 809ms 1.22% std::set::erase (inline) 22ms 0.033% 77.84% 805ms 1.22% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 77.84% 787ms 1.19% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 77.84% 781ms 1.18% boost::numeric::ublas::vector_binary::operator() (inline) 36ms 0.054% 77.89% 776ms 1.17% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 26ms 0.039% 77.93% 751ms 1.14% CellPropertyRegistry::Get 739ms 1.12% 79.05% 739ms 1.12% [libchaste_mesh.so] 47ms 0.071% 79.12% 719ms 1.09% std::less::operator() (inline) 8ms 0.012% 79.13% 688ms 1.04% boost::numeric::ublas::detail::expression_type_check (inline) 682ms 1.03% 80.17% 682ms 1.03% [libstdc++.so.6.0.33] 562ms 0.85% 81.02% 672ms 1.02% std::operator< (inline) 78ms 0.12% 81.13% 662ms 1.00% boost::numeric::ublas::detail::equals 0 0% 81.13% 626ms 0.95% std::_Rb_tree::clear (inline) 620ms 0.94% 82.07% 620ms 0.94% std::_Rb_tree_insert_and_rebalance 2ms 0.003% 82.08% 613ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.08% 610ms 0.92% tcache_get (inline) 610ms 0.92% 83.00% 610ms 0.92% tcache_get_n (inline) 0 0% 83.00% 609ms 0.92% std::map::clear (inline) 0 0% 83.00% 595ms 0.9% VertexMeshWriter::MakeVtkMesh 16ms 0.024% 83.02% 587ms 0.89% MutableElement::RegisterWithEdges (inline) 15ms 0.023% 83.05% 579ms 0.88% Edge::AddElement 510ms 0.77% 83.82% 574ms 0.87% CellPropertyCollection::GetProperty 0 0% 83.82% 571ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 19ms 0.029% 83.85% 571ms 0.86% boost::numeric::ublas::c_vector::swap 80ms 0.12% 83.97% 552ms 0.84% std::swap_ranges (inline) 0 0% 83.97% 541ms 0.82% boost::numeric::ublas::norm_inf (inline) 217ms 0.33% 84.30% 541ms 0.82% boost::numeric::ublas::vector_norm_inf::apply (inline) 60ms 0.091% 84.39% 525ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 284ms 0.43% 84.82% 523ms 0.79% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 120ms 0.18% 85.00% 480ms 0.73% MutableElement::GetNodeLocalIndex 0 0% 85.00% 472ms 0.71% std::iter_swap (inline) 472ms 0.71% 85.71% 472ms 0.71% std::swap (inline) 467ms 0.71% 86.42% 467ms 0.71% std::vector::size 8ms 0.012% 86.43% 455ms 0.69% AbstractNumericalMethod::DetectStepSizeExceptions 42ms 0.064% 86.50% 455ms 0.69% std::_Rb_tree::find (inline) 93ms 0.14% 86.64% 447ms 0.68% VertexBasedCellPopulation::CheckForStepSizeException (partial-inline) 0 0% 86.64% 427ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.03% 86.67% 427ms 0.65% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.67% 420ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.67% 411ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.67% 410ms 0.62% vtkPolygon::New 0 0% 86.67% 409ms 0.62% vtkPolygon::vtkPolygon 204ms 0.31% 86.97% 393ms 0.59% Edge::GetMapIndex 2ms 0.003% 86.98% 380ms 0.58% std::map::find (inline) 7ms 0.011% 86.99% 379ms 0.57% Cylindrical2dVertexMesh::GetMeshForVtk 11ms 0.017% 87.01% 366ms 0.55% MutableElement::RegisterWithNodes (inline) 19ms 0.029% 87.03% 359ms 0.54% Node::AddElement 337ms 0.51% 87.54% 337ms 0.51% operator delete 0 0% 87.54% 337ms 0.51% std::map::map (inline)