File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 68999ms, 89.14% of 77407ms total Dropped 1057 nodes (cum <= 387.04ms) flat flat% sum% cum cum% 0 0% 0% 77215ms 99.75% __libc_start_call_main 0 0% 0% 77215ms 99.75% __libc_start_main_impl 0 0% 0% 77215ms 99.75% _start 0 0% 0% 77199ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 77199ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 77199ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 77199ms 99.73% main 0 0% 0% 77161ms 99.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 77161ms 99.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 77161ms 99.68% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0026% 0.0026% 77154ms 99.67% AbstractCellBasedSimulation::Solve 12ms 0.016% 0.018% 40344ms 52.12% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.014% 0.032% 37643ms 48.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 51ms 0.066% 0.098% 36916ms 47.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 257ms 0.33% 0.43% 28712ms 37.09% NagaiHondaForce::AddForceContribution 1ms 0.0013% 0.43% 27184ms 35.12% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0039% 0.44% 16423ms 21.22% VertexBasedCellPopulation::Update 0 0% 0.44% 16317ms 21.08% MutableVertexMesh::ReMesh 6719ms 8.68% 9.12% 13016ms 16.82% Cylindrical2dVertexMesh::GetVectorFromAtoB 85ms 0.11% 9.23% 12650ms 16.34% Cell::ReadyToDivide 50ms 0.065% 9.29% 11819ms 15.27% NagaiHondaForce::GetAdhesionParameter 20ms 0.026% 9.32% 11753ms 15.18% AbstractPhaseBasedCellCycleModel::ReadyToDivide 660ms 0.85% 10.17% 10054ms 12.99% std::__new_allocator::allocate (inline) 47ms 0.061% 10.23% 9990ms 12.91% SimpleWntCellCycleModel::UpdateCellCyclePhase 300ms 0.39% 10.62% 9741ms 12.58% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.62% 9658ms 12.48% std::allocator_traits::allocate (inline) 0 0% 10.62% 9450ms 12.21% std::_Rb_tree::_M_create_node (inline) 724ms 0.94% 11.55% 9327ms 12.05% operator new 123ms 0.16% 11.71% 9267ms 11.97% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.71% 9171ms 11.85% std::_Rb_tree::_M_get_node (inline) 201ms 0.26% 11.97% 8734ms 11.28% boost::numeric::ublas::vector_assign (inline) 2730ms 3.53% 15.50% 8318ms 10.75% __GI___libc_malloc 0 0% 15.50% 8129ms 10.50% std::_Rb_tree::_Alloc_node::operator() (inline) 67ms 0.087% 15.58% 7904ms 10.21% VertexBasedCellPopulation::GetDampingConstant 38ms 0.049% 15.63% 7808ms 10.09% AbstractTargetAreaModifier::UpdateTargetAreas 20ms 0.026% 15.66% 7732ms 9.99% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 65ms 0.084% 15.74% 7535ms 9.73% AbstractCellProperty::IsSubType (inline) 1815ms 2.34% 18.09% 7469ms 9.65% __dynamic_cast 6ms 0.0078% 18.10% 7454ms 9.63% AbstractCellBasedSimulation::DoCellBirth 88ms 0.11% 18.21% 7353ms 9.50% MutableVertexMesh::CheckForIntersections 326ms 0.42% 18.63% 6651ms 8.59% std::map::operator[] (partial-inline) 749ms 0.97% 19.60% 6633ms 8.57% std::_Rb_tree::_M_erase 0 0% 19.60% 6519ms 8.42% std::_Rb_tree::_M_drop_node (inline) 1924ms 2.49% 22.08% 6305ms 8.15% boost::numeric::ublas::indexing_vector_assign 254ms 0.33% 22.41% 6206ms 8.02% std::_Rb_tree::~_Rb_tree (inline) 0 0% 22.41% 5915ms 7.64% std::set::~set (inline) 13ms 0.017% 22.43% 5865ms 7.58% MutableVertexMesh::RemoveDeletedNodesAndElements 26ms 0.034% 22.46% 5827ms 7.53% VertexBasedCellPopulation::GetLocationOfCellCentre 73ms 0.094% 22.56% 5800ms 7.49% std::__new_allocator::deallocate (inline) 0 0% 22.56% 5781ms 7.47% std::allocator_traits::deallocate (inline) 39ms 0.05% 22.61% 5749ms 7.43% Cell::GetMutationState 0 0% 22.61% 5736ms 7.41% std::_Rb_tree::_M_put_node (inline) 288ms 0.37% 22.98% 5657ms 7.31% VertexMesh::GetNextEdgeGradientOfElementAtNode 1576ms 2.04% 25.01% 5634ms 7.28% __GI___libc_free 0 0% 25.01% 5616ms 7.26% std::set::insert (inline) 408ms 0.53% 25.54% 5540ms 7.16% VertexMesh::GetCentroidOfElement 364ms 0.47% 26.01% 5506ms 7.11% VertexMesh::ElementIncludesPoint 83ms 0.11% 26.12% 5480ms 7.08% std::_Rb_tree::_Rb_tree (partial-inline) 541ms 0.7% 26.82% 5267ms 6.80% std::_Rb_tree::_M_copy (inline) 657ms 0.85% 27.67% 5158ms 6.66% std::_Rb_tree::_M_insert_ (inline) 12ms 0.016% 27.68% 5112ms 6.60% std::set::set (inline) 1700ms 2.20% 29.88% 4795ms 6.19% std::_Rb_tree::_M_lower_bound (inline) 4711ms 6.09% 35.96% 4711ms 6.09% boost::numeric::ublas::c_vector::operator() 592ms 0.76% 36.73% 4588ms 5.93% std::_Rb_tree::_M_clone_node (inline) 4471ms 5.78% 42.51% 4471ms 5.78% __strcmp_evex 35ms 0.045% 42.55% 4470ms 5.77% std::set_intersection (inline) 177ms 0.23% 42.78% 4435ms 5.73% std::__set_intersection 100ms 0.13% 42.91% 4359ms 5.63% SimpleWntCellCycleModel::GetWntLevel 673ms 0.87% 43.78% 4275ms 5.52% AbstractMesh::GetDistanceBetweenNodes 19ms 0.025% 43.80% 4191ms 5.41% MutableVertexMesh::RemoveDeletedNodes 100ms 0.13% 43.93% 4178ms 5.40% WntConcentration::GetWntLevel 0 0% 43.93% 4103ms 5.30% std::_Rb_tree::lower_bound (inline) 0 0% 43.93% 4103ms 5.30% std::map::lower_bound (inline) 32ms 0.041% 43.97% 4089ms 5.28% EdgeHelper::RemoveDeletedEdges 3453ms 4.46% 48.43% 4046ms 5.23% _int_malloc 3673ms 4.75% 53.18% 4028ms 5.20% _int_free 11ms 0.014% 53.19% 3941ms 5.09% EdgeHelper::UpdateEdgesMapKey 436ms 0.56% 53.76% 3936ms 5.08% boost::numeric::ublas::c_vector::operator[] (inline) 1813ms 2.34% 56.10% 3678ms 4.75% __cxxabiv1::__si_class_type_info::__do_dyncast 118ms 0.15% 56.25% 3634ms 4.69% MutableElement::ResetIndex 56ms 0.072% 56.32% 3554ms 4.59% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.32% 3540ms 4.57% std::insert_iterator::operator= (inline) 0 0% 56.32% 3306ms 4.27% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0026% 56.33% 3300ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 3179ms 4.11% 60.43% 3179ms 4.11% boost::numeric::ublas::same_impl_ex 16ms 0.021% 60.45% 3144ms 4.06% Cell::GetCellProliferativeType 2745ms 3.55% 64.00% 2745ms 3.55% std::_Rb_tree::_S_right (inline) 106ms 0.14% 64.14% 2549ms 3.29% AbstractCellProperty::IsType (inline) 2546ms 3.29% 67.43% 2546ms 3.29% [libchaste_cell_based.so] 45ms 0.058% 67.48% 2532ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 654ms 0.84% 68.33% 2375ms 3.07% AbstractElement::GetNodeLocation 0 0% 68.33% 2310ms 2.98% std::_Rb_tree::_M_insert_unique 71ms 0.092% 68.42% 2301ms 2.97% boost::detail::shared_count::~shared_count (inline) 0 0% 68.42% 2301ms 2.97% boost::shared_ptr::~shared_ptr (inline) 71ms 0.092% 68.51% 2285ms 2.95% Cell::SetCellProliferativeType 33ms 0.043% 68.55% 2182ms 2.82% std::_Rb_tree::_M_emplace_hint_unique 2177ms 2.81% 71.37% 2180ms 2.82% boost::detail::sp_counted_base::release 180ms 0.23% 71.60% 2147ms 2.77% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.0052% 71.60% 2135ms 2.76% AbstractCellPopulation::Iterator::operator++ (inline) 51ms 0.066% 71.67% 2119ms 2.74% std::_Rb_tree::erase 0 0% 71.67% 1907ms 2.46% boost::numeric::ublas::c_vector::assign (inline) 12ms 0.016% 71.69% 1902ms 2.46% Cell::GetCellData 63ms 0.081% 71.77% 1796ms 2.32% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.77% 1795ms 2.32% AbstractCellPopulation::WriteResultsToFiles 1795ms 2.32% 74.09% 1795ms 2.32% [libchaste_mesh.so] 211ms 0.27% 74.36% 1795ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 25ms 0.032% 74.39% 1779ms 2.30% CellPropertyCollection::HasProperty 0 0% 74.39% 1740ms 2.25% Cell::HasCellProperty (inline) 43ms 0.056% 74.45% 1731ms 2.24% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 210ms 0.27% 74.72% 1651ms 2.13% VertexMesh::GetAreaGradientOfElementAtNode 337ms 0.44% 75.15% 1630ms 2.11% AbstractCellProperty::IsSame 9ms 0.012% 75.17% 1603ms 2.07% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 75.17% 1601ms 2.07% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 75.17% 1467ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0013% 75.17% 1461ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 225ms 0.29% 75.46% 1438ms 1.86% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 77ms 0.099% 75.56% 1361ms 1.76% VertexMesh::GetVolumeOfElement 0 0% 75.56% 1321ms 1.71% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.56% 1317ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 104ms 0.13% 75.69% 1293ms 1.67% std::type_info::operator== (inline) 1ms 0.0013% 75.69% 1291ms 1.67% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.69% 1291ms 1.67% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.69% 1281ms 1.65% tcache_get (inline) 1281ms 1.65% 77.35% 1281ms 1.65% tcache_get_n (inline) 43ms 0.056% 77.40% 1249ms 1.61% AbstractCellPopulation::GetLocationIndexUsingCell 100ms 0.13% 77.53% 1227ms 1.59% CellPropertyCollection::AddProperty 736ms 0.95% 78.48% 1161ms 1.50% std::_Rb_tree::equal_range (inline) 1ms 0.0013% 78.48% 1106ms 1.43% OffLatticeSimulation::ApplyBoundaries 50ms 0.065% 78.55% 1089ms 1.41% MutableVertexMesh::CheckForSwapsFromShortEdges 56ms 0.072% 78.62% 1085ms 1.40% VertexMesh::GetSurfaceAreaOfElement 1072ms 1.38% 80.01% 1072ms 1.38% std::_Rb_tree_increment 16ms 0.021% 80.03% 1049ms 1.36% Node::RemoveElement 1ms 0.0013% 80.03% 1033ms 1.33% std::set::erase (inline) 44ms 0.057% 80.08% 1030ms 1.33% std::_Rb_tree::_M_erase_aux (partial-inline) 37ms 0.048% 80.13% 988ms 1.28% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.13% 936ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 14ms 0.018% 80.15% 840ms 1.09% MutableElement::RegisterWithEdges (inline) 37ms 0.048% 80.20% 837ms 1.08% Edge::AddElement 0 0% 80.20% 834ms 1.08% CellPropertyCollection::~CellPropertyCollection (inline) 54ms 0.07% 80.27% 833ms 1.08% boost::numeric::ublas::vector_reference::operator() (inline) 40ms 0.052% 80.32% 811ms 1.05% CellPropertyRegistry::Get 804ms 1.04% 81.36% 804ms 1.04% std::_Rb_tree_insert_and_rebalance 0 0% 81.36% 787ms 1.02% std::__new_allocator::destroy (inline) 0 0% 81.36% 787ms 1.02% std::allocator_traits::destroy (inline) 786ms 1.02% 82.37% 786ms 1.02% [libstdc++.so.6.0.33] 0 0% 82.37% 783ms 1.01% std::_Rb_tree::_M_destroy_node (inline) 13ms 0.017% 82.39% 782ms 1.01% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.39% 758ms 0.98% boost::numeric::ublas::norm_2 (inline) 142ms 0.18% 82.57% 750ms 0.97% boost::numeric::ublas::detail::equals 363ms 0.47% 83.04% 740ms 0.96% boost::numeric::ublas::vector_norm_2::apply 9ms 0.012% 83.05% 733ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 70ms 0.09% 83.14% 731ms 0.94% std::_Rb_tree::find (inline) 0 0% 83.14% 729ms 0.94% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0039% 83.15% 729ms 0.94% boost::numeric::ublas::c_vector::swap 103ms 0.13% 83.28% 726ms 0.94% std::swap_ranges (inline) 694ms 0.9% 84.18% 694ms 0.9% Node::rGetLocation 0 0% 84.18% 682ms 0.88% std::_Rb_tree::clear (inline) 49ms 0.063% 84.24% 668ms 0.86% std::less::operator() (inline) 0 0% 84.24% 667ms 0.86% std::map::clear (inline) 1ms 0.0013% 84.24% 666ms 0.86% VertexMeshWriter::MakeVtkMesh 42ms 0.054% 84.30% 650ms 0.84% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.30% 623ms 0.8% std::iter_swap (inline) 623ms 0.8% 85.10% 623ms 0.8% std::swap (inline) 466ms 0.6% 85.70% 619ms 0.8% std::operator< (inline) 0 0% 85.70% 614ms 0.79% std::map::find (inline) 467ms 0.6% 86.31% 576ms 0.74% CellPropertyCollection::GetProperty 0 0% 86.31% 575ms 0.74% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.032% 86.34% 575ms 0.74% std::_Rb_tree::_M_insert_node (inline) 61ms 0.079% 86.42% 539ms 0.7% MutableElement::GetNodeLocalIndex 0 0% 86.42% 537ms 0.69% boost::numeric::ublas::norm_inf (inline) 225ms 0.29% 86.71% 537ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 534ms 0.69% 87.40% 534ms 0.69% std::vector::size (inline) 256ms 0.33% 87.73% 532ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 16ms 0.021% 87.75% 496ms 0.64% MutableElement::RegisterWithNodes (inline) 1ms 0.0013% 87.75% 486ms 0.63% std::_Vector_base::_M_allocate (inline) 31ms 0.04% 87.79% 472ms 0.61% Node::AddElement 0 0% 87.79% 467ms 0.6% vtkPolygon::New 0 0% 87.79% 467ms 0.6% vtkPolygon::vtkPolygon 228ms 0.29% 88.09% 434ms 0.56% Edge::GetMapIndex 0 0% 88.09% 424ms 0.55% std::map::map (inline) 417ms 0.54% 88.63% 417ms 0.54% Node::GetIndex 4ms 0.0052% 88.63% 400ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.63% 400ms 0.52% boost::numeric::ublas::vector::vector (inline) 393ms 0.51% 89.14% 393ms 0.51% tcache_put (inline)