File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97231ms, 88.52% of 109841ms total Dropped 1127 nodes (cum <= 549.21ms) flat flat% sum% cum cum% 0 0% 0% 109386ms 99.59% __libc_start_call_main 0 0% 0% 109386ms 99.59% __libc_start_main_impl 0 0% 0% 109386ms 99.59% _start 0 0% 0% 109365ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109365ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109365ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109365ms 99.57% main 0 0% 0% 109325ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109325ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109325ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 109317ms 99.52% AbstractCellBasedSimulation::Solve 11ms 0.01% 0.014% 56567ms 51.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.026% 53237ms 48.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 135ms 0.12% 0.15% 51747ms 47.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 353ms 0.32% 0.47% 39757ms 36.20% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.47% 39564ms 36.02% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.47% 24561ms 22.36% VertexBasedCellPopulation::Update 1ms 0.00091% 0.47% 24456ms 22.26% MutableVertexMesh::ReMesh 14426ms 13.13% 13.61% 22752ms 20.71% Cylindrical2dVertexMesh::GetVectorFromAtoB 139ms 0.13% 13.73% 17703ms 16.12% Cell::ReadyToDivide 83ms 0.076% 13.81% 16382ms 14.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 283ms 0.26% 14.07% 14713ms 13.39% NagaiHondaForce::GetAdhesionParameter 442ms 0.4% 14.47% 14407ms 13.12% boost::numeric::ublas::c_vector::c_vector (partial-inline) 142ms 0.13% 14.60% 13975ms 12.72% CellPropertyCollection::GetPropertiesType (inline) 117ms 0.11% 14.71% 13922ms 12.67% SimpleWntCellCycleModel::UpdateCellCyclePhase 391ms 0.36% 15.06% 12845ms 11.69% boost::numeric::ublas::vector_assign (inline) 122ms 0.11% 15.17% 12030ms 10.95% MutableVertexMesh::CheckForIntersections 55ms 0.05% 15.22% 11487ms 10.46% VertexBasedCellPopulation::GetDampingConstant 3395ms 3.09% 18.31% 11484ms 10.46% __dynamic_cast 73ms 0.066% 18.38% 11377ms 10.36% AbstractCellProperty::IsSubType (inline) 84ms 0.076% 18.46% 10656ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.046% 18.50% 10543ms 9.60% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1307ms 1.19% 19.69% 10341ms 9.41% std::__new_allocator::allocate (inline) 24ms 0.022% 19.71% 10337ms 9.41% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.71% 9797ms 8.92% std::allocator_traits::allocate (inline) 0 0% 19.71% 9769ms 8.89% std::_Rb_tree::_M_create_node (inline) 2687ms 2.45% 22.16% 9504ms 8.65% boost::numeric::ublas::indexing_vector_assign 1354ms 1.23% 23.39% 9471ms 8.62% std::_Rb_tree::_M_erase 867ms 0.79% 24.18% 9212ms 8.39% operator new 0 0% 24.18% 9078ms 8.26% std::_Rb_tree::_M_get_node (inline) 78ms 0.071% 24.25% 8962ms 8.16% Cell::GetMutationState 788ms 0.72% 24.97% 8954ms 8.15% VertexMesh::ElementIncludesPoint 29ms 0.026% 25.00% 8766ms 7.98% VertexBasedCellPopulation::GetLocationOfCellCentre 395ms 0.36% 25.36% 8705ms 7.93% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.36% 8609ms 7.84% std::_Rb_tree::_M_drop_node (inline) 241ms 0.22% 25.58% 8591ms 7.82% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.58% 8560ms 7.79% std::_Rb_tree::_Alloc_node::operator() (inline) 279ms 0.25% 25.83% 8396ms 7.64% std::__new_allocator::deallocate (inline) 0 0% 25.83% 8356ms 7.61% std::allocator_traits::deallocate (inline) 3204ms 2.92% 28.75% 8295ms 7.55% __GI___libc_free 0 0% 28.75% 8271ms 7.53% std::_Rb_tree::_M_put_node (inline) 472ms 0.43% 29.18% 8235ms 7.50% VertexMesh::GetCentroidOfElement 3315ms 3.02% 32.20% 8143ms 7.41% __GI___libc_malloc 0 0% 32.20% 8103ms 7.38% std::set::~set (inline) 15ms 0.014% 32.21% 7937ms 7.23% MutableVertexMesh::RemoveDeletedNodesAndElements 469ms 0.43% 32.64% 7633ms 6.95% std::map::operator[] (partial-inline) 146ms 0.13% 32.77% 6984ms 6.36% std::_Rb_tree::_Rb_tree (partial-inline) 1208ms 1.10% 33.87% 6971ms 6.35% AbstractMesh::GetDistanceBetweenNodes 655ms 0.6% 34.47% 6575ms 5.99% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 34.48% 6518ms 5.93% std::set::set (inline) 6511ms 5.93% 40.41% 6511ms 5.93% __strcmp_avx2 98ms 0.089% 40.49% 6309ms 5.74% SimpleWntCellCycleModel::GetWntLevel 135ms 0.12% 40.62% 6118ms 5.57% WntConcentration::GetWntLevel 2494ms 2.27% 42.89% 6106ms 5.56% std::_Rb_tree::_M_lower_bound (inline) 6007ms 5.47% 48.36% 6007ms 5.47% boost::numeric::ublas::c_vector::operator() 0 0% 48.36% 5637ms 5.13% std::set::insert (inline) 695ms 0.63% 48.99% 5623ms 5.12% std::_Rb_tree::_M_clone_node (inline) 2658ms 2.42% 51.41% 5596ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.025% 51.44% 5584ms 5.08% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 51.47% 5407ms 4.92% EdgeHelper::RemoveDeletedEdges 44ms 0.04% 51.51% 5104ms 4.65% EdgeHelper::UpdateEdgesMapKey 4760ms 4.33% 55.84% 5085ms 4.63% _int_free 228ms 0.21% 56.05% 4909ms 4.47% MutableElement::ResetIndex 0 0% 56.05% 4894ms 4.46% std::_Rb_tree::lower_bound (inline) 0 0% 56.05% 4894ms 4.46% std::map::lower_bound (inline) 1520ms 1.38% 57.43% 4826ms 4.39% boost::numeric::ublas::c_vector::operator[] (inline) 596ms 0.54% 57.97% 4760ms 4.33% std::_Rb_tree::_M_insert_ (inline) 1ms 0.00091% 57.98% 4655ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 69ms 0.063% 58.04% 4499ms 4.10% std::set_intersection (inline) 262ms 0.24% 58.28% 4430ms 4.03% std::__set_intersection 96ms 0.087% 58.36% 4162ms 3.79% AbstractCellPopulation::GetCellUsingLocationIndex 4060ms 3.70% 62.06% 4060ms 3.70% boost::numeric::ublas::same_impl_ex 48ms 0.044% 62.10% 4048ms 3.69% Cell::GetCellProliferativeType 66ms 0.06% 62.16% 3703ms 3.37% AbstractCellProperty::IsType (inline) 8ms 0.0073% 62.17% 3529ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.17% 3297ms 3.00% std::insert_iterator::operator= (inline) 823ms 0.75% 62.92% 3198ms 2.91% AbstractElement::GetNodeLocation 45ms 0.041% 62.96% 3198ms 2.91% Cell::SetCellProliferativeType 2185ms 1.99% 64.95% 3176ms 2.89% _int_malloc 44ms 0.04% 64.99% 3072ms 2.80% std::_Rb_tree::erase 3051ms 2.78% 67.77% 3051ms 2.78% std::_Rb_tree::_S_right (inline) 641ms 0.58% 68.35% 2924ms 2.66% boost::numeric::ublas::vector_binary::size (inline) 6ms 0.0055% 68.36% 2898ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 3ms 0.0027% 68.36% 2739ms 2.49% std::_Rb_tree::_M_insert_unique (inline) 387ms 0.35% 68.71% 2733ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 672ms 0.61% 69.32% 2665ms 2.43% AbstractCellProperty::IsSame 37ms 0.034% 69.36% 2601ms 2.37% CellPropertyCollection::HasProperty 0 0% 69.36% 2573ms 2.34% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.36% 2506ms 2.28% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.36% 2500ms 2.28% Cell::HasCellProperty (inline) 24ms 0.022% 69.38% 2483ms 2.26% Cell::GetCellData 213ms 0.19% 69.57% 2432ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.57% 2423ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 108ms 0.098% 69.67% 2358ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 100ms 0.091% 69.76% 2269ms 2.07% VertexMesh::GetVolumeOfElement 1ms 0.00091% 69.76% 2227ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 37ms 0.034% 69.80% 2214ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 205ms 0.19% 69.98% 2209ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 2148ms 1.96% 71.94% 2148ms 1.96% std::_Rb_tree_increment 1368ms 1.25% 73.19% 2057ms 1.87% std::_Rb_tree::equal_range (inline) 0 0% 73.19% 2056ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 73.19% 2044ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 505ms 0.46% 73.65% 1993ms 1.81% std::type_info::operator== (inline) 3ms 0.0027% 73.65% 1925ms 1.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.65% 1925ms 1.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 72ms 0.066% 73.72% 1856ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00091% 73.72% 1838ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 21ms 0.019% 73.74% 1769ms 1.61% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.026% 73.76% 1624ms 1.48% VertexMesh::GetSurfaceAreaOfElement 151ms 0.14% 73.90% 1616ms 1.47% CellPropertyCollection::AddProperty 35ms 0.032% 73.93% 1596ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.069% 74.00% 1553ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 73ms 0.066% 74.07% 1541ms 1.40% Node::RemoveElement 18ms 0.016% 74.08% 1479ms 1.35% std::set::erase (inline) 0 0% 74.08% 1478ms 1.35% tcache_get (inline) 1478ms 1.35% 75.43% 1478ms 1.35% tcache_get_n (inline) 147ms 0.13% 75.56% 1463ms 1.33% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.56% 1368ms 1.25% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00091% 75.56% 1338ms 1.22% OffLatticeSimulation::ApplyBoundaries 93ms 0.085% 75.65% 1290ms 1.17% std::less::operator() (inline) 0 0% 75.65% 1241ms 1.13% boost::numeric::ublas::norm_2 (inline) 540ms 0.49% 76.14% 1226ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.14% 1209ms 1.10% std::_Rb_tree::_Auto_node::_Auto_node (inline) 974ms 0.89% 77.03% 1197ms 1.09% std::operator< (inline) 1179ms 1.07% 78.10% 1179ms 1.07% [libchaste_cell_based.so] 88ms 0.08% 78.18% 1175ms 1.07% std::_Rb_tree::find (inline) 66ms 0.06% 78.24% 1164ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 21ms 0.019% 78.26% 1124ms 1.02% CellPropertyRegistry::Get 0 0% 78.26% 1124ms 1.02% std::_Rb_tree::clear (inline) 14ms 0.013% 78.27% 1111ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.27% 1107ms 1.01% std::map::clear (inline) 1106ms 1.01% 79.28% 1106ms 1.01% std::_Rb_tree_insert_and_rebalance 1102ms 1.00% 80.28% 1102ms 1.00% Node::rGetLocation 10ms 0.0091% 80.29% 1070ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1016ms 0.92% 81.22% 1016ms 0.92% std::vector::size (inline) 1000ms 0.91% 82.13% 1000ms 0.91% [libchaste_mesh.so] 150ms 0.14% 82.26% 993ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 82.26% 993ms 0.9% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.26% 983ms 0.89% std::map::find (inline) 23ms 0.021% 82.28% 928ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 388ms 0.35% 82.64% 923ms 0.84% Edge::GetMapIndex 0 0% 82.64% 912ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 82.64% 912ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 79ms 0.072% 82.71% 907ms 0.83% std::swap_ranges (inline) 169ms 0.15% 82.87% 899ms 0.82% boost::numeric::ublas::detail::equals 0 0% 82.87% 894ms 0.81% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.87% 856ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 82.87% 828ms 0.75% std::iter_swap (inline) 828ms 0.75% 83.62% 828ms 0.75% std::swap (inline) 807ms 0.73% 84.36% 812ms 0.74% boost::detail::sp_counted_base::release 101ms 0.092% 84.45% 802ms 0.73% MutableElement::GetNodeLocalIndex 28ms 0.025% 84.47% 782ms 0.71% Edge::AddElement 131ms 0.12% 84.59% 775ms 0.71% boost::shared_ptr::shared_ptr (inline) 14ms 0.013% 84.61% 771ms 0.7% MutableElement::RegisterWithEdges (inline) 136ms 0.12% 84.73% 747ms 0.68% std::__new_allocator::construct (inline) 0 0% 84.73% 747ms 0.68% std::allocator_traits::construct (inline) 104ms 0.095% 84.82% 742ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 443ms 0.4% 85.23% 728ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.23% 718ms 0.65% std::_Vector_base::_M_allocate (inline) 701ms 0.64% 85.87% 701ms 0.64% Node::GetIndex 14ms 0.013% 85.88% 692ms 0.63% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.88% 691ms 0.63% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.88% 684ms 0.62% boost::numeric::ublas::norm_inf (inline) 334ms 0.3% 86.18% 684ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 92ms 0.084% 86.27% 678ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 20ms 0.018% 86.28% 650ms 0.59% MutableElement::RegisterWithNodes (inline) 0 0% 86.28% 650ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.015% 86.30% 650ms 0.59% std::_Rb_tree::_M_insert_node (inline) 618ms 0.56% 86.86% 644ms 0.59% boost::detail::shared_count::shared_count (inline) 31ms 0.028% 86.89% 635ms 0.58% Node::AddElement 0 0% 86.89% 620ms 0.56% vtkPolygon::New 2ms 0.0018% 86.89% 620ms 0.56% vtkPolygon::vtkPolygon 7ms 0.0064% 86.90% 612ms 0.56% std::vector::_M_default_append (inline) 0 0% 86.90% 602ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 596ms 0.54% 87.44% 596ms 0.54% [libstdc++.so.6.0.33] 589ms 0.54% 87.98% 589ms 0.54% operator delete 580ms 0.53% 88.51% 580ms 0.53% boost::shared_ptr::operator-> (inline) 16ms 0.015% 88.52% 560ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.52% 560ms 0.51% boost::numeric::ublas::vector::vector (inline)