File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95792ms, 88.52% of 108214ms total Dropped 1127 nodes (cum <= 541.07ms) flat flat% sum% cum cum% 0 0% 0% 107955ms 99.76% __libc_start_call_main 0 0% 0% 107955ms 99.76% __libc_start_main_impl 0 0% 0% 107955ms 99.76% _start 0 0% 0% 107932ms 99.74% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107932ms 99.74% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107932ms 99.74% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107932ms 99.74% main 0 0% 0% 107896ms 99.71% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107896ms 99.71% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107896ms 99.71% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 107889ms 99.70% AbstractCellBasedSimulation::Solve 5ms 0.0046% 0.0092% 57051ms 52.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 28ms 0.026% 0.035% 53438ms 49.38% ForwardEulerNumericalMethod::UpdateAllNodePositions 79ms 0.073% 0.11% 52344ms 48.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 344ms 0.32% 0.43% 40680ms 37.59% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.43% 37694ms 34.83% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.43% 22512ms 20.80% VertexBasedCellPopulation::Update 1ms 0.00092% 0.43% 22362ms 20.66% MutableVertexMesh::ReMesh 9401ms 8.69% 9.12% 18158ms 16.78% Cylindrical2dVertexMesh::GetVectorFromAtoB 55ms 0.051% 9.17% 17943ms 16.58% Cell::ReadyToDivide 25ms 0.023% 9.19% 16950ms 15.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 114ms 0.11% 9.30% 16839ms 15.56% NagaiHondaForce::GetAdhesionParameter 93ms 0.086% 9.38% 14630ms 13.52% SimpleWntCellCycleModel::UpdateCellCyclePhase 827ms 0.76% 10.15% 14210ms 13.13% std::__new_allocator::allocate (inline) 420ms 0.39% 10.53% 14084ms 13.01% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.53% 13672ms 12.63% std::allocator_traits::allocate (inline) 0 0% 10.53% 13438ms 12.42% std::_Rb_tree::_M_create_node (inline) 929ms 0.86% 11.39% 13277ms 12.27% operator new 0 0% 11.39% 13058ms 12.07% std::_Rb_tree::_M_get_node (inline) 78ms 0.072% 11.47% 12965ms 11.98% CellPropertyCollection::GetPropertiesType (inline) 256ms 0.24% 11.70% 12678ms 11.72% boost::numeric::ublas::vector_assign (inline) 4151ms 3.84% 15.54% 12001ms 11.09% __GI___libc_malloc 0 0% 15.54% 11557ms 10.68% std::_Rb_tree::_Alloc_node::operator() (inline) 89ms 0.082% 15.62% 11285ms 10.43% VertexBasedCellPopulation::GetDampingConstant 13ms 0.012% 15.63% 10656ms 9.85% AbstractCellBasedSimulation::DoCellBirth 57ms 0.053% 15.68% 10649ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 43ms 0.04% 15.72% 10545ms 9.74% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 99ms 0.091% 15.82% 10515ms 9.72% AbstractCellProperty::IsSubType (inline) 3098ms 2.86% 18.68% 10395ms 9.61% __dynamic_cast 173ms 0.16% 18.84% 9931ms 9.18% MutableVertexMesh::CheckForIntersections 0 0% 18.84% 9579ms 8.85% std::_Rb_tree::_M_drop_node (inline) 1035ms 0.96% 19.80% 9537ms 8.81% std::_Rb_tree::_M_erase 549ms 0.51% 20.30% 9211ms 8.51% std::map::operator[] (partial-inline) 2712ms 2.51% 22.81% 9173ms 8.48% boost::numeric::ublas::indexing_vector_assign 343ms 0.32% 23.13% 8973ms 8.29% std::_Rb_tree::~_Rb_tree (inline) 128ms 0.12% 23.24% 8679ms 8.02% std::__new_allocator::deallocate (inline) 0 0% 23.24% 8654ms 8.00% std::allocator_traits::deallocate (inline) 0 0% 23.24% 8591ms 7.94% std::_Rb_tree::_M_put_node (inline) 0 0% 23.24% 8560ms 7.91% std::set::~set (inline) 65ms 0.06% 23.30% 8483ms 7.84% VertexBasedCellPopulation::GetLocationOfCellCentre 2224ms 2.06% 25.36% 8451ms 7.81% __GI___libc_free 74ms 0.068% 25.43% 8405ms 7.77% Cell::GetMutationState 0 0% 25.43% 8401ms 7.76% std::set::insert (inline) 432ms 0.4% 25.83% 8014ms 7.41% VertexMesh::GetNextEdgeGradientOfElementAtNode 12ms 0.011% 25.84% 8008ms 7.40% MutableVertexMesh::RemoveDeletedNodesAndElements 688ms 0.64% 26.47% 7957ms 7.35% VertexMesh::GetCentroidOfElement 909ms 0.84% 27.31% 7715ms 7.13% std::_Rb_tree::_M_insert_ (inline) 546ms 0.5% 27.82% 7295ms 6.74% VertexMesh::ElementIncludesPoint 172ms 0.16% 27.98% 7254ms 6.70% std::_Rb_tree::_Rb_tree (partial-inline) 701ms 0.65% 28.62% 6891ms 6.37% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 28.64% 6788ms 6.27% std::set::set (inline) 56ms 0.052% 28.69% 6621ms 6.12% std::set_intersection (inline) 253ms 0.23% 28.92% 6565ms 6.07% std::__set_intersection 2577ms 2.38% 31.30% 6474ms 5.98% std::_Rb_tree::_M_lower_bound (inline) 144ms 0.13% 31.44% 6464ms 5.97% SimpleWntCellCycleModel::GetWntLevel 6419ms 5.93% 37.37% 6419ms 5.93% boost::numeric::ublas::c_vector::operator() 1073ms 0.99% 38.36% 6294ms 5.82% AbstractMesh::GetDistanceBetweenNodes 138ms 0.13% 38.49% 6182ms 5.71% WntConcentration::GetWntLevel 5376ms 4.97% 43.45% 6166ms 5.70% _int_free 748ms 0.69% 44.15% 5994ms 5.54% std::_Rb_tree::_M_clone_node (inline) 21ms 0.019% 44.17% 5830ms 5.39% MutableVertexMesh::RemoveDeletedNodes 4845ms 4.48% 48.64% 5769ms 5.33% _int_malloc 68ms 0.063% 48.71% 5656ms 5.23% EdgeHelper::RemoveDeletedEdges 0 0% 48.71% 5574ms 5.15% std::_Rb_tree::lower_bound (inline) 0 0% 48.71% 5574ms 5.15% std::map::lower_bound (inline) 5467ms 5.05% 53.76% 5467ms 5.05% __strcmp_evex 0 0% 53.76% 5388ms 4.98% std::insert_iterator::operator= (inline) 23ms 0.021% 53.78% 5359ms 4.95% EdgeHelper::UpdateEdgesMapKey 572ms 0.53% 54.31% 5285ms 4.88% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 54.31% 5053ms 4.67% std::_Rb_tree::_M_insert_unique_ (inline) 68ms 0.063% 54.37% 4910ms 4.54% AbstractCellPopulation::GetCellUsingLocationIndex 112ms 0.1% 54.47% 4809ms 4.44% MutableElement::ResetIndex 2491ms 2.30% 56.78% 4806ms 4.44% __cxxabiv1::__si_class_type_info::__do_dyncast 4588ms 4.24% 61.02% 4588ms 4.24% boost::numeric::ublas::same_impl_ex 0 0% 61.02% 4513ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 18ms 0.017% 61.03% 4373ms 4.04% Cell::GetCellProliferativeType 59ms 0.055% 61.09% 3514ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 161ms 0.15% 61.24% 3370ms 3.11% AbstractCellProperty::IsType (inline) 1ms 0.00092% 61.24% 3348ms 3.09% std::_Rb_tree::_M_insert_unique 3312ms 3.06% 64.30% 3312ms 3.06% [libchaste_cell_based.so] 3284ms 3.03% 67.33% 3284ms 3.03% std::_Rb_tree::_S_right (inline) 126ms 0.12% 67.45% 3273ms 3.02% Cell::SetCellProliferativeType 854ms 0.79% 68.24% 3272ms 3.02% AbstractElement::GetNodeLocation 35ms 0.032% 68.27% 3037ms 2.81% std::_Rb_tree::_M_emplace_hint_unique 130ms 0.12% 68.39% 3033ms 2.80% boost::detail::shared_count::~shared_count (inline) 0 0% 68.39% 3033ms 2.80% boost::shared_ptr::~shared_ptr (inline) 2839ms 2.62% 71.01% 2848ms 2.63% boost::detail::sp_counted_base::release 0 0% 71.01% 2820ms 2.61% boost::numeric::ublas::c_vector::operator-= (inline) 11ms 0.01% 71.02% 2818ms 2.60% AbstractCellPopulation::Iterator::operator++ (inline) 192ms 0.18% 71.20% 2812ms 2.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 71ms 0.066% 71.27% 2736ms 2.53% std::_Rb_tree::erase 126ms 0.12% 71.38% 2617ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.38% 2610ms 2.41% boost::numeric::ublas::c_vector::assign (inline) 0 0% 71.38% 2463ms 2.28% AbstractCellPopulation::WriteResultsToFiles 18ms 0.017% 71.40% 2415ms 2.23% Cell::GetCellData 2377ms 2.20% 73.60% 2377ms 2.20% [libchaste_mesh.so] 271ms 0.25% 73.85% 2370ms 2.19% std::_Rb_tree_const_iterator::operator++ (inline) 56ms 0.052% 73.90% 2273ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 267ms 0.25% 74.14% 2201ms 2.03% VertexMesh::GetAreaGradientOfElementAtNode 28ms 0.026% 74.17% 2180ms 2.01% CellPropertyCollection::HasProperty 29ms 0.027% 74.20% 2180ms 2.01% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.20% 2131ms 1.97% Cell::HasCellProperty (inline) 452ms 0.42% 74.62% 2101ms 1.94% AbstractCellProperty::IsSame 0 0% 74.62% 2031ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 74.62% 2017ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 330ms 0.3% 74.92% 1993ms 1.84% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 95ms 0.088% 75.01% 1934ms 1.79% VertexMesh::GetVolumeOfElement 0 0% 75.01% 1881ms 1.74% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.01% 1824ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 132ms 0.12% 75.13% 1806ms 1.67% CellPropertyCollection::AddProperty 89ms 0.082% 75.21% 1747ms 1.61% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.0037% 75.22% 1732ms 1.60% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.22% 1732ms 1.60% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 67ms 0.062% 75.28% 1723ms 1.59% MutableVertexMesh::CheckForSwapsFromShortEdges 195ms 0.18% 75.46% 1649ms 1.52% std::type_info::operator== (inline) 2ms 0.0018% 75.46% 1649ms 1.52% tcache_get (inline) 1647ms 1.52% 76.98% 1647ms 1.52% tcache_get_n (inline) 73ms 0.067% 77.05% 1563ms 1.44% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 77.05% 1520ms 1.40% boost::numeric::ublas::vector_binary::operator() (inline) 74ms 0.068% 77.12% 1514ms 1.40% VertexMesh::GetSurfaceAreaOfElement 0 0% 77.12% 1487ms 1.37% OffLatticeSimulation::ApplyBoundaries 1453ms 1.34% 78.46% 1453ms 1.34% std::_Rb_tree_increment 50ms 0.046% 78.51% 1342ms 1.24% Node::RemoveElement 52ms 0.048% 78.56% 1335ms 1.23% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.00092% 78.56% 1293ms 1.19% std::set::erase (inline) 770ms 0.71% 79.27% 1271ms 1.17% std::_Rb_tree::equal_range (inline) 0 0% 79.27% 1228ms 1.13% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 79.27% 1228ms 1.13% boost::numeric::ublas::c_vector::swap (inline) 413ms 0.38% 79.66% 1223ms 1.13% std::swap_ranges (inline) 8ms 0.0074% 79.66% 1205ms 1.11% MutableElement::RegisterWithEdges (inline) 40ms 0.037% 79.70% 1203ms 1.11% Edge::AddElement 119ms 0.11% 79.81% 1202ms 1.11% boost::numeric::ublas::vector_reference::operator() (inline) 45ms 0.042% 79.85% 1175ms 1.09% CellPropertyRegistry::Get 0 0% 79.85% 1145ms 1.06% CellPropertyCollection::~CellPropertyCollection (inline) 16ms 0.015% 79.87% 1144ms 1.06% boost::numeric::ublas::detail::expression_type_check (inline) 1110ms 1.03% 80.89% 1110ms 1.03% [libstdc++.so.6.0.33] 207ms 0.19% 81.08% 1101ms 1.02% boost::numeric::ublas::detail::equals 1094ms 1.01% 82.09% 1094ms 1.01% Node::rGetLocation 1069ms 0.99% 83.08% 1069ms 0.99% std::_Rb_tree_insert_and_rebalance 0 0% 83.08% 996ms 0.92% boost::numeric::ublas::norm_2 (inline) 0 0% 83.08% 995ms 0.92% std::__new_allocator::destroy (inline) 0 0% 83.08% 995ms 0.92% std::allocator_traits::destroy (inline) 0 0% 83.08% 990ms 0.91% std::_Rb_tree::_M_destroy_node (inline) 119ms 0.11% 83.19% 964ms 0.89% std::_Rb_tree::find (inline) 14ms 0.013% 83.21% 961ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 490ms 0.45% 83.66% 960ms 0.89% boost::numeric::ublas::vector_norm_2::apply 0 0% 83.66% 943ms 0.87% VertexMeshWriter::MakeVtkMesh 0 0% 83.66% 911ms 0.84% std::_Rb_tree::clear (inline) 907ms 0.84% 84.50% 907ms 0.84% tcache_put (inline) 0 0% 84.50% 889ms 0.82% std::map::clear (inline) 692ms 0.64% 85.14% 870ms 0.8% CellPropertyCollection::GetProperty 61ms 0.056% 85.19% 841ms 0.78% std::less::operator() (inline) 1ms 0.00092% 85.19% 815ms 0.75% std::map::find (inline) 811ms 0.75% 85.94% 811ms 0.75% std::swap (inline) 0 0% 85.94% 810ms 0.75% std::iter_swap (inline) 49ms 0.045% 85.99% 804ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 369ms 0.34% 86.33% 787ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 621ms 0.57% 86.90% 780ms 0.72% std::operator< (inline) 0 0% 86.90% 758ms 0.7% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.92% 758ms 0.7% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.92% 748ms 0.69% boost::numeric::ublas::norm_inf (inline) 258ms 0.24% 87.16% 748ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 723ms 0.67% 87.83% 723ms 0.67% std::vector::size (inline) 22ms 0.02% 87.85% 668ms 0.62% MutableElement::RegisterWithNodes (inline) 63ms 0.058% 87.91% 663ms 0.61% MutableElement::GetNodeLocalIndex 0 0% 87.91% 652ms 0.6% vtkPolygon::New 0 0% 87.91% 651ms 0.6% vtkPolygon::vtkPolygon 66ms 0.061% 87.97% 645ms 0.6% Node::AddElement 0 0% 87.97% 609ms 0.56% std::_Vector_base::_M_allocate (inline) 587ms 0.54% 88.51% 587ms 0.54% Node::GetIndex 12ms 0.011% 88.52% 550ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.52% 550ms 0.51% boost::numeric::ublas::vector::vector (inline) 0 0% 88.52% 548ms 0.51% std::map::map (inline)