File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 83366ms, 88.15% of 94570ms total Dropped 1052 nodes (cum <= 472.85ms) flat flat% sum% cum cum% 0 0% 0% 94326ms 99.74% __libc_start_call_main 0 0% 0% 94326ms 99.74% __libc_start_main_impl 0 0% 0% 94326ms 99.74% _start 0 0% 0% 94303ms 99.72% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 94303ms 99.72% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 94303ms 99.72% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 94303ms 99.72% main 0 0% 0% 94271ms 99.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 94271ms 99.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 94271ms 99.68% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0021% 0.0021% 94264ms 99.68% AbstractCellBasedSimulation::Solve 12ms 0.013% 0.015% 49510ms 52.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 10ms 0.011% 0.025% 46155ms 48.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 54ms 0.057% 0.082% 44830ms 47.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 321ms 0.34% 0.42% 34757ms 36.75% NagaiHondaForce::AddForceContribution 1ms 0.0011% 0.42% 32971ms 34.86% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0032% 0.43% 19515ms 20.64% VertexBasedCellPopulation::Update 0 0% 0.43% 19415ms 20.53% MutableVertexMesh::ReMesh 105ms 0.11% 0.54% 15936ms 16.85% Cell::ReadyToDivide 8046ms 8.51% 9.05% 15590ms 16.49% Cylindrical2dVertexMesh::GetVectorFromAtoB 31ms 0.033% 9.08% 14834ms 15.69% AbstractPhaseBasedCellCycleModel::ReadyToDivide 76ms 0.08% 9.16% 14331ms 15.15% NagaiHondaForce::GetAdhesionParameter 79ms 0.084% 9.24% 12671ms 13.40% SimpleWntCellCycleModel::UpdateCellCyclePhase 392ms 0.41% 9.66% 12158ms 12.86% boost::numeric::ublas::c_vector::c_vector (partial-inline) 65ms 0.069% 9.73% 11970ms 12.66% CellPropertyCollection::GetPropertiesType (inline) 735ms 0.78% 10.50% 11905ms 12.59% std::__new_allocator::allocate (inline) 0 0% 10.50% 11474ms 12.13% std::allocator_traits::allocate (inline) 0 0% 10.50% 11285ms 11.93% std::_Rb_tree::_M_create_node (inline) 793ms 0.84% 11.34% 11120ms 11.76% operator new 0 0% 11.34% 10942ms 11.57% std::_Rb_tree::_M_get_node (inline) 229ms 0.24% 11.58% 10875ms 11.50% boost::numeric::ublas::vector_assign (inline) 3471ms 3.67% 15.25% 10004ms 10.58% __GI___libc_malloc 69ms 0.073% 15.33% 9807ms 10.37% AbstractCellProperty::IsSubType (inline) 2566ms 2.71% 18.04% 9773ms 10.33% __dynamic_cast 97ms 0.1% 18.14% 9744ms 10.30% VertexBasedCellPopulation::GetDampingConstant 0 0% 18.14% 9712ms 10.27% std::_Rb_tree::_Alloc_node::operator() (inline) 35ms 0.037% 18.18% 9685ms 10.24% AbstractTargetAreaModifier::UpdateTargetAreas 39ms 0.041% 18.22% 9621ms 10.17% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 3ms 0.0032% 18.22% 9476ms 10.02% AbstractCellBasedSimulation::DoCellBirth 143ms 0.15% 18.37% 8719ms 9.22% MutableVertexMesh::CheckForIntersections 945ms 1% 19.37% 8203ms 8.67% std::_Rb_tree::_M_erase 0 0% 19.37% 8167ms 8.64% std::_Rb_tree::_M_drop_node (inline) 472ms 0.5% 19.87% 7944ms 8.40% std::map::operator[] (partial-inline) 2261ms 2.39% 22.26% 7904ms 8.36% boost::numeric::ublas::indexing_vector_assign 284ms 0.3% 22.56% 7708ms 8.15% std::_Rb_tree::~_Rb_tree (inline) 71ms 0.075% 22.64% 7459ms 7.89% Cell::GetMutationState 91ms 0.096% 22.74% 7367ms 7.79% std::__new_allocator::deallocate (inline) 0 0% 22.74% 7351ms 7.77% std::allocator_traits::deallocate (inline) 0 0% 22.74% 7328ms 7.75% std::set::~set (inline) 0 0% 22.74% 7288ms 7.71% std::_Rb_tree::_M_put_node (inline) 1856ms 1.96% 24.70% 7137ms 7.55% __GI___libc_free 51ms 0.054% 24.75% 7081ms 7.49% VertexBasedCellPopulation::GetLocationOfCellCentre 7ms 0.0074% 24.76% 6946ms 7.34% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 24.76% 6928ms 7.33% std::set::insert (inline) 360ms 0.38% 25.14% 6830ms 7.22% VertexMesh::GetNextEdgeGradientOfElementAtNode 523ms 0.55% 25.69% 6590ms 6.97% VertexMesh::GetCentroidOfElement 463ms 0.49% 26.18% 6475ms 6.85% VertexMesh::ElementIncludesPoint 795ms 0.84% 27.02% 6380ms 6.75% std::_Rb_tree::_M_insert_ (inline) 92ms 0.097% 27.12% 6219ms 6.58% std::_Rb_tree::_Rb_tree (partial-inline) 618ms 0.65% 27.77% 5972ms 6.31% std::_Rb_tree::_M_copy (inline) 7ms 0.0074% 27.78% 5814ms 6.15% std::set::set (inline) 5699ms 6.03% 33.81% 5699ms 6.03% boost::numeric::ublas::c_vector::operator() 2220ms 2.35% 36.16% 5683ms 6.01% std::_Rb_tree::_M_lower_bound (inline) 5622ms 5.94% 42.10% 5622ms 5.94% __strcmp_evex 59ms 0.062% 42.16% 5542ms 5.86% std::set_intersection (inline) 224ms 0.24% 42.40% 5483ms 5.80% std::__set_intersection 121ms 0.13% 42.53% 5275ms 5.58% SimpleWntCellCycleModel::GetWntLevel 853ms 0.9% 43.43% 5236ms 5.54% AbstractMesh::GetDistanceBetweenNodes 4548ms 4.81% 48.24% 5231ms 5.53% _int_free 656ms 0.69% 48.93% 5209ms 5.51% std::_Rb_tree::_M_clone_node (inline) 23ms 0.024% 48.96% 5067ms 5.36% MutableVertexMesh::RemoveDeletedNodes 101ms 0.11% 49.06% 5048ms 5.34% WntConcentration::GetWntLevel 47ms 0.05% 49.11% 4944ms 5.23% EdgeHelper::RemoveDeletedEdges 0 0% 49.11% 4864ms 5.14% std::_Rb_tree::lower_bound (inline) 0 0% 49.11% 4864ms 5.14% std::map::lower_bound (inline) 4013ms 4.24% 53.36% 4799ms 5.07% _int_malloc 2320ms 2.45% 55.81% 4795ms 5.07% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.019% 55.83% 4719ms 4.99% EdgeHelper::UpdateEdgesMapKey 545ms 0.58% 56.40% 4666ms 4.93% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 56.40% 4242ms 4.49% std::insert_iterator::operator= (inline) 85ms 0.09% 56.49% 4188ms 4.43% MutableElement::ResetIndex 27ms 0.029% 56.52% 4144ms 4.38% Cell::GetCellProliferativeType 52ms 0.055% 56.58% 4015ms 4.25% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.58% 3967ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 56.58% 3927ms 4.15% std::_Rb_tree::_M_insert_unique_ (inline) 3870ms 4.09% 60.67% 3870ms 4.09% boost::numeric::ublas::same_impl_ex 124ms 0.13% 60.80% 3194ms 3.38% AbstractCellProperty::IsType (inline) 3124ms 3.30% 64.10% 3124ms 3.30% [libchaste_cell_based.so] 50ms 0.053% 64.16% 3081ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 87ms 0.092% 64.25% 3061ms 3.24% Cell::SetCellProliferativeType 2ms 0.0021% 64.25% 3001ms 3.17% std::_Rb_tree::_M_insert_unique 2966ms 3.14% 67.39% 2966ms 3.14% std::_Rb_tree::_S_right (inline) 706ms 0.75% 68.13% 2764ms 2.92% AbstractElement::GetNodeLocation 115ms 0.12% 68.26% 2733ms 2.89% boost::detail::shared_count::~shared_count (inline) 0 0% 68.26% 2733ms 2.89% boost::shared_ptr::~shared_ptr (inline) 12ms 0.013% 68.27% 2610ms 2.76% AbstractCellPopulation::Iterator::operator++ (inline) 185ms 0.2% 68.46% 2595ms 2.74% AbstractCellPopulation::Iterator::IsRealCell (inline) 30ms 0.032% 68.50% 2570ms 2.72% std::_Rb_tree::_M_emplace_hint_unique 2549ms 2.70% 71.19% 2569ms 2.72% boost::detail::sp_counted_base::release 74ms 0.078% 71.27% 2428ms 2.57% std::_Rb_tree::erase 25ms 0.026% 71.30% 2361ms 2.50% Cell::GetCellData 0 0% 71.30% 2315ms 2.45% boost::numeric::ublas::c_vector::assign (inline) 129ms 0.14% 71.43% 2236ms 2.36% boost::numeric::ublas::vector_binary::size (inline) 301ms 0.32% 71.75% 2171ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 29ms 0.031% 71.78% 2147ms 2.27% CellPropertyCollection::HasProperty 59ms 0.062% 71.84% 2115ms 2.24% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0011% 71.85% 2111ms 2.23% Cell::HasCellProperty (inline) 0 0% 71.85% 2078ms 2.20% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 71.85% 2070ms 2.19% AbstractCellPopulation::WriteResultsToFiles 2027ms 2.14% 73.99% 2027ms 2.14% [libchaste_mesh.so] 418ms 0.44% 74.43% 2022ms 2.14% AbstractCellProperty::IsSame 23ms 0.024% 74.45% 1990ms 2.10% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 212ms 0.22% 74.68% 1885ms 1.99% VertexMesh::GetAreaGradientOfElementAtNode 291ms 0.31% 74.99% 1821ms 1.93% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.99% 1706ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0011% 74.99% 1702ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 123ms 0.13% 75.12% 1692ms 1.79% CellPropertyCollection::AddProperty 91ms 0.096% 75.21% 1646ms 1.74% VertexMesh::GetVolumeOfElement 192ms 0.2% 75.42% 1604ms 1.70% std::type_info::operator== (inline) 69ms 0.073% 75.49% 1574ms 1.66% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.49% 1573ms 1.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0021% 75.49% 1560ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.49% 1560ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.49% 1529ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.0042% 75.50% 1477ms 1.56% OffLatticeSimulation::ApplyBoundaries 0 0% 75.50% 1440ms 1.52% boost::numeric::ublas::vector_binary::operator() (inline) 51ms 0.054% 75.55% 1397ms 1.48% MutableVertexMesh::CheckForSwapsFromShortEdges 3ms 0.0032% 75.55% 1369ms 1.45% tcache_get (inline) 1366ms 1.44% 77.00% 1366ms 1.44% tcache_get_n (inline) 59ms 0.062% 77.06% 1338ms 1.41% std::_Rb_tree::_M_erase_aux (partial-inline) 1287ms 1.36% 78.42% 1287ms 1.36% std::_Rb_tree_increment 59ms 0.062% 78.48% 1285ms 1.36% VertexMesh::GetSurfaceAreaOfElement 48ms 0.051% 78.53% 1284ms 1.36% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 36ms 0.038% 78.57% 1185ms 1.25% Node::RemoveElement 706ms 0.75% 79.32% 1170ms 1.24% std::_Rb_tree::equal_range (inline) 0 0% 79.32% 1149ms 1.21% std::set::erase (inline) 97ms 0.1% 79.42% 1139ms 1.20% boost::numeric::ublas::vector_reference::operator() (inline) 41ms 0.043% 79.46% 1136ms 1.20% CellPropertyRegistry::Get 13ms 0.014% 79.48% 1056ms 1.12% MutableElement::RegisterWithEdges (inline) 38ms 0.04% 79.52% 1049ms 1.11% Edge::AddElement 7ms 0.0074% 79.53% 1031ms 1.09% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.53% 1009ms 1.07% CellPropertyCollection::~CellPropertyCollection (inline) 1003ms 1.06% 80.59% 1003ms 1.06% [libstdc++.so.6.0.33] 174ms 0.18% 80.77% 1003ms 1.06% boost::numeric::ublas::detail::equals 921ms 0.97% 81.74% 921ms 0.97% Node::rGetLocation 921ms 0.97% 82.72% 921ms 0.97% std::_Rb_tree_insert_and_rebalance 0 0% 82.72% 881ms 0.93% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.72% 881ms 0.93% std::__new_allocator::destroy (inline) 0 0% 82.72% 881ms 0.93% std::allocator_traits::destroy (inline) 105ms 0.11% 82.83% 880ms 0.93% std::_Rb_tree::find (inline) 0 0% 82.83% 855ms 0.9% boost::numeric::ublas::norm_2 (inline) 11ms 0.012% 82.84% 849ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 313ms 0.33% 83.17% 837ms 0.89% boost::numeric::ublas::vector_norm_2::apply 3ms 0.0032% 83.18% 804ms 0.85% VertexMeshWriter::MakeVtkMesh 0 0% 83.18% 799ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0021% 83.18% 799ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 133ms 0.14% 83.32% 797ms 0.84% std::swap_ranges (inline) 1ms 0.0011% 83.32% 789ms 0.83% std::_Rb_tree::clear (inline) 45ms 0.048% 83.37% 785ms 0.83% std::less::operator() (inline) 0 0% 83.37% 765ms 0.81% std::map::clear (inline) 0 0% 83.37% 760ms 0.8% std::map::find (inline) 606ms 0.64% 84.01% 752ms 0.8% CellPropertyCollection::GetProperty 746ms 0.79% 84.80% 746ms 0.79% tcache_put (inline) 579ms 0.61% 85.41% 740ms 0.78% std::operator< (inline) 44ms 0.047% 85.46% 722ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.46% 715ms 0.76% boost::numeric::ublas::norm_inf (inline) 258ms 0.27% 85.73% 715ms 0.76% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.73% 664ms 0.7% std::iter_swap (inline) 664ms 0.7% 86.43% 664ms 0.7% std::swap (inline) 0 0% 86.43% 662ms 0.7% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.027% 86.46% 662ms 0.7% std::_Rb_tree::_M_insert_node (inline) 57ms 0.06% 86.52% 622ms 0.66% MutableElement::GetNodeLocalIndex 621ms 0.66% 87.17% 621ms 0.66% std::vector::size (inline) 280ms 0.3% 87.47% 601ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 22ms 0.023% 87.49% 582ms 0.62% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 87.49% 572ms 0.6% vtkPolygon::New 1ms 0.0011% 87.49% 572ms 0.6% vtkPolygon::vtkPolygon 92ms 0.097% 87.59% 560ms 0.59% VertexBasedCellPopulation::CheckForStepSizeException 10ms 0.011% 87.60% 537ms 0.57% MutableElement::RegisterWithNodes (inline) 0 0% 87.60% 530ms 0.56% std::_Vector_base::_M_allocate (inline) 38ms 0.04% 87.64% 518ms 0.55% Node::AddElement 482ms 0.51% 88.15% 482ms 0.51% Node::GetIndex 0 0% 88.15% 475ms 0.5% std::map::map (inline)