File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97399ms, 88.57% of 109973ms total Dropped 1105 nodes (cum <= 549.87ms) flat flat% sum% cum cum% 0 0% 0% 109481ms 99.55% __libc_start_call_main 0 0% 0% 109481ms 99.55% __libc_start_main_impl 0 0% 0% 109481ms 99.55% _start 0 0% 0% 109460ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109460ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109460ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109460ms 99.53% main 0 0% 0% 109424ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109424ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109424ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 109416ms 99.49% AbstractCellBasedSimulation::Solve 15ms 0.014% 0.016% 56495ms 51.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.029% 53149ms 48.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 147ms 0.13% 0.16% 51550ms 46.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 345ms 0.31% 0.48% 39860ms 36.25% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.48% 39791ms 36.18% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0036% 0.48% 24796ms 22.55% VertexBasedCellPopulation::Update 1ms 0.00091% 0.48% 24653ms 22.42% MutableVertexMesh::ReMesh 14512ms 13.20% 13.68% 22890ms 20.81% Cylindrical2dVertexMesh::GetVectorFromAtoB 148ms 0.13% 13.81% 17598ms 16.00% Cell::ReadyToDivide 115ms 0.1% 13.92% 16261ms 14.79% AbstractPhaseBasedCellCycleModel::ReadyToDivide 346ms 0.31% 14.23% 14546ms 13.23% NagaiHondaForce::GetAdhesionParameter 406ms 0.37% 14.60% 14346ms 13.05% boost::numeric::ublas::c_vector::c_vector (partial-inline) 109ms 0.099% 14.70% 13831ms 12.58% SimpleWntCellCycleModel::UpdateCellCyclePhase 136ms 0.12% 14.82% 13742ms 12.50% CellPropertyCollection::GetPropertiesType (inline) 369ms 0.34% 15.16% 12843ms 11.68% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.28% 12112ms 11.01% MutableVertexMesh::CheckForIntersections 3265ms 2.97% 18.25% 11386ms 10.35% __dynamic_cast 61ms 0.055% 18.31% 11263ms 10.24% AbstractCellProperty::IsSubType (inline) 83ms 0.075% 18.38% 11168ms 10.16% VertexBasedCellPopulation::GetDampingConstant 78ms 0.071% 18.45% 10630ms 9.67% AbstractTargetAreaModifier::UpdateTargetAreas 87ms 0.079% 18.53% 10514ms 9.56% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 26ms 0.024% 18.56% 10297ms 9.36% AbstractCellBasedSimulation::DoCellBirth 1371ms 1.25% 19.80% 10109ms 9.19% std::__new_allocator::allocate (inline) 2794ms 2.54% 22.34% 9673ms 8.80% boost::numeric::ublas::indexing_vector_assign 0 0% 22.34% 9588ms 8.72% std::allocator_traits::allocate (inline) 0 0% 22.34% 9544ms 8.68% std::_Rb_tree::_M_create_node (inline) 353ms 0.32% 22.66% 9065ms 8.24% VertexMesh::GetNextEdgeGradientOfElementAtNode 1412ms 1.28% 23.95% 9032ms 8.21% std::_Rb_tree::_M_erase 797ms 0.72% 24.67% 8963ms 8.15% VertexMesh::ElementIncludesPoint 861ms 0.78% 25.46% 8914ms 8.11% operator new 0 0% 25.46% 8858ms 8.05% std::_Rb_tree::_M_get_node (inline) 31ms 0.028% 25.48% 8711ms 7.92% VertexBasedCellPopulation::GetLocationOfCellCentre 80ms 0.073% 25.56% 8575ms 7.80% Cell::GetMutationState 0 0% 25.56% 8344ms 7.59% std::_Rb_tree::_Alloc_node::operator() (inline) 508ms 0.46% 26.02% 8245ms 7.50% VertexMesh::GetCentroidOfElement 226ms 0.21% 26.22% 8160ms 7.42% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.22% 8041ms 7.31% std::_Rb_tree::_M_drop_node (inline) 17ms 0.015% 26.24% 8022ms 7.29% MutableVertexMesh::RemoveDeletedNodesAndElements 3192ms 2.90% 29.14% 7870ms 7.16% __GI___libc_malloc 235ms 0.21% 29.36% 7836ms 7.13% std::__new_allocator::deallocate (inline) 0 0% 29.36% 7803ms 7.10% std::allocator_traits::deallocate (inline) 0 0% 29.36% 7709ms 7.01% std::_Rb_tree::_M_put_node (inline) 3003ms 2.73% 32.09% 7674ms 6.98% __GI___libc_free 0 0% 32.09% 7664ms 6.97% std::set::~set (inline) 442ms 0.4% 32.49% 7453ms 6.78% std::map::operator[] (partial-inline) 1453ms 1.32% 33.81% 7166ms 6.52% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 162ms 0.15% 33.96% 6992ms 6.36% std::_Rb_tree::_Rb_tree (partial-inline) 643ms 0.58% 34.54% 6588ms 5.99% std::_Rb_tree::_M_copy (inline) 6546ms 5.95% 40.49% 6546ms 5.95% __strcmp_avx2 8ms 0.0073% 40.50% 6498ms 5.91% std::set::set (inline) 108ms 0.098% 40.60% 6280ms 5.71% SimpleWntCellCycleModel::GetWntLevel 6138ms 5.58% 46.18% 6138ms 5.58% boost::numeric::ublas::c_vector::operator() 130ms 0.12% 46.30% 6074ms 5.52% WntConcentration::GetWntLevel 2469ms 2.25% 48.54% 5902ms 5.37% std::_Rb_tree::_M_lower_bound (inline) 2723ms 2.48% 51.02% 5693ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 764ms 0.69% 51.72% 5649ms 5.14% std::_Rb_tree::_M_clone_node (inline) 29ms 0.026% 51.74% 5630ms 5.12% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.74% 5465ms 4.97% std::set::insert (inline) 32ms 0.029% 51.77% 5440ms 4.95% EdgeHelper::RemoveDeletedEdges 22ms 0.02% 51.79% 5157ms 4.69% EdgeHelper::UpdateEdgesMapKey 232ms 0.21% 52.00% 4998ms 4.54% MutableElement::ResetIndex 1554ms 1.41% 53.41% 4833ms 4.39% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.41% 4743ms 4.31% std::_Rb_tree::lower_bound (inline) 0 0% 53.41% 4743ms 4.31% std::map::lower_bound (inline) 1ms 0.00091% 53.42% 4690ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 4372ms 3.98% 57.39% 4667ms 4.24% _int_free 565ms 0.51% 57.91% 4576ms 4.16% std::_Rb_tree::_M_insert_ (inline) 48ms 0.044% 57.95% 4465ms 4.06% std::set_intersection (inline) 265ms 0.24% 58.19% 4417ms 4.02% std::__set_intersection 117ms 0.11% 58.30% 4043ms 3.68% AbstractCellPopulation::GetCellUsingLocationIndex 48ms 0.044% 58.34% 4036ms 3.67% Cell::GetCellProliferativeType 3945ms 3.59% 61.93% 3945ms 3.59% boost::numeric::ublas::same_impl_ex 62ms 0.056% 61.98% 3770ms 3.43% AbstractCellProperty::IsType (inline) 9ms 0.0082% 61.99% 3574ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 888ms 0.81% 62.80% 3381ms 3.07% AbstractElement::GetNodeLocation 0 0% 62.80% 3268ms 2.97% std::insert_iterator::operator= (inline) 47ms 0.043% 62.84% 3239ms 2.95% std::_Rb_tree::erase 2192ms 1.99% 64.84% 3183ms 2.89% _int_malloc 29ms 0.026% 64.86% 3173ms 2.89% Cell::SetCellProliferativeType 2891ms 2.63% 67.49% 2891ms 2.63% std::_Rb_tree::_S_right (inline) 5ms 0.0045% 67.49% 2866ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 617ms 0.56% 68.06% 2793ms 2.54% boost::numeric::ublas::vector_binary::size (inline) 699ms 0.64% 68.69% 2742ms 2.49% AbstractCellProperty::IsSame 380ms 0.35% 69.04% 2706ms 2.46% std::_Rb_tree_const_iterator::operator++ (inline) 37ms 0.034% 69.07% 2673ms 2.43% CellPropertyCollection::HasProperty 1ms 0.00091% 69.07% 2599ms 2.36% std::_Rb_tree::_M_insert_unique 0 0% 69.07% 2584ms 2.35% Cell::HasCellProperty (inline) 236ms 0.21% 69.29% 2562ms 2.33% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.29% 2528ms 2.30% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.29% 2463ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.29% 2395ms 2.18% boost::numeric::ublas::c_vector::operator-= (inline) 18ms 0.016% 69.30% 2384ms 2.17% Cell::GetCellData 114ms 0.1% 69.41% 2291ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0018% 69.41% 2278ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 239ms 0.22% 69.63% 2273ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 1517ms 1.38% 71.00% 2234ms 2.03% std::_Rb_tree::equal_range (inline) 97ms 0.088% 71.09% 2220ms 2.02% VertexMesh::GetVolumeOfElement 38ms 0.035% 71.13% 2216ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 2180ms 1.98% 73.11% 2180ms 1.98% std::_Rb_tree_increment 506ms 0.46% 73.57% 2043ms 1.86% std::type_info::operator== (inline) 0 0% 73.57% 2018ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.57% 2003ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 4ms 0.0036% 73.57% 1910ms 1.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.57% 1910ms 1.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 73ms 0.066% 73.64% 1842ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00091% 73.64% 1809ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 34ms 0.031% 73.67% 1746ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 28ms 0.025% 73.70% 1708ms 1.55% VertexMesh::GetSurfaceAreaOfElement 46ms 0.042% 73.74% 1689ms 1.54% Node::RemoveElement 22ms 0.02% 73.76% 1655ms 1.50% std::set::erase (inline) 166ms 0.15% 73.91% 1534ms 1.39% CellPropertyCollection::AddProperty 98ms 0.089% 74.00% 1522ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 25ms 0.023% 74.02% 1506ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 124ms 0.11% 74.14% 1471ms 1.34% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.14% 1394ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.14% 1313ms 1.19% tcache_get (inline) 1313ms 1.19% 75.33% 1313ms 1.19% tcache_get_n (inline) 2ms 0.0018% 75.33% 1308ms 1.19% OffLatticeSimulation::ApplyBoundaries 68ms 0.062% 75.39% 1306ms 1.19% std::less::operator() (inline) 998ms 0.91% 76.30% 1238ms 1.13% std::operator< (inline) 0 0% 76.30% 1227ms 1.12% boost::numeric::ublas::norm_2 (inline) 537ms 0.49% 76.79% 1212ms 1.10% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1202ms 1.09% 77.88% 1202ms 1.09% Node::rGetLocation 0 0% 77.88% 1200ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 20ms 0.018% 77.90% 1161ms 1.06% CellPropertyRegistry::Get 85ms 0.077% 77.98% 1161ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 112ms 0.1% 78.08% 1140ms 1.04% std::_Rb_tree::find (inline) 1125ms 1.02% 79.10% 1125ms 1.02% std::_Rb_tree_insert_and_rebalance 14ms 0.013% 79.11% 1115ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.11% 1103ms 1.00% std::_Rb_tree::clear (inline) 0 0% 79.11% 1088ms 0.99% std::map::clear (inline) 1078ms 0.98% 80.10% 1078ms 0.98% [libchaste_cell_based.so] 10ms 0.0091% 80.10% 1060ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 483ms 0.44% 80.54% 1024ms 0.93% Edge::GetMapIndex 1024ms 0.93% 81.47% 1024ms 0.93% [libchaste_mesh.so] 120ms 0.11% 81.58% 1013ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.58% 1013ms 0.92% boost::shared_ptr::~shared_ptr (inline) 1000ms 0.91% 82.49% 1000ms 0.91% std::vector::size (inline) 0 0% 82.49% 935ms 0.85% std::map::find (inline) 0 0% 82.49% 920ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 82.50% 920ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 78ms 0.071% 82.57% 913ms 0.83% std::swap_ranges (inline) 25ms 0.023% 82.59% 908ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 151ms 0.14% 82.73% 875ms 0.8% boost::numeric::ublas::detail::equals 858ms 0.78% 83.51% 865ms 0.79% boost::detail::sp_counted_base::release 0 0% 83.51% 862ms 0.78% VertexMeshWriter::MakeVtkMesh 131ms 0.12% 83.63% 837ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 836ms 0.76% 84.39% 836ms 0.76% std::swap (inline) 0 0% 84.39% 835ms 0.76% std::iter_swap (inline) 109ms 0.099% 84.49% 799ms 0.73% MutableElement::GetNodeLocalIndex 165ms 0.15% 84.64% 780ms 0.71% boost::shared_ptr::shared_ptr (inline) 14ms 0.013% 84.65% 771ms 0.7% MutableElement::RegisterWithEdges (inline) 28ms 0.025% 84.68% 766ms 0.7% Edge::AddElement 765ms 0.7% 85.37% 765ms 0.7% Node::GetIndex 447ms 0.41% 85.78% 757ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 17ms 0.015% 85.79% 736ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 121ms 0.11% 85.90% 732ms 0.67% std::__new_allocator::construct (inline) 0 0% 85.90% 732ms 0.67% std::allocator_traits::construct (inline) 0 0% 85.90% 724ms 0.66% std::_Vector_base::_M_allocate (inline) 93ms 0.085% 85.99% 719ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 85.99% 686ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.99% 683ms 0.62% boost::numeric::ublas::norm_inf (inline) 337ms 0.31% 86.30% 683ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.30% 675ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 30ms 0.027% 86.32% 675ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.32% 657ms 0.6% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.00091% 86.32% 636ms 0.58% vtkPolygon::New 0 0% 86.32% 635ms 0.58% vtkPolygon::vtkPolygon 632ms 0.57% 86.90% 632ms 0.57% boost::shared_ptr::operator-> (inline) 10ms 0.0091% 86.91% 630ms 0.57% std::vector::_M_default_append (inline) 31ms 0.028% 86.94% 616ms 0.56% MutableElement::RegisterWithNodes (inline) 591ms 0.54% 87.47% 615ms 0.56% boost::detail::shared_count::shared_count (inline) 610ms 0.55% 88.03% 610ms 0.55% [libstdc++.so.6.0.33] 31ms 0.028% 88.06% 590ms 0.54% Node::AddElement 0 0% 88.06% 588ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 561ms 0.51% 88.57% 561ms 0.51% operator delete