File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 73705ms, 87.44% of 84291ms total Dropped 1098 nodes (cum <= 421.45ms) flat flat% sum% cum cum% 0 0% 0% 83982ms 99.63% __libc_start_call_main 0 0% 0% 83982ms 99.63% __libc_start_main_impl 0 0% 0% 83982ms 99.63% _start 0 0% 0% 83964ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 83964ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 83964ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 83964ms 99.61% main 0 0% 0% 83922ms 99.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 83922ms 99.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 83922ms 99.56% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0059% 0.0059% 83916ms 99.56% AbstractCellBasedSimulation::Solve 18ms 0.021% 0.027% 43652ms 51.79% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.011% 0.038% 41089ms 48.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 134ms 0.16% 0.2% 39935ms 47.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 212ms 0.25% 0.45% 30569ms 36.27% NagaiHondaForce::AddForceContribution 1ms 0.0012% 0.45% 29947ms 35.53% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0036% 0.45% 18363ms 21.79% VertexBasedCellPopulation::Update 0 0% 0.45% 18236ms 21.63% MutableVertexMesh::ReMesh 11387ms 13.51% 13.96% 18126ms 21.50% Cylindrical2dVertexMesh::GetVectorFromAtoB 70ms 0.083% 14.05% 13818ms 16.39% Cell::ReadyToDivide 65ms 0.077% 14.12% 12736ms 15.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 147ms 0.17% 14.30% 10941ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 266ms 0.32% 14.61% 10874ms 12.90% NagaiHondaForce::GetAdhesionParameter 386ms 0.46% 15.07% 10826ms 12.84% boost::numeric::ublas::c_vector::c_vector (partial-inline) 81ms 0.096% 15.17% 10800ms 12.81% CellPropertyCollection::GetPropertiesType (inline) 230ms 0.27% 15.44% 9645ms 11.44% boost::numeric::ublas::vector_assign (inline) 2633ms 3.12% 18.56% 9303ms 11.04% __dynamic_cast 32ms 0.038% 18.60% 9186ms 10.90% AbstractCellProperty::IsSubType (inline) 110ms 0.13% 18.73% 9168ms 10.88% MutableVertexMesh::CheckForIntersections 71ms 0.084% 18.82% 8908ms 10.57% VertexBasedCellPopulation::GetDampingConstant 66ms 0.078% 18.89% 8307ms 9.86% AbstractTargetAreaModifier::UpdateTargetAreas 24ms 0.028% 18.92% 8219ms 9.75% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.026% 18.95% 8000ms 9.49% AbstractCellBasedSimulation::DoCellBirth 972ms 1.15% 20.10% 7541ms 8.95% std::__new_allocator::allocate (inline) 312ms 0.37% 20.47% 7407ms 8.79% VertexMesh::GetNextEdgeGradientOfElementAtNode 2257ms 2.68% 23.15% 7404ms 8.78% boost::numeric::ublas::indexing_vector_assign 0 0% 23.15% 7169ms 8.51% std::_Rb_tree::_M_create_node (inline) 0 0% 23.15% 7135ms 8.46% std::allocator_traits::allocate (inline) 29ms 0.034% 23.18% 6764ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 915ms 1.09% 24.27% 6707ms 7.96% std::_Rb_tree::_M_erase 616ms 0.73% 25.00% 6692ms 7.94% VertexMesh::ElementIncludesPoint 55ms 0.065% 25.07% 6669ms 7.91% Cell::GetMutationState 609ms 0.72% 25.79% 6653ms 7.89% operator new 0 0% 25.79% 6580ms 7.81% std::_Rb_tree::_M_get_node (inline) 358ms 0.42% 26.21% 6371ms 7.56% VertexMesh::GetCentroidOfElement 0 0% 26.21% 6296ms 7.47% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.21% 6065ms 7.20% std::_Rb_tree::_M_drop_node (inline) 177ms 0.21% 26.42% 6056ms 7.18% std::_Rb_tree::~_Rb_tree (inline) 2257ms 2.68% 29.10% 5895ms 6.99% __GI___libc_malloc 168ms 0.2% 29.30% 5882ms 6.98% std::__new_allocator::deallocate (inline) 0 0% 29.30% 5866ms 6.96% std::allocator_traits::deallocate (inline) 0 0% 29.30% 5811ms 6.89% std::_Rb_tree::_M_put_node (inline) 1119ms 1.33% 30.63% 5782ms 6.86% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 415ms 0.49% 31.12% 5780ms 6.86% std::map::operator[] (partial-inline) 9ms 0.011% 31.13% 5776ms 6.85% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 31.13% 5725ms 6.79% std::set::~set (inline) 1834ms 2.18% 33.31% 5549ms 6.58% __GI___libc_free 166ms 0.2% 33.50% 5535ms 6.57% std::_Rb_tree::_Rb_tree (partial-inline) 5417ms 6.43% 39.93% 5417ms 6.43% __strcmp_evex 27ms 0.032% 39.96% 5183ms 6.15% std::set::set (inline) 662ms 0.79% 40.75% 5156ms 6.12% std::_Rb_tree::_M_copy (inline) 96ms 0.11% 40.86% 4858ms 5.76% SimpleWntCellCycleModel::GetWntLevel 4766ms 5.65% 46.52% 4766ms 5.65% boost::numeric::ublas::c_vector::operator() 113ms 0.13% 46.65% 4700ms 5.58% WntConcentration::GetWntLevel 1874ms 2.22% 48.87% 4534ms 5.38% std::_Rb_tree::_M_lower_bound (inline) 576ms 0.68% 49.56% 4301ms 5.10% std::_Rb_tree::_M_clone_node (inline) 2284ms 2.71% 52.27% 4165ms 4.94% __cxxabiv1::__si_class_type_info::__do_dyncast 1519ms 1.80% 54.07% 4112ms 4.88% boost::numeric::ublas::c_vector::operator[] (inline) 13ms 0.015% 54.08% 3991ms 4.73% MutableVertexMesh::RemoveDeletedNodes 0 0% 54.08% 3960ms 4.70% std::set::insert (inline) 24ms 0.028% 54.11% 3848ms 4.57% EdgeHelper::RemoveDeletedEdges 3363ms 3.99% 58.10% 3693ms 4.38% _int_free 0 0% 58.10% 3688ms 4.38% std::_Rb_tree::lower_bound (inline) 0 0% 58.10% 3688ms 4.38% std::map::lower_bound (inline) 30ms 0.036% 58.14% 3625ms 4.30% EdgeHelper::UpdateEdgesMapKey 145ms 0.17% 58.31% 3585ms 4.25% MutableElement::ResetIndex 0 0% 58.31% 3571ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 113ms 0.13% 58.44% 3386ms 4.02% AbstractCellPopulation::GetCellUsingLocationIndex 350ms 0.42% 58.86% 3305ms 3.92% std::_Rb_tree::_M_insert_ (inline) 81ms 0.096% 58.95% 3220ms 3.82% std::set_intersection (inline) 22ms 0.026% 58.98% 3168ms 3.76% Cell::GetCellProliferativeType 151ms 0.18% 59.16% 3139ms 3.72% std::__set_intersection 39ms 0.046% 59.21% 3124ms 3.71% AbstractCellProperty::IsType (inline) 2919ms 3.46% 62.67% 2919ms 3.46% boost::numeric::ublas::same_impl_ex 5ms 0.0059% 62.67% 2690ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 36ms 0.043% 62.72% 2462ms 2.92% Cell::SetCellProliferativeType 1674ms 1.99% 64.70% 2426ms 2.88% _int_malloc 0 0% 64.70% 2424ms 2.88% std::insert_iterator::operator= (inline) 668ms 0.79% 65.50% 2365ms 2.81% AbstractElement::GetNodeLocation 59ms 0.07% 65.57% 2276ms 2.70% std::_Rb_tree::erase 638ms 0.76% 66.32% 2272ms 2.70% AbstractCellProperty::IsSame 22ms 0.026% 66.35% 2236ms 2.65% CellPropertyCollection::HasProperty 2196ms 2.61% 68.95% 2196ms 2.61% std::_Rb_tree::_S_right (inline) 0 0% 68.95% 2170ms 2.57% Cell::HasCellProperty (inline) 3ms 0.0036% 68.96% 2102ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.96% 2076ms 2.46% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.96% 2062ms 2.45% boost::numeric::ublas::c_vector::operator-= (inline) 174ms 0.21% 69.16% 2027ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.16% 1979ms 2.35% AbstractCellPopulation::WriteResultsToFiles 465ms 0.55% 69.72% 1970ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 18ms 0.021% 69.74% 1966ms 2.33% Cell::GetCellData 199ms 0.24% 69.97% 1955ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0012% 69.97% 1858ms 2.20% std::_Rb_tree::_M_insert_unique (inline) 57ms 0.068% 70.04% 1775ms 2.11% VertexMesh::GetVolumeOfElement 35ms 0.042% 70.08% 1717ms 2.04% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0036% 70.09% 1670ms 1.98% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.09% 1670ms 1.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 34ms 0.04% 70.13% 1649ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 367ms 0.44% 70.56% 1634ms 1.94% std::type_info::operator== (inline) 0 0% 70.56% 1620ms 1.92% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0012% 70.56% 1615ms 1.92% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0036% 70.57% 1610ms 1.91% AbstractCellPopulation::Iterator::operator++ (inline) 117ms 0.14% 70.71% 1596ms 1.89% AbstractCellPopulation::Iterator::IsRealCell (inline) 1575ms 1.87% 72.57% 1575ms 1.87% std::_Rb_tree_increment 1ms 0.0012% 72.58% 1455ms 1.73% VertexMeshWriter::WriteVtkUsingMesh 1000ms 1.19% 73.76% 1446ms 1.72% std::_Rb_tree::equal_range (inline) 45ms 0.053% 73.82% 1445ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 24ms 0.028% 73.84% 1255ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.034% 73.88% 1189ms 1.41% VertexMesh::GetSurfaceAreaOfElement 38ms 0.045% 73.92% 1130ms 1.34% Node::RemoveElement 0 0% 73.92% 1125ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 17ms 0.02% 73.94% 1103ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 65ms 0.077% 74.02% 1100ms 1.31% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 6ms 0.0071% 74.03% 1095ms 1.30% std::set::erase (inline) 41ms 0.049% 74.08% 1085ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.08% 1059ms 1.26% tcache_get (inline) 1059ms 1.26% 75.33% 1059ms 1.26% tcache_get_n (inline) 0 0% 75.33% 1055ms 1.25% boost::numeric::ublas::norm_2 (inline) 103ms 0.12% 75.46% 1046ms 1.24% CellPropertyCollection::AddProperty 483ms 0.57% 76.03% 1046ms 1.24% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.03% 1033ms 1.23% OffLatticeSimulation::ApplyBoundaries 1003ms 1.19% 77.22% 1003ms 1.19% [libchaste_cell_based.so] 42ms 0.05% 77.27% 959ms 1.14% std::less::operator() (inline) 25ms 0.03% 77.30% 952ms 1.13% CellPropertyRegistry::Get 62ms 0.074% 77.37% 920ms 1.09% std::_Rb_tree::_M_erase_aux (partial-inline) 727ms 0.86% 78.23% 917ms 1.09% std::operator< (inline) 0 0% 78.23% 873ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 10ms 0.012% 78.25% 863ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.25% 860ms 1.02% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0095% 78.26% 860ms 1.02% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.089% 78.34% 854ms 1.01% std::_Rb_tree::find (inline) 68ms 0.081% 78.42% 852ms 1.01% std::swap_ranges (inline) 1ms 0.0012% 78.43% 845ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 78.43% 834ms 0.99% std::_Rb_tree::clear (inline) 820ms 0.97% 79.40% 820ms 0.97% std::_Rb_tree_insert_and_rebalance 0 0% 79.40% 818ms 0.97% std::map::clear (inline) 118ms 0.14% 79.54% 794ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 79.54% 794ms 0.94% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.54% 784ms 0.93% std::iter_swap (inline) 784ms 0.93% 80.47% 784ms 0.93% std::swap (inline) 13ms 0.015% 80.48% 774ms 0.92% boost::numeric::ublas::detail::expression_type_check (inline) 124ms 0.15% 80.63% 746ms 0.89% boost::numeric::ublas::detail::equals 743ms 0.88% 81.51% 743ms 0.88% Node::rGetLocation 1ms 0.0012% 81.51% 695ms 0.82% VertexMeshWriter::MakeVtkMesh 0 0% 81.51% 695ms 0.82% std::map::find (inline) 631ms 0.75% 82.26% 651ms 0.77% boost::detail::sp_counted_base::release 199ms 0.24% 82.50% 649ms 0.77% std::__new_allocator::construct (inline) 0 0% 82.50% 649ms 0.77% std::allocator_traits::construct (inline) 86ms 0.1% 82.60% 645ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 631ms 0.75% 83.35% 631ms 0.75% std::vector::size (inline) 0 0% 83.35% 615ms 0.73% boost::numeric::ublas::norm_inf (inline) 311ms 0.37% 83.72% 615ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 596ms 0.71% 84.43% 596ms 0.71% [libchaste_mesh.so] 324ms 0.38% 84.81% 594ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 155ms 0.18% 84.99% 589ms 0.7% boost::shared_ptr::shared_ptr (inline) 0 0% 84.99% 589ms 0.7% std::_Rb_tree::_M_construct_node (inline) 14ms 0.017% 85.01% 587ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 85.01% 585ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 22ms 0.026% 85.04% 584ms 0.69% Edge::AddElement 296ms 0.35% 85.39% 560ms 0.66% Edge::GetMapIndex 2ms 0.0024% 85.39% 554ms 0.66% std::_Vector_base::_M_allocate (inline) 0 0% 85.39% 544ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 537ms 0.64% 86.03% 537ms 0.64% [libstdc++.so.6.0.33] 17ms 0.02% 86.05% 528ms 0.63% AbstractNumericalMethod::DetectStepSizeExceptions 128ms 0.15% 86.20% 517ms 0.61% MutableElement::GetNodeLocalIndex 89ms 0.11% 86.30% 511ms 0.61% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.30% 494ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 9ms 0.011% 86.32% 494ms 0.59% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.32% 488ms 0.58% vtkPolygon::New 0 0% 86.32% 488ms 0.58% vtkPolygon::vtkPolygon 471ms 0.56% 86.87% 471ms 0.56% Node::GetIndex 25ms 0.03% 86.90% 470ms 0.56% MutableElement::RegisterWithNodes (inline) 5ms 0.0059% 86.91% 458ms 0.54% std::vector::_M_default_append (inline) 23ms 0.027% 86.94% 441ms 0.52% Node::AddElement 407ms 0.48% 87.42% 434ms 0.51% boost::detail::shared_count::shared_count (inline) 18ms 0.021% 87.44% 424ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.44% 424ms 0.5% boost::numeric::ublas::vector::vector (inline)