File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95449ms, 88.33% of 108058ms total Dropped 1092 nodes (cum <= 540.29ms) flat flat% sum% cum cum% 0 0% 0% 107586ms 99.56% __libc_start_call_main 0 0% 0% 107586ms 99.56% __libc_start_main_impl 0 0% 0% 107586ms 99.56% _start 0 0% 0% 107567ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107567ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107567ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107567ms 99.55% main 0 0% 0% 107529ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107529ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107529ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00093% 0.00093% 107522ms 99.50% AbstractCellBasedSimulation::Solve 11ms 0.01% 0.011% 55794ms 51.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.024% 52660ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 130ms 0.12% 0.14% 51149ms 47.33% AbstractNumericalMethod::ComputeForcesIncludingDamping 355ms 0.33% 0.47% 39533ms 36.58% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.47% 38692ms 35.81% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.48% 23920ms 22.14% VertexBasedCellPopulation::Update 0 0% 0.48% 23798ms 22.02% MutableVertexMesh::ReMesh 14298ms 13.23% 13.71% 22805ms 21.10% Cylindrical2dVertexMesh::GetVectorFromAtoB 106ms 0.098% 13.81% 17563ms 16.25% Cell::ReadyToDivide 76ms 0.07% 13.88% 16291ms 15.08% AbstractPhaseBasedCellCycleModel::ReadyToDivide 328ms 0.3% 14.18% 14670ms 13.58% NagaiHondaForce::GetAdhesionParameter 407ms 0.38% 14.56% 14406ms 13.33% boost::numeric::ublas::c_vector::c_vector (partial-inline) 101ms 0.093% 14.65% 13868ms 12.83% SimpleWntCellCycleModel::UpdateCellCyclePhase 139ms 0.13% 14.78% 13726ms 12.70% CellPropertyCollection::GetPropertiesType (inline) 416ms 0.38% 15.17% 12928ms 11.96% boost::numeric::ublas::vector_assign (inline) 114ms 0.11% 15.27% 12062ms 11.16% MutableVertexMesh::CheckForIntersections 3318ms 3.07% 18.34% 11542ms 10.68% __dynamic_cast 71ms 0.066% 18.41% 11415ms 10.56% AbstractCellProperty::IsSubType (inline) 78ms 0.072% 18.48% 11100ms 10.27% VertexBasedCellPopulation::GetDampingConstant 83ms 0.077% 18.56% 10593ms 9.80% AbstractTargetAreaModifier::UpdateTargetAreas 45ms 0.042% 18.60% 10488ms 9.71% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 33ms 0.031% 18.63% 10257ms 9.49% AbstractCellBasedSimulation::DoCellBirth 1248ms 1.15% 19.78% 10083ms 9.33% std::__new_allocator::allocate (inline) 2792ms 2.58% 22.37% 9629ms 8.91% boost::numeric::ublas::indexing_vector_assign 0 0% 22.37% 9568ms 8.85% std::allocator_traits::allocate (inline) 0 0% 22.37% 9557ms 8.84% std::_Rb_tree::_M_create_node (inline) 909ms 0.84% 23.21% 8967ms 8.30% operator new 0 0% 23.21% 8937ms 8.27% std::_Rb_tree::_M_get_node (inline) 767ms 0.71% 23.92% 8936ms 8.27% VertexMesh::ElementIncludesPoint 1328ms 1.23% 25.15% 8836ms 8.18% std::_Rb_tree::_M_erase 344ms 0.32% 25.47% 8754ms 8.10% VertexMesh::GetNextEdgeGradientOfElementAtNode 29ms 0.027% 25.49% 8637ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 79ms 0.073% 25.56% 8485ms 7.85% Cell::GetMutationState 0 0% 25.56% 8362ms 7.74% std::_Rb_tree::_Alloc_node::operator() (inline) 479ms 0.44% 26.01% 8199ms 7.59% VertexMesh::GetCentroidOfElement 223ms 0.21% 26.21% 8053ms 7.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.21% 7949ms 7.36% std::_Rb_tree::_M_drop_node (inline) 3159ms 2.92% 29.14% 7883ms 7.30% __GI___libc_malloc 224ms 0.21% 29.35% 7733ms 7.16% std::__new_allocator::deallocate (inline) 0 0% 29.35% 7701ms 7.13% std::allocator_traits::deallocate (inline) 0 0% 29.35% 7629ms 7.06% std::_Rb_tree::_M_put_node (inline) 0 0% 29.35% 7627ms 7.06% std::set::~set (inline) 2942ms 2.72% 32.07% 7620ms 7.05% __GI___libc_free 12ms 0.011% 32.08% 7368ms 6.82% MutableVertexMesh::RemoveDeletedNodesAndElements 496ms 0.46% 32.54% 7256ms 6.71% std::map::operator[] (partial-inline) 1242ms 1.15% 33.69% 7124ms 6.59% AbstractMesh::GetDistanceBetweenNodes 145ms 0.13% 33.82% 6880ms 6.37% std::_Rb_tree::_Rb_tree (partial-inline) 6699ms 6.20% 40.02% 6699ms 6.20% __strcmp_avx2 649ms 0.6% 40.62% 6502ms 6.02% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 40.63% 6464ms 5.98% std::set::set (inline) 120ms 0.11% 40.75% 6298ms 5.83% SimpleWntCellCycleModel::GetWntLevel 6246ms 5.78% 46.53% 6246ms 5.78% boost::numeric::ublas::c_vector::operator() 144ms 0.13% 46.66% 6043ms 5.59% WntConcentration::GetWntLevel 2670ms 2.47% 49.13% 5739ms 5.31% __cxxabiv1::__si_class_type_info::__do_dyncast 2397ms 2.22% 51.35% 5591ms 5.17% std::_Rb_tree::_M_lower_bound (inline) 756ms 0.7% 52.05% 5571ms 5.16% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.05% 5403ms 5.00% std::set::insert (inline) 36ms 0.033% 52.08% 5190ms 4.80% MutableVertexMesh::RemoveDeletedNodes 36ms 0.033% 52.11% 5029ms 4.65% EdgeHelper::RemoveDeletedEdges 1517ms 1.40% 53.52% 4929ms 4.56% boost::numeric::ublas::c_vector::operator[] (inline) 34ms 0.031% 53.55% 4788ms 4.43% EdgeHelper::UpdateEdgesMapKey 4340ms 4.02% 57.57% 4673ms 4.32% _int_free 212ms 0.2% 57.76% 4604ms 4.26% MutableElement::ResetIndex 526ms 0.49% 58.25% 4570ms 4.23% std::_Rb_tree::_M_insert_ (inline) 65ms 0.06% 58.31% 4558ms 4.22% std::set_intersection (inline) 0 0% 58.31% 4539ms 4.20% std::_Rb_tree::lower_bound (inline) 0 0% 58.31% 4539ms 4.20% std::map::lower_bound (inline) 1ms 0.00093% 58.31% 4508ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 289ms 0.27% 58.58% 4493ms 4.16% std::__set_intersection 37ms 0.034% 58.61% 4003ms 3.70% Cell::GetCellProliferativeType 3961ms 3.67% 62.28% 3961ms 3.67% boost::numeric::ublas::same_impl_ex 87ms 0.081% 62.36% 3909ms 3.62% AbstractCellPopulation::GetCellUsingLocationIndex 62ms 0.057% 62.42% 3803ms 3.52% AbstractCellProperty::IsType (inline) 4ms 0.0037% 62.42% 3498ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.42% 3293ms 3.05% std::insert_iterator::operator= (inline) 41ms 0.038% 62.46% 3287ms 3.04% Cell::SetCellProliferativeType 778ms 0.72% 63.18% 3118ms 2.89% AbstractElement::GetNodeLocation 2186ms 2.02% 65.20% 3111ms 2.88% _int_malloc 6ms 0.0056% 65.21% 2892ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 38ms 0.035% 65.24% 2886ms 2.67% std::_Rb_tree::erase 616ms 0.57% 65.81% 2759ms 2.55% boost::numeric::ublas::vector_binary::size (inline) 722ms 0.67% 66.48% 2735ms 2.53% AbstractCellProperty::IsSame 428ms 0.4% 66.88% 2691ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 38ms 0.035% 66.91% 2652ms 2.45% CellPropertyCollection::HasProperty 2633ms 2.44% 69.35% 2633ms 2.44% std::_Rb_tree::_S_right (inline) 241ms 0.22% 69.57% 2553ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.57% 2552ms 2.36% Cell::HasCellProperty (inline) 0 0% 69.57% 2517ms 2.33% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0019% 69.57% 2511ms 2.32% std::_Rb_tree::_M_insert_unique 18ms 0.017% 69.59% 2491ms 2.31% Cell::GetCellData 1ms 0.00093% 69.59% 2423ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.59% 2372ms 2.20% boost::numeric::ublas::c_vector::operator-= (inline) 106ms 0.098% 69.69% 2317ms 2.14% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 116ms 0.11% 69.79% 2186ms 2.02% VertexMesh::GetVolumeOfElement 227ms 0.21% 70.00% 2184ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.00093% 70.01% 2183ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 30ms 0.028% 70.03% 2175ms 2.01% std::_Rb_tree::_M_emplace_hint_unique 2075ms 1.92% 71.95% 2075ms 1.92% std::_Rb_tree_increment 449ms 0.42% 72.37% 2013ms 1.86% std::type_info::operator== (inline) 0 0% 72.37% 1977ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00093% 72.37% 1963ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00093% 72.37% 1935ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.37% 1935ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1280ms 1.18% 73.56% 1879ms 1.74% std::_Rb_tree::equal_range (inline) 52ms 0.048% 73.60% 1868ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.60% 1769ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.023% 73.63% 1695ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 17ms 0.016% 73.64% 1624ms 1.50% VertexMesh::GetSurfaceAreaOfElement 57ms 0.053% 73.70% 1538ms 1.42% Node::RemoveElement 163ms 0.15% 73.85% 1519ms 1.41% CellPropertyCollection::AddProperty 23ms 0.021% 73.87% 1497ms 1.39% std::set::erase (inline) 124ms 0.11% 73.98% 1496ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 27ms 0.025% 74.01% 1495ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 94ms 0.087% 74.09% 1480ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.09% 1447ms 1.34% tcache_get (inline) 1447ms 1.34% 75.43% 1447ms 1.34% tcache_get_n (inline) 0 0% 75.43% 1369ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.43% 1242ms 1.15% OffLatticeSimulation::ApplyBoundaries 0 0% 75.43% 1226ms 1.13% boost::numeric::ublas::norm_2 (inline) 515ms 0.48% 75.91% 1213ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 75.91% 1195ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 89ms 0.082% 75.99% 1183ms 1.09% std::_Rb_tree::_M_erase_aux (partial-inline) 60ms 0.056% 76.05% 1160ms 1.07% std::less::operator() (inline) 33ms 0.031% 76.08% 1142ms 1.06% CellPropertyRegistry::Get 1109ms 1.03% 77.10% 1109ms 1.03% std::_Rb_tree_insert_and_rebalance 1107ms 1.02% 78.13% 1107ms 1.02% [libchaste_cell_based.so] 1105ms 1.02% 79.15% 1105ms 1.02% Node::rGetLocation 896ms 0.83% 79.98% 1100ms 1.02% std::operator< (inline) 12ms 0.011% 79.99% 1056ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 104ms 0.096% 80.09% 1052ms 0.97% std::_Rb_tree::find (inline) 0 0% 80.09% 1009ms 0.93% std::_Rb_tree::clear (inline) 998ms 0.92% 81.01% 998ms 0.92% [libchaste_mesh.so] 128ms 0.12% 81.13% 998ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.13% 998ms 0.92% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.13% 983ms 0.91% std::map::clear (inline) 970ms 0.9% 82.03% 970ms 0.9% std::vector::size (inline) 6ms 0.0056% 82.03% 960ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 20ms 0.019% 82.05% 954ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 169ms 0.16% 82.21% 925ms 0.86% boost::numeric::ublas::detail::equals 0 0% 82.21% 901ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0093% 82.22% 901ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 383ms 0.35% 82.57% 896ms 0.83% Edge::GetMapIndex 72ms 0.067% 82.64% 891ms 0.82% std::swap_ranges (inline) 0 0% 82.64% 846ms 0.78% VertexMeshWriter::MakeVtkMesh 837ms 0.77% 83.41% 844ms 0.78% boost::detail::sp_counted_base::release 0 0% 83.41% 835ms 0.77% std::map::find (inline) 0 0% 83.41% 819ms 0.76% std::iter_swap (inline) 819ms 0.76% 84.17% 819ms 0.76% std::swap (inline) 118ms 0.11% 84.28% 787ms 0.73% MutableElement::GetNodeLocalIndex 103ms 0.095% 84.38% 787ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 24ms 0.022% 84.40% 754ms 0.7% MutableElement::RegisterWithEdges (inline) 22ms 0.02% 84.42% 741ms 0.69% Edge::AddElement 721ms 0.67% 85.09% 721ms 0.67% Node::GetIndex 14ms 0.013% 85.10% 714ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.10% 709ms 0.66% boost::numeric::ublas::norm_inf (inline) 371ms 0.34% 85.44% 709ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 105ms 0.097% 85.54% 700ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 131ms 0.12% 85.66% 694ms 0.64% boost::shared_ptr::shared_ptr (inline) 0 0% 85.66% 691ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.027% 85.69% 691ms 0.64% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.69% 688ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 421ms 0.39% 86.08% 686ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 122ms 0.11% 86.19% 669ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.19% 669ms 0.62% std::allocator_traits::construct (inline) 1ms 0.00093% 86.19% 627ms 0.58% std::_Vector_base::_M_allocate (inline) 0 0% 86.19% 620ms 0.57% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.19% 612ms 0.57% vtkPolygon::New 1ms 0.00093% 86.19% 612ms 0.57% vtkPolygon::vtkPolygon 0 0% 86.19% 586ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 583ms 0.54% 86.73% 583ms 0.54% [libstdc++.so.6.0.33] 31ms 0.029% 86.76% 579ms 0.54% MutableElement::RegisterWithNodes (inline) 572ms 0.53% 87.29% 572ms 0.53% boost::shared_ptr::operator-> (inline) 537ms 0.5% 87.79% 563ms 0.52% boost::detail::shared_count::shared_count (inline) 563ms 0.52% 88.31% 563ms 0.52% operator delete 26ms 0.024% 88.33% 542ms 0.5% Node::AddElement