File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 86402ms, 88.54% of 97585ms total Dropped 1103 nodes (cum <= 487.93ms) flat flat% sum% cum cum% 0 0% 0% 97169ms 99.57% __libc_start_call_main 0 0% 0% 97169ms 99.57% __libc_start_main_impl 0 0% 0% 97169ms 99.57% _start 0 0% 0% 97149ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 97149ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 97149ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 97149ms 99.55% main 0 0% 0% 97111ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 97111ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 97111ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 97103ms 99.51% AbstractCellBasedSimulation::Solve 23ms 0.024% 0.024% 45199ms 46.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.014% 0.038% 42590ms 43.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 130ms 0.13% 0.17% 41523ms 42.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 3ms 0.0031% 0.17% 38880ms 39.84% AbstractCellBasedSimulation::UpdateCellPopulation 471ms 0.48% 0.66% 29982ms 30.72% NagaiHondaForce::AddForceContribution 4ms 0.0041% 0.66% 24338ms 24.94% VertexBasedCellPopulation::Update 0 0% 0.66% 24204ms 24.80% MutableVertexMesh::ReMesh 14593ms 14.95% 15.62% 22908ms 23.47% Cylindrical2dVertexMesh::GetVectorFromAtoB 87ms 0.089% 15.70% 17415ms 17.85% Cell::ReadyToDivide 38ms 0.039% 15.74% 16254ms 16.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 156ms 0.16% 15.90% 14041ms 14.39% CellPropertyCollection::GetPropertiesType (inline) 409ms 0.42% 16.32% 13991ms 14.34% boost::numeric::ublas::c_vector::c_vector (partial-inline) 128ms 0.13% 16.45% 13864ms 14.21% SimpleWntCellCycleModel::UpdateCellCyclePhase 444ms 0.45% 16.91% 12440ms 12.75% boost::numeric::ublas::vector_assign (inline) 127ms 0.13% 17.04% 12132ms 12.43% MutableVertexMesh::CheckForIntersections 3573ms 3.66% 20.70% 11596ms 11.88% __dynamic_cast 128ms 0.13% 20.83% 11526ms 11.81% AbstractCellProperty::IsSubType (inline) 251ms 0.26% 21.09% 11034ms 11.31% VertexBasedCellPopulation::GetDampingConstant 86ms 0.088% 21.18% 10519ms 10.78% AbstractTargetAreaModifier::UpdateTargetAreas 61ms 0.063% 21.24% 10403ms 10.66% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.032% 21.27% 10220ms 10.47% AbstractCellBasedSimulation::DoCellBirth 2579ms 2.64% 23.91% 9391ms 9.62% boost::numeric::ublas::indexing_vector_assign 810ms 0.83% 24.74% 9077ms 9.30% VertexMesh::ElementIncludesPoint 84ms 0.086% 24.83% 9068ms 9.29% Cell::GetMutationState 464ms 0.48% 25.31% 8899ms 9.12% VertexMesh::GetNextEdgeGradientOfElementAtNode 23ms 0.024% 25.33% 8647ms 8.86% VertexBasedCellPopulation::GetLocationOfCellCentre 473ms 0.48% 25.81% 8056ms 8.26% VertexMesh::GetCentroidOfElement 10ms 0.01% 25.82% 7628ms 7.82% MutableVertexMesh::RemoveDeletedNodesAndElements 459ms 0.47% 26.29% 7520ms 7.71% std::map::operator[] (partial-inline) 1412ms 1.45% 27.74% 7246ms 7.43% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 6337ms 6.49% 34.23% 6337ms 6.49% __strcmp_avx2 92ms 0.094% 34.33% 6329ms 6.49% SimpleWntCellCycleModel::GetWntLevel 138ms 0.14% 34.47% 6156ms 6.31% WntConcentration::GetWntLevel 6133ms 6.28% 40.76% 6133ms 6.28% boost::numeric::ublas::c_vector::operator() 2556ms 2.62% 43.37% 6107ms 6.26% std::_Rb_tree::_M_lower_bound (inline) 2666ms 2.73% 46.11% 5640ms 5.78% __cxxabiv1::__si_class_type_info::__do_dyncast 130ms 0.13% 46.24% 5486ms 5.62% NagaiHondaForce::GetAdhesionParameter 24ms 0.025% 46.26% 5394ms 5.53% MutableVertexMesh::RemoveDeletedNodes 44ms 0.045% 46.31% 5242ms 5.37% EdgeHelper::RemoveDeletedEdges 31ms 0.032% 46.34% 4964ms 5.09% EdgeHelper::UpdateEdgesMapKey 0 0% 46.34% 4858ms 4.98% std::_Rb_tree::lower_bound (inline) 0 0% 46.34% 4858ms 4.98% std::map::lower_bound (inline) 412ms 0.42% 46.76% 4853ms 4.97% std::__new_allocator::allocate (inline) 1491ms 1.53% 48.29% 4832ms 4.95% boost::numeric::ublas::c_vector::operator[] (inline) 215ms 0.22% 48.51% 4723ms 4.84% MutableElement::ResetIndex 458ms 0.47% 48.98% 4634ms 4.75% operator new 0 0% 48.98% 4404ms 4.51% std::allocator_traits::allocate (inline) 0 0% 48.98% 4357ms 4.46% std::_Rb_tree::_M_create_node (inline) 0 0% 48.98% 4312ms 4.42% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 48.98% 4207ms 4.31% std::set::insert (inline) 103ms 0.11% 49.09% 4156ms 4.26% AbstractCellPopulation::GetCellUsingLocationIndex 1763ms 1.81% 50.89% 4061ms 4.16% __GI___libc_malloc 4005ms 4.10% 55.00% 4005ms 4.10% boost::numeric::ublas::same_impl_ex 39ms 0.04% 55.04% 3963ms 4.06% Cell::GetCellProliferativeType 0 0% 55.04% 3955ms 4.05% std::_Rb_tree::_M_get_node (inline) 20ms 0.02% 55.06% 3948ms 4.05% std::set_intersection (inline) 379ms 0.39% 55.45% 3928ms 4.03% std::__set_intersection 968ms 0.99% 56.44% 3752ms 3.84% std::_Rb_tree::_M_erase 498ms 0.51% 56.95% 3528ms 3.62% std::_Rb_tree::_M_insert_ (inline) 358ms 0.37% 57.32% 3490ms 3.58% std::_Rb_tree_const_iterator::operator++ (inline) 61ms 0.063% 57.38% 3482ms 3.57% AbstractCellProperty::IsType (inline) 4ms 0.0041% 57.38% 3404ms 3.49% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 57.38% 3380ms 3.46% std::_Rb_tree::_M_drop_node (inline) 1389ms 1.42% 58.81% 3353ms 3.44% __GI___libc_free 857ms 0.88% 59.68% 3333ms 3.42% AbstractElement::GetNodeLocation 56ms 0.057% 59.74% 3208ms 3.29% Cell::SetCellProliferativeType 0 0% 59.74% 3179ms 3.26% std::_Rb_tree::_Alloc_node::operator() (inline) 171ms 0.18% 59.92% 3150ms 3.23% std::__new_allocator::deallocate (inline) 0 0% 59.92% 3123ms 3.20% std::allocator_traits::deallocate (inline) 0 0% 59.92% 3061ms 3.14% std::_Rb_tree::_M_put_node (inline) 3018ms 3.09% 63.01% 3018ms 3.09% std::_Rb_tree::_S_right (inline) 37ms 0.038% 63.05% 3007ms 3.08% std::_Rb_tree::erase 2980ms 3.05% 66.10% 2980ms 3.05% std::_Rb_tree_increment 200ms 0.2% 66.31% 2906ms 2.98% std::_Rb_tree::~_Rb_tree (inline) 638ms 0.65% 66.96% 2785ms 2.85% boost::numeric::ublas::vector_binary::size (inline) 254ms 0.26% 67.22% 2580ms 2.64% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 67.22% 2559ms 2.62% std::set::~set (inline) 706ms 0.72% 67.94% 2535ms 2.60% AbstractCellProperty::IsSame 3ms 0.0031% 67.95% 2517ms 2.58% std::_Rb_tree::_M_insert_unique 0 0% 67.95% 2479ms 2.54% AbstractCellPopulation::WriteResultsToFiles 44ms 0.045% 67.99% 2478ms 2.54% CellPropertyCollection::HasProperty 0 0% 67.99% 2453ms 2.51% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 67.99% 2440ms 2.50% boost::numeric::ublas::c_vector::assign (inline) 17ms 0.017% 68.01% 2410ms 2.47% Cell::GetCellData 0 0% 68.01% 2369ms 2.43% Cell::HasCellProperty (inline) 126ms 0.13% 68.14% 2332ms 2.39% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.002% 68.14% 2298ms 2.35% AbstractCellPopulation::Iterator::operator++ (inline) 234ms 0.24% 68.38% 2286ms 2.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 90ms 0.092% 68.47% 2214ms 2.27% VertexMesh::GetVolumeOfElement 36ms 0.037% 68.51% 2154ms 2.21% std::_Rb_tree::_M_emplace_hint_unique 0 0% 68.51% 2110ms 2.16% std::insert_iterator::operator= (inline) 1377ms 1.41% 69.92% 2047ms 2.10% std::_Rb_tree::equal_range (inline) 0 0% 69.92% 2032ms 2.08% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.002% 69.92% 2021ms 2.07% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1780ms 1.82% 71.75% 1954ms 2.00% _int_free 79ms 0.081% 71.83% 1891ms 1.94% MutableVertexMesh::CheckForSwapsFromShortEdges 3ms 0.0031% 71.83% 1829ms 1.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.83% 1829ms 1.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 466ms 0.48% 72.31% 1829ms 1.87% std::type_info::operator== (inline) 0 0% 72.31% 1826ms 1.87% VertexMeshWriter::WriteVtkUsingMesh 17ms 0.017% 72.32% 1788ms 1.83% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.025% 72.35% 1749ms 1.79% VertexMesh::GetSurfaceAreaOfElement 4ms 0.0041% 72.35% 1690ms 1.73% std::_Rb_tree::_M_insert_unique_ (inline) 15ms 0.015% 72.37% 1579ms 1.62% std::set::set (inline) 93ms 0.095% 72.46% 1576ms 1.62% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 27ms 0.028% 72.49% 1572ms 1.61% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.078% 72.57% 1561ms 1.60% std::_Rb_tree::_Rb_tree 48ms 0.049% 72.62% 1539ms 1.58% Node::RemoveElement 987ms 1.01% 73.63% 1512ms 1.55% _int_malloc 20ms 0.02% 73.65% 1507ms 1.54% std::set::erase (inline) 157ms 0.16% 73.81% 1498ms 1.54% CellPropertyCollection::AddProperty 127ms 0.13% 73.94% 1467ms 1.50% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 73.94% 1414ms 1.45% boost::numeric::ublas::vector_binary::operator() (inline) 115ms 0.12% 74.06% 1347ms 1.38% std::_Rb_tree::_M_copy (inline) 4ms 0.0041% 74.06% 1250ms 1.28% OffLatticeSimulation::ApplyBoundaries 503ms 0.52% 74.58% 1229ms 1.26% std::_Rb_tree::_M_clone_node (inline) 1221ms 1.25% 75.83% 1221ms 1.25% Node::rGetLocation 0 0% 75.83% 1198ms 1.23% boost::numeric::ublas::norm_2 (inline) 63ms 0.065% 75.89% 1196ms 1.23% std::less::operator() (inline) 527ms 0.54% 76.43% 1190ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 79ms 0.081% 76.52% 1182ms 1.21% std::_Rb_tree::find (inline) 0 0% 76.52% 1178ms 1.21% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1166ms 1.19% 77.71% 1166ms 1.19% std::_Rb_tree_insert_and_rebalance 74ms 0.076% 77.79% 1142ms 1.17% std::_Rb_tree::_M_erase_aux (partial-inline) 902ms 0.92% 78.71% 1133ms 1.16% std::operator< (inline) 14ms 0.014% 78.73% 1065ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.73% 1053ms 1.08% std::_Rb_tree::clear (inline) 0 0% 78.73% 1036ms 1.06% std::map::clear (inline) 997ms 1.02% 79.75% 997ms 1.02% std::vector::size (inline) 150ms 0.15% 79.90% 975ms 1% boost::detail::shared_count::~shared_count (inline) 0 0% 79.90% 975ms 1% boost::shared_ptr::~shared_ptr (inline) 23ms 0.024% 79.92% 974ms 1% CellPropertyRegistry::Get 416ms 0.43% 80.35% 973ms 1% Edge::GetMapIndex 972ms 1% 81.35% 972ms 1% [libchaste_mesh.so] 1ms 0.001% 81.35% 965ms 0.99% std::map::find (inline) 0 0% 81.35% 958ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.002% 81.35% 958ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 90ms 0.092% 81.44% 956ms 0.98% std::swap_ranges (inline) 920ms 0.94% 82.38% 920ms 0.94% [libchaste_cell_based.so] 0 0% 82.38% 866ms 0.89% std::iter_swap (inline) 866ms 0.89% 83.27% 866ms 0.89% std::swap (inline) 9ms 0.0092% 83.28% 862ms 0.88% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.001% 83.28% 852ms 0.87% VertexMeshWriter::MakeVtkMesh 18ms 0.018% 83.30% 833ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 805ms 0.82% 84.13% 810ms 0.83% boost::detail::sp_counted_base::release 140ms 0.14% 84.27% 806ms 0.83% boost::numeric::ublas::detail::equals 180ms 0.18% 84.45% 798ms 0.82% boost::shared_ptr::shared_ptr (inline) 114ms 0.12% 84.57% 785ms 0.8% MutableElement::GetNodeLocalIndex 111ms 0.11% 84.68% 785ms 0.8% boost::numeric::ublas::c_vector::operator= (inline) 22ms 0.023% 84.71% 770ms 0.79% Edge::AddElement 16ms 0.016% 84.72% 768ms 0.79% MutableElement::RegisterWithEdges (inline) 738ms 0.76% 85.48% 738ms 0.76% Node::GetIndex 0 0% 85.48% 730ms 0.75% tcache_get (inline) 730ms 0.75% 86.23% 730ms 0.75% tcache_get_n (inline) 0 0% 86.23% 711ms 0.73% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.23% 660ms 0.68% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.03% 86.26% 660ms 0.68% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.26% 632ms 0.65% boost::numeric::ublas::norm_inf (inline) 311ms 0.32% 86.58% 632ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 591ms 0.61% 87.18% 618ms 0.63% boost::detail::shared_count::shared_count (inline) 0 0% 87.18% 615ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.002% 87.18% 607ms 0.62% vtkPolygon::New 0 0% 87.18% 605ms 0.62% vtkPolygon::vtkPolygon 330ms 0.34% 87.52% 598ms 0.61% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 31ms 0.032% 87.55% 571ms 0.59% MutableElement::RegisterWithNodes (inline) 556ms 0.57% 88.12% 556ms 0.57% boost::shared_ptr::operator-> (inline) 32ms 0.033% 88.16% 531ms 0.54% Node::AddElement 329ms 0.34% 88.49% 529ms 0.54% CellPropertyCollection::GetProperty 31ms 0.032% 88.52% 496ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 15ms 0.015% 88.54% 488ms 0.5% Cylindrical2dVertexMesh::GetMeshForVtk