File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94807ms, 87.68% of 108131ms total Dropped 1137 nodes (cum <= 540.65ms) flat flat% sum% cum cum% 0 0% 0% 107787ms 99.68% __libc_start_call_main 0 0% 0% 107787ms 99.68% __libc_start_main_impl 0 0% 0% 107787ms 99.68% _start 0 0% 0% 107767ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107767ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107767ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107767ms 99.66% main 0 0% 0% 107720ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107720ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107720ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107712ms 99.61% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.015% 56066ms 51.85% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.018% 0.032% 52794ms 48.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 163ms 0.15% 0.18% 51672ms 47.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 349ms 0.32% 0.51% 39897ms 36.90% NagaiHondaForce::AddForceContribution 0 0% 0.51% 38707ms 35.80% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.51% 23864ms 22.07% VertexBasedCellPopulation::Update 1ms 0.00092% 0.51% 23714ms 21.93% MutableVertexMesh::ReMesh 14676ms 13.57% 14.08% 23296ms 21.54% Cylindrical2dVertexMesh::GetVectorFromAtoB 90ms 0.083% 14.16% 17513ms 16.20% Cell::ReadyToDivide 50ms 0.046% 14.21% 16316ms 15.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 324ms 0.3% 14.51% 14460ms 13.37% NagaiHondaForce::GetAdhesionParameter 158ms 0.15% 14.66% 14012ms 12.96% SimpleWntCellCycleModel::UpdateCellCyclePhase 484ms 0.45% 15.10% 13745ms 12.71% boost::numeric::ublas::c_vector::c_vector (partial-inline) 102ms 0.094% 15.20% 13555ms 12.54% CellPropertyCollection::GetPropertiesType (inline) 272ms 0.25% 15.45% 12300ms 11.38% boost::numeric::ublas::vector_assign (inline) 137ms 0.13% 15.58% 11830ms 10.94% MutableVertexMesh::CheckForIntersections 3593ms 3.32% 18.90% 11554ms 10.69% __dynamic_cast 92ms 0.085% 18.98% 11464ms 10.60% AbstractCellProperty::IsSubType (inline) 81ms 0.075% 19.06% 11224ms 10.38% VertexBasedCellPopulation::GetDampingConstant 72ms 0.067% 19.12% 10451ms 9.67% AbstractTargetAreaModifier::UpdateTargetAreas 37ms 0.034% 19.16% 10364ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.025% 19.18% 10194ms 9.43% AbstractCellBasedSimulation::DoCellBirth 1302ms 1.20% 20.39% 9824ms 9.09% std::__new_allocator::allocate (inline) 343ms 0.32% 20.71% 9386ms 8.68% VertexMesh::GetNextEdgeGradientOfElementAtNode 2779ms 2.57% 23.28% 9344ms 8.64% boost::numeric::ublas::indexing_vector_assign 0 0% 23.28% 9313ms 8.61% std::_Rb_tree::_M_create_node (inline) 0 0% 23.28% 9261ms 8.56% std::allocator_traits::allocate (inline) 1257ms 1.16% 24.44% 9073ms 8.39% std::_Rb_tree::_M_erase 37ms 0.034% 24.47% 8763ms 8.10% VertexBasedCellPopulation::GetLocationOfCellCentre 872ms 0.81% 25.28% 8689ms 8.04% VertexMesh::ElementIncludesPoint 109ms 0.1% 25.38% 8650ms 8.00% Cell::GetMutationState 0 0% 25.38% 8597ms 7.95% std::_Rb_tree::_M_get_node (inline) 796ms 0.74% 26.12% 8529ms 7.89% operator new 482ms 0.45% 26.56% 8282ms 7.66% VertexMesh::GetCentroidOfElement 0 0% 26.56% 8247ms 7.63% std::_Rb_tree::_Alloc_node::operator() (inline) 194ms 0.18% 26.74% 8215ms 7.60% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.74% 8136ms 7.52% std::_Rb_tree::_M_drop_node (inline) 240ms 0.22% 26.96% 7875ms 7.28% std::__new_allocator::deallocate (inline) 0 0% 26.96% 7863ms 7.27% std::allocator_traits::deallocate (inline) 0 0% 26.96% 7807ms 7.22% std::_Rb_tree::_M_put_node (inline) 0 0% 26.96% 7796ms 7.21% std::set::~set (inline) 13ms 0.012% 26.97% 7631ms 7.06% MutableVertexMesh::RemoveDeletedNodesAndElements 476ms 0.44% 27.41% 7596ms 7.02% std::map::operator[] (partial-inline) 2827ms 2.61% 30.03% 7533ms 6.97% __GI___libc_malloc 1447ms 1.34% 31.37% 7434ms 6.87% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2317ms 2.14% 33.51% 7373ms 6.82% __GI___libc_free 232ms 0.21% 33.72% 7082ms 6.55% std::_Rb_tree::_Rb_tree (partial-inline) 34ms 0.031% 33.76% 6638ms 6.14% std::set::set (inline) 692ms 0.64% 34.40% 6604ms 6.11% std::_Rb_tree::_M_copy (inline) 114ms 0.11% 34.50% 6292ms 5.82% SimpleWntCellCycleModel::GetWntLevel 6122ms 5.66% 40.16% 6122ms 5.66% boost::numeric::ublas::c_vector::operator() 6111ms 5.65% 45.81% 6111ms 5.65% __strcmp_avx2 177ms 0.16% 45.98% 6094ms 5.64% WntConcentration::GetWntLevel 2502ms 2.31% 48.29% 5928ms 5.48% std::_Rb_tree::_M_lower_bound (inline) 789ms 0.73% 49.02% 5686ms 5.26% std::_Rb_tree::_M_clone_node (inline) 2935ms 2.71% 51.74% 5392ms 4.99% __cxxabiv1::__si_class_type_info::__do_dyncast 1964ms 1.82% 53.55% 5345ms 4.94% boost::numeric::ublas::c_vector::operator[] (inline) 20ms 0.018% 53.57% 5312ms 4.91% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.57% 5198ms 4.81% std::set::insert (inline) 27ms 0.025% 53.60% 5146ms 4.76% EdgeHelper::RemoveDeletedEdges 4609ms 4.26% 57.86% 5040ms 4.66% _int_free 0 0% 57.86% 4861ms 4.50% std::_Rb_tree::lower_bound (inline) 0 0% 57.86% 4861ms 4.50% std::map::lower_bound (inline) 39ms 0.036% 57.89% 4827ms 4.46% EdgeHelper::UpdateEdgesMapKey 194ms 0.18% 58.07% 4640ms 4.29% MutableElement::ResetIndex 0 0% 58.07% 4635ms 4.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 117ms 0.11% 58.18% 4370ms 4.04% AbstractCellPopulation::GetCellUsingLocationIndex 471ms 0.44% 58.62% 4351ms 4.02% std::_Rb_tree::_M_insert_ (inline) 104ms 0.096% 58.71% 4235ms 3.92% std::set_intersection (inline) 240ms 0.22% 58.94% 4131ms 3.82% std::__set_intersection 45ms 0.042% 58.98% 3920ms 3.63% Cell::GetCellProliferativeType 3782ms 3.50% 62.48% 3782ms 3.50% boost::numeric::ublas::same_impl_ex 51ms 0.047% 62.52% 3604ms 3.33% AbstractCellProperty::IsType (inline) 15ms 0.014% 62.54% 3545ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.54% 3175ms 2.94% std::insert_iterator::operator= (inline) 950ms 0.88% 63.41% 3129ms 2.89% AbstractElement::GetNodeLocation 72ms 0.067% 63.48% 3110ms 2.88% Cell::SetCellProliferativeType 2240ms 2.07% 65.55% 3093ms 2.86% _int_malloc 54ms 0.05% 65.60% 2896ms 2.68% std::_Rb_tree::erase 2886ms 2.67% 68.27% 2886ms 2.67% std::_Rb_tree::_S_right (inline) 9ms 0.0083% 68.28% 2740ms 2.53% std::_Rb_tree::_M_insert_unique_ (inline) 213ms 0.2% 68.48% 2628ms 2.43% VertexMesh::GetAreaGradientOfElementAtNode 633ms 0.59% 69.06% 2598ms 2.40% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.06% 2571ms 2.38% boost::numeric::ublas::c_vector::assign (inline) 747ms 0.69% 69.75% 2562ms 2.37% AbstractCellProperty::IsSame 25ms 0.023% 69.78% 2538ms 2.35% CellPropertyCollection::HasProperty 291ms 0.27% 70.05% 2518ms 2.33% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.05% 2505ms 2.32% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.05% 2459ms 2.27% AbstractCellPopulation::WriteResultsToFiles 1ms 0.00092% 70.05% 2458ms 2.27% std::_Rb_tree::_M_insert_unique 0 0% 70.05% 2441ms 2.26% Cell::HasCellProperty (inline) 69ms 0.064% 70.11% 2372ms 2.19% VertexMesh::GetVolumeOfElement 31ms 0.029% 70.14% 2331ms 2.16% Cell::GetCellData 58ms 0.054% 70.19% 2235ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 46ms 0.043% 70.24% 2204ms 2.04% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.0046% 70.24% 2126ms 1.97% AbstractCellPopulation::Iterator::operator++ (inline) 174ms 0.16% 70.40% 2113ms 1.95% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.0018% 70.40% 2078ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.40% 2078ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 70.40% 2006ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 70.40% 1993ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1973ms 1.82% 72.23% 1973ms 1.82% std::_Rb_tree_increment 1265ms 1.17% 73.40% 1917ms 1.77% std::_Rb_tree::equal_range (inline) 90ms 0.083% 73.48% 1865ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 494ms 0.46% 73.94% 1815ms 1.68% std::type_info::operator== (inline) 1ms 0.00092% 73.94% 1792ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.023% 73.96% 1651ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 36ms 0.033% 74.00% 1586ms 1.47% VertexMesh::GetSurfaceAreaOfElement 78ms 0.072% 74.07% 1520ms 1.41% Node::RemoveElement 48ms 0.044% 74.11% 1477ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 79ms 0.073% 74.19% 1465ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 9ms 0.0083% 74.19% 1444ms 1.34% std::set::erase (inline) 0 0% 74.19% 1423ms 1.32% tcache_get (inline) 1423ms 1.32% 75.51% 1423ms 1.32% tcache_get_n (inline) 144ms 0.13% 75.64% 1386ms 1.28% CellPropertyCollection::AddProperty 65ms 0.06% 75.70% 1347ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 1343ms 1.24% 76.95% 1343ms 1.24% [libchaste_cell_based.so] 0 0% 76.95% 1319ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 76.95% 1316ms 1.22% OffLatticeSimulation::ApplyBoundaries 0 0% 76.95% 1314ms 1.22% boost::numeric::ublas::norm_2 (inline) 628ms 0.58% 77.53% 1302ms 1.20% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 66ms 0.061% 77.59% 1244ms 1.15% std::less::operator() (inline) 960ms 0.89% 78.48% 1178ms 1.09% std::operator< (inline) 1174ms 1.09% 79.56% 1174ms 1.09% std::_Rb_tree_insert_and_rebalance 92ms 0.085% 79.65% 1142ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 31ms 0.029% 79.68% 1132ms 1.05% CellPropertyRegistry::Get 14ms 0.013% 79.69% 1107ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 86ms 0.08% 79.77% 1087ms 1.01% std::_Rb_tree::find (inline) 0 0% 79.77% 1066ms 0.99% std::_Rb_tree::_Auto_node::_Auto_node (inline) 9ms 0.0083% 79.78% 1058ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.78% 1057ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 19ms 0.018% 79.79% 1057ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 0 0% 79.79% 1055ms 0.98% std::_Rb_tree::clear (inline) 0 0% 79.79% 1042ms 0.96% std::map::clear (inline) 90ms 0.083% 79.88% 1038ms 0.96% std::swap_ranges (inline) 6ms 0.0055% 79.88% 1026ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 171ms 0.16% 80.04% 1006ms 0.93% boost::numeric::ublas::detail::equals 1005ms 0.93% 80.97% 1005ms 0.93% Node::rGetLocation 117ms 0.11% 81.08% 996ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.08% 996ms 0.92% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.08% 948ms 0.88% std::iter_swap (inline) 948ms 0.88% 81.96% 948ms 0.88% std::swap (inline) 1ms 0.00092% 81.96% 904ms 0.84% std::map::find (inline) 0 0% 81.96% 848ms 0.78% VertexMeshWriter::MakeVtkMesh 810ms 0.75% 82.71% 839ms 0.78% boost::detail::sp_counted_base::release 806ms 0.75% 83.45% 806ms 0.75% std::vector::size (inline) 22ms 0.02% 83.47% 801ms 0.74% Edge::AddElement 18ms 0.017% 83.49% 798ms 0.74% MutableElement::RegisterWithEdges (inline) 428ms 0.4% 83.88% 780ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 222ms 0.21% 84.09% 777ms 0.72% std::__new_allocator::construct (inline) 0 0% 84.09% 777ms 0.72% std::allocator_traits::construct (inline) 773ms 0.71% 84.80% 773ms 0.71% [libchaste_mesh.so] 102ms 0.094% 84.90% 767ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.90% 764ms 0.71% boost::numeric::ublas::norm_inf (inline) 371ms 0.34% 85.24% 764ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 378ms 0.35% 85.59% 741ms 0.69% Edge::GetMapIndex 148ms 0.14% 85.73% 737ms 0.68% boost::shared_ptr::shared_ptr (inline) 0 0% 85.73% 737ms 0.68% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 85.75% 737ms 0.68% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.75% 716ms 0.66% std::_Rb_tree::_M_construct_node (inline) 146ms 0.14% 85.89% 703ms 0.65% MutableElement::GetNodeLocalIndex 0 0% 85.89% 696ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.89% 677ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.00092% 85.89% 662ms 0.61% std::_Vector_base::_M_allocate (inline) 657ms 0.61% 86.50% 657ms 0.61% [libstdc++.so.6.0.33] 0 0% 86.50% 624ms 0.58% vtkPolygon::New 2ms 0.0018% 86.50% 624ms 0.58% vtkPolygon::vtkPolygon 621ms 0.57% 87.07% 621ms 0.57% Node::GetIndex 30ms 0.028% 87.10% 592ms 0.55% MutableElement::RegisterWithNodes (inline) 27ms 0.025% 87.12% 590ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.12% 590ms 0.55% boost::numeric::ublas::vector::vector (inline) 556ms 0.51% 87.64% 589ms 0.54% boost::detail::shared_count::shared_count (inline) 32ms 0.03% 87.67% 559ms 0.52% Node::AddElement 10ms 0.0092% 87.68% 559ms 0.52% std::vector::_M_default_append (inline)