File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 102648ms, 88.08% of 116541ms total Dropped 1090 nodes (cum <= 582.71ms) flat flat% sum% cum cum% 0 0% 0% 116275ms 99.77% __libc_start_call_main 0 0% 0% 116275ms 99.77% __libc_start_main_impl 0 0% 0% 116275ms 99.77% _start 0 0% 0% 116256ms 99.76% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 116256ms 99.76% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 116256ms 99.76% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 116256ms 99.76% main 0 0% 0% 116219ms 99.72% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 116219ms 99.72% CxxTest::TestRunner::runTest (inline) 0 0% 0% 116219ms 99.72% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 7ms 0.006% 0.006% 116212ms 99.72% AbstractCellBasedSimulation::Solve 19ms 0.016% 0.022% 61811ms 53.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 26ms 0.022% 0.045% 58110ms 49.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 142ms 0.12% 0.17% 56636ms 48.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 577ms 0.5% 0.66% 44568ms 38.24% NagaiHondaForce::AddForceContribution 0 0% 0.66% 39710ms 34.07% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.0051% 0.67% 22755ms 19.53% VertexBasedCellPopulation::Update 1ms 0.00086% 0.67% 22620ms 19.41% MutableVertexMesh::ReMesh 81ms 0.07% 0.74% 20435ms 17.53% Cell::ReadyToDivide 9849ms 8.45% 9.19% 19997ms 17.16% Cylindrical2dVertexMesh::GetVectorFromAtoB 77ms 0.066% 9.25% 19294ms 16.56% AbstractPhaseBasedCellCycleModel::ReadyToDivide 424ms 0.36% 9.62% 17697ms 15.19% boost::numeric::ublas::c_vector::c_vector (partial-inline) 108ms 0.093% 9.71% 17001ms 14.59% NagaiHondaForce::GetAdhesionParameter 98ms 0.084% 9.79% 16411ms 14.08% SimpleWntCellCycleModel::UpdateCellCyclePhase 542ms 0.47% 10.26% 15739ms 13.51% boost::numeric::ublas::vector_assign (inline) 1274ms 1.09% 11.35% 14720ms 12.63% std::__new_allocator::allocate (inline) 75ms 0.064% 11.42% 14667ms 12.59% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.42% 13984ms 12.00% std::allocator_traits::allocate (inline) 0 0% 11.42% 13650ms 11.71% std::_Rb_tree::_M_create_node (inline) 901ms 0.77% 12.19% 13381ms 11.48% operator new 0 0% 12.19% 13197ms 11.32% std::_Rb_tree::_M_get_node (inline) 74ms 0.063% 12.25% 12095ms 10.38% AbstractTargetAreaModifier::UpdateTargetAreas 7ms 0.006% 12.26% 12053ms 10.34% AbstractCellBasedSimulation::DoCellBirth 0 0% 12.26% 11945ms 10.25% std::_Rb_tree::_Alloc_node::operator() (inline) 39ms 0.033% 12.29% 11938ms 10.24% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 4029ms 3.46% 15.75% 11864ms 10.18% __GI___libc_malloc 131ms 0.11% 15.86% 11696ms 10.04% AbstractCellProperty::IsSubType (inline) 3921ms 3.36% 19.23% 11641ms 9.99% __dynamic_cast 73ms 0.063% 19.29% 11565ms 9.92% VertexBasedCellPopulation::GetDampingConstant 2956ms 2.54% 21.83% 11345ms 9.73% boost::numeric::ublas::indexing_vector_assign 160ms 0.14% 21.96% 10623ms 9.12% MutableVertexMesh::CheckForIntersections 1178ms 1.01% 22.97% 9605ms 8.24% std::_Rb_tree::_M_erase 677ms 0.58% 23.56% 9601ms 8.24% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.56% 9467ms 8.12% std::_Rb_tree::_M_drop_node (inline) 80ms 0.069% 23.62% 9418ms 8.08% VertexBasedCellPopulation::GetLocationOfCellCentre 53ms 0.045% 23.67% 9215ms 7.91% Cell::GetMutationState 346ms 0.3% 23.97% 9015ms 7.74% std::_Rb_tree::~_Rb_tree (inline) 772ms 0.66% 24.63% 8970ms 7.70% VertexMesh::GetCentroidOfElement 250ms 0.21% 24.84% 8675ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 24.84% 8672ms 7.44% std::allocator_traits::deallocate (inline) 2021ms 1.73% 26.58% 8583ms 7.36% __GI___libc_free 0 0% 26.58% 8578ms 7.36% std::set::~set (inline) 0 0% 26.58% 8575ms 7.36% std::_Rb_tree::_M_put_node (inline) 647ms 0.56% 27.13% 8508ms 7.30% std::map::operator[] (partial-inline) 146ms 0.13% 27.26% 8435ms 7.24% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.26% 8155ms 7.00% std::set::insert (inline) 667ms 0.57% 27.83% 8114ms 6.96% std::_Rb_tree::_M_copy (inline) 22ms 0.019% 27.85% 8037ms 6.90% MutableVertexMesh::RemoveDeletedNodesAndElements 612ms 0.53% 28.37% 7958ms 6.83% VertexMesh::ElementIncludesPoint 18ms 0.015% 28.39% 7749ms 6.65% std::set::set (inline) 7312ms 6.27% 34.66% 7312ms 6.27% boost::numeric::ublas::c_vector::operator() 912ms 0.78% 35.45% 7298ms 6.26% std::_Rb_tree::_M_insert_ (inline) 166ms 0.14% 35.59% 7196ms 6.17% SimpleWntCellCycleModel::GetWntLevel 1151ms 0.99% 36.58% 7171ms 6.15% std::_Rb_tree::_M_clone_node (inline) 120ms 0.1% 36.68% 6895ms 5.92% WntConcentration::GetWntLevel 5544ms 4.76% 41.44% 6249ms 5.36% _int_free 2354ms 2.02% 43.46% 6036ms 5.18% std::_Rb_tree::_M_lower_bound (inline) 870ms 0.75% 44.20% 5956ms 5.11% AbstractMesh::GetDistanceBetweenNodes 30ms 0.026% 44.23% 5892ms 5.06% std::set_intersection (inline) 195ms 0.17% 44.40% 5862ms 5.03% std::__set_intersection 5664ms 4.86% 49.26% 5664ms 4.86% __strcmp_evex 4405ms 3.78% 53.04% 5574ms 4.78% _int_malloc 22ms 0.019% 53.06% 5465ms 4.69% MutableVertexMesh::RemoveDeletedNodes 961ms 0.82% 53.88% 5435ms 4.66% boost::numeric::ublas::c_vector::operator[] (inline) 2511ms 2.15% 56.03% 5395ms 4.63% __cxxabiv1::__si_class_type_info::__do_dyncast 69ms 0.059% 56.09% 5297ms 4.55% EdgeHelper::RemoveDeletedEdges 0 0% 56.09% 5121ms 4.39% std::_Rb_tree::lower_bound (inline) 0 0% 56.09% 5121ms 4.39% std::map::lower_bound (inline) 80ms 0.069% 56.16% 5037ms 4.32% AbstractCellPopulation::GetCellUsingLocationIndex 21ms 0.018% 56.18% 5025ms 4.31% EdgeHelper::UpdateEdgesMapKey 150ms 0.13% 56.31% 4996ms 4.29% MutableElement::ResetIndex 4983ms 4.28% 60.58% 4983ms 4.28% boost::numeric::ublas::same_impl_ex 1ms 0.00086% 60.59% 4892ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 32ms 0.027% 60.61% 4763ms 4.09% Cell::GetCellProliferativeType 0 0% 60.61% 4753ms 4.08% std::insert_iterator::operator= (inline) 0 0% 60.61% 4553ms 3.91% std::_Rb_tree::_M_insert_unique_ (inline) 179ms 0.15% 60.77% 4053ms 3.48% AbstractCellProperty::IsType (inline) 949ms 0.81% 61.58% 3913ms 3.36% AbstractElement::GetNodeLocation 56ms 0.048% 61.63% 3700ms 3.17% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00086% 61.63% 3602ms 3.09% std::_Rb_tree::_M_insert_unique 92ms 0.079% 61.71% 3557ms 3.05% Cell::SetCellProliferativeType 783ms 0.67% 62.38% 3404ms 2.92% boost::numeric::ublas::vector_binary::size (inline) 3319ms 2.85% 65.23% 3319ms 2.85% [libchaste_cell_based.so] 0 0% 65.23% 3129ms 2.68% boost::numeric::ublas::c_vector::assign (inline) 3029ms 2.60% 67.83% 3029ms 2.60% std::_Rb_tree::_S_right (inline) 56ms 0.048% 67.88% 2903ms 2.49% std::_Rb_tree::erase 431ms 0.37% 68.25% 2845ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 47ms 0.04% 68.29% 2771ms 2.38% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.0069% 68.29% 2747ms 2.36% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.18% 68.47% 2739ms 2.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 145ms 0.12% 68.59% 2695ms 2.31% boost::detail::shared_count::~shared_count (inline) 0 0% 68.59% 2695ms 2.31% boost::shared_ptr::~shared_ptr (inline) 37ms 0.032% 68.63% 2687ms 2.31% std::_Rb_tree::_M_emplace_hint_unique 18ms 0.015% 68.64% 2631ms 2.26% Cell::GetCellData 329ms 0.28% 68.92% 2629ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 54ms 0.046% 68.97% 2601ms 2.23% CellPropertyCollection::HasProperty 0 0% 68.97% 2556ms 2.19% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.97% 2534ms 2.17% Cell::HasCellProperty (inline) 686ms 0.59% 69.56% 2493ms 2.14% AbstractCellProperty::IsSame 2436ms 2.09% 71.65% 2481ms 2.13% boost::detail::sp_counted_base::release 0 0% 71.65% 2457ms 2.11% boost::numeric::ublas::c_vector::operator-= (inline) 2345ms 2.01% 73.66% 2345ms 2.01% [libchaste_mesh.so] 161ms 0.14% 73.80% 2223ms 1.91% VertexMesh::GetVolumeOfElement 41ms 0.035% 73.83% 2157ms 1.85% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.83% 2096ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.83% 2075ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 142ms 0.12% 73.96% 2070ms 1.78% CellPropertyCollection::AddProperty 3ms 0.0026% 73.96% 1968ms 1.69% tcache_get (inline) 1965ms 1.69% 75.65% 1965ms 1.69% tcache_get_n (inline) 1ms 0.00086% 75.65% 1905ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 229ms 0.2% 75.84% 1873ms 1.61% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 1818ms 1.56% 77.40% 1818ms 1.56% std::_Rb_tree_increment 15ms 0.013% 77.42% 1816ms 1.56% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.42% 1816ms 1.56% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 465ms 0.4% 77.81% 1807ms 1.55% std::type_info::operator== (inline) 169ms 0.15% 77.96% 1754ms 1.51% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 77.96% 1705ms 1.46% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.96% 1683ms 1.44% boost::numeric::ublas::vector_binary::operator() (inline) 88ms 0.076% 78.04% 1603ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 121ms 0.1% 78.14% 1591ms 1.37% std::_Rb_tree::_M_erase_aux (partial-inline) 898ms 0.77% 78.91% 1486ms 1.28% std::_Rb_tree::equal_range (inline) 87ms 0.075% 78.98% 1483ms 1.27% VertexMesh::GetSurfaceAreaOfElement 76ms 0.065% 79.05% 1453ms 1.25% MutableVertexMesh::CheckForSwapsFromShortEdges 1440ms 1.24% 80.29% 1440ms 1.24% [libstdc++.so.6.0.33] 2ms 0.0017% 80.29% 1410ms 1.21% OffLatticeSimulation::ApplyBoundaries 35ms 0.03% 80.32% 1406ms 1.21% Node::RemoveElement 13ms 0.011% 80.33% 1371ms 1.18% std::set::erase (inline) 54ms 0.046% 80.37% 1336ms 1.15% CellPropertyRegistry::Get 43ms 0.037% 80.41% 1250ms 1.07% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1198ms 1.03% 81.44% 1198ms 1.03% Node::rGetLocation 22ms 0.019% 81.46% 1175ms 1.01% MutableElement::RegisterWithEdges (inline) 8ms 0.0069% 81.46% 1168ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 28ms 0.024% 81.49% 1160ms 1% Edge::AddElement 43ms 0.037% 81.53% 1148ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 254ms 0.22% 81.74% 1077ms 0.92% boost::numeric::ublas::detail::equals 0 0% 81.74% 1040ms 0.89% boost::numeric::ublas::norm_2 (inline) 0 0% 81.74% 1012ms 0.87% CellPropertyCollection::~CellPropertyCollection (inline) 201ms 0.17% 81.92% 1004ms 0.86% boost::numeric::ublas::vector_norm_2::apply 3ms 0.0026% 81.92% 990ms 0.85% VertexMeshWriter::MakeVtkMesh 116ms 0.1% 82.02% 978ms 0.84% std::_Rb_tree::find (inline) 967ms 0.83% 82.85% 967ms 0.83% std::_Rb_tree_insert_and_rebalance 0 0% 82.85% 942ms 0.81% std::_Rb_tree::clear (inline) 0 0% 82.85% 924ms 0.79% std::map::clear (inline) 0 0% 82.85% 900ms 0.77% std::__new_allocator::destroy (inline) 0 0% 82.85% 900ms 0.77% std::allocator_traits::destroy (inline) 43ms 0.037% 82.88% 899ms 0.77% std::less::operator() (inline) 0 0% 82.88% 892ms 0.77% std::_Rb_tree::_M_destroy_node (inline) 643ms 0.55% 83.44% 856ms 0.73% std::operator< (inline) 496ms 0.43% 83.86% 843ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 816ms 0.7% 84.56% 816ms 0.7% tcache_put (inline) 0 0% 84.56% 812ms 0.7% std::map::find (inline) 4ms 0.0034% 84.57% 785ms 0.67% std::_Vector_base::_M_allocate (inline) 0 0% 84.57% 784ms 0.67% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 84.57% 784ms 0.67% boost::numeric::ublas::c_vector::swap (inline) 77ms 0.066% 84.63% 784ms 0.67% std::swap_ranges (inline) 100ms 0.086% 84.72% 783ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.72% 777ms 0.67% boost::numeric::ublas::norm_inf (inline) 409ms 0.35% 85.07% 777ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 38ms 0.033% 85.10% 774ms 0.66% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.10% 774ms 0.66% boost::numeric::ublas::vector::vector (inline) 619ms 0.53% 85.63% 743ms 0.64% CellPropertyCollection::GetProperty 740ms 0.63% 86.27% 740ms 0.63% std::vector::size (inline) 0 0% 86.27% 738ms 0.63% std::map::map (inline) 87ms 0.075% 86.34% 736ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 86.34% 707ms 0.61% std::iter_swap (inline) 707ms 0.61% 86.95% 707ms 0.61% std::swap (inline) 20ms 0.017% 86.97% 701ms 0.6% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 86.97% 701ms 0.6% vtkPolygon::New 0 0% 86.97% 699ms 0.6% vtkPolygon::vtkPolygon 26ms 0.022% 86.99% 686ms 0.59% MutableElement::RegisterWithNodes (inline) 24ms 0.021% 87.01% 663ms 0.57% Node::AddElement 0 0% 87.01% 654ms 0.56% std::_Rb_tree::_Auto_node::_M_insert (inline) 30ms 0.026% 87.03% 654ms 0.56% std::_Rb_tree::_M_insert_node (inline) 6ms 0.0051% 87.04% 632ms 0.54% std::vector::_M_default_append (inline) 630ms 0.54% 87.58% 630ms 0.54% Node::GetIndex 106ms 0.091% 87.67% 627ms 0.54% VertexBasedCellPopulation::CheckForStepSizeException 475ms 0.41% 88.08% 586ms 0.5% malloc_consolidate