File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96901ms, 88.54% of 109447ms total Dropped 1069 nodes (cum <= 547.24ms) flat flat% sum% cum cum% 0 0% 0% 108971ms 99.57% __libc_start_call_main 0 0% 0% 108971ms 99.57% __libc_start_main_impl 0 0% 0% 108971ms 99.57% _start 0 0% 0% 108950ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108950ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108950ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108950ms 99.55% main 0 0% 0% 108915ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108915ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108915ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 108908ms 99.51% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.018% 56870ms 51.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.015% 0.033% 53693ms 49.06% ForwardEulerNumericalMethod::UpdateAllNodePositions 132ms 0.12% 0.15% 52638ms 48.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 375ms 0.34% 0.5% 40625ms 37.12% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.5% 39009ms 35.64% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.5% 24084ms 22.01% VertexBasedCellPopulation::Update 0 0% 0.5% 23939ms 21.87% MutableVertexMesh::ReMesh 14370ms 13.13% 13.63% 22611ms 20.66% Cylindrical2dVertexMesh::GetVectorFromAtoB 68ms 0.062% 13.69% 17760ms 16.23% Cell::ReadyToDivide 74ms 0.068% 13.76% 16528ms 15.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 378ms 0.35% 14.10% 15284ms 13.96% NagaiHondaForce::GetAdhesionParameter 450ms 0.41% 14.52% 14313ms 13.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 104ms 0.095% 14.61% 14133ms 12.91% SimpleWntCellCycleModel::UpdateCellCyclePhase 125ms 0.11% 14.72% 13662ms 12.48% CellPropertyCollection::GetPropertiesType (inline) 348ms 0.32% 15.04% 12737ms 11.64% boost::numeric::ublas::vector_assign (inline) 153ms 0.14% 15.18% 12048ms 11.01% MutableVertexMesh::CheckForIntersections 71ms 0.065% 15.25% 11480ms 10.49% VertexBasedCellPopulation::GetDampingConstant 3077ms 2.81% 18.06% 11293ms 10.32% __dynamic_cast 56ms 0.051% 18.11% 11166ms 10.20% AbstractCellProperty::IsSubType (inline) 68ms 0.062% 18.17% 10626ms 9.71% AbstractTargetAreaModifier::UpdateTargetAreas 49ms 0.045% 18.22% 10527ms 9.62% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1338ms 1.22% 19.44% 10361ms 9.47% std::__new_allocator::allocate (inline) 25ms 0.023% 19.46% 10347ms 9.45% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.46% 9885ms 9.03% std::_Rb_tree::_M_create_node (inline) 0 0% 19.46% 9840ms 8.99% std::allocator_traits::allocate (inline) 2723ms 2.49% 21.95% 9355ms 8.55% boost::numeric::ublas::indexing_vector_assign 0 0% 21.95% 9218ms 8.42% std::_Rb_tree::_M_get_node (inline) 810ms 0.74% 22.69% 9069ms 8.29% operator new 1341ms 1.23% 23.92% 9062ms 8.28% std::_Rb_tree::_M_erase 34ms 0.031% 23.95% 8925ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 782ms 0.71% 24.66% 8873ms 8.11% VertexMesh::ElementIncludesPoint 63ms 0.058% 24.72% 8801ms 8.04% Cell::GetMutationState 0 0% 24.72% 8689ms 7.94% std::_Rb_tree::_Alloc_node::operator() (inline) 351ms 0.32% 25.04% 8676ms 7.93% VertexMesh::GetNextEdgeGradientOfElementAtNode 469ms 0.43% 25.47% 8442ms 7.71% VertexMesh::GetCentroidOfElement 196ms 0.18% 25.65% 8270ms 7.56% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.65% 8109ms 7.41% std::_Rb_tree::_M_drop_node (inline) 3176ms 2.90% 28.55% 8042ms 7.35% __GI___libc_malloc 269ms 0.25% 28.79% 7911ms 7.23% std::__new_allocator::deallocate (inline) 0 0% 28.79% 7882ms 7.20% std::allocator_traits::deallocate (inline) 0 0% 28.79% 7857ms 7.18% std::set::~set (inline) 0 0% 28.79% 7811ms 7.14% std::_Rb_tree::_M_put_node (inline) 3039ms 2.78% 31.57% 7721ms 7.05% __GI___libc_free 425ms 0.39% 31.96% 7568ms 6.91% std::map::operator[] (partial-inline) 16ms 0.015% 31.97% 7500ms 6.85% MutableVertexMesh::RemoveDeletedNodesAndElements 190ms 0.17% 32.15% 7331ms 6.70% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.019% 32.17% 6932ms 6.33% std::set::set (inline) 1439ms 1.31% 33.48% 6902ms 6.31% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 691ms 0.63% 34.11% 6846ms 6.26% std::_Rb_tree::_M_copy (inline) 6657ms 6.08% 40.20% 6657ms 6.08% __strcmp_avx2 102ms 0.093% 40.29% 6474ms 5.92% SimpleWntCellCycleModel::GetWntLevel 151ms 0.14% 40.43% 6285ms 5.74% WntConcentration::GetWntLevel 6130ms 5.60% 46.03% 6130ms 5.60% boost::numeric::ublas::c_vector::operator() 2530ms 2.31% 48.34% 6068ms 5.54% std::_Rb_tree::_M_lower_bound (inline) 809ms 0.74% 49.08% 5803ms 5.30% std::_Rb_tree::_M_clone_node (inline) 2700ms 2.47% 51.55% 5652ms 5.16% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.55% 5645ms 5.16% std::set::insert (inline) 34ms 0.031% 51.58% 5365ms 4.90% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 51.61% 5201ms 4.75% EdgeHelper::RemoveDeletedEdges 36ms 0.033% 51.64% 4931ms 4.51% EdgeHelper::UpdateEdgesMapKey 1482ms 1.35% 53.00% 4890ms 4.47% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.00% 4889ms 4.47% std::_Rb_tree::lower_bound (inline) 0 0% 53.00% 4889ms 4.47% std::map::lower_bound (inline) 542ms 0.5% 53.49% 4795ms 4.38% std::_Rb_tree::_M_insert_ (inline) 4316ms 3.94% 57.43% 4671ms 4.27% _int_free 187ms 0.17% 57.61% 4629ms 4.23% MutableElement::ResetIndex 4ms 0.0037% 57.61% 4568ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 54ms 0.049% 57.66% 4561ms 4.17% std::set_intersection (inline) 263ms 0.24% 57.90% 4507ms 4.12% std::__set_intersection 103ms 0.094% 57.99% 4163ms 3.80% AbstractCellPopulation::GetCellUsingLocationIndex 4061ms 3.71% 61.70% 4061ms 3.71% boost::numeric::ublas::same_impl_ex 77ms 0.07% 61.77% 3948ms 3.61% AbstractCellProperty::IsType (inline) 38ms 0.035% 61.81% 3733ms 3.41% Cell::GetCellProliferativeType 7ms 0.0064% 61.81% 3562ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 61.81% 3422ms 3.13% std::insert_iterator::operator= (inline) 859ms 0.78% 62.60% 3323ms 3.04% AbstractElement::GetNodeLocation 2264ms 2.07% 64.67% 3093ms 2.83% _int_malloc 37ms 0.034% 64.70% 3026ms 2.76% Cell::SetCellProliferativeType 5ms 0.0046% 64.71% 2986ms 2.73% std::_Rb_tree::_M_insert_unique_ (inline) 2931ms 2.68% 67.38% 2931ms 2.68% std::_Rb_tree::_S_right (inline) 46ms 0.042% 67.43% 2898ms 2.65% std::_Rb_tree::erase 618ms 0.56% 67.99% 2830ms 2.59% boost::numeric::ublas::vector_binary::size (inline) 777ms 0.71% 68.70% 2784ms 2.54% AbstractCellProperty::IsSame 48ms 0.044% 68.74% 2739ms 2.50% CellPropertyCollection::HasProperty 362ms 0.33% 69.08% 2730ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.0027% 69.08% 2659ms 2.43% std::_Rb_tree::_M_insert_unique 0 0% 69.08% 2618ms 2.39% Cell::HasCellProperty (inline) 244ms 0.22% 69.30% 2535ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.30% 2481ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.30% 2415ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.30% 2383ms 2.18% AbstractCellPopulation::WriteResultsToFiles 25ms 0.023% 69.32% 2300ms 2.10% Cell::GetCellData 147ms 0.13% 69.46% 2297ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 85ms 0.078% 69.54% 2261ms 2.07% VertexMesh::GetVolumeOfElement 38ms 0.035% 69.57% 2206ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 2183ms 1.99% 71.57% 2183ms 1.99% std::_Rb_tree_increment 3ms 0.0027% 71.57% 2169ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 217ms 0.2% 71.77% 2141ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 517ms 0.47% 72.24% 2007ms 1.83% std::type_info::operator== (inline) 3ms 0.0027% 72.24% 1978ms 1.81% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.24% 1978ms 1.81% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.24% 1963ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0027% 72.24% 1951ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1297ms 1.19% 73.43% 1932ms 1.77% std::_Rb_tree::equal_range (inline) 86ms 0.079% 73.51% 1829ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.51% 1745ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 22ms 0.02% 73.53% 1677ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 175ms 0.16% 73.69% 1602ms 1.46% CellPropertyCollection::AddProperty 20ms 0.018% 73.71% 1597ms 1.46% VertexMesh::GetSurfaceAreaOfElement 48ms 0.044% 73.75% 1581ms 1.44% Node::RemoveElement 0 0% 73.75% 1544ms 1.41% tcache_get (inline) 1544ms 1.41% 75.16% 1544ms 1.41% tcache_get_n (inline) 16ms 0.015% 75.18% 1543ms 1.41% std::set::erase (inline) 26ms 0.024% 75.20% 1522ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 143ms 0.13% 75.33% 1502ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 75ms 0.069% 75.40% 1471ms 1.34% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.40% 1332ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 3ms 0.0027% 75.40% 1266ms 1.16% OffLatticeSimulation::ApplyBoundaries 27ms 0.025% 75.43% 1261ms 1.15% CellPropertyRegistry::Get 64ms 0.058% 75.48% 1253ms 1.14% std::less::operator() (inline) 0 0% 75.48% 1213ms 1.11% boost::numeric::ublas::norm_2 (inline) 520ms 0.48% 75.96% 1198ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 75.96% 1196ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1189ms 1.09% 77.05% 1189ms 1.09% Node::rGetLocation 982ms 0.9% 77.94% 1189ms 1.09% std::operator< (inline) 98ms 0.09% 78.03% 1176ms 1.07% std::_Rb_tree::find (inline) 1144ms 1.05% 79.08% 1144ms 1.05% std::_Rb_tree_insert_and_rebalance 1133ms 1.04% 80.11% 1133ms 1.04% [libchaste_cell_based.so] 66ms 0.06% 80.17% 1131ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1083ms 0.99% 81.16% 1083ms 0.99% std::vector::size (inline) 20ms 0.018% 81.18% 1057ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 14ms 0.013% 81.19% 1050ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 222ms 0.2% 81.40% 1031ms 0.94% boost::numeric::ublas::detail::equals 0 0% 81.40% 991ms 0.91% std::_Rb_tree::clear (inline) 0 0% 81.40% 974ms 0.89% std::map::clear (inline) 127ms 0.12% 81.51% 971ms 0.89% MutableElement::GetNodeLocalIndex 7ms 0.0064% 81.52% 965ms 0.88% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.52% 939ms 0.86% std::map::find (inline) 936ms 0.86% 82.37% 936ms 0.86% [libchaste_mesh.so] 129ms 0.12% 82.49% 934ms 0.85% boost::detail::shared_count::~shared_count (inline) 0 0% 82.49% 934ms 0.85% boost::shared_ptr::~shared_ptr (inline) 362ms 0.33% 82.82% 925ms 0.85% Edge::GetMapIndex 0 0% 82.82% 877ms 0.8% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 82.83% 877ms 0.8% boost::numeric::ublas::c_vector::swap (inline) 79ms 0.072% 82.90% 872ms 0.8% std::swap_ranges (inline) 1ms 0.00091% 82.90% 853ms 0.78% VertexMeshWriter::MakeVtkMesh 815ms 0.74% 83.65% 815ms 0.74% Node::GetIndex 24ms 0.022% 83.67% 810ms 0.74% MutableElement::RegisterWithEdges (inline) 33ms 0.03% 83.70% 806ms 0.74% Edge::AddElement 0 0% 83.70% 793ms 0.72% std::iter_swap (inline) 793ms 0.72% 84.42% 793ms 0.72% std::swap (inline) 778ms 0.71% 85.13% 784ms 0.72% boost::detail::sp_counted_base::release 0 0% 85.13% 766ms 0.7% boost::numeric::ublas::norm_inf (inline) 378ms 0.35% 85.48% 766ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 458ms 0.42% 85.90% 765ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 132ms 0.12% 86.02% 753ms 0.69% boost::shared_ptr::shared_ptr (inline) 112ms 0.1% 86.12% 747ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 114ms 0.1% 86.22% 714ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.22% 714ms 0.65% std::allocator_traits::construct (inline) 0 0% 86.22% 667ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.22% 663ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.026% 86.25% 663ms 0.61% std::_Rb_tree::_M_insert_node (inline) 637ms 0.58% 86.83% 637ms 0.58% operator delete 0 0% 86.83% 634ms 0.58% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.0018% 86.83% 622ms 0.57% std::_Vector_base::_M_allocate (inline) 596ms 0.54% 87.38% 621ms 0.57% boost::detail::shared_count::shared_count (inline) 619ms 0.57% 87.94% 619ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 87.94% 616ms 0.56% vtkPolygon::New 1ms 0.00091% 87.94% 615ms 0.56% vtkPolygon::vtkPolygon 28ms 0.026% 87.97% 611ms 0.56% MutableElement::RegisterWithNodes (inline) 586ms 0.54% 88.51% 586ms 0.54% [libstdc++.so.6.0.33] 34ms 0.031% 88.54% 576ms 0.53% Node::AddElement 0 0% 88.54% 549ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)