File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 100834ms, 88.20% of 114326ms total Dropped 1083 nodes (cum <= 571.63ms) flat flat% sum% cum cum% 0 0% 0% 113906ms 99.63% __libc_start_call_main 0 0% 0% 113906ms 99.63% __libc_start_main_impl 0 0% 0% 113906ms 99.63% _start 0 0% 0% 113887ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 113887ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 113887ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 113887ms 99.62% main 0 0% 0% 113851ms 99.58% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 113851ms 99.58% CxxTest::TestRunner::runTest (inline) 0 0% 0% 113851ms 99.58% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00087% 0.00087% 113843ms 99.58% AbstractCellBasedSimulation::Solve 20ms 0.017% 0.018% 56960ms 49.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.0096% 0.028% 53682ms 46.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 73ms 0.064% 0.092% 52034ms 45.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.00087% 0.093% 43857ms 38.36% AbstractCellBasedSimulation::UpdateCellPopulation 412ms 0.36% 0.45% 40021ms 35.01% NagaiHondaForce::AddForceContribution 0 0% 0.45% 25310ms 22.14% VertexBasedCellPopulation::Update 0 0% 0.45% 25190ms 22.03% MutableVertexMesh::ReMesh 15744ms 13.77% 14.22% 24993ms 21.86% Cylindrical2dVertexMesh::GetVectorFromAtoB 83ms 0.073% 14.30% 17508ms 15.31% Cell::ReadyToDivide 394ms 0.34% 14.64% 17180ms 15.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 64ms 0.056% 14.70% 16373ms 14.32% AbstractPhaseBasedCellCycleModel::ReadyToDivide 610ms 0.53% 15.23% 14883ms 13.02% boost::numeric::ublas::vector_assign (inline) 300ms 0.26% 15.49% 14792ms 12.94% NagaiHondaForce::GetAdhesionParameter 132ms 0.12% 15.61% 13869ms 12.13% SimpleWntCellCycleModel::UpdateCellCyclePhase 116ms 0.1% 15.71% 13372ms 11.70% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.024% 15.73% 12742ms 11.15% VertexBasedCellPopulation::GetLocationOfCellCentre 433ms 0.38% 16.11% 12279ms 10.74% VertexMesh::GetCentroidOfElement 140ms 0.12% 16.24% 12102ms 10.59% MutableVertexMesh::CheckForIntersections 4066ms 3.56% 19.79% 11468ms 10.03% boost::numeric::ublas::indexing_vector_assign 3132ms 2.74% 22.53% 10962ms 9.59% __dynamic_cast 75ms 0.066% 22.60% 10827ms 9.47% AbstractCellProperty::IsSubType (inline) 58ms 0.051% 22.65% 10585ms 9.26% AbstractTargetAreaModifier::UpdateTargetAreas 206ms 0.18% 22.83% 10583ms 9.26% VertexBasedCellPopulation::GetDampingConstant 75ms 0.066% 22.89% 10497ms 9.18% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 17ms 0.015% 22.91% 10035ms 8.78% AbstractCellBasedSimulation::DoCellBirth 966ms 0.84% 23.75% 9873ms 8.64% std::__new_allocator::allocate (inline) 1280ms 1.12% 24.87% 9393ms 8.22% std::_Rb_tree::_M_erase 0 0% 24.87% 9393ms 8.22% std::allocator_traits::allocate (inline) 0 0% 24.87% 9372ms 8.20% std::_Rb_tree::_M_create_node (inline) 9082ms 7.94% 32.82% 9082ms 7.94% boost::numeric::ublas::c_vector::operator() 821ms 0.72% 33.53% 9027ms 7.90% operator new 775ms 0.68% 34.21% 9006ms 7.88% VertexMesh::ElementIncludesPoint 346ms 0.3% 34.52% 9000ms 7.87% VertexMesh::GetNextEdgeGradientOfElementAtNode 1427ms 1.25% 35.76% 8824ms 7.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 35.76% 8733ms 7.64% std::_Rb_tree::_M_get_node (inline) 0 0% 35.76% 8612ms 7.53% std::_Rb_tree::_M_drop_node (inline) 255ms 0.22% 35.99% 8590ms 7.51% std::_Rb_tree::~_Rb_tree (inline) 0 0% 35.99% 8496ms 7.43% AbstractCellBasedSimulation::DoCellRemoval (inline) 279ms 0.24% 36.23% 8359ms 7.31% std::__new_allocator::deallocate (inline) 0 0% 36.23% 8327ms 7.28% std::allocator_traits::deallocate (inline) 126ms 0.11% 36.34% 8319ms 7.28% Cell::GetMutationState 0 0% 36.34% 8268ms 7.23% std::_Rb_tree::_M_put_node (inline) 0 0% 36.34% 8215ms 7.19% std::_Rb_tree::_Alloc_node::operator() (inline) 3167ms 2.77% 39.11% 8213ms 7.18% __GI___libc_free 0 0% 39.11% 8126ms 7.11% std::set::~set (inline) 3105ms 2.72% 41.83% 8022ms 7.02% __GI___libc_malloc 1481ms 1.30% 43.12% 7444ms 6.51% boost::numeric::ublas::c_vector::operator[] (inline) 12ms 0.01% 43.13% 7432ms 6.50% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 13ms 0.011% 43.14% 7427ms 6.50% MutableVertexMesh::RemoveDeletedNodesAndElements 494ms 0.43% 43.58% 6776ms 5.93% std::map::operator[] (partial-inline) 157ms 0.14% 43.71% 6512ms 5.70% std::_Rb_tree::_Rb_tree (partial-inline) 116ms 0.1% 43.82% 6421ms 5.62% SimpleWntCellCycleModel::GetWntLevel 152ms 0.13% 43.95% 6168ms 5.40% WntConcentration::GetWntLevel 606ms 0.53% 44.48% 6160ms 5.39% std::_Rb_tree::_M_copy (inline) 6086ms 5.32% 49.80% 6086ms 5.32% __strcmp_avx2 11ms 0.0096% 49.81% 6020ms 5.27% std::set::set (inline) 0 0% 49.81% 5552ms 4.86% std::set::insert (inline) 2729ms 2.39% 52.20% 5411ms 4.73% __cxxabiv1::__si_class_type_info::__do_dyncast 728ms 0.64% 52.83% 5304ms 4.64% std::_Rb_tree::_M_clone_node (inline) 5277ms 4.62% 57.45% 5277ms 4.62% boost::numeric::ublas::same_impl_ex 33ms 0.029% 57.48% 5078ms 4.44% MutableVertexMesh::RemoveDeletedNodes 2289ms 2.00% 59.48% 5076ms 4.44% std::_Rb_tree::_M_lower_bound (inline) 4629ms 4.05% 63.53% 5040ms 4.41% _int_free 31ms 0.027% 63.56% 4896ms 4.28% EdgeHelper::RemoveDeletedEdges 533ms 0.47% 64.02% 4738ms 4.14% std::_Rb_tree::_M_insert_ (inline) 126ms 0.11% 64.13% 4704ms 4.11% MutableElement::ResetIndex 23ms 0.02% 64.15% 4627ms 4.05% EdgeHelper::UpdateEdgesMapKey 50ms 0.044% 64.20% 4560ms 3.99% std::set_intersection (inline) 286ms 0.25% 64.45% 4510ms 3.94% std::__set_intersection 88ms 0.077% 64.53% 4210ms 3.68% Cell::GetCellProliferativeType 0 0% 64.53% 4088ms 3.58% std::_Rb_tree::lower_bound (inline) 0 0% 64.53% 4088ms 3.58% std::map::lower_bound (inline) 0 0% 64.53% 4006ms 3.50% boost::numeric::ublas::c_vector::assign (inline) 852ms 0.75% 65.27% 3809ms 3.33% AbstractElement::GetNodeLocation 164ms 0.14% 65.41% 3756ms 3.29% AbstractCellPopulation::GetCellUsingLocationIndex 609ms 0.53% 65.95% 3592ms 3.14% boost::numeric::ublas::vector_binary::size (inline) 70ms 0.061% 66.01% 3482ms 3.05% AbstractCellProperty::IsType (inline) 0 0% 66.01% 3265ms 2.86% std::insert_iterator::operator= (inline) 73ms 0.064% 66.07% 3241ms 2.83% MutableVertexMesh::CheckForSwapsFromShortEdges 65ms 0.057% 66.13% 3178ms 2.78% Cell::SetCellProliferativeType 2203ms 1.93% 68.06% 3072ms 2.69% _int_malloc 7ms 0.0061% 68.06% 2881ms 2.52% std::_Rb_tree::_M_insert_unique_ (inline) 468ms 0.41% 68.47% 2700ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0017% 68.47% 2671ms 2.34% std::_Rb_tree::_M_insert_unique 80ms 0.07% 68.54% 2639ms 2.31% std::_Rb_tree::erase 0 0% 68.54% 2481ms 2.17% boost::numeric::ublas::c_vector::operator-= (inline) 223ms 0.2% 68.74% 2476ms 2.17% VertexMesh::GetAreaGradientOfElementAtNode 50ms 0.044% 68.78% 2443ms 2.14% CellPropertyCollection::HasProperty 636ms 0.56% 69.34% 2433ms 2.13% AbstractCellProperty::IsSame 104ms 0.091% 69.43% 2421ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.43% 2420ms 2.12% AbstractCellPopulation::WriteResultsToFiles 16ms 0.014% 69.44% 2366ms 2.07% Cell::GetCellData 0 0% 69.44% 2327ms 2.04% Cell::HasCellProperty (inline) 2269ms 1.98% 71.43% 2269ms 1.98% std::_Rb_tree::_S_right (inline) 94ms 0.082% 71.51% 2192ms 1.92% VertexMesh::GetVolumeOfElement 32ms 0.028% 71.54% 2144ms 1.88% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0026% 71.54% 2101ms 1.84% AbstractCellPopulation::Iterator::operator++ (inline) 161ms 0.14% 71.68% 2092ms 1.83% AbstractCellPopulation::Iterator::IsRealCell (inline) 2071ms 1.81% 73.49% 2071ms 1.81% std::_Rb_tree_increment 0 0% 73.49% 1986ms 1.74% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00087% 73.49% 1971ms 1.72% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0017% 73.50% 1922ms 1.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.50% 1922ms 1.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 488ms 0.43% 73.92% 1804ms 1.58% Node::RemoveElement 418ms 0.37% 74.29% 1797ms 1.57% std::type_info::operator== (inline) 0 0% 74.29% 1761ms 1.54% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.017% 74.31% 1686ms 1.47% VertexMesh::GetSurfaceAreaOfElement 160ms 0.14% 74.45% 1670ms 1.46% CellPropertyCollection::AddProperty 0 0% 74.45% 1659ms 1.45% tcache_get (inline) 1659ms 1.45% 75.90% 1659ms 1.45% tcache_get_n (inline) 29ms 0.025% 75.92% 1642ms 1.44% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 147ms 0.13% 76.05% 1632ms 1.43% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.05% 1502ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 918ms 0.8% 76.85% 1480ms 1.29% std::_Rb_tree::equal_range (inline) 22ms 0.019% 76.87% 1438ms 1.26% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.066% 76.94% 1417ms 1.24% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 17ms 0.015% 76.95% 1324ms 1.16% std::set::erase (inline) 95ms 0.083% 77.04% 1305ms 1.14% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 77.04% 1273ms 1.11% boost::numeric::ublas::norm_2 (inline) 537ms 0.47% 77.51% 1267ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 77.51% 1257ms 1.10% OffLatticeSimulation::ApplyBoundaries 19ms 0.017% 77.52% 1169ms 1.02% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 77.52% 1157ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1152ms 1.01% 78.53% 1152ms 1.01% std::_Rb_tree_insert_and_rebalance 1113ms 0.97% 79.50% 1113ms 0.97% [libchaste_cell_based.so] 1108ms 0.97% 80.47% 1108ms 0.97% Node::rGetLocation 73ms 0.064% 80.54% 1103ms 0.96% std::less::operator() (inline) 1ms 0.00087% 80.54% 1064ms 0.93% std::_Rb_tree::clear (inline) 24ms 0.021% 80.56% 1058ms 0.93% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.56% 1041ms 0.91% std::map::clear (inline) 837ms 0.73% 81.29% 1030ms 0.9% std::operator< (inline) 34ms 0.03% 81.32% 1029ms 0.9% CellPropertyRegistry::Get 51ms 0.045% 81.37% 1014ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 144ms 0.13% 81.49% 1012ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 81.49% 1012ms 0.89% boost::shared_ptr::~shared_ptr (inline) 90ms 0.079% 81.57% 997ms 0.87% std::_Rb_tree::find (inline) 111ms 0.097% 81.67% 996ms 0.87% std::__new_allocator::construct (inline) 0 0% 81.67% 996ms 0.87% std::allocator_traits::construct (inline) 983ms 0.86% 82.53% 983ms 0.86% std::vector::size (inline) 0 0% 82.53% 939ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0052% 82.53% 939ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 86ms 0.075% 82.61% 933ms 0.82% std::swap_ranges (inline) 924ms 0.81% 83.42% 924ms 0.81% [libchaste_mesh.so] 127ms 0.11% 83.53% 885ms 0.77% MutableElement::GetNodeLocalIndex 14ms 0.012% 83.54% 885ms 0.77% boost::numeric::ublas::detail::expression_type_check (inline) 172ms 0.15% 83.69% 860ms 0.75% boost::numeric::ublas::detail::equals 836ms 0.73% 84.42% 849ms 0.74% boost::detail::sp_counted_base::release 1ms 0.00087% 84.42% 848ms 0.74% VertexMeshWriter::MakeVtkMesh 0 0% 84.42% 847ms 0.74% std::iter_swap (inline) 847ms 0.74% 85.16% 847ms 0.74% std::swap (inline) 345ms 0.3% 85.46% 842ms 0.74% Edge::GetMapIndex 188ms 0.16% 85.63% 828ms 0.72% boost::shared_ptr::shared_ptr (inline) 0 0% 85.63% 822ms 0.72% std::map::find (inline) 0 0% 85.63% 778ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 14ms 0.012% 85.64% 744ms 0.65% MutableElement::RegisterWithEdges (inline) 31ms 0.027% 85.67% 740ms 0.65% Edge::AddElement 100ms 0.087% 85.76% 736ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 729ms 0.64% 86.39% 729ms 0.64% Node::GetIndex 21ms 0.018% 86.41% 721ms 0.63% VertexBasedCellPopulation::SetNode 413ms 0.36% 86.77% 697ms 0.61% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 3ms 0.0026% 86.78% 670ms 0.59% ChastePoint::ChastePoint (partial-inline) 0 0% 86.78% 661ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.018% 86.79% 661ms 0.58% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0017% 86.80% 659ms 0.58% std::_Vector_base::_M_allocate (inline) 0 0% 86.80% 650ms 0.57% boost::numeric::ublas::norm_inf (inline) 324ms 0.28% 87.08% 650ms 0.57% boost::numeric::ublas::vector_norm_inf::apply (inline) 610ms 0.53% 87.61% 640ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 87.61% 639ms 0.56% std::_Rb_tree::_M_construct_node (inline) 36ms 0.031% 87.64% 624ms 0.55% MutableElement::RegisterWithNodes (inline) 1ms 0.00087% 87.64% 617ms 0.54% vtkPolygon::New 0 0% 87.64% 615ms 0.54% vtkPolygon::vtkPolygon 609ms 0.53% 88.18% 609ms 0.53% [libstdc++.so.6.0.33] 24ms 0.021% 88.20% 589ms 0.52% Node::AddElement 0 0% 88.20% 586ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)