File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 56728ms, 88.48% of 64111ms total Dropped 991 nodes (cum <= 320.56ms) flat flat% sum% cum cum% 0 0% 0% 63856ms 99.60% __libc_start_call_main 0 0% 0% 63856ms 99.60% __libc_start_main_impl 0 0% 0% 63856ms 99.60% _start 0 0% 0% 63840ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63840ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63840ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63840ms 99.58% main 0 0% 0% 63806ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63806ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63806ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0016% 0.0016% 63801ms 99.52% AbstractCellBasedSimulation::Solve 22ms 0.034% 0.036% 33443ms 52.16% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.012% 0.048% 31260ms 48.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 45ms 0.07% 0.12% 30435ms 47.47% AbstractNumericalMethod::ComputeForcesIncludingDamping 175ms 0.27% 0.39% 23409ms 36.51% NagaiHondaForce::AddForceContribution 2ms 0.0031% 0.39% 22465ms 35.04% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0016% 0.4% 13786ms 21.50% VertexBasedCellPopulation::Update 0 0% 0.4% 13681ms 21.34% MutableVertexMesh::ReMesh 6778ms 10.57% 10.97% 11817ms 18.43% Cylindrical2dVertexMesh::GetVectorFromAtoB 38ms 0.059% 11.03% 10436ms 16.28% Cell::ReadyToDivide 25ms 0.039% 11.07% 9750ms 15.21% AbstractPhaseBasedCellCycleModel::ReadyToDivide 55ms 0.086% 11.15% 9498ms 14.81% NagaiHondaForce::GetAdhesionParameter 30ms 0.047% 11.20% 8427ms 13.14% SimpleWntCellCycleModel::UpdateCellCyclePhase 213ms 0.33% 11.53% 7978ms 12.44% boost::numeric::ublas::c_vector::c_vector (partial-inline) 54ms 0.084% 11.62% 7600ms 11.85% CellPropertyCollection::GetPropertiesType (inline) 534ms 0.83% 12.45% 7085ms 11.05% std::__new_allocator::allocate (inline) 196ms 0.31% 12.75% 7065ms 11.02% boost::numeric::ublas::vector_assign (inline) 0 0% 12.75% 6811ms 10.62% std::allocator_traits::allocate (inline) 28ms 0.044% 12.80% 6785ms 10.58% VertexBasedCellPopulation::GetDampingConstant 0 0% 12.80% 6698ms 10.45% std::_Rb_tree::_M_create_node (inline) 610ms 0.95% 13.75% 6579ms 10.26% operator new 0 0% 13.75% 6455ms 10.07% std::_Rb_tree::_M_get_node (inline) 67ms 0.1% 13.85% 6431ms 10.03% MutableVertexMesh::CheckForIntersections 31ms 0.048% 13.90% 6389ms 9.97% AbstractTargetAreaModifier::UpdateTargetAreas 24ms 0.037% 13.94% 6329ms 9.87% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1591ms 2.48% 16.42% 6276ms 9.79% __dynamic_cast 35ms 0.055% 16.48% 6254ms 9.75% AbstractCellProperty::IsSubType (inline) 6ms 0.0094% 16.49% 6105ms 9.52% AbstractCellBasedSimulation::DoCellBirth 675ms 1.05% 17.54% 6098ms 9.51% std::_Rb_tree::_M_erase 0 0% 17.54% 5933ms 9.25% std::_Rb_tree::_M_drop_node (inline) 0 0% 17.54% 5851ms 9.13% std::_Rb_tree::_Alloc_node::operator() (inline) 2545ms 3.97% 21.51% 5841ms 9.11% __GI___libc_malloc 272ms 0.42% 21.93% 5769ms 9.00% std::_Rb_tree::~_Rb_tree (inline) 0 0% 21.93% 5499ms 8.58% std::set::~set (inline) 1681ms 2.62% 24.55% 5281ms 8.24% boost::numeric::ublas::indexing_vector_assign 59ms 0.092% 24.65% 5215ms 8.13% std::__new_allocator::deallocate (inline) 0 0% 24.65% 5214ms 8.13% std::allocator_traits::deallocate (inline) 0 0% 24.65% 5181ms 8.08% std::_Rb_tree::_M_put_node (inline) 51ms 0.08% 24.73% 4982ms 7.77% Cell::GetMutationState 197ms 0.31% 25.03% 4887ms 7.62% VertexMesh::GetNextEdgeGradientOfElementAtNode 953ms 1.49% 26.52% 4848ms 7.56% __GI___libc_free 10ms 0.016% 26.54% 4822ms 7.52% MutableVertexMesh::RemoveDeletedNodesAndElements 257ms 0.4% 26.94% 4718ms 7.36% std::map::operator[] (partial-inline) 17ms 0.027% 26.96% 4627ms 7.22% VertexBasedCellPopulation::GetLocationOfCellCentre 430ms 0.67% 27.63% 4606ms 7.18% VertexMesh::ElementIncludesPoint 368ms 0.57% 28.21% 4389ms 6.85% VertexMesh::GetCentroidOfElement 0 0% 28.21% 4384ms 6.84% std::set::insert (inline) 830ms 1.29% 29.50% 4129ms 6.44% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 116ms 0.18% 29.68% 3995ms 6.23% std::_Rb_tree::_Rb_tree (partial-inline) 605ms 0.94% 30.63% 3911ms 6.10% std::_Rb_tree::_M_insert_ (inline) 3664ms 5.72% 36.34% 3870ms 6.04% _int_free 408ms 0.64% 36.98% 3762ms 5.87% std::_Rb_tree::_M_copy (inline) 1ms 0.0016% 36.98% 3697ms 5.77% std::set::set (inline) 3687ms 5.75% 42.73% 3687ms 5.75% boost::numeric::ublas::c_vector::operator() 98ms 0.15% 42.88% 3529ms 5.50% SimpleWntCellCycleModel::GetWntLevel 57ms 0.089% 42.97% 3459ms 5.40% std::set_intersection (inline) 1529ms 2.38% 45.36% 3448ms 5.38% std::_Rb_tree::_M_lower_bound (inline) 3417ms 5.33% 50.69% 3417ms 5.33% __strcmp_evex 160ms 0.25% 50.94% 3402ms 5.31% std::__set_intersection 92ms 0.14% 51.08% 3359ms 5.24% WntConcentration::GetWntLevel 2018ms 3.15% 54.23% 3333ms 5.20% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.016% 54.24% 3291ms 5.13% MutableVertexMesh::RemoveDeletedNodes 413ms 0.64% 54.89% 3215ms 5.01% std::_Rb_tree::_M_clone_node (inline) 25ms 0.039% 54.93% 3186ms 4.97% EdgeHelper::RemoveDeletedEdges 35ms 0.055% 54.98% 3041ms 4.74% EdgeHelper::UpdateEdgesMapKey 842ms 1.31% 56.29% 2987ms 4.66% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 56.29% 2940ms 4.59% std::_Rb_tree::lower_bound (inline) 0 0% 56.29% 2940ms 4.59% std::map::lower_bound (inline) 81ms 0.13% 56.42% 2924ms 4.56% MutableElement::ResetIndex 76ms 0.12% 56.54% 2759ms 4.30% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.54% 2648ms 4.13% std::insert_iterator::operator= (inline) 1ms 0.0016% 56.54% 2563ms 4.00% AbstractCellBasedSimulation::DoCellRemoval (inline) 45ms 0.07% 56.61% 2560ms 3.99% Cell::GetCellProliferativeType 1970ms 3.07% 59.68% 2492ms 3.89% _int_malloc 8ms 0.012% 59.70% 2434ms 3.80% std::_Rb_tree::_M_insert_unique_ (inline) 2397ms 3.74% 63.44% 2397ms 3.74% boost::numeric::ublas::same_impl_ex 103ms 0.16% 63.60% 2303ms 3.59% boost::detail::shared_count::~shared_count (inline) 0 0% 63.60% 2303ms 3.59% boost::shared_ptr::~shared_ptr (inline) 2175ms 3.39% 66.99% 2183ms 3.41% boost::detail::sp_counted_base::release 75ms 0.12% 67.11% 2119ms 3.31% AbstractCellProperty::IsType (inline) 78ms 0.12% 67.23% 2100ms 3.28% Cell::SetCellProliferativeType 33ms 0.051% 67.28% 2000ms 3.12% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 67.28% 1950ms 3.04% std::_Rb_tree::_M_insert_unique 22ms 0.034% 67.31% 1715ms 2.68% std::_Rb_tree::erase 448ms 0.7% 68.01% 1693ms 2.64% AbstractElement::GetNodeLocation 0 0% 68.01% 1663ms 2.59% boost::numeric::ublas::c_vector::assign (inline) 19ms 0.03% 68.04% 1602ms 2.50% CellPropertyCollection::HasProperty 154ms 0.24% 68.28% 1599ms 2.49% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0031% 68.28% 1598ms 2.49% AbstractCellPopulation::Iterator::operator++ (inline) 282ms 0.44% 68.72% 1589ms 2.48% boost::numeric::ublas::vector_binary::size (inline) 132ms 0.21% 68.93% 1588ms 2.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.93% 1544ms 2.41% Cell::HasCellProperty (inline) 1538ms 2.40% 71.33% 1538ms 2.40% std::_Rb_tree::_S_right (inline) 9ms 0.014% 71.34% 1526ms 2.38% Cell::GetCellData 20ms 0.031% 71.37% 1502ms 2.34% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.37% 1494ms 2.33% AbstractCellPopulation::WriteResultsToFiles 330ms 0.51% 71.89% 1477ms 2.30% AbstractCellProperty::IsSame 264ms 0.41% 72.30% 1467ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0031% 72.30% 1409ms 2.20% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.30% 1409ms 2.20% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 23ms 0.036% 72.34% 1287ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 72.34% 1232ms 1.92% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0031% 72.34% 1224ms 1.91% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 72.34% 1224ms 1.91% boost::numeric::ublas::c_vector::operator-= (inline) 7ms 0.011% 72.35% 1157ms 1.80% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 140ms 0.22% 72.57% 1147ms 1.79% std::type_info::operator== (inline) 0 0% 72.57% 1121ms 1.75% VertexMeshWriter::WriteVtkUsingMesh 63ms 0.098% 72.67% 1117ms 1.74% VertexMesh::GetVolumeOfElement 86ms 0.13% 72.80% 1096ms 1.71% CellPropertyCollection::AddProperty 1053ms 1.64% 74.45% 1053ms 1.64% std::_Rb_tree_increment 194ms 0.3% 74.75% 1027ms 1.60% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 38ms 0.059% 74.81% 998ms 1.56% MutableVertexMesh::CheckForSwapsFromShortEdges 55ms 0.086% 74.90% 993ms 1.55% boost::numeric::ublas::vector_reference::operator() (inline) 16ms 0.025% 74.92% 938ms 1.46% VertexMesh::GetSurfaceAreaOfElement 38ms 0.059% 74.98% 930ms 1.45% Node::RemoveElement 55ms 0.086% 75.07% 922ms 1.44% std::_Rb_tree::_M_erase_aux (partial-inline) 899ms 1.40% 76.47% 899ms 1.40% [libchaste_cell_based.so] 0 0% 76.47% 894ms 1.39% boost::numeric::ublas::norm_2 (inline) 3ms 0.0047% 76.47% 892ms 1.39% std::set::erase (inline) 535ms 0.83% 77.31% 887ms 1.38% std::_Rb_tree::equal_range (inline) 361ms 0.56% 77.87% 881ms 1.37% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 77.87% 852ms 1.33% OffLatticeSimulation::ApplyBoundaries 0 0% 77.87% 847ms 1.32% std::_Rb_tree::_Auto_node::_Auto_node (inline) 30ms 0.047% 77.92% 789ms 1.23% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 77.92% 777ms 1.21% CellPropertyCollection::~CellPropertyCollection (inline) 774ms 1.21% 79.12% 774ms 1.21% [libchaste_mesh.so] 59ms 0.092% 79.22% 761ms 1.19% std::less::operator() (inline) 0 0% 79.22% 755ms 1.18% std::__new_allocator::destroy (inline) 0 0% 79.22% 755ms 1.18% std::allocator_traits::destroy (inline) 0 0% 79.22% 753ms 1.17% std::_Rb_tree::_M_destroy_node (inline) 41ms 0.064% 79.28% 739ms 1.15% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.28% 705ms 1.10% boost::numeric::ublas::vector_binary::operator() (inline) 607ms 0.95% 80.23% 702ms 1.09% std::operator< (inline) 10ms 0.016% 80.24% 696ms 1.09% CellPropertyRegistry::Get 10ms 0.016% 80.26% 652ms 1.02% boost::numeric::ublas::detail::expression_type_check (inline) 1ms 0.0016% 80.26% 649ms 1.01% tcache_get (inline) 648ms 1.01% 81.27% 648ms 1.01% tcache_get_n (inline) 10ms 0.016% 81.29% 630ms 0.98% MutableElement::RegisterWithEdges (inline) 11ms 0.017% 81.30% 627ms 0.98% Edge::AddElement 66ms 0.1% 81.41% 627ms 0.98% boost::numeric::ublas::detail::equals 621ms 0.97% 82.37% 621ms 0.97% std::_Rb_tree_insert_and_rebalance 0 0% 82.37% 603ms 0.94% std::_Rb_tree::clear (inline) 593ms 0.92% 83.30% 593ms 0.92% [libstdc++.so.6.0.33] 0 0% 83.30% 592ms 0.92% std::map::clear (inline) 2ms 0.0031% 83.30% 587ms 0.92% VertexMeshWriter::MakeVtkMesh 0 0% 83.30% 582ms 0.91% boost::numeric::ublas::c_vector::assign_temporary (inline) 19ms 0.03% 83.33% 582ms 0.91% boost::numeric::ublas::c_vector::swap (inline) 508ms 0.79% 84.12% 577ms 0.9% CellPropertyCollection::GetProperty 109ms 0.17% 84.29% 563ms 0.88% std::swap_ranges (inline) 4ms 0.0062% 84.30% 540ms 0.84% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 84.30% 519ms 0.81% boost::numeric::ublas::norm_inf (inline) 197ms 0.31% 84.61% 519ms 0.81% boost::numeric::ublas::vector_norm_inf::apply (inline) 63ms 0.098% 84.71% 508ms 0.79% std::_Rb_tree::find (inline) 97ms 0.15% 84.86% 505ms 0.79% MutableElement::GetNodeLocalIndex 491ms 0.77% 85.62% 491ms 0.77% std::vector::size (inline) 42ms 0.066% 85.69% 477ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 251ms 0.39% 86.08% 469ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.08% 454ms 0.71% std::iter_swap (inline) 454ms 0.71% 86.79% 454ms 0.71% std::swap (inline) 12ms 0.019% 86.81% 438ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 229ms 0.36% 87.16% 438ms 0.68% Edge::GetMapIndex 0 0% 87.16% 428ms 0.67% vtkPolygon::New 0 0% 87.16% 428ms 0.67% vtkPolygon::vtkPolygon 82ms 0.13% 87.29% 426ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException (partial-inline) 22ms 0.034% 87.33% 420ms 0.66% MutableElement::RegisterWithNodes (inline) 0 0% 87.33% 418ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.025% 87.35% 418ms 0.65% std::_Rb_tree::_M_insert_node (inline) 29ms 0.045% 87.40% 402ms 0.63% Node::AddElement 1ms 0.0016% 87.40% 398ms 0.62% std::map::find (inline) 0 0% 87.40% 386ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 354ms 0.55% 87.95% 354ms 0.55% operator delete 0 0% 87.95% 353ms 0.55% std::_Vector_base::_M_allocate (inline) 341ms 0.53% 88.48% 341ms 0.53% Node::GetIndex 1ms 0.0016% 88.48% 335ms 0.52% vtkCell::vtkCell