File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94770ms, 88.75% of 106779ms total Dropped 1049 nodes (cum <= 533.89ms) flat flat% sum% cum cum% 0 0% 0% 106306ms 99.56% __libc_start_call_main 0 0% 0% 106306ms 99.56% __libc_start_main_impl 0 0% 0% 106306ms 99.56% _start 0 0% 0% 106288ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106288ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106288ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106288ms 99.54% main 0 0% 0% 106252ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106252ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106252ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00094% 0.00094% 106244ms 99.50% AbstractCellBasedSimulation::Solve 20ms 0.019% 0.02% 55463ms 51.94% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.031% 52394ms 49.07% ForwardEulerNumericalMethod::UpdateAllNodePositions 100ms 0.094% 0.12% 51346ms 48.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 352ms 0.33% 0.45% 39895ms 37.36% NagaiHondaForce::AddForceContribution 1ms 0.00094% 0.46% 38256ms 35.83% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.46% 23669ms 22.17% VertexBasedCellPopulation::Update 0 0% 0.46% 23551ms 22.06% MutableVertexMesh::ReMesh 14541ms 13.62% 14.07% 23131ms 21.66% Cylindrical2dVertexMesh::GetVectorFromAtoB 90ms 0.084% 14.16% 17186ms 16.09% Cell::ReadyToDivide 94ms 0.088% 14.25% 15965ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 375ms 0.35% 14.60% 14961ms 14.01% NagaiHondaForce::GetAdhesionParameter 396ms 0.37% 14.97% 14428ms 13.51% boost::numeric::ublas::c_vector::c_vector (partial-inline) 136ms 0.13% 15.09% 13584ms 12.72% SimpleWntCellCycleModel::UpdateCellCyclePhase 131ms 0.12% 15.22% 13156ms 12.32% CellPropertyCollection::GetPropertiesType (inline) 363ms 0.34% 15.56% 12842ms 12.03% boost::numeric::ublas::vector_assign (inline) 148ms 0.14% 15.70% 11978ms 11.22% MutableVertexMesh::CheckForIntersections 3089ms 2.89% 18.59% 11021ms 10.32% __dynamic_cast 81ms 0.076% 18.66% 10956ms 10.26% VertexBasedCellPopulation::GetDampingConstant 78ms 0.073% 18.74% 10916ms 10.22% AbstractCellProperty::IsSubType (inline) 63ms 0.059% 18.80% 10212ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 48ms 0.045% 18.84% 10129ms 9.49% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 18.87% 10107ms 9.47% AbstractCellBasedSimulation::DoCellBirth 2711ms 2.54% 21.40% 9578ms 8.97% boost::numeric::ublas::indexing_vector_assign 1207ms 1.13% 22.53% 9527ms 8.92% std::__new_allocator::allocate (inline) 1333ms 1.25% 23.78% 9332ms 8.74% std::_Rb_tree::_M_erase 353ms 0.33% 24.11% 9111ms 8.53% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 24.11% 9002ms 8.43% std::_Rb_tree::_M_create_node (inline) 0 0% 24.11% 8991ms 8.42% std::allocator_traits::allocate (inline) 794ms 0.74% 24.86% 8937ms 8.37% VertexMesh::ElementIncludesPoint 37ms 0.035% 24.89% 8662ms 8.11% VertexBasedCellPopulation::GetLocationOfCellCentre 215ms 0.2% 25.09% 8559ms 8.02% std::_Rb_tree::~_Rb_tree (inline) 81ms 0.076% 25.17% 8515ms 7.97% Cell::GetMutationState 804ms 0.75% 25.92% 8425ms 7.89% operator new 0 0% 25.92% 8411ms 7.88% std::_Rb_tree::_M_get_node (inline) 0 0% 25.92% 8360ms 7.83% std::_Rb_tree::_M_drop_node (inline) 502ms 0.47% 26.39% 8234ms 7.71% VertexMesh::GetCentroidOfElement 250ms 0.23% 26.63% 8124ms 7.61% std::__new_allocator::deallocate (inline) 0 0% 26.63% 8091ms 7.58% std::set::~set (inline) 0 0% 26.63% 8089ms 7.58% std::allocator_traits::deallocate (inline) 0 0% 26.63% 8048ms 7.54% std::_Rb_tree::_M_put_node (inline) 3187ms 2.98% 29.61% 7936ms 7.43% __GI___libc_free 0 0% 29.61% 7878ms 7.38% std::_Rb_tree::_Alloc_node::operator() (inline) 3023ms 2.83% 32.44% 7458ms 6.98% __GI___libc_malloc 1355ms 1.27% 33.71% 7380ms 6.91% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 13ms 0.012% 33.72% 7148ms 6.69% MutableVertexMesh::RemoveDeletedNodesAndElements 459ms 0.43% 34.15% 7014ms 6.57% std::map::operator[] (partial-inline) 149ms 0.14% 34.29% 6626ms 6.21% std::_Rb_tree::_Rb_tree (partial-inline) 6295ms 5.90% 40.19% 6295ms 5.90% __strcmp_avx2 683ms 0.64% 40.83% 6258ms 5.86% std::_Rb_tree::_M_copy (inline) 118ms 0.11% 40.94% 6255ms 5.86% SimpleWntCellCycleModel::GetWntLevel 16ms 0.015% 40.95% 6236ms 5.84% std::set::set (inline) 6136ms 5.75% 46.70% 6136ms 5.75% boost::numeric::ublas::c_vector::operator() 131ms 0.12% 46.82% 6041ms 5.66% WntConcentration::GetWntLevel 2722ms 2.55% 49.37% 5533ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 2259ms 2.12% 51.49% 5294ms 4.96% std::_Rb_tree::_M_lower_bound (inline) 707ms 0.66% 52.15% 5291ms 4.96% std::_Rb_tree::_M_clone_node (inline) 26ms 0.024% 52.17% 5209ms 4.88% MutableVertexMesh::RemoveDeletedNodes 0 0% 52.17% 5201ms 4.87% std::set::insert (inline) 51ms 0.048% 52.22% 5063ms 4.74% EdgeHelper::RemoveDeletedEdges 41ms 0.038% 52.26% 4786ms 4.48% EdgeHelper::UpdateEdgesMapKey 4415ms 4.13% 56.39% 4741ms 4.44% _int_free 1485ms 1.39% 57.78% 4712ms 4.41% boost::numeric::ublas::c_vector::operator[] (inline) 51ms 0.048% 57.83% 4647ms 4.35% std::set_intersection (inline) 299ms 0.28% 58.11% 4596ms 4.30% std::__set_intersection 1ms 0.00094% 58.11% 4467ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 180ms 0.17% 58.28% 4407ms 4.13% MutableElement::ResetIndex 513ms 0.48% 58.76% 4353ms 4.08% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.76% 4287ms 4.01% std::_Rb_tree::lower_bound (inline) 0 0% 58.76% 4287ms 4.01% std::map::lower_bound (inline) 4093ms 3.83% 62.60% 4093ms 3.83% boost::numeric::ublas::same_impl_ex 39ms 0.037% 62.63% 3875ms 3.63% Cell::GetCellProliferativeType 111ms 0.1% 62.74% 3745ms 3.51% AbstractCellPopulation::GetCellUsingLocationIndex 76ms 0.071% 62.81% 3656ms 3.42% AbstractCellProperty::IsType (inline) 4ms 0.0037% 62.81% 3505ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.81% 3234ms 3.03% std::insert_iterator::operator= (inline) 787ms 0.74% 63.55% 3048ms 2.85% AbstractElement::GetNodeLocation 41ms 0.038% 63.59% 3020ms 2.83% Cell::SetCellProliferativeType 641ms 0.6% 64.19% 2933ms 2.75% boost::numeric::ublas::vector_binary::size (inline) 2137ms 2.00% 66.19% 2926ms 2.74% _int_malloc 6ms 0.0056% 66.19% 2832ms 2.65% std::_Rb_tree::_M_insert_unique_ (inline) 32ms 0.03% 66.22% 2774ms 2.60% std::_Rb_tree::erase 431ms 0.4% 66.63% 2734ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 667ms 0.62% 67.25% 2590ms 2.43% AbstractCellProperty::IsSame 38ms 0.036% 67.29% 2524ms 2.36% CellPropertyCollection::HasProperty 2498ms 2.34% 69.63% 2498ms 2.34% std::_Rb_tree::_S_right (inline) 266ms 0.25% 69.88% 2480ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.88% 2437ms 2.28% Cell::HasCellProperty (inline) 0 0% 69.88% 2408ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.88% 2369ms 2.22% std::_Rb_tree::_M_insert_unique 0 0% 69.88% 2341ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.00094% 69.88% 2294ms 2.15% AbstractCellPopulation::WriteResultsToFiles 34ms 0.032% 69.91% 2279ms 2.13% Cell::GetCellData 104ms 0.097% 70.01% 2265ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 100ms 0.094% 70.10% 2251ms 2.11% VertexMesh::GetVolumeOfElement 34ms 0.032% 70.13% 2215ms 2.07% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.0047% 70.14% 2142ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 2122ms 1.99% 72.12% 2122ms 1.99% std::_Rb_tree_increment 195ms 0.18% 72.31% 2099ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0028% 72.31% 1940ms 1.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.31% 1940ms 1.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 463ms 0.43% 72.74% 1923ms 1.80% std::type_info::operator== (inline) 66ms 0.062% 72.80% 1904ms 1.78% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 72.80% 1866ms 1.75% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00094% 72.81% 1863ms 1.74% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1242ms 1.16% 73.97% 1806ms 1.69% std::_Rb_tree::equal_range (inline) 0 0% 73.97% 1685ms 1.58% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.024% 73.99% 1617ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 138ms 0.13% 74.12% 1612ms 1.51% boost::numeric::ublas::vector_reference::operator() (inline) 18ms 0.017% 74.14% 1608ms 1.51% VertexMesh::GetSurfaceAreaOfElement 48ms 0.045% 74.18% 1498ms 1.40% Node::RemoveElement 0 0% 74.18% 1462ms 1.37% boost::numeric::ublas::vector_binary::operator() (inline) 20ms 0.019% 74.20% 1460ms 1.37% std::set::erase (inline) 88ms 0.082% 74.29% 1423ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 23ms 0.022% 74.31% 1422ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 175ms 0.16% 74.47% 1418ms 1.33% CellPropertyCollection::AddProperty 0 0% 74.47% 1331ms 1.25% tcache_get (inline) 1331ms 1.25% 75.72% 1331ms 1.25% tcache_get_n (inline) 0 0% 75.72% 1197ms 1.12% boost::numeric::ublas::norm_2 (inline) 498ms 0.47% 76.18% 1184ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1184ms 1.11% 77.29% 1184ms 1.11% std::_Rb_tree_insert_and_rebalance 2ms 0.0019% 77.29% 1163ms 1.09% OffLatticeSimulation::ApplyBoundaries 65ms 0.061% 77.36% 1141ms 1.07% std::less::operator() (inline) 0 0% 77.36% 1124ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1109ms 1.04% 78.39% 1109ms 1.04% Node::rGetLocation 75ms 0.07% 78.46% 1105ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1097ms 1.03% 79.49% 1097ms 1.03% [libchaste_cell_based.so] 896ms 0.84% 80.33% 1076ms 1.01% std::operator< (inline) 29ms 0.027% 80.36% 1051ms 0.98% CellPropertyRegistry::Get 103ms 0.096% 80.45% 1012ms 0.95% std::_Rb_tree::find (inline) 2ms 0.0019% 80.46% 998ms 0.93% std::_Rb_tree::clear (inline) 19ms 0.018% 80.47% 993ms 0.93% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.47% 980ms 0.92% std::map::clear (inline) 974ms 0.91% 81.39% 974ms 0.91% std::vector::size (inline) 967ms 0.91% 82.29% 967ms 0.91% [libchaste_mesh.so] 19ms 0.018% 82.31% 946ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 155ms 0.15% 82.45% 945ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 82.45% 945ms 0.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.45% 938ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0075% 82.46% 938ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 88ms 0.082% 82.54% 930ms 0.87% std::swap_ranges (inline) 142ms 0.13% 82.68% 919ms 0.86% boost::numeric::ublas::detail::equals 5ms 0.0047% 82.68% 912ms 0.85% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 122ms 0.11% 82.80% 867ms 0.81% MutableElement::GetNodeLocalIndex 369ms 0.35% 83.14% 864ms 0.81% Edge::GetMapIndex 843ms 0.79% 83.93% 843ms 0.79% std::swap (inline) 0 0% 83.93% 842ms 0.79% std::iter_swap (inline) 0 0% 83.93% 821ms 0.77% VertexMeshWriter::MakeVtkMesh 0 0% 83.93% 817ms 0.77% std::map::find (inline) 0 0% 83.93% 816ms 0.76% CellPropertyCollection::~CellPropertyCollection (inline) 167ms 0.16% 84.09% 796ms 0.75% boost::shared_ptr::shared_ptr (inline) 463ms 0.43% 84.52% 769ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 753ms 0.71% 85.23% 759ms 0.71% boost::detail::sp_counted_base::release 112ms 0.1% 85.33% 756ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.33% 743ms 0.7% boost::numeric::ublas::norm_inf (inline) 374ms 0.35% 85.68% 743ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.68% 739ms 0.69% std::_Rb_tree::_Auto_node::_M_insert (inline) 30ms 0.028% 85.71% 739ms 0.69% std::_Rb_tree::_M_insert_node (inline) 722ms 0.68% 86.39% 722ms 0.68% Node::GetIndex 22ms 0.021% 86.41% 686ms 0.64% MutableElement::RegisterWithEdges (inline) 26ms 0.024% 86.43% 680ms 0.64% Edge::AddElement 91ms 0.085% 86.52% 642ms 0.6% std::__new_allocator::construct (inline) 0 0% 86.52% 642ms 0.6% std::allocator_traits::construct (inline) 605ms 0.57% 87.08% 629ms 0.59% boost::detail::shared_count::shared_count (inline) 31ms 0.029% 87.11% 623ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 87.11% 591ms 0.55% std::_Rb_tree::_M_construct_node (inline) 26ms 0.024% 87.14% 588ms 0.55% Node::AddElement 0 0% 87.14% 586ms 0.55% vtkPolygon::New 2ms 0.0019% 87.14% 586ms 0.55% vtkPolygon::vtkPolygon 0 0% 87.14% 579ms 0.54% std::_Vector_base::_M_allocate (inline) 577ms 0.54% 87.68% 577ms 0.54% operator delete 569ms 0.53% 88.21% 569ms 0.53% [libstdc++.so.6.0.33] 33ms 0.031% 88.24% 569ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.24% 569ms 0.53% boost::numeric::ublas::vector::vector (inline) 546ms 0.51% 88.75% 546ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 88.75% 544ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)