File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 74355ms, 88.13% of 84366ms total Dropped 1038 nodes (cum <= 421.83ms) flat flat% sum% cum cum% 0 0% 0% 84085ms 99.67% __libc_start_call_main 0 0% 0% 84085ms 99.67% __libc_start_main_impl 0 0% 0% 84085ms 99.67% _start 0 0% 0% 84068ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 84068ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 84068ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 84068ms 99.65% main 0 0% 0% 84031ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 84031ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 84031ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0024% 0.0024% 84025ms 99.60% AbstractCellBasedSimulation::Solve 14ms 0.017% 0.019% 43741ms 51.85% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.019% 0.038% 41260ms 48.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 121ms 0.14% 0.18% 40377ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 265ms 0.31% 0.5% 30948ms 36.68% NagaiHondaForce::AddForceContribution 0 0% 0.5% 30153ms 35.74% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0012% 0.5% 18604ms 22.05% VertexBasedCellPopulation::Update 1ms 0.0012% 0.5% 18498ms 21.93% MutableVertexMesh::ReMesh 11216ms 13.29% 13.79% 18030ms 21.37% Cylindrical2dVertexMesh::GetVectorFromAtoB 75ms 0.089% 13.88% 13605ms 16.13% Cell::ReadyToDivide 51ms 0.06% 13.94% 12611ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 271ms 0.32% 14.26% 11266ms 13.35% NagaiHondaForce::GetAdhesionParameter 131ms 0.16% 14.42% 10847ms 12.86% SimpleWntCellCycleModel::UpdateCellCyclePhase 392ms 0.46% 14.88% 10630ms 12.60% boost::numeric::ublas::c_vector::c_vector (partial-inline) 75ms 0.089% 14.97% 10520ms 12.47% CellPropertyCollection::GetPropertiesType (inline) 241ms 0.29% 15.26% 9465ms 11.22% boost::numeric::ublas::vector_assign (inline) 101ms 0.12% 15.38% 9129ms 10.82% MutableVertexMesh::CheckForIntersections 2759ms 3.27% 18.65% 9090ms 10.77% __dynamic_cast 49ms 0.058% 18.71% 8983ms 10.65% AbstractCellProperty::IsSubType (inline) 65ms 0.077% 18.78% 8951ms 10.61% VertexBasedCellPopulation::GetDampingConstant 40ms 0.047% 18.83% 8151ms 9.66% AbstractTargetAreaModifier::UpdateTargetAreas 36ms 0.043% 18.87% 8094ms 9.59% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.026% 18.90% 8045ms 9.54% AbstractCellBasedSimulation::DoCellBirth 1045ms 1.24% 20.14% 7859ms 9.32% std::__new_allocator::allocate (inline) 0 0% 20.14% 7381ms 8.75% std::allocator_traits::allocate (inline) 0 0% 20.14% 7376ms 8.74% std::_Rb_tree::_M_create_node (inline) 284ms 0.34% 20.47% 7293ms 8.64% VertexMesh::GetNextEdgeGradientOfElementAtNode 2121ms 2.51% 22.99% 7225ms 8.56% boost::numeric::ublas::indexing_vector_assign 1018ms 1.21% 24.19% 7057ms 8.36% std::_Rb_tree::_M_erase 602ms 0.71% 24.91% 6839ms 8.11% operator new 0 0% 24.91% 6837ms 8.10% std::_Rb_tree::_M_get_node (inline) 625ms 0.74% 25.65% 6773ms 8.03% VertexMesh::ElementIncludesPoint 19ms 0.023% 25.67% 6712ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 72ms 0.085% 25.76% 6599ms 7.82% Cell::GetMutationState 0 0% 25.76% 6478ms 7.68% std::_Rb_tree::_Alloc_node::operator() (inline) 173ms 0.21% 25.96% 6427ms 7.62% std::_Rb_tree::~_Rb_tree (inline) 334ms 0.4% 26.36% 6291ms 7.46% VertexMesh::GetCentroidOfElement 0 0% 26.36% 6258ms 7.42% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.36% 6134ms 7.27% std::set::~set (inline) 361ms 0.43% 26.79% 6108ms 7.24% std::map::operator[] (partial-inline) 2283ms 2.71% 29.49% 6084ms 7.21% __GI___libc_malloc 166ms 0.2% 29.69% 6078ms 7.20% std::__new_allocator::deallocate (inline) 0 0% 29.69% 6068ms 7.19% std::allocator_traits::deallocate (inline) 0 0% 29.69% 6019ms 7.13% std::_Rb_tree::_M_put_node (inline) 1195ms 1.42% 31.10% 5902ms 7.00% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 13ms 0.015% 31.12% 5870ms 6.96% MutableVertexMesh::RemoveDeletedNodesAndElements 1849ms 2.19% 33.31% 5679ms 6.73% __GI___libc_free 142ms 0.17% 33.48% 5636ms 6.68% std::_Rb_tree::_Rb_tree (partial-inline) 594ms 0.7% 34.18% 5304ms 6.29% std::_Rb_tree::_M_copy (inline) 19ms 0.023% 34.21% 5282ms 6.26% std::set::set (inline) 5044ms 5.98% 40.19% 5044ms 5.98% __strcmp_evex 92ms 0.11% 40.29% 4961ms 5.88% SimpleWntCellCycleModel::GetWntLevel 1966ms 2.33% 42.62% 4893ms 5.80% std::_Rb_tree::_M_lower_bound (inline) 4837ms 5.73% 48.36% 4837ms 5.73% boost::numeric::ublas::c_vector::operator() 181ms 0.21% 48.57% 4814ms 5.71% WntConcentration::GetWntLevel 626ms 0.74% 49.31% 4510ms 5.35% std::_Rb_tree::_M_clone_node (inline) 1520ms 1.80% 51.12% 4205ms 4.98% boost::numeric::ublas::c_vector::operator[] (inline) 13ms 0.015% 51.13% 4126ms 4.89% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.13% 4067ms 4.82% std::set::insert (inline) 0 0% 51.13% 4030ms 4.78% std::_Rb_tree::lower_bound (inline) 0 0% 51.13% 4030ms 4.78% std::map::lower_bound (inline) 29ms 0.034% 51.17% 3992ms 4.73% EdgeHelper::RemoveDeletedEdges 2196ms 2.60% 53.77% 3943ms 4.67% __cxxabiv1::__si_class_type_info::__do_dyncast 3447ms 4.09% 57.86% 3823ms 4.53% _int_free 27ms 0.032% 57.89% 3752ms 4.45% EdgeHelper::UpdateEdgesMapKey 99ms 0.12% 58.00% 3687ms 4.37% AbstractCellPopulation::GetCellUsingLocationIndex 158ms 0.19% 58.19% 3660ms 4.34% MutableElement::ResetIndex 0 0% 58.19% 3495ms 4.14% AbstractCellBasedSimulation::DoCellRemoval (inline) 386ms 0.46% 58.65% 3376ms 4.00% std::_Rb_tree::_M_insert_ (inline) 71ms 0.084% 58.73% 3304ms 3.92% std::set_intersection (inline) 157ms 0.19% 58.92% 3233ms 3.83% std::__set_intersection 30ms 0.036% 58.96% 3071ms 3.64% Cell::GetCellProliferativeType 44ms 0.052% 59.01% 2899ms 3.44% AbstractCellProperty::IsType (inline) 2874ms 3.41% 62.41% 2874ms 3.41% boost::numeric::ublas::same_impl_ex 5ms 0.0059% 62.42% 2615ms 3.10% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1775ms 2.10% 64.52% 2517ms 2.98% _int_malloc 0 0% 64.52% 2510ms 2.98% std::insert_iterator::operator= (inline) 2480ms 2.94% 67.46% 2480ms 2.94% std::_Rb_tree::_S_right (inline) 755ms 0.89% 68.36% 2467ms 2.92% AbstractElement::GetNodeLocation 34ms 0.04% 68.40% 2385ms 2.83% Cell::SetCellProliferativeType 46ms 0.055% 68.45% 2312ms 2.74% std::_Rb_tree::erase 4ms 0.0047% 68.46% 2172ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 545ms 0.65% 69.10% 2091ms 2.48% AbstractCellProperty::IsSame 34ms 0.04% 69.14% 2061ms 2.44% CellPropertyCollection::HasProperty 489ms 0.58% 69.72% 2014ms 2.39% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.72% 1982ms 2.35% Cell::HasCellProperty (inline) 161ms 0.19% 69.91% 1968ms 2.33% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.91% 1957ms 2.32% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.91% 1956ms 2.32% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.91% 1922ms 2.28% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.91% 1895ms 2.25% std::_Rb_tree::_M_insert_unique (inline) 21ms 0.025% 69.94% 1877ms 2.22% Cell::GetCellData 221ms 0.26% 70.20% 1856ms 2.20% std::_Rb_tree_const_iterator::operator++ (inline) 71ms 0.084% 70.29% 1802ms 2.14% VertexMesh::GetVolumeOfElement 3ms 0.0036% 70.29% 1720ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 129ms 0.15% 70.44% 1710ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 36ms 0.043% 70.48% 1704ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0012% 70.49% 1689ms 2.00% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.49% 1689ms 2.00% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 23ms 0.027% 70.51% 1687ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0012% 70.51% 1608ms 1.91% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0012% 70.52% 1594ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1026ms 1.22% 71.73% 1566ms 1.86% std::_Rb_tree::equal_range (inline) 364ms 0.43% 72.16% 1546ms 1.83% std::type_info::operator== (inline) 47ms 0.056% 72.22% 1532ms 1.82% MutableVertexMesh::CheckForSwapsFromShortEdges 1463ms 1.73% 73.95% 1463ms 1.73% std::_Rb_tree_increment 0 0% 73.95% 1428ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 32ms 0.038% 73.99% 1309ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.028% 74.02% 1218ms 1.44% VertexMesh::GetSurfaceAreaOfElement 33ms 0.039% 74.06% 1188ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 51ms 0.06% 74.12% 1158ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.12% 1150ms 1.36% tcache_get (inline) 1150ms 1.36% 75.48% 1150ms 1.36% tcache_get_n (inline) 38ms 0.045% 75.53% 1141ms 1.35% Node::RemoveElement 6ms 0.0071% 75.53% 1105ms 1.31% std::set::erase (inline) 0 0% 75.53% 1078ms 1.28% boost::numeric::ublas::norm_2 (inline) 91ms 0.11% 75.64% 1069ms 1.27% CellPropertyCollection::AddProperty 480ms 0.57% 76.21% 1066ms 1.26% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 62ms 0.073% 76.28% 1052ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0012% 76.29% 1033ms 1.22% OffLatticeSimulation::ApplyBoundaries 0 0% 76.29% 1009ms 1.20% boost::numeric::ublas::vector_binary::operator() (inline) 1004ms 1.19% 77.48% 1004ms 1.19% [libchaste_cell_based.so] 51ms 0.06% 77.54% 1003ms 1.19% std::less::operator() (inline) 788ms 0.93% 78.47% 952ms 1.13% std::operator< (inline) 0 0% 78.47% 898ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 20ms 0.024% 78.49% 885ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 24ms 0.028% 78.52% 862ms 1.02% CellPropertyRegistry::Get 4ms 0.0047% 78.53% 855ms 1.01% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 74ms 0.088% 78.61% 854ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 70ms 0.083% 78.70% 852ms 1.01% std::_Rb_tree::find (inline) 847ms 1.00% 79.70% 847ms 1.00% std::_Rb_tree_insert_and_rebalance 0 0% 79.70% 815ms 0.97% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0095% 79.71% 815ms 0.97% boost::numeric::ublas::c_vector::swap (inline) 70ms 0.083% 79.79% 807ms 0.96% std::swap_ranges (inline) 0 0% 79.79% 805ms 0.95% std::_Rb_tree::clear (inline) 0 0% 79.79% 792ms 0.94% std::map::clear (inline) 84ms 0.1% 79.89% 784ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 79.89% 784ms 0.93% boost::shared_ptr::~shared_ptr (inline) 776ms 0.92% 80.81% 776ms 0.92% Node::rGetLocation 12ms 0.014% 80.83% 760ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.83% 744ms 0.88% std::map::find (inline) 0 0% 80.83% 737ms 0.87% std::iter_swap (inline) 737ms 0.87% 81.70% 737ms 0.87% std::swap (inline) 95ms 0.11% 81.81% 734ms 0.87% boost::numeric::ublas::detail::equals 3ms 0.0036% 81.82% 694ms 0.82% VertexMeshWriter::MakeVtkMesh 642ms 0.76% 82.58% 668ms 0.79% boost::detail::sp_counted_base::release 667ms 0.79% 83.37% 667ms 0.79% std::vector::size (inline) 0 0% 83.37% 611ms 0.72% boost::numeric::ublas::norm_inf (inline) 289ms 0.34% 83.71% 611ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 338ms 0.4% 84.11% 610ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 65ms 0.077% 84.19% 604ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 18ms 0.021% 84.21% 591ms 0.7% MutableElement::RegisterWithEdges (inline) 183ms 0.22% 84.43% 588ms 0.7% std::__new_allocator::construct (inline) 0 0% 84.43% 588ms 0.7% std::allocator_traits::construct (inline) 275ms 0.33% 84.75% 583ms 0.69% Edge::GetMapIndex 0 0% 84.75% 581ms 0.69% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 14ms 0.017% 84.77% 580ms 0.69% Edge::AddElement 578ms 0.69% 85.46% 578ms 0.69% [libchaste_mesh.so] 0 0% 85.46% 575ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 571ms 0.68% 86.13% 571ms 0.68% [libstdc++.so.6.0.33] 0 0% 86.13% 539ms 0.64% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.13% 538ms 0.64% std::_Vector_base::_M_allocate (inline) 76ms 0.09% 86.22% 536ms 0.64% MutableElement::GetNodeLocalIndex 162ms 0.19% 86.41% 521ms 0.62% boost::shared_ptr::shared_ptr (inline) 0 0% 86.41% 506ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.02% 86.43% 506ms 0.6% std::_Rb_tree::_M_insert_node (inline) 21ms 0.025% 86.46% 499ms 0.59% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.46% 499ms 0.59% boost::numeric::ublas::vector::vector (inline) 489ms 0.58% 87.04% 489ms 0.58% Node::GetIndex 1ms 0.0012% 87.04% 485ms 0.57% vtkPolygon::New 0 0% 87.04% 483ms 0.57% vtkPolygon::vtkPolygon 16ms 0.019% 87.06% 481ms 0.57% MutableElement::RegisterWithNodes (inline) 24ms 0.028% 87.09% 466ms 0.55% Node::AddElement 9ms 0.011% 87.10% 463ms 0.55% std::vector::_M_default_append (inline) 439ms 0.52% 87.62% 439ms 0.52% tcache_put (inline) 435ms 0.52% 88.13% 435ms 0.52% boost::shared_ptr::operator-> (inline)