File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 90180ms, 88.07% of 102391ms total Dropped 1108 nodes (cum <= 511.95ms) flat flat% sum% cum cum% 0 0% 0% 102138ms 99.75% __libc_start_call_main 0 0% 0% 102138ms 99.75% __libc_start_main_impl 0 0% 0% 102138ms 99.75% _start 0 0% 0% 102116ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 102116ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 102116ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 102116ms 99.73% main 0 0% 0% 102080ms 99.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 102080ms 99.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 102080ms 99.70% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00098% 0.00098% 102073ms 99.69% AbstractCellBasedSimulation::Solve 6ms 0.0059% 0.0068% 53454ms 52.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.015% 0.021% 50075ms 48.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 75ms 0.073% 0.095% 48654ms 47.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 357ms 0.35% 0.44% 37689ms 36.81% NagaiHondaForce::AddForceContribution 0 0% 0.44% 35626ms 34.79% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0029% 0.45% 21095ms 20.60% VertexBasedCellPopulation::Update 3ms 0.0029% 0.45% 20961ms 20.47% MutableVertexMesh::ReMesh 109ms 0.11% 0.56% 17456ms 17.05% Cell::ReadyToDivide 8787ms 8.58% 9.14% 16979ms 16.58% Cylindrical2dVertexMesh::GetVectorFromAtoB 31ms 0.03% 9.17% 16277ms 15.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 101ms 0.099% 9.27% 15436ms 15.08% NagaiHondaForce::GetAdhesionParameter 78ms 0.076% 9.34% 13932ms 13.61% SimpleWntCellCycleModel::UpdateCellCyclePhase 385ms 0.38% 9.72% 13102ms 12.80% boost::numeric::ublas::c_vector::c_vector (partial-inline) 66ms 0.064% 9.78% 12905ms 12.60% CellPropertyCollection::GetPropertiesType (inline) 736ms 0.72% 10.50% 12808ms 12.51% std::__new_allocator::allocate (inline) 0 0% 10.50% 12298ms 12.01% std::allocator_traits::allocate (inline) 0 0% 10.50% 12055ms 11.77% std::_Rb_tree::_M_create_node (inline) 862ms 0.84% 11.34% 12008ms 11.73% operator new 258ms 0.25% 11.60% 11719ms 11.45% boost::numeric::ublas::vector_assign (inline) 0 0% 11.60% 11696ms 11.42% std::_Rb_tree::_M_get_node (inline) 3683ms 3.60% 15.19% 10813ms 10.56% __GI___libc_malloc 108ms 0.11% 15.30% 10715ms 10.46% AbstractCellProperty::IsSubType (inline) 53ms 0.052% 15.35% 10676ms 10.43% AbstractTargetAreaModifier::UpdateTargetAreas 108ms 0.11% 15.46% 10599ms 10.35% VertexBasedCellPopulation::GetDampingConstant 45ms 0.044% 15.50% 10584ms 10.34% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 2652ms 2.59% 18.09% 10576ms 10.33% __dynamic_cast 0 0% 18.09% 10379ms 10.14% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.0078% 18.10% 10282ms 10.04% AbstractCellBasedSimulation::DoCellBirth 166ms 0.16% 18.26% 9474ms 9.25% MutableVertexMesh::CheckForIntersections 993ms 0.97% 19.23% 8905ms 8.70% std::_Rb_tree::_M_erase 0 0% 19.23% 8893ms 8.69% std::_Rb_tree::_M_drop_node (inline) 469ms 0.46% 19.69% 8470ms 8.27% std::map::operator[] (partial-inline) 356ms 0.35% 20.03% 8453ms 8.26% std::_Rb_tree::~_Rb_tree (inline) 2476ms 2.42% 22.45% 8452ms 8.25% boost::numeric::ublas::indexing_vector_assign 0 0% 22.45% 8060ms 7.87% std::set::~set (inline) 97ms 0.095% 22.55% 8042ms 7.85% std::__new_allocator::deallocate (inline) 0 0% 22.55% 8026ms 7.84% std::allocator_traits::deallocate (inline) 63ms 0.062% 22.61% 8013ms 7.83% Cell::GetMutationState 0 0% 22.61% 7961ms 7.78% std::_Rb_tree::_M_put_node (inline) 2051ms 2.00% 24.61% 7792ms 7.61% __GI___libc_free 52ms 0.051% 24.66% 7740ms 7.56% VertexBasedCellPopulation::GetLocationOfCellCentre 8ms 0.0078% 24.67% 7461ms 7.29% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 24.67% 7459ms 7.28% std::set::insert (inline) 398ms 0.39% 25.06% 7453ms 7.28% VertexMesh::GetNextEdgeGradientOfElementAtNode 556ms 0.54% 25.60% 7239ms 7.07% VertexMesh::GetCentroidOfElement 555ms 0.54% 26.14% 7065ms 6.90% VertexMesh::ElementIncludesPoint 826ms 0.81% 26.95% 6900ms 6.74% std::_Rb_tree::_M_insert_ (inline) 100ms 0.098% 27.05% 6511ms 6.36% std::_Rb_tree::_Rb_tree (partial-inline) 6395ms 6.25% 33.29% 6395ms 6.25% __strcmp_evex 605ms 0.59% 33.89% 6203ms 6.06% std::_Rb_tree::_M_copy (inline) 6176ms 6.03% 39.92% 6176ms 6.03% boost::numeric::ublas::c_vector::operator() 7ms 0.0068% 39.92% 6120ms 5.98% std::set::set (inline) 2361ms 2.31% 42.23% 6039ms 5.90% std::_Rb_tree::_M_lower_bound (inline) 71ms 0.069% 42.30% 6028ms 5.89% std::set_intersection (inline) 213ms 0.21% 42.51% 5957ms 5.82% std::__set_intersection 141ms 0.14% 42.65% 5865ms 5.73% SimpleWntCellCycleModel::GetWntLevel 949ms 0.93% 43.57% 5792ms 5.66% AbstractMesh::GetDistanceBetweenNodes 4942ms 4.83% 48.40% 5683ms 5.55% _int_free 142ms 0.14% 48.54% 5618ms 5.49% WntConcentration::GetWntLevel 699ms 0.68% 49.22% 5420ms 5.29% std::_Rb_tree::_M_clone_node (inline) 20ms 0.02% 49.24% 5400ms 5.27% MutableVertexMesh::RemoveDeletedNodes 4408ms 4.31% 53.54% 5263ms 5.14% _int_malloc 54ms 0.053% 53.60% 5249ms 5.13% EdgeHelper::RemoveDeletedEdges 0 0% 53.60% 5164ms 5.04% std::_Rb_tree::lower_bound (inline) 0 0% 53.60% 5164ms 5.04% std::map::lower_bound (inline) 2427ms 2.37% 55.97% 5146ms 5.03% __cxxabiv1::__si_class_type_info::__do_dyncast 593ms 0.58% 56.55% 5092ms 4.97% boost::numeric::ublas::c_vector::operator[] (inline) 23ms 0.022% 56.57% 4998ms 4.88% EdgeHelper::UpdateEdgesMapKey 0 0% 56.57% 4652ms 4.54% std::insert_iterator::operator= (inline) 33ms 0.032% 56.60% 4507ms 4.40% Cell::GetCellProliferativeType 99ms 0.097% 56.70% 4498ms 4.39% MutableElement::ResetIndex 57ms 0.056% 56.75% 4429ms 4.33% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.75% 4344ms 4.24% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 56.75% 4241ms 4.14% AbstractCellBasedSimulation::DoCellRemoval (inline) 4173ms 4.08% 60.83% 4173ms 4.08% boost::numeric::ublas::same_impl_ex 148ms 0.14% 60.97% 3458ms 3.38% AbstractCellProperty::IsType (inline) 97ms 0.095% 61.07% 3311ms 3.23% Cell::SetCellProliferativeType 47ms 0.046% 61.11% 3310ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3265ms 3.19% 64.30% 3265ms 3.19% [libchaste_cell_based.so] 3133ms 3.06% 67.36% 3133ms 3.06% std::_Rb_tree::_S_right (inline) 4ms 0.0039% 67.37% 3115ms 3.04% std::_Rb_tree::_M_insert_unique 135ms 0.13% 67.50% 2974ms 2.90% boost::detail::shared_count::~shared_count (inline) 0 0% 67.50% 2974ms 2.90% boost::shared_ptr::~shared_ptr (inline) 728ms 0.71% 68.21% 2877ms 2.81% AbstractElement::GetNodeLocation 10ms 0.0098% 68.22% 2831ms 2.76% AbstractCellPopulation::Iterator::operator++ (inline) 201ms 0.2% 68.42% 2827ms 2.76% AbstractCellPopulation::Iterator::IsRealCell (inline) 2762ms 2.70% 71.11% 2792ms 2.73% boost::detail::sp_counted_base::release 33ms 0.032% 71.15% 2785ms 2.72% std::_Rb_tree::_M_emplace_hint_unique 55ms 0.054% 71.20% 2567ms 2.51% std::_Rb_tree::erase 14ms 0.014% 71.21% 2508ms 2.45% Cell::GetCellData 0 0% 71.21% 2444ms 2.39% boost::numeric::ublas::c_vector::assign (inline) 45ms 0.044% 71.26% 2410ms 2.35% CellPropertyCollection::HasProperty 147ms 0.14% 71.40% 2401ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.40% 2345ms 2.29% Cell::HasCellProperty (inline) 0 0% 71.40% 2301ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 57ms 0.056% 71.46% 2287ms 2.23% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.46% 2284ms 2.23% AbstractCellPopulation::WriteResultsToFiles 471ms 0.46% 71.92% 2274ms 2.22% AbstractCellProperty::IsSame 353ms 0.34% 72.26% 2259ms 2.21% std::_Rb_tree_const_iterator::operator++ (inline) 23ms 0.022% 72.28% 2195ms 2.14% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2174ms 2.12% 74.41% 2174ms 2.12% [libchaste_mesh.so] 313ms 0.31% 74.71% 2007ms 1.96% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 236ms 0.23% 74.94% 2004ms 1.96% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 74.94% 1884ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.94% 1870ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 216ms 0.21% 75.15% 1803ms 1.76% std::type_info::operator== (inline) 101ms 0.099% 75.25% 1786ms 1.74% VertexMesh::GetVolumeOfElement 85ms 0.083% 75.34% 1747ms 1.71% AbstractCellPopulation::GetLocationIndexUsingCell 142ms 0.14% 75.47% 1738ms 1.70% CellPropertyCollection::AddProperty 4ms 0.0039% 75.48% 1699ms 1.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.48% 1699ms 1.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.002% 75.48% 1677ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.48% 1676ms 1.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 65ms 0.063% 75.54% 1539ms 1.50% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.002% 75.55% 1512ms 1.48% OffLatticeSimulation::ApplyBoundaries 0 0% 75.55% 1491ms 1.46% boost::numeric::ublas::vector_binary::operator() (inline) 4ms 0.0039% 75.55% 1476ms 1.44% tcache_get (inline) 1472ms 1.44% 76.99% 1472ms 1.44% tcache_get_n (inline) 63ms 0.062% 77.05% 1425ms 1.39% std::_Rb_tree::_M_erase_aux (partial-inline) 86ms 0.084% 77.13% 1404ms 1.37% VertexMesh::GetSurfaceAreaOfElement 62ms 0.061% 77.19% 1327ms 1.30% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1323ms 1.29% 78.49% 1323ms 1.29% std::_Rb_tree_increment 784ms 0.77% 79.25% 1259ms 1.23% std::_Rb_tree::equal_range (inline) 44ms 0.043% 79.29% 1214ms 1.19% Node::RemoveElement 58ms 0.057% 79.35% 1202ms 1.17% CellPropertyRegistry::Get 2ms 0.002% 79.35% 1171ms 1.14% std::set::erase (inline) 112ms 0.11% 79.46% 1169ms 1.14% boost::numeric::ublas::vector_reference::operator() (inline) 13ms 0.013% 79.47% 1144ms 1.12% MutableElement::RegisterWithEdges (inline) 37ms 0.036% 79.51% 1131ms 1.10% Edge::AddElement 0 0% 79.51% 1049ms 1.02% CellPropertyCollection::~CellPropertyCollection (inline) 9ms 0.0088% 79.52% 1046ms 1.02% boost::numeric::ublas::detail::expression_type_check (inline) 1022ms 1% 80.52% 1022ms 1% [libstdc++.so.6.0.33] 149ms 0.15% 80.66% 1013ms 0.99% boost::numeric::ublas::detail::equals 1007ms 0.98% 81.65% 1007ms 0.98% std::_Rb_tree_insert_and_rebalance 1001ms 0.98% 82.62% 1001ms 0.98% Node::rGetLocation 0 0% 82.62% 978ms 0.96% boost::numeric::ublas::norm_2 (inline) 359ms 0.35% 82.98% 954ms 0.93% boost::numeric::ublas::vector_norm_2::apply 103ms 0.1% 83.08% 954ms 0.93% std::_Rb_tree::find (inline) 0 0% 83.08% 942ms 0.92% std::__new_allocator::destroy (inline) 0 0% 83.08% 942ms 0.92% std::allocator_traits::destroy (inline) 0 0% 83.08% 936ms 0.91% std::_Rb_tree::_M_destroy_node (inline) 12ms 0.012% 83.09% 903ms 0.88% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.09% 874ms 0.85% VertexMeshWriter::MakeVtkMesh 671ms 0.66% 83.74% 872ms 0.85% CellPropertyCollection::GetProperty 0 0% 83.74% 861ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.00098% 83.74% 861ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 145ms 0.14% 83.89% 860ms 0.84% std::swap_ranges (inline) 834ms 0.81% 84.70% 834ms 0.81% tcache_put (inline) 0 0% 84.70% 821ms 0.8% std::map::find (inline) 0 0% 84.70% 817ms 0.8% std::_Rb_tree::clear (inline) 57ms 0.056% 84.76% 794ms 0.78% std::less::operator() (inline) 0 0% 84.76% 792ms 0.77% std::map::clear (inline) 49ms 0.048% 84.80% 745ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.80% 737ms 0.72% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.026% 84.83% 737ms 0.72% std::_Rb_tree::_M_insert_node (inline) 563ms 0.55% 85.38% 737ms 0.72% std::operator< (inline) 0 0% 85.38% 731ms 0.71% boost::numeric::ublas::norm_inf (inline) 249ms 0.24% 85.62% 731ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.62% 715ms 0.7% std::iter_swap (inline) 715ms 0.7% 86.32% 715ms 0.7% std::swap (inline) 27ms 0.026% 86.35% 669ms 0.65% AbstractNumericalMethod::DetectStepSizeExceptions 312ms 0.3% 86.65% 660ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 659ms 0.64% 87.30% 659ms 0.64% std::vector::size (inline) 71ms 0.069% 87.37% 651ms 0.64% MutableElement::GetNodeLocalIndex 0 0% 87.37% 648ms 0.63% vtkPolygon::New 0 0% 87.37% 645ms 0.63% vtkPolygon::vtkPolygon 103ms 0.1% 87.47% 642ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 1ms 0.00098% 87.47% 602ms 0.59% std::_Vector_base::_M_allocate (inline) 22ms 0.021% 87.49% 595ms 0.58% MutableElement::RegisterWithNodes (inline) 45ms 0.044% 87.53% 549ms 0.54% Node::AddElement 541ms 0.53% 88.06% 541ms 0.53% Node::GetIndex 12ms 0.012% 88.07% 522ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.07% 522ms 0.51% boost::numeric::ublas::vector::vector (inline) 2ms 0.002% 88.07% 515ms 0.5% vtkCell::vtkCell