File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96135ms, 88.29% of 108886ms total Dropped 1050 nodes (cum <= 544.43ms) flat flat% sum% cum cum% 0 0% 0% 108439ms 99.59% __libc_start_call_main 0 0% 0% 108439ms 99.59% __libc_start_main_impl 0 0% 0% 108439ms 99.59% _start 0 0% 0% 108420ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108420ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108420ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108420ms 99.57% main 0 0% 0% 108385ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108385ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108385ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00092% 0.00092% 108378ms 99.53% AbstractCellBasedSimulation::Solve 19ms 0.017% 0.018% 55928ms 51.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.032% 52578ms 48.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 144ms 0.13% 0.16% 51549ms 47.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 373ms 0.34% 0.51% 40153ms 36.88% NagaiHondaForce::AddForceContribution 0 0% 0.51% 39770ms 36.52% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.51% 24995ms 22.96% VertexBasedCellPopulation::Update 0 0% 0.51% 24872ms 22.84% MutableVertexMesh::ReMesh 15008ms 13.78% 14.29% 23715ms 21.78% Cylindrical2dVertexMesh::GetVectorFromAtoB 99ms 0.091% 14.38% 17334ms 15.92% Cell::ReadyToDivide 80ms 0.073% 14.45% 16120ms 14.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 421ms 0.39% 14.84% 15231ms 13.99% boost::numeric::ublas::c_vector::c_vector (partial-inline) 370ms 0.34% 15.18% 14994ms 13.77% NagaiHondaForce::GetAdhesionParameter 127ms 0.12% 15.30% 13755ms 12.63% SimpleWntCellCycleModel::UpdateCellCyclePhase 389ms 0.36% 15.65% 13627ms 12.51% boost::numeric::ublas::vector_assign (inline) 127ms 0.12% 15.77% 13114ms 12.04% MutableVertexMesh::CheckForIntersections 114ms 0.1% 15.88% 13055ms 11.99% CellPropertyCollection::GetPropertiesType (inline) 63ms 0.058% 15.93% 10864ms 9.98% VertexBasedCellPopulation::GetDampingConstant 3081ms 2.83% 18.76% 10718ms 9.84% __dynamic_cast 101ms 0.093% 18.86% 10618ms 9.75% AbstractCellProperty::IsSubType (inline) 75ms 0.069% 18.93% 10308ms 9.47% AbstractTargetAreaModifier::UpdateTargetAreas 63ms 0.058% 18.98% 10205ms 9.37% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.025% 19.01% 10159ms 9.33% AbstractCellBasedSimulation::DoCellBirth 2895ms 2.66% 21.67% 10152ms 9.32% boost::numeric::ublas::indexing_vector_assign 1263ms 1.16% 22.83% 9981ms 9.17% std::__new_allocator::allocate (inline) 0 0% 22.83% 9432ms 8.66% std::allocator_traits::allocate (inline) 0 0% 22.83% 9422ms 8.65% std::_Rb_tree::_M_create_node (inline) 1335ms 1.23% 24.05% 9332ms 8.57% std::_Rb_tree::_M_erase 771ms 0.71% 24.76% 9181ms 8.43% VertexMesh::ElementIncludesPoint 322ms 0.3% 25.06% 8993ms 8.26% VertexMesh::GetNextEdgeGradientOfElementAtNode 26ms 0.024% 25.08% 8886ms 8.16% VertexBasedCellPopulation::GetLocationOfCellCentre 871ms 0.8% 25.88% 8803ms 8.08% operator new 0 0% 25.88% 8766ms 8.05% std::_Rb_tree::_M_get_node (inline) 202ms 0.19% 26.07% 8563ms 7.86% std::_Rb_tree::~_Rb_tree (inline) 519ms 0.48% 26.54% 8441ms 7.75% VertexMesh::GetCentroidOfElement 80ms 0.073% 26.62% 8375ms 7.69% Cell::GetMutationState 0 0% 26.62% 8330ms 7.65% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.62% 8316ms 7.64% std::_Rb_tree::_M_drop_node (inline) 224ms 0.21% 26.82% 8105ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 26.82% 8090ms 7.43% std::set::~set (inline) 3176ms 2.92% 29.74% 8081ms 7.42% __GI___libc_free 0 0% 29.74% 8075ms 7.42% std::allocator_traits::deallocate (inline) 0 0% 29.74% 8027ms 7.37% std::_Rb_tree::_M_put_node (inline) 3342ms 3.07% 32.81% 7716ms 7.09% __GI___libc_malloc 29ms 0.027% 32.83% 7428ms 6.82% MutableVertexMesh::RemoveDeletedNodesAndElements 496ms 0.46% 33.29% 7227ms 6.64% std::map::operator[] (partial-inline) 1435ms 1.32% 34.61% 7171ms 6.59% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 128ms 0.12% 34.73% 6772ms 6.22% std::_Rb_tree::_Rb_tree (partial-inline) 122ms 0.11% 34.84% 6494ms 5.96% SimpleWntCellCycleModel::GetWntLevel 634ms 0.58% 35.42% 6398ms 5.88% std::_Rb_tree::_M_copy (inline) 7ms 0.0064% 35.43% 6347ms 5.83% std::set::set (inline) 6284ms 5.77% 41.20% 6284ms 5.77% boost::numeric::ublas::c_vector::operator() 119ms 0.11% 41.31% 6249ms 5.74% WntConcentration::GetWntLevel 6069ms 5.57% 46.88% 6069ms 5.57% __strcmp_avx2 2431ms 2.23% 49.11% 5723ms 5.26% std::_Rb_tree::_M_lower_bound (inline) 715ms 0.66% 49.77% 5525ms 5.07% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.77% 5398ms 4.96% std::set::insert (inline) 2654ms 2.44% 52.21% 5302ms 4.87% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.02% 52.23% 5154ms 4.73% MutableVertexMesh::RemoveDeletedNodes 1838ms 1.69% 53.92% 5097ms 4.68% boost::numeric::ublas::c_vector::operator[] (inline) 42ms 0.039% 53.95% 4994ms 4.59% EdgeHelper::RemoveDeletedEdges 4583ms 4.21% 58.16% 4901ms 4.50% _int_free 38ms 0.035% 58.20% 4762ms 4.37% EdgeHelper::UpdateEdgesMapKey 205ms 0.19% 58.39% 4646ms 4.27% MutableElement::ResetIndex 0 0% 58.39% 4594ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.39% 4578ms 4.20% std::_Rb_tree::lower_bound (inline) 0 0% 58.39% 4578ms 4.20% std::map::lower_bound (inline) 54ms 0.05% 58.44% 4569ms 4.20% std::set_intersection (inline) 514ms 0.47% 58.91% 4545ms 4.17% std::_Rb_tree::_M_insert_ (inline) 272ms 0.25% 59.16% 4515ms 4.15% std::__set_intersection 4211ms 3.87% 63.02% 4211ms 3.87% boost::numeric::ublas::same_impl_ex 87ms 0.08% 63.10% 3892ms 3.57% AbstractCellPopulation::GetCellUsingLocationIndex 28ms 0.026% 63.13% 3851ms 3.54% Cell::GetCellProliferativeType 70ms 0.064% 63.19% 3620ms 3.32% AbstractCellProperty::IsType (inline) 9ms 0.0083% 63.20% 3510ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 766ms 0.7% 63.91% 3366ms 3.09% AbstractElement::GetNodeLocation 0 0% 63.91% 3247ms 2.98% std::insert_iterator::operator= (inline) 0 0% 63.91% 3048ms 2.80% boost::numeric::ublas::c_vector::assign (inline) 2157ms 1.98% 65.89% 3022ms 2.78% _int_malloc 67ms 0.062% 65.95% 3013ms 2.77% Cell::SetCellProliferativeType 33ms 0.03% 65.98% 2880ms 2.64% std::_Rb_tree::erase 0 0% 65.98% 2877ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 629ms 0.58% 66.56% 2871ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 450ms 0.41% 66.97% 2822ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 2754ms 2.53% 69.50% 2754ms 2.53% std::_Rb_tree::_S_right (inline) 277ms 0.25% 69.75% 2621ms 2.41% VertexMesh::GetAreaGradientOfElementAtNode 668ms 0.61% 70.37% 2562ms 2.35% AbstractCellProperty::IsSame 2ms 0.0018% 70.37% 2521ms 2.32% std::_Rb_tree::_M_insert_unique 49ms 0.045% 70.41% 2491ms 2.29% CellPropertyCollection::HasProperty 0 0% 70.41% 2491ms 2.29% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.41% 2389ms 2.19% Cell::HasCellProperty (inline) 0 0% 70.41% 2354ms 2.16% AbstractCellPopulation::WriteResultsToFiles 129ms 0.12% 70.53% 2303ms 2.12% VertexMesh::GetVolumeOfElement 3ms 0.0028% 70.54% 2273ms 2.09% AbstractCellPopulation::Iterator::operator++ (inline) 100ms 0.092% 70.63% 2267ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 186ms 0.17% 70.80% 2226ms 2.04% AbstractCellPopulation::Iterator::IsRealCell (inline) 28ms 0.026% 70.82% 2193ms 2.01% Cell::GetCellData 2193ms 2.01% 72.84% 2193ms 2.01% std::_Rb_tree_increment 25ms 0.023% 72.86% 2112ms 1.94% std::_Rb_tree::_M_emplace_hint_unique 1274ms 1.17% 74.03% 1924ms 1.77% std::_Rb_tree::equal_range (inline) 0 0% 74.03% 1922ms 1.77% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.03% 1916ms 1.76% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00092% 74.03% 1915ms 1.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.03% 1915ms 1.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 436ms 0.4% 74.43% 1894ms 1.74% std::type_info::operator== (inline) 76ms 0.07% 74.50% 1877ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 30ms 0.028% 74.53% 1737ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.53% 1726ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.017% 74.55% 1577ms 1.45% VertexMesh::GetSurfaceAreaOfElement 30ms 0.028% 74.57% 1546ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 96ms 0.088% 74.66% 1541ms 1.42% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 143ms 0.13% 74.79% 1527ms 1.40% boost::numeric::ublas::vector_reference::operator() (inline) 54ms 0.05% 74.84% 1490ms 1.37% Node::RemoveElement 163ms 0.15% 74.99% 1483ms 1.36% CellPropertyCollection::AddProperty 19ms 0.017% 75.01% 1444ms 1.33% std::set::erase (inline) 0 0% 75.01% 1418ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.01% 1413ms 1.30% OffLatticeSimulation::ApplyBoundaries 78ms 0.072% 75.08% 1182ms 1.09% std::less::operator() (inline) 0 0% 75.08% 1182ms 1.09% tcache_get (inline) 1182ms 1.09% 76.17% 1182ms 1.09% tcache_get_n (inline) 1160ms 1.07% 77.23% 1160ms 1.07% [libchaste_cell_based.so] 0 0% 77.23% 1152ms 1.06% boost::numeric::ublas::norm_2 (inline) 501ms 0.46% 77.69% 1142ms 1.05% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1133ms 1.04% 78.73% 1133ms 1.04% Node::rGetLocation 22ms 0.02% 78.75% 1119ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 82ms 0.075% 78.83% 1105ms 1.01% std::_Rb_tree::find (inline) 908ms 0.83% 79.66% 1104ms 1.01% std::operator< (inline) 71ms 0.065% 79.73% 1101ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 79.73% 1092ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1091ms 1.00% 80.73% 1091ms 1.00% std::_Rb_tree_insert_and_rebalance 4ms 0.0037% 80.73% 1042ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 23ms 0.021% 80.75% 1025ms 0.94% CellPropertyRegistry::Get 23ms 0.021% 80.78% 1010ms 0.93% boost::numeric::ublas::detail::expression_type_check (inline) 158ms 0.15% 80.92% 979ms 0.9% boost::numeric::ublas::detail::equals 0 0% 80.92% 974ms 0.89% std::_Rb_tree::clear (inline) 0 0% 80.92% 957ms 0.88% std::map::clear (inline) 129ms 0.12% 81.04% 937ms 0.86% boost::detail::shared_count::~shared_count (inline) 0 0% 81.04% 937ms 0.86% boost::shared_ptr::~shared_ptr (inline) 936ms 0.86% 81.90% 936ms 0.86% [libchaste_mesh.so] 0 0% 81.90% 917ms 0.84% std::map::find (inline) 0 0% 81.90% 898ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 81.90% 898ms 0.82% boost::numeric::ublas::c_vector::swap 85ms 0.078% 81.98% 893ms 0.82% std::swap_ranges (inline) 884ms 0.81% 82.79% 884ms 0.81% std::vector::size (inline) 371ms 0.34% 83.13% 875ms 0.8% Edge::GetMapIndex 183ms 0.17% 83.30% 828ms 0.76% boost::shared_ptr::shared_ptr (inline) 1ms 0.00092% 83.30% 827ms 0.76% VertexMeshWriter::MakeVtkMesh 809ms 0.74% 84.05% 809ms 0.74% std::swap (inline) 0 0% 84.05% 808ms 0.74% std::iter_swap (inline) 115ms 0.11% 84.15% 795ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 101ms 0.093% 84.24% 794ms 0.73% MutableElement::GetNodeLocalIndex 36ms 0.033% 84.28% 791ms 0.73% Edge::AddElement 24ms 0.022% 84.30% 790ms 0.73% MutableElement::RegisterWithEdges (inline) 780ms 0.72% 85.02% 790ms 0.73% boost::detail::sp_counted_base::release 465ms 0.43% 85.44% 774ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.44% 763ms 0.7% boost::numeric::ublas::norm_inf (inline) 385ms 0.35% 85.80% 763ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.80% 756ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 724ms 0.66% 86.46% 724ms 0.66% Node::GetIndex 104ms 0.096% 86.56% 708ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.56% 708ms 0.65% std::allocator_traits::construct (inline) 0 0% 86.56% 689ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 32ms 0.029% 86.59% 689ms 0.63% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.59% 666ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.59% 656ms 0.6% std::_Rb_tree::_M_construct_node (inline) 605ms 0.56% 87.14% 645ms 0.59% boost::detail::shared_count::shared_count (inline) 25ms 0.023% 87.17% 618ms 0.57% MutableElement::RegisterWithNodes (inline) 594ms 0.55% 87.71% 594ms 0.55% [libstdc++.so.6.0.33] 0 0% 87.71% 587ms 0.54% vtkPolygon::New 0 0% 87.71% 586ms 0.54% vtkPolygon::vtkPolygon 28ms 0.026% 87.74% 577ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.74% 577ms 0.53% boost::numeric::ublas::vector::vector (inline) 34ms 0.031% 87.77% 573ms 0.53% Node::AddElement 9ms 0.0083% 87.78% 565ms 0.52% std::vector::_M_default_append (inline) 559ms 0.51% 88.29% 559ms 0.51% operator delete 0 0% 88.29% 557ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)