File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 53583ms, 88.83% of 60321ms total Dropped 941 nodes (cum <= 301.61ms) flat flat% sum% cum cum% 0 0% 0% 60061ms 99.57% __libc_start_call_main 0 0% 0% 60061ms 99.57% __libc_start_main_impl 0 0% 0% 60061ms 99.57% _start 0 0% 0% 60046ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60046ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60046ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60046ms 99.54% main 0 0% 0% 60012ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60012ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60012ms 99.49% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0017% 0.0017% 60007ms 99.48% AbstractCellBasedSimulation::Solve 11ms 0.018% 0.02% 31386ms 52.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.013% 0.033% 29315ms 48.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 51ms 0.085% 0.12% 28768ms 47.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 137ms 0.23% 0.34% 21974ms 36.43% NagaiHondaForce::AddForceContribution 0 0% 0.34% 21221ms 35.18% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.005% 0.35% 12869ms 21.33% VertexBasedCellPopulation::Update 1ms 0.0017% 0.35% 12785ms 21.19% MutableVertexMesh::ReMesh 6491ms 10.76% 11.11% 11370ms 18.85% Cylindrical2dVertexMesh::GetVectorFromAtoB 38ms 0.063% 11.18% 9961ms 16.51% Cell::ReadyToDivide 30ms 0.05% 11.22% 9385ms 15.56% AbstractPhaseBasedCellCycleModel::ReadyToDivide 59ms 0.098% 11.32% 8676ms 14.38% NagaiHondaForce::GetAdhesionParameter 23ms 0.038% 11.36% 8142ms 13.50% SimpleWntCellCycleModel::UpdateCellCyclePhase 211ms 0.35% 11.71% 7774ms 12.89% boost::numeric::ublas::c_vector::c_vector (partial-inline) 45ms 0.075% 11.79% 7256ms 12.03% CellPropertyCollection::GetPropertiesType (inline) 212ms 0.35% 12.14% 6852ms 11.36% boost::numeric::ublas::vector_assign (inline) 42ms 0.07% 12.21% 6570ms 10.89% VertexBasedCellPopulation::GetDampingConstant 399ms 0.66% 12.87% 6479ms 10.74% std::__new_allocator::allocate (inline) 68ms 0.11% 12.98% 6232ms 10.33% MutableVertexMesh::CheckForIntersections 0 0% 12.98% 6219ms 10.31% std::allocator_traits::allocate (inline) 1354ms 2.24% 15.23% 6103ms 10.12% __dynamic_cast 619ms 1.03% 16.25% 6096ms 10.11% operator new 43ms 0.071% 16.32% 6080ms 10.08% AbstractCellProperty::IsSubType (inline) 0 0% 16.32% 6037ms 10.01% std::_Rb_tree::_M_create_node (inline) 29ms 0.048% 16.37% 5963ms 9.89% AbstractTargetAreaModifier::UpdateTargetAreas 18ms 0.03% 16.40% 5917ms 9.81% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 16.40% 5848ms 9.69% std::_Rb_tree::_M_get_node (inline) 5ms 0.0083% 16.41% 5824ms 9.66% AbstractCellBasedSimulation::DoCellBirth 605ms 1.00% 17.41% 5770ms 9.57% std::_Rb_tree::_M_erase 0 0% 17.41% 5679ms 9.41% std::_Rb_tree::_M_drop_node (inline) 269ms 0.45% 17.86% 5534ms 9.17% std::_Rb_tree::~_Rb_tree (inline) 2287ms 3.79% 21.65% 5356ms 8.88% __GI___libc_malloc 0 0% 21.65% 5270ms 8.74% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 21.65% 5254ms 8.71% std::set::~set (inline) 1558ms 2.58% 24.23% 5126ms 8.50% boost::numeric::ublas::indexing_vector_assign 84ms 0.14% 24.37% 4943ms 8.19% std::__new_allocator::deallocate (inline) 0 0% 24.37% 4943ms 8.19% std::allocator_traits::deallocate (inline) 42ms 0.07% 24.44% 4924ms 8.16% Cell::GetMutationState 0 0% 24.44% 4910ms 8.14% std::_Rb_tree::_M_put_node (inline) 155ms 0.26% 24.70% 4755ms 7.88% VertexMesh::GetNextEdgeGradientOfElementAtNode 882ms 1.46% 26.16% 4566ms 7.57% __GI___libc_free 27ms 0.045% 26.20% 4461ms 7.40% VertexBasedCellPopulation::GetLocationOfCellCentre 483ms 0.8% 27.01% 4422ms 7.33% VertexMesh::ElementIncludesPoint 7ms 0.012% 27.02% 4341ms 7.20% MutableVertexMesh::RemoveDeletedNodesAndElements 279ms 0.46% 27.48% 4267ms 7.07% std::map::operator[] (partial-inline) 349ms 0.58% 28.06% 4258ms 7.06% VertexMesh::GetCentroidOfElement 893ms 1.48% 29.54% 4052ms 6.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 29.54% 3977ms 6.59% std::set::insert (inline) 105ms 0.17% 29.71% 3678ms 6.10% std::_Rb_tree::_Rb_tree (partial-inline) 3478ms 5.77% 35.48% 3669ms 6.08% _int_free 3572ms 5.92% 41.40% 3572ms 5.92% boost::numeric::ublas::c_vector::operator() 584ms 0.97% 42.37% 3537ms 5.86% std::_Rb_tree::_M_insert_ (inline) 383ms 0.63% 43.00% 3497ms 5.80% std::_Rb_tree::_M_copy (inline) 3450ms 5.72% 48.72% 3450ms 5.72% __strcmp_evex 1938ms 3.21% 51.94% 3445ms 5.71% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.0066% 51.94% 3424ms 5.68% std::set::set (inline) 62ms 0.1% 52.04% 3297ms 5.47% SimpleWntCellCycleModel::GetWntLevel 85ms 0.14% 52.19% 3164ms 5.25% WntConcentration::GetWntLevel 53ms 0.088% 52.27% 3148ms 5.22% std::set_intersection (inline) 148ms 0.25% 52.52% 3095ms 5.13% std::__set_intersection 1484ms 2.46% 54.98% 3028ms 5.02% std::_Rb_tree::_M_lower_bound (inline) 420ms 0.7% 55.68% 2975ms 4.93% std::_Rb_tree::_M_clone_node (inline) 13ms 0.022% 55.70% 2900ms 4.81% MutableVertexMesh::RemoveDeletedNodes 841ms 1.39% 57.09% 2872ms 4.76% boost::numeric::ublas::c_vector::operator[] (inline) 16ms 0.027% 57.12% 2800ms 4.64% EdgeHelper::RemoveDeletedEdges 64ms 0.11% 57.22% 2662ms 4.41% MutableElement::ResetIndex 19ms 0.031% 57.26% 2655ms 4.40% EdgeHelper::UpdateEdgesMapKey 53ms 0.088% 57.34% 2632ms 4.36% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.34% 2611ms 4.33% std::_Rb_tree::lower_bound (inline) 0 0% 57.34% 2611ms 4.33% std::map::lower_bound (inline) 0 0% 57.34% 2523ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 2413ms 4.00% 61.34% 2413ms 4.00% boost::numeric::ublas::same_impl_ex 0 0% 61.34% 2412ms 4.00% std::insert_iterator::operator= (inline) 1872ms 3.10% 64.45% 2359ms 3.91% _int_malloc 34ms 0.056% 64.50% 2348ms 3.89% Cell::GetCellProliferativeType 103ms 0.17% 64.67% 2240ms 3.71% boost::detail::shared_count::~shared_count (inline) 0 0% 64.67% 2240ms 3.71% boost::shared_ptr::~shared_ptr (inline) 8ms 0.013% 64.69% 2223ms 3.69% std::_Rb_tree::_M_insert_unique_ (inline) 2114ms 3.50% 68.19% 2116ms 3.51% boost::detail::sp_counted_base::release 58ms 0.096% 68.29% 2066ms 3.43% AbstractCellProperty::IsType (inline) 56ms 0.093% 68.38% 1963ms 3.25% Cell::SetCellProliferativeType 35ms 0.058% 68.44% 1927ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 68.44% 1754ms 2.91% std::_Rb_tree::_M_insert_unique 430ms 0.71% 69.15% 1675ms 2.78% AbstractElement::GetNodeLocation 0 0% 69.15% 1580ms 2.62% boost::numeric::ublas::c_vector::assign (inline) 34ms 0.056% 69.21% 1568ms 2.60% std::_Rb_tree::erase 128ms 0.21% 69.42% 1561ms 2.59% VertexMesh::GetAreaGradientOfElementAtNode 17ms 0.028% 69.45% 1550ms 2.57% CellPropertyCollection::HasProperty 270ms 0.45% 69.90% 1547ms 2.56% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.90% 1513ms 2.51% Cell::HasCellProperty (inline) 4ms 0.0066% 69.90% 1485ms 2.46% AbstractCellPopulation::Iterator::operator++ (inline) 98ms 0.16% 70.07% 1478ms 2.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 385ms 0.64% 70.70% 1455ms 2.41% AbstractCellProperty::IsSame 0 0% 70.70% 1426ms 2.36% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0099% 70.71% 1410ms 2.34% Cell::GetCellData 20ms 0.033% 70.75% 1353ms 2.24% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.005% 70.75% 1345ms 2.23% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.75% 1345ms 2.23% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 260ms 0.43% 71.18% 1326ms 2.20% std::_Rb_tree_const_iterator::operator++ (inline) 19ms 0.031% 71.21% 1205ms 2.00% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.21% 1165ms 1.93% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0033% 71.22% 1159ms 1.92% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1149ms 1.90% 73.12% 1149ms 1.90% std::_Rb_tree::_S_right (inline) 0 0% 73.12% 1125ms 1.87% boost::numeric::ublas::c_vector::operator-= (inline) 6ms 0.0099% 73.13% 1084ms 1.80% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 66ms 0.11% 73.24% 1076ms 1.78% VertexMesh::GetVolumeOfElement 139ms 0.23% 73.47% 1070ms 1.77% std::type_info::operator== (inline) 0 0% 73.47% 1051ms 1.74% VertexMeshWriter::WriteVtkUsingMesh 104ms 0.17% 73.64% 1012ms 1.68% CellPropertyCollection::AddProperty 188ms 0.31% 73.96% 945ms 1.57% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 30ms 0.05% 74.01% 944ms 1.56% MutableVertexMesh::CheckForSwapsFromShortEdges 48ms 0.08% 74.09% 939ms 1.56% boost::numeric::ublas::vector_reference::operator() (inline) 935ms 1.55% 75.64% 935ms 1.55% std::_Rb_tree_increment 58ms 0.096% 75.73% 905ms 1.50% std::_Rb_tree::_M_erase_aux (partial-inline) 20ms 0.033% 75.76% 897ms 1.49% VertexMesh::GetSurfaceAreaOfElement 0 0% 75.76% 854ms 1.42% boost::numeric::ublas::norm_2 (inline) 337ms 0.56% 76.32% 840ms 1.39% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 829ms 1.37% 77.70% 829ms 1.37% [libchaste_cell_based.so] 38ms 0.063% 77.76% 818ms 1.36% Node::RemoveElement 0 0% 77.76% 810ms 1.34% OffLatticeSimulation::ApplyBoundaries 6ms 0.0099% 77.77% 782ms 1.30% std::set::erase (inline) 0 0% 77.77% 770ms 1.28% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.77% 770ms 1.28% std::__new_allocator::destroy (inline) 0 0% 77.77% 770ms 1.28% std::allocator_traits::destroy (inline) 0 0% 77.77% 767ms 1.27% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.77% 766ms 1.27% CellPropertyCollection::~CellPropertyCollection (inline) 755ms 1.25% 79.02% 755ms 1.25% [libchaste_mesh.so] 470ms 0.78% 79.80% 743ms 1.23% std::_Rb_tree::equal_range (inline) 24ms 0.04% 79.84% 723ms 1.20% AbstractCellPopulation::GetLocationIndexUsingCell 32ms 0.053% 79.89% 720ms 1.19% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.89% 674ms 1.12% boost::numeric::ublas::vector_binary::operator() (inline) 50ms 0.083% 79.98% 661ms 1.10% std::less::operator() (inline) 17ms 0.028% 80.01% 630ms 1.04% CellPropertyRegistry::Get 619ms 1.03% 81.03% 619ms 1.03% [libstdc++.so.6.0.33] 527ms 0.87% 81.91% 611ms 1.01% std::operator< (inline) 5ms 0.0083% 81.91% 599ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 9ms 0.015% 81.93% 584ms 0.97% MutableElement::RegisterWithEdges (inline) 1ms 0.0017% 81.93% 582ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 54ms 0.09% 82.02% 582ms 0.96% boost::numeric::ublas::detail::equals 581ms 0.96% 82.98% 581ms 0.96% std::_Rb_tree_insert_and_rebalance 15ms 0.025% 83.01% 579ms 0.96% Edge::AddElement 2ms 0.0033% 83.01% 568ms 0.94% tcache_get (inline) 566ms 0.94% 83.95% 566ms 0.94% tcache_get_n (inline) 488ms 0.81% 84.76% 553ms 0.92% CellPropertyCollection::GetProperty 0 0% 84.76% 548ms 0.91% VertexMeshWriter::MakeVtkMesh 0 0% 84.76% 540ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 53ms 0.088% 84.85% 540ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 0 0% 84.85% 507ms 0.84% std::_Rb_tree::clear (inline) 0 0% 84.85% 494ms 0.82% std::map::clear (inline) 0 0% 84.85% 491ms 0.81% boost::numeric::ublas::norm_inf (inline) 223ms 0.37% 85.22% 491ms 0.81% boost::numeric::ublas::vector_norm_inf::apply (inline) 82ms 0.14% 85.35% 487ms 0.81% std::swap_ranges (inline) 50ms 0.083% 85.43% 469ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 442ms 0.73% 86.17% 442ms 0.73% std::vector::size 54ms 0.09% 86.26% 424ms 0.7% std::_Rb_tree::find (inline) 233ms 0.39% 86.64% 415ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.64% 405ms 0.67% std::iter_swap (inline) 405ms 0.67% 87.31% 405ms 0.67% std::swap (inline) 1ms 0.0017% 87.32% 404ms 0.67% vtkPolygon::New 1ms 0.0017% 87.32% 403ms 0.67% vtkPolygon::vtkPolygon 69ms 0.11% 87.43% 401ms 0.66% MutableElement::GetNodeLocalIndex 0 0% 87.43% 385ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.027% 87.46% 385ms 0.64% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.46% 383ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.46% 366ms 0.61% std::_Vector_base::_M_allocate (inline) 177ms 0.29% 87.75% 362ms 0.6% Edge::GetMapIndex 20ms 0.033% 87.79% 347ms 0.58% MutableElement::RegisterWithNodes (inline) 2ms 0.0033% 87.79% 345ms 0.57% std::map::find (inline) 14ms 0.023% 87.81% 327ms 0.54% Node::AddElement 308ms 0.51% 88.32% 308ms 0.51% Node::GetIndex 3ms 0.005% 88.33% 306ms 0.51% std::vector::_M_default_append (inline) 1ms 0.0017% 88.33% 305ms 0.51% vtkCell::vtkCell 302ms 0.5% 88.83% 302ms 0.5% operator delete