File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97838ms, 88.73% of 110260ms total Dropped 1084 nodes (cum <= 551.30ms) flat flat% sum% cum cum% 0 0% 0% 109781ms 99.57% __libc_start_call_main 0 0% 0% 109781ms 99.57% __libc_start_main_impl 0 0% 0% 109781ms 99.57% _start 0 0% 0% 109760ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109760ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109760ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109760ms 99.55% main 0 0% 0% 109719ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109719ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109719ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 109712ms 99.50% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.014% 57320ms 51.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.016% 0.03% 54221ms 49.18% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.16% 53204ms 48.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 358ms 0.32% 0.48% 40733ms 36.94% NagaiHondaForce::AddForceContribution 0 0% 0.48% 39275ms 35.62% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.48% 24247ms 21.99% VertexBasedCellPopulation::Update 0 0% 0.48% 24119ms 21.87% MutableVertexMesh::ReMesh 14667ms 13.30% 13.78% 22985ms 20.85% Cylindrical2dVertexMesh::GetVectorFromAtoB 74ms 0.067% 13.85% 17687ms 16.04% Cell::ReadyToDivide 75ms 0.068% 13.92% 16512ms 14.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 343ms 0.31% 14.23% 15225ms 13.81% NagaiHondaForce::GetAdhesionParameter 426ms 0.39% 14.62% 14281ms 12.95% boost::numeric::ublas::c_vector::c_vector (partial-inline) 149ms 0.14% 14.75% 14226ms 12.90% CellPropertyCollection::GetPropertiesType (inline) 112ms 0.1% 14.85% 14117ms 12.80% SimpleWntCellCycleModel::UpdateCellCyclePhase 391ms 0.35% 15.21% 12711ms 11.53% boost::numeric::ublas::vector_assign (inline) 141ms 0.13% 15.34% 12028ms 10.91% MutableVertexMesh::CheckForIntersections 85ms 0.077% 15.41% 11981ms 10.87% VertexBasedCellPopulation::GetDampingConstant 3509ms 3.18% 18.60% 11701ms 10.61% __dynamic_cast 76ms 0.069% 18.66% 11611ms 10.53% AbstractCellProperty::IsSubType (inline) 87ms 0.079% 18.74% 10641ms 9.65% AbstractTargetAreaModifier::UpdateTargetAreas 73ms 0.066% 18.81% 10528ms 9.55% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 36ms 0.033% 18.84% 10399ms 9.43% AbstractCellBasedSimulation::DoCellBirth 1363ms 1.24% 20.08% 10227ms 9.28% std::__new_allocator::allocate (inline) 0 0% 20.08% 9689ms 8.79% std::allocator_traits::allocate (inline) 0 0% 20.08% 9683ms 8.78% std::_Rb_tree::_M_create_node (inline) 2714ms 2.46% 22.54% 9522ms 8.64% boost::numeric::ublas::indexing_vector_assign 1419ms 1.29% 23.83% 9454ms 8.57% std::_Rb_tree::_M_erase 67ms 0.061% 23.89% 9224ms 8.37% Cell::GetMutationState 0 0% 23.89% 9028ms 8.19% std::_Rb_tree::_M_get_node (inline) 394ms 0.36% 24.25% 9001ms 8.16% VertexMesh::GetNextEdgeGradientOfElementAtNode 837ms 0.76% 25.00% 8989ms 8.15% operator new 797ms 0.72% 25.73% 8924ms 8.09% VertexMesh::ElementIncludesPoint 33ms 0.03% 25.76% 8855ms 8.03% VertexBasedCellPopulation::GetLocationOfCellCentre 274ms 0.25% 26.01% 8662ms 7.86% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.01% 8553ms 7.76% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.01% 8374ms 7.59% std::_Rb_tree::_M_drop_node (inline) 501ms 0.45% 26.46% 8326ms 7.55% VertexMesh::GetCentroidOfElement 0 0% 26.46% 8235ms 7.47% std::set::~set (inline) 288ms 0.26% 26.72% 8102ms 7.35% std::__new_allocator::deallocate (inline) 0 0% 26.72% 8078ms 7.33% std::allocator_traits::deallocate (inline) 0 0% 26.72% 8026ms 7.28% std::_Rb_tree::_M_put_node (inline) 3242ms 2.94% 29.66% 7964ms 7.22% __GI___libc_malloc 3066ms 2.78% 32.44% 7744ms 7.02% __GI___libc_free 446ms 0.4% 32.85% 7603ms 6.90% std::map::operator[] (partial-inline) 20ms 0.018% 32.87% 7587ms 6.88% MutableVertexMesh::RemoveDeletedNodesAndElements 1432ms 1.30% 34.16% 7242ms 6.57% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 156ms 0.14% 34.31% 6991ms 6.34% std::_Rb_tree::_Rb_tree (partial-inline) 6660ms 6.04% 40.35% 6660ms 6.04% __strcmp_avx2 638ms 0.58% 40.92% 6600ms 5.99% std::_Rb_tree::_M_copy (inline) 6ms 0.0054% 40.93% 6576ms 5.96% std::set::set (inline) 99ms 0.09% 41.02% 6420ms 5.82% SimpleWntCellCycleModel::GetWntLevel 135ms 0.12% 41.14% 6234ms 5.65% WntConcentration::GetWntLevel 2474ms 2.24% 43.39% 6103ms 5.54% std::_Rb_tree::_M_lower_bound (inline) 6070ms 5.51% 48.89% 6070ms 5.51% boost::numeric::ublas::c_vector::operator() 765ms 0.69% 49.58% 5668ms 5.14% std::_Rb_tree::_M_clone_node (inline) 2647ms 2.40% 51.99% 5565ms 5.05% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.99% 5476ms 4.97% std::set::insert (inline) 23ms 0.021% 52.01% 5348ms 4.85% MutableVertexMesh::RemoveDeletedNodes 44ms 0.04% 52.05% 5193ms 4.71% EdgeHelper::RemoveDeletedEdges 0 0% 52.05% 5016ms 4.55% std::_Rb_tree::lower_bound (inline) 0 0% 52.05% 5016ms 4.55% std::map::lower_bound (inline) 42ms 0.038% 52.08% 4903ms 4.45% EdgeHelper::UpdateEdgesMapKey 220ms 0.2% 52.28% 4738ms 4.30% MutableElement::ResetIndex 1461ms 1.33% 53.61% 4731ms 4.29% boost::numeric::ublas::c_vector::operator[] (inline) 4354ms 3.95% 57.56% 4672ms 4.24% _int_free 65ms 0.059% 57.62% 4662ms 4.23% std::set_intersection (inline) 501ms 0.45% 58.07% 4640ms 4.21% std::_Rb_tree::_M_insert_ (inline) 1ms 0.00091% 58.07% 4622ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 244ms 0.22% 58.29% 4597ms 4.17% std::__set_intersection 99ms 0.09% 58.38% 4386ms 3.98% AbstractCellPopulation::GetCellUsingLocationIndex 3975ms 3.61% 61.99% 3975ms 3.61% boost::numeric::ublas::same_impl_ex 34ms 0.031% 62.02% 3931ms 3.57% Cell::GetCellProliferativeType 50ms 0.045% 62.06% 3851ms 3.49% AbstractCellProperty::IsType (inline) 14ms 0.013% 62.08% 3540ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.08% 3285ms 2.98% std::insert_iterator::operator= (inline) 846ms 0.77% 62.84% 3224ms 2.92% AbstractElement::GetNodeLocation 2292ms 2.08% 64.92% 3172ms 2.88% _int_malloc 37ms 0.034% 64.96% 3155ms 2.86% Cell::SetCellProliferativeType 3098ms 2.81% 67.77% 3098ms 2.81% std::_Rb_tree::_S_right (inline) 411ms 0.37% 68.14% 2990ms 2.71% std::_Rb_tree_const_iterator::operator++ (inline) 35ms 0.032% 68.17% 2978ms 2.70% std::_Rb_tree::erase 639ms 0.58% 68.75% 2902ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.0045% 68.75% 2831ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 740ms 0.67% 69.43% 2705ms 2.45% AbstractCellProperty::IsSame 0 0% 69.43% 2645ms 2.40% std::_Rb_tree::_M_insert_unique 278ms 0.25% 69.68% 2643ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 53ms 0.048% 69.73% 2613ms 2.37% CellPropertyCollection::HasProperty 0 0% 69.73% 2497ms 2.26% Cell::HasCellProperty (inline) 0 0% 69.73% 2450ms 2.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.73% 2410ms 2.19% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.73% 2389ms 2.17% boost::numeric::ublas::c_vector::assign (inline) 2384ms 2.16% 71.89% 2384ms 2.16% std::_Rb_tree_increment 28ms 0.025% 71.91% 2374ms 2.15% Cell::GetCellData 112ms 0.1% 72.02% 2303ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 242ms 0.22% 72.23% 2278ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0027% 72.24% 2278ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 88ms 0.08% 72.32% 2196ms 1.99% VertexMesh::GetVolumeOfElement 38ms 0.034% 72.35% 2103ms 1.91% std::_Rb_tree::_M_emplace_hint_unique 0 0% 72.35% 2009ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 72.35% 1996ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1330ms 1.21% 73.56% 1996ms 1.81% std::_Rb_tree::equal_range (inline) 445ms 0.4% 73.96% 1965ms 1.78% std::type_info::operator== (inline) 70ms 0.063% 74.03% 1931ms 1.75% MutableVertexMesh::CheckForSwapsFromShortEdges 5ms 0.0045% 74.03% 1861ms 1.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.03% 1861ms 1.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.00091% 74.03% 1792ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 32ms 0.029% 74.06% 1760ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 182ms 0.17% 74.23% 1651ms 1.50% CellPropertyCollection::AddProperty 27ms 0.024% 74.25% 1575ms 1.43% VertexMesh::GetSurfaceAreaOfElement 39ms 0.035% 74.29% 1569ms 1.42% Node::RemoveElement 24ms 0.022% 74.31% 1546ms 1.40% std::set::erase (inline) 88ms 0.08% 74.39% 1524ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 39ms 0.035% 74.42% 1508ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 130ms 0.12% 74.54% 1502ms 1.36% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.54% 1399ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.54% 1364ms 1.24% tcache_get (inline) 1364ms 1.24% 75.78% 1364ms 1.24% tcache_get_n (inline) 5ms 0.0045% 75.78% 1266ms 1.15% OffLatticeSimulation::ApplyBoundaries 0 0% 75.78% 1212ms 1.10% boost::numeric::ublas::norm_2 (inline) 569ms 0.52% 76.30% 1199ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 62ms 0.056% 76.35% 1192ms 1.08% std::less::operator() (inline) 1158ms 1.05% 77.41% 1158ms 1.05% Node::rGetLocation 92ms 0.083% 77.49% 1156ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 1141ms 1.03% 78.52% 1141ms 1.03% [libchaste_cell_based.so] 0 0% 78.52% 1130ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 942ms 0.85% 79.38% 1130ms 1.02% std::operator< (inline) 25ms 0.023% 79.40% 1107ms 1.00% CellPropertyRegistry::Get 88ms 0.08% 79.48% 1083ms 0.98% std::_Rb_tree::find (inline) 9ms 0.0082% 79.49% 1077ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.49% 1072ms 0.97% std::_Rb_tree::clear (inline) 1068ms 0.97% 80.46% 1068ms 0.97% std::_Rb_tree_insert_and_rebalance 133ms 0.12% 80.58% 1058ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 80.58% 1058ms 0.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.58% 1054ms 0.96% std::map::clear (inline) 9ms 0.0082% 80.59% 1044ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1006ms 0.91% 81.50% 1006ms 0.91% std::vector::size (inline) 966ms 0.88% 82.37% 966ms 0.88% [libchaste_mesh.so] 0 0% 82.37% 941ms 0.85% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0027% 82.38% 941ms 0.85% boost::numeric::ublas::c_vector::swap 74ms 0.067% 82.44% 938ms 0.85% std::swap_ranges (inline) 15ms 0.014% 82.46% 909ms 0.82% boost::numeric::ublas::detail::expression_type_check (inline) 896ms 0.81% 83.27% 902ms 0.82% boost::detail::sp_counted_base::release 368ms 0.33% 83.60% 895ms 0.81% Edge::GetMapIndex 0 0% 83.60% 889ms 0.81% std::map::find (inline) 170ms 0.15% 83.76% 877ms 0.8% boost::numeric::ublas::detail::equals 1ms 0.00091% 83.76% 865ms 0.78% VertexMeshWriter::MakeVtkMesh 865ms 0.78% 84.54% 865ms 0.78% std::swap (inline) 0 0% 84.54% 864ms 0.78% std::iter_swap (inline) 119ms 0.11% 84.65% 838ms 0.76% MutableElement::GetNodeLocalIndex 97ms 0.088% 84.74% 789ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 784ms 0.71% 85.45% 784ms 0.71% Node::GetIndex 134ms 0.12% 85.57% 762ms 0.69% boost::shared_ptr::shared_ptr (inline) 22ms 0.02% 85.59% 761ms 0.69% MutableElement::RegisterWithEdges (inline) 25ms 0.023% 85.61% 748ms 0.68% Edge::AddElement 440ms 0.4% 86.01% 732ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 122ms 0.11% 86.12% 702ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.12% 702ms 0.64% std::allocator_traits::construct (inline) 0 0% 86.12% 686ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 680ms 0.62% 86.74% 680ms 0.62% operator delete 3ms 0.0027% 86.74% 659ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.74% 655ms 0.59% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.74% 649ms 0.59% boost::numeric::ublas::norm_inf (inline) 302ms 0.27% 87.02% 649ms 0.59% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 87.02% 646ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 87.04% 646ms 0.59% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.04% 637ms 0.58% vtkPolygon::New 1ms 0.00091% 87.04% 636ms 0.58% vtkPolygon::vtkPolygon 594ms 0.54% 87.58% 628ms 0.57% boost::detail::shared_count::shared_count (inline) 36ms 0.033% 87.61% 622ms 0.56% MutableElement::RegisterWithNodes (inline) 600ms 0.54% 88.15% 600ms 0.54% [libstdc++.so.6.0.33] 27ms 0.024% 88.18% 573ms 0.52% Node::AddElement 32ms 0.029% 88.21% 570ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.21% 570ms 0.52% boost::numeric::ublas::vector::vector (inline) 569ms 0.52% 88.72% 569ms 0.52% boost::shared_ptr::operator-> (inline) 11ms 0.01% 88.73% 566ms 0.51% std::vector::_M_default_append (inline) 0 0% 88.73% 552ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)