File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96864ms, 88.60% of 109323ms total Dropped 1112 nodes (cum <= 546.62ms) flat flat% sum% cum cum% 0 0% 0% 108830ms 99.55% __libc_start_call_main 0 0% 0% 108830ms 99.55% __libc_start_main_impl 0 0% 0% 108830ms 99.55% _start 0 0% 0% 108811ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108811ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108811ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108811ms 99.53% main 0 0% 0% 108768ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108768ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108768ms 99.49% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0055% 0.0055% 108760ms 99.49% AbstractCellBasedSimulation::Solve 15ms 0.014% 0.019% 56439ms 51.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.018% 0.038% 53203ms 48.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 122ms 0.11% 0.15% 51723ms 47.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 341ms 0.31% 0.46% 39796ms 36.40% NagaiHondaForce::AddForceContribution 0 0% 0.46% 39236ms 35.89% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.46% 24411ms 22.33% VertexBasedCellPopulation::Update 0 0% 0.46% 24287ms 22.22% MutableVertexMesh::ReMesh 14635ms 13.39% 13.85% 22986ms 21.03% Cylindrical2dVertexMesh::GetVectorFromAtoB 103ms 0.094% 13.94% 17477ms 15.99% Cell::ReadyToDivide 77ms 0.07% 14.01% 16212ms 14.83% AbstractPhaseBasedCellCycleModel::ReadyToDivide 355ms 0.32% 14.34% 14689ms 13.44% NagaiHondaForce::GetAdhesionParameter 455ms 0.42% 14.75% 14295ms 13.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 118ms 0.11% 14.86% 13849ms 12.67% SimpleWntCellCycleModel::UpdateCellCyclePhase 128ms 0.12% 14.98% 13772ms 12.60% CellPropertyCollection::GetPropertiesType (inline) 351ms 0.32% 15.30% 12706ms 11.62% boost::numeric::ublas::vector_assign (inline) 159ms 0.15% 15.45% 12144ms 11.11% MutableVertexMesh::CheckForIntersections 3326ms 3.04% 18.49% 11426ms 10.45% __dynamic_cast 78ms 0.071% 18.56% 11420ms 10.45% VertexBasedCellPopulation::GetDampingConstant 82ms 0.075% 18.63% 11327ms 10.36% AbstractCellProperty::IsSubType (inline) 85ms 0.078% 18.71% 10577ms 9.67% AbstractTargetAreaModifier::UpdateTargetAreas 63ms 0.058% 18.77% 10468ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1254ms 1.15% 19.92% 10255ms 9.38% std::__new_allocator::allocate (inline) 41ms 0.038% 19.95% 10202ms 9.33% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.95% 9734ms 8.90% std::allocator_traits::allocate (inline) 0 0% 19.95% 9715ms 8.89% std::_Rb_tree::_M_create_node (inline) 2664ms 2.44% 22.39% 9468ms 8.66% boost::numeric::ublas::indexing_vector_assign 826ms 0.76% 23.15% 9179ms 8.40% operator new 0 0% 23.15% 9049ms 8.28% std::_Rb_tree::_M_get_node (inline) 1364ms 1.25% 24.39% 9017ms 8.25% std::_Rb_tree::_M_erase 757ms 0.69% 25.09% 8954ms 8.19% VertexMesh::ElementIncludesPoint 358ms 0.33% 25.41% 8835ms 8.08% VertexMesh::GetNextEdgeGradientOfElementAtNode 19ms 0.017% 25.43% 8692ms 7.95% VertexBasedCellPopulation::GetLocationOfCellCentre 94ms 0.086% 25.52% 8670ms 7.93% Cell::GetMutationState 0 0% 25.52% 8476ms 7.75% std::_Rb_tree::_Alloc_node::operator() (inline) 519ms 0.47% 25.99% 8258ms 7.55% VertexMesh::GetCentroidOfElement 268ms 0.25% 26.24% 8250ms 7.55% std::_Rb_tree::~_Rb_tree (inline) 3185ms 2.91% 29.15% 8171ms 7.47% __GI___libc_malloc 0 0% 29.15% 8093ms 7.40% std::_Rb_tree::_M_drop_node (inline) 256ms 0.23% 29.39% 7845ms 7.18% std::__new_allocator::deallocate (inline) 0 0% 29.39% 7816ms 7.15% std::allocator_traits::deallocate (inline) 0 0% 29.39% 7769ms 7.11% std::set::~set (inline) 0 0% 29.39% 7752ms 7.09% std::_Rb_tree::_M_put_node (inline) 3028ms 2.77% 32.16% 7740ms 7.08% __GI___libc_free 24ms 0.022% 32.18% 7702ms 7.05% MutableVertexMesh::RemoveDeletedNodesAndElements 443ms 0.41% 32.58% 7463ms 6.83% std::map::operator[] (partial-inline) 1366ms 1.25% 33.83% 7166ms 6.55% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 193ms 0.18% 34.01% 6965ms 6.37% std::_Rb_tree::_Rb_tree (partial-inline) 6610ms 6.05% 40.05% 6610ms 6.05% __strcmp_avx2 647ms 0.59% 40.65% 6551ms 5.99% std::_Rb_tree::_M_copy (inline) 11ms 0.01% 40.66% 6521ms 5.96% std::set::set (inline) 106ms 0.097% 40.75% 6298ms 5.76% SimpleWntCellCycleModel::GetWntLevel 6173ms 5.65% 46.40% 6173ms 5.65% boost::numeric::ublas::c_vector::operator() 169ms 0.15% 46.55% 6125ms 5.60% WntConcentration::GetWntLevel 2523ms 2.31% 48.86% 5827ms 5.33% std::_Rb_tree::_M_lower_bound (inline) 713ms 0.65% 49.51% 5632ms 5.15% std::_Rb_tree::_M_clone_node (inline) 2689ms 2.46% 51.97% 5519ms 5.05% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.97% 5430ms 4.97% std::set::insert (inline) 24ms 0.022% 52.00% 5380ms 4.92% MutableVertexMesh::RemoveDeletedNodes 34ms 0.031% 52.03% 5216ms 4.77% EdgeHelper::RemoveDeletedEdges 35ms 0.032% 52.06% 4920ms 4.50% EdgeHelper::UpdateEdgesMapKey 1505ms 1.38% 53.44% 4866ms 4.45% boost::numeric::ublas::c_vector::operator[] (inline) 223ms 0.2% 53.64% 4803ms 4.39% MutableElement::ResetIndex 0 0% 53.64% 4736ms 4.33% std::_Rb_tree::lower_bound (inline) 0 0% 53.64% 4736ms 4.33% std::map::lower_bound (inline) 4376ms 4.00% 57.64% 4702ms 4.30% _int_free 0 0% 57.64% 4616ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 513ms 0.47% 58.11% 4594ms 4.20% std::_Rb_tree::_M_insert_ (inline) 52ms 0.048% 58.16% 4460ms 4.08% std::set_intersection (inline) 267ms 0.24% 58.40% 4408ms 4.03% std::__set_intersection 114ms 0.1% 58.51% 4138ms 3.79% AbstractCellPopulation::GetCellUsingLocationIndex 3999ms 3.66% 62.17% 3999ms 3.66% boost::numeric::ublas::same_impl_ex 40ms 0.037% 62.20% 3956ms 3.62% Cell::GetCellProliferativeType 73ms 0.067% 62.27% 3908ms 3.57% AbstractCellProperty::IsType (inline) 13ms 0.012% 62.28% 3564ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.28% 3280ms 3.00% std::insert_iterator::operator= (inline) 2265ms 2.07% 64.35% 3218ms 2.94% _int_malloc 830ms 0.76% 65.11% 3162ms 2.89% AbstractElement::GetNodeLocation 40ms 0.037% 65.15% 3162ms 2.89% Cell::SetCellProliferativeType 37ms 0.034% 65.18% 3069ms 2.81% std::_Rb_tree::erase 7ms 0.0064% 65.19% 2868ms 2.62% std::_Rb_tree::_M_insert_unique_ (inline) 585ms 0.54% 65.72% 2830ms 2.59% boost::numeric::ublas::vector_binary::size (inline) 749ms 0.69% 66.41% 2809ms 2.57% AbstractCellProperty::IsSame 2803ms 2.56% 68.97% 2803ms 2.56% std::_Rb_tree::_S_right (inline) 386ms 0.35% 69.33% 2738ms 2.50% std::_Rb_tree_const_iterator::operator++ (inline) 42ms 0.038% 69.37% 2714ms 2.48% CellPropertyCollection::HasProperty 0 0% 69.37% 2614ms 2.39% Cell::HasCellProperty (inline) 2ms 0.0018% 69.37% 2562ms 2.34% std::_Rb_tree::_M_insert_unique 12ms 0.011% 69.38% 2507ms 2.29% Cell::GetCellData 0 0% 69.38% 2476ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.38% 2471ms 2.26% AbstractCellPopulation::WriteResultsToFiles 221ms 0.2% 69.58% 2439ms 2.23% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.58% 2355ms 2.15% boost::numeric::ublas::c_vector::assign (inline) 111ms 0.1% 69.68% 2285ms 2.09% VertexMesh::GetVolumeOfElement 86ms 0.079% 69.76% 2267ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 38ms 0.035% 69.80% 2246ms 2.05% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00091% 69.80% 2196ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 227ms 0.21% 70.00% 2187ms 2.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 2165ms 1.98% 71.98% 2165ms 1.98% std::_Rb_tree_increment 1387ms 1.27% 73.25% 2073ms 1.90% std::_Rb_tree::equal_range (inline) 466ms 0.43% 73.68% 2060ms 1.88% std::type_info::operator== (inline) 0 0% 73.68% 2009ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.68% 1995ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0027% 73.68% 1944ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.68% 1944ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 68ms 0.062% 73.74% 1870ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.74% 1802ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.024% 73.77% 1699ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 26ms 0.024% 73.79% 1687ms 1.54% VertexMesh::GetSurfaceAreaOfElement 40ms 0.037% 73.83% 1601ms 1.46% Node::RemoveElement 18ms 0.016% 73.84% 1575ms 1.44% std::set::erase (inline) 0 0% 73.84% 1564ms 1.43% tcache_get (inline) 1564ms 1.43% 75.28% 1564ms 1.43% tcache_get_n (inline) 180ms 0.16% 75.44% 1527ms 1.40% CellPropertyCollection::AddProperty 139ms 0.13% 75.57% 1524ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 37ms 0.034% 75.60% 1518ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 90ms 0.082% 75.68% 1515ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.68% 1427ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.68% 1239ms 1.13% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.68% 1225ms 1.12% boost::numeric::ublas::norm_2 (inline) 1ms 0.00091% 75.68% 1223ms 1.12% OffLatticeSimulation::ApplyBoundaries 528ms 0.48% 76.17% 1215ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 26ms 0.024% 76.19% 1196ms 1.09% CellPropertyRegistry::Get 79ms 0.072% 76.26% 1168ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 58ms 0.053% 76.32% 1155ms 1.06% std::less::operator() (inline) 1150ms 1.05% 77.37% 1150ms 1.05% Node::rGetLocation 1115ms 1.02% 78.39% 1115ms 1.02% [libchaste_cell_based.so] 891ms 0.82% 79.20% 1097ms 1.00% std::operator< (inline) 1090ms 1% 80.20% 1090ms 1% std::_Rb_tree_insert_and_rebalance 105ms 0.096% 80.30% 1075ms 0.98% std::_Rb_tree::find (inline) 14ms 0.013% 80.31% 1042ms 0.95% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.31% 1038ms 0.95% std::_Rb_tree::clear (inline) 1027ms 0.94% 81.25% 1027ms 0.94% std::vector::size (inline) 0 0% 81.25% 1025ms 0.94% std::map::clear (inline) 156ms 0.14% 81.39% 1016ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 81.39% 1016ms 0.93% boost::shared_ptr::~shared_ptr (inline) 9ms 0.0082% 81.40% 1003ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 968ms 0.89% 82.28% 968ms 0.89% [libchaste_mesh.so] 19ms 0.017% 82.30% 952ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 152ms 0.14% 82.44% 923ms 0.84% boost::numeric::ublas::detail::equals 367ms 0.34% 82.78% 922ms 0.84% Edge::GetMapIndex 0 0% 82.78% 883ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.78% 883ms 0.81% boost::numeric::ublas::c_vector::swap 94ms 0.086% 82.87% 879ms 0.8% std::swap_ranges (inline) 0 0% 82.87% 876ms 0.8% std::map::find (inline) 1ms 0.00091% 82.87% 856ms 0.78% VertexMeshWriter::MakeVtkMesh 829ms 0.76% 83.63% 834ms 0.76% boost::detail::sp_counted_base::release 90ms 0.082% 83.71% 821ms 0.75% MutableElement::GetNodeLocalIndex 156ms 0.14% 83.85% 808ms 0.74% boost::shared_ptr::shared_ptr (inline) 786ms 0.72% 84.57% 786ms 0.72% std::swap (inline) 0 0% 84.57% 785ms 0.72% std::iter_swap (inline) 770ms 0.7% 85.27% 770ms 0.7% Node::GetIndex 13ms 0.012% 85.29% 742ms 0.68% MutableElement::RegisterWithEdges (inline) 103ms 0.094% 85.38% 741ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 445ms 0.41% 85.79% 739ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 31ms 0.028% 85.82% 733ms 0.67% Edge::AddElement 120ms 0.11% 85.93% 721ms 0.66% std::__new_allocator::construct (inline) 0 0% 85.93% 721ms 0.66% std::allocator_traits::construct (inline) 0 0% 85.93% 719ms 0.66% boost::numeric::ublas::norm_inf (inline) 359ms 0.33% 86.25% 719ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 11ms 0.01% 86.26% 701ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 104ms 0.095% 86.36% 690ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.36% 688ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.36% 682ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.36% 666ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.36% 653ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 86.38% 653ms 0.6% std::_Rb_tree::_M_insert_node (inline) 628ms 0.57% 86.96% 652ms 0.6% boost::detail::shared_count::shared_count (inline) 28ms 0.026% 86.98% 640ms 0.59% MutableElement::RegisterWithNodes (inline) 0 0% 86.98% 614ms 0.56% vtkPolygon::New 2ms 0.0018% 86.98% 614ms 0.56% vtkPolygon::vtkPolygon 28ms 0.026% 87.01% 611ms 0.56% Node::AddElement 575ms 0.53% 87.53% 575ms 0.53% [libstdc++.so.6.0.33] 0 0% 87.53% 572ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 566ms 0.52% 88.05% 566ms 0.52% boost::shared_ptr::operator-> (inline) 559ms 0.51% 88.56% 559ms 0.51% operator delete 14ms 0.013% 88.58% 553ms 0.51% std::vector::_M_default_append (inline) 30ms 0.027% 88.60% 551ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.60% 551ms 0.5% boost::numeric::ublas::vector::vector (inline)