File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95899ms, 88.53% of 108326ms total Dropped 1119 nodes (cum <= 541.63ms) flat flat% sum% cum cum% 0 0% 0% 107832ms 99.54% __libc_start_call_main 0 0% 0% 107832ms 99.54% __libc_start_main_impl 0 0% 0% 107832ms 99.54% _start 0 0% 0% 107811ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107811ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107811ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107811ms 99.52% main 0 0% 0% 107776ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107776ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107776ms 99.49% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107769ms 99.49% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.015% 56083ms 51.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.025% 52837ms 48.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 133ms 0.12% 0.15% 51349ms 47.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 350ms 0.32% 0.47% 39606ms 36.56% NagaiHondaForce::AddForceContribution 0 0% 0.47% 38768ms 35.79% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.47% 23974ms 22.13% VertexBasedCellPopulation::Update 0 0% 0.47% 23850ms 22.02% MutableVertexMesh::ReMesh 14504ms 13.39% 13.86% 22730ms 20.98% Cylindrical2dVertexMesh::GetVectorFromAtoB 73ms 0.067% 13.93% 17341ms 16.01% Cell::ReadyToDivide 72ms 0.066% 14.00% 16114ms 14.88% AbstractPhaseBasedCellCycleModel::ReadyToDivide 354ms 0.33% 14.32% 14793ms 13.66% NagaiHondaForce::GetAdhesionParameter 440ms 0.41% 14.73% 14118ms 13.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 128ms 0.12% 14.85% 13709ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 156ms 0.14% 14.99% 13690ms 12.64% CellPropertyCollection::GetPropertiesType (inline) 373ms 0.34% 15.34% 12517ms 11.55% boost::numeric::ublas::vector_assign (inline) 127ms 0.12% 15.45% 11999ms 11.08% MutableVertexMesh::CheckForIntersections 85ms 0.078% 15.53% 11254ms 10.39% VertexBasedCellPopulation::GetDampingConstant 3138ms 2.90% 18.43% 11250ms 10.39% __dynamic_cast 61ms 0.056% 18.48% 11101ms 10.25% AbstractCellProperty::IsSubType (inline) 73ms 0.067% 18.55% 10499ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 61ms 0.056% 18.61% 10389ms 9.59% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.63% 10199ms 9.42% AbstractCellBasedSimulation::DoCellBirth 1289ms 1.19% 19.82% 10073ms 9.30% std::__new_allocator::allocate (inline) 0 0% 19.82% 9568ms 8.83% std::_Rb_tree::_M_create_node (inline) 0 0% 19.82% 9556ms 8.82% std::allocator_traits::allocate (inline) 2470ms 2.28% 22.10% 9180ms 8.47% boost::numeric::ublas::indexing_vector_assign 1395ms 1.29% 23.39% 9091ms 8.39% std::_Rb_tree::_M_erase 787ms 0.73% 24.11% 8972ms 8.28% VertexMesh::ElementIncludesPoint 0 0% 24.11% 8909ms 8.22% std::_Rb_tree::_M_get_node (inline) 890ms 0.82% 24.93% 8896ms 8.21% operator new 370ms 0.34% 25.28% 8730ms 8.06% VertexMesh::GetNextEdgeGradientOfElementAtNode 81ms 0.075% 25.35% 8608ms 7.95% Cell::GetMutationState 19ms 0.018% 25.37% 8537ms 7.88% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.37% 8399ms 7.75% std::_Rb_tree::_Alloc_node::operator() (inline) 206ms 0.19% 25.56% 8267ms 7.63% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.56% 8154ms 7.53% std::_Rb_tree::_M_drop_node (inline) 471ms 0.43% 25.99% 8032ms 7.41% VertexMesh::GetCentroidOfElement 273ms 0.25% 26.25% 7970ms 7.36% std::__new_allocator::deallocate (inline) 0 0% 26.25% 7935ms 7.33% std::allocator_traits::deallocate (inline) 3099ms 2.86% 29.11% 7900ms 7.29% __GI___libc_free 0 0% 29.11% 7852ms 7.25% std::_Rb_tree::_M_put_node (inline) 3193ms 2.95% 32.05% 7834ms 7.23% __GI___libc_malloc 0 0% 32.05% 7815ms 7.21% std::set::~set (inline) 18ms 0.017% 32.07% 7428ms 6.86% MutableVertexMesh::RemoveDeletedNodesAndElements 439ms 0.41% 32.48% 7386ms 6.82% std::map::operator[] (partial-inline) 1373ms 1.27% 33.74% 7125ms 6.58% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 138ms 0.13% 33.87% 6989ms 6.45% std::_Rb_tree::_Rb_tree (partial-inline) 683ms 0.63% 34.50% 6608ms 6.10% std::_Rb_tree::_M_copy (inline) 11ms 0.01% 34.51% 6565ms 6.06% std::set::set (inline) 6488ms 5.99% 40.50% 6488ms 5.99% __strcmp_avx2 85ms 0.078% 40.58% 6097ms 5.63% SimpleWntCellCycleModel::GetWntLevel 5954ms 5.50% 46.08% 5954ms 5.50% boost::numeric::ublas::c_vector::operator() 141ms 0.13% 46.21% 5922ms 5.47% WntConcentration::GetWntLevel 2536ms 2.34% 48.55% 5851ms 5.40% std::_Rb_tree::_M_lower_bound (inline) 772ms 0.71% 49.26% 5649ms 5.21% std::_Rb_tree::_M_clone_node (inline) 2721ms 2.51% 51.77% 5571ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.77% 5508ms 5.08% std::set::insert (inline) 36ms 0.033% 51.80% 5229ms 4.83% MutableVertexMesh::RemoveDeletedNodes 43ms 0.04% 51.84% 5046ms 4.66% EdgeHelper::RemoveDeletedEdges 4446ms 4.10% 55.95% 4798ms 4.43% _int_free 41ms 0.038% 55.99% 4760ms 4.39% EdgeHelper::UpdateEdgesMapKey 0 0% 55.99% 4745ms 4.38% std::_Rb_tree::lower_bound (inline) 0 0% 55.99% 4745ms 4.38% std::map::lower_bound (inline) 1450ms 1.34% 57.33% 4742ms 4.38% boost::numeric::ublas::c_vector::operator[] (inline) 613ms 0.57% 57.89% 4663ms 4.30% std::_Rb_tree::_M_insert_ (inline) 230ms 0.21% 58.10% 4636ms 4.28% MutableElement::ResetIndex 1ms 0.00092% 58.10% 4586ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 66ms 0.061% 58.17% 4499ms 4.15% std::set_intersection (inline) 282ms 0.26% 58.43% 4433ms 4.09% std::__set_intersection 4083ms 3.77% 62.19% 4083ms 3.77% boost::numeric::ublas::same_impl_ex 56ms 0.052% 62.25% 4030ms 3.72% Cell::GetCellProliferativeType 126ms 0.12% 62.36% 4021ms 3.71% AbstractCellPopulation::GetCellUsingLocationIndex 62ms 0.057% 62.42% 3733ms 3.45% AbstractCellProperty::IsType (inline) 9ms 0.0083% 62.43% 3534ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 47ms 0.043% 62.47% 3287ms 3.03% Cell::SetCellProliferativeType 0 0% 62.47% 3235ms 2.99% std::insert_iterator::operator= (inline) 822ms 0.76% 63.23% 3063ms 2.83% AbstractElement::GetNodeLocation 2192ms 2.02% 65.25% 3037ms 2.80% _int_malloc 628ms 0.58% 65.83% 2994ms 2.76% boost::numeric::ublas::vector_binary::size (inline) 46ms 0.042% 65.88% 2938ms 2.71% std::_Rb_tree::erase 7ms 0.0065% 65.88% 2883ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 2764ms 2.55% 68.43% 2764ms 2.55% std::_Rb_tree::_S_right (inline) 718ms 0.66% 69.10% 2750ms 2.54% AbstractCellProperty::IsSame 425ms 0.39% 69.49% 2701ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0018% 69.49% 2625ms 2.42% std::_Rb_tree::_M_insert_unique 56ms 0.052% 69.54% 2623ms 2.42% CellPropertyCollection::HasProperty 0 0% 69.54% 2505ms 2.31% Cell::HasCellProperty (inline) 30ms 0.028% 69.57% 2467ms 2.28% Cell::GetCellData 214ms 0.2% 69.77% 2460ms 2.27% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.77% 2395ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.77% 2394ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.77% 2326ms 2.15% boost::numeric::ublas::c_vector::assign (inline) 127ms 0.12% 69.89% 2309ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 92ms 0.085% 69.97% 2225ms 2.05% VertexMesh::GetVolumeOfElement 2ms 0.0018% 69.97% 2185ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 239ms 0.22% 70.19% 2184ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 33ms 0.03% 70.22% 2162ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 2091ms 1.93% 72.15% 2091ms 1.93% std::_Rb_tree_increment 536ms 0.49% 72.65% 2032ms 1.88% std::type_info::operator== (inline) 3ms 0.0028% 72.65% 2008ms 1.85% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.65% 2008ms 1.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.65% 1962ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.65% 1949ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1327ms 1.23% 73.88% 1918ms 1.77% std::_Rb_tree::equal_range (inline) 79ms 0.073% 73.95% 1916ms 1.77% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.95% 1736ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 23ms 0.021% 73.97% 1716ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 149ms 0.14% 74.11% 1637ms 1.51% CellPropertyCollection::AddProperty 19ms 0.018% 74.13% 1606ms 1.48% VertexMesh::GetSurfaceAreaOfElement 41ms 0.038% 74.16% 1580ms 1.46% Node::RemoveElement 17ms 0.016% 74.18% 1547ms 1.43% std::set::erase (inline) 87ms 0.08% 74.26% 1527ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 26ms 0.024% 74.28% 1518ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 106ms 0.098% 74.38% 1437ms 1.33% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00092% 74.38% 1384ms 1.28% tcache_get (inline) 1383ms 1.28% 75.66% 1383ms 1.28% tcache_get_n (inline) 0 0% 75.66% 1328ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 75.66% 1300ms 1.20% OffLatticeSimulation::ApplyBoundaries 0 0% 75.66% 1252ms 1.16% boost::numeric::ublas::norm_2 (inline) 555ms 0.51% 76.17% 1243ms 1.15% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 58ms 0.054% 76.23% 1196ms 1.10% std::less::operator() (inline) 54ms 0.05% 76.28% 1194ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 76.28% 1169ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1152ms 1.06% 77.34% 1152ms 1.06% Node::rGetLocation 910ms 0.84% 78.18% 1138ms 1.05% std::operator< (inline) 98ms 0.09% 78.27% 1125ms 1.04% std::_Rb_tree::find (inline) 1112ms 1.03% 79.30% 1112ms 1.03% [libchaste_cell_based.so] 1103ms 1.02% 80.31% 1103ms 1.02% std::_Rb_tree_insert_and_rebalance 14ms 0.013% 80.33% 1087ms 1.00% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 25ms 0.023% 80.35% 1075ms 0.99% CellPropertyRegistry::Get 1ms 0.00092% 80.35% 1035ms 0.96% std::_Rb_tree::clear (inline) 0 0% 80.35% 1021ms 0.94% std::map::clear (inline) 8ms 0.0074% 80.36% 1002ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 21ms 0.019% 80.38% 997ms 0.92% boost::numeric::ublas::detail::expression_type_check (inline) 141ms 0.13% 80.51% 988ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.51% 988ms 0.91% boost::shared_ptr::~shared_ptr (inline) 181ms 0.17% 80.68% 972ms 0.9% boost::numeric::ublas::detail::equals 919ms 0.85% 81.52% 919ms 0.85% [libchaste_mesh.so] 0 0% 81.52% 918ms 0.85% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 81.53% 918ms 0.85% boost::numeric::ublas::c_vector::swap (inline) 87ms 0.08% 81.61% 912ms 0.84% std::swap_ranges (inline) 905ms 0.84% 82.45% 905ms 0.84% std::vector::size (inline) 0 0% 82.45% 896ms 0.83% std::map::find (inline) 2ms 0.0018% 82.45% 848ms 0.78% VertexMeshWriter::MakeVtkMesh 331ms 0.31% 82.75% 831ms 0.77% Edge::GetMapIndex 826ms 0.76% 83.52% 826ms 0.76% std::swap (inline) 0 0% 83.52% 825ms 0.76% std::iter_swap (inline) 806ms 0.74% 84.26% 816ms 0.75% boost::detail::sp_counted_base::release 115ms 0.11% 84.37% 792ms 0.73% boost::shared_ptr::shared_ptr (inline) 98ms 0.09% 84.46% 789ms 0.73% MutableElement::GetNodeLocalIndex 116ms 0.11% 84.56% 765ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.56% 762ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.56% 756ms 0.7% boost::numeric::ublas::norm_inf (inline) 407ms 0.38% 84.94% 756ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 24ms 0.022% 84.96% 726ms 0.67% MutableElement::RegisterWithEdges (inline) 431ms 0.4% 85.36% 726ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 21ms 0.019% 85.38% 714ms 0.66% Edge::AddElement 708ms 0.65% 86.03% 708ms 0.65% Node::GetIndex 119ms 0.11% 86.14% 706ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.14% 706ms 0.65% std::allocator_traits::construct (inline) 16ms 0.015% 86.16% 689ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 642ms 0.59% 86.75% 677ms 0.62% boost::detail::shared_count::shared_count (inline) 96ms 0.089% 86.84% 673ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.84% 659ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.84% 653ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.86% 653ms 0.6% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.86% 645ms 0.6% std::_Vector_base::_M_allocate (inline) 34ms 0.031% 86.89% 602ms 0.56% MutableElement::RegisterWithNodes (inline) 0 0% 86.89% 599ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.89% 595ms 0.55% vtkPolygon::New 1ms 0.00092% 86.89% 595ms 0.55% vtkPolygon::vtkPolygon 578ms 0.53% 87.42% 578ms 0.53% [libstdc++.so.6.0.33] 570ms 0.53% 87.95% 570ms 0.53% boost::shared_ptr::operator-> (inline) 567ms 0.52% 88.47% 567ms 0.52% operator delete 24ms 0.022% 88.49% 563ms 0.52% Node::AddElement 29ms 0.027% 88.52% 546ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.52% 546ms 0.5% boost::numeric::ublas::vector::vector (inline) 7ms 0.0065% 88.53% 543ms 0.5% std::vector::_M_default_append (inline)