File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96295ms, 88.86% of 108373ms total Dropped 1018 nodes (cum <= 541.87ms) flat flat% sum% cum cum% 0 0% 0% 107880ms 99.55% __libc_start_call_main 0 0% 0% 107880ms 99.55% __libc_start_main_impl 0 0% 0% 107880ms 99.55% _start 0 0% 0% 107861ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107861ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107861ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107861ms 99.53% main 0 0% 0% 107827ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107827ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107827ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 107820ms 99.49% AbstractCellBasedSimulation::Solve 22ms 0.02% 0.024% 56423ms 52.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 25ms 0.023% 0.047% 53221ms 49.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 106ms 0.098% 0.14% 52146ms 48.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 378ms 0.35% 0.49% 40590ms 37.45% NagaiHondaForce::AddForceContribution 0 0% 0.49% 38722ms 35.73% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.49% 23908ms 22.06% VertexBasedCellPopulation::Update 0 0% 0.49% 23782ms 21.94% MutableVertexMesh::ReMesh 14593ms 13.47% 13.96% 22926ms 21.15% Cylindrical2dVertexMesh::GetVectorFromAtoB 96ms 0.089% 14.05% 17333ms 15.99% Cell::ReadyToDivide 78ms 0.072% 14.12% 16109ms 14.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 415ms 0.38% 14.50% 15047ms 13.88% boost::numeric::ublas::c_vector::c_vector (partial-inline) 373ms 0.34% 14.85% 14922ms 13.77% NagaiHondaForce::GetAdhesionParameter 146ms 0.13% 14.98% 13785ms 12.72% SimpleWntCellCycleModel::UpdateCellCyclePhase 407ms 0.38% 15.36% 13422ms 12.39% boost::numeric::ublas::vector_assign (inline) 142ms 0.13% 15.49% 13336ms 12.31% CellPropertyCollection::GetPropertiesType (inline) 138ms 0.13% 15.62% 12013ms 11.08% MutableVertexMesh::CheckForIntersections 72ms 0.066% 15.68% 11064ms 10.21% VertexBasedCellPopulation::GetDampingConstant 3288ms 3.03% 18.72% 11062ms 10.21% __dynamic_cast 96ms 0.089% 18.81% 10975ms 10.13% AbstractCellProperty::IsSubType (inline) 80ms 0.074% 18.88% 10348ms 9.55% AbstractTargetAreaModifier::UpdateTargetAreas 56ms 0.052% 18.93% 10255ms 9.46% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 21ms 0.019% 18.95% 10232ms 9.44% AbstractCellBasedSimulation::DoCellBirth 1302ms 1.20% 20.15% 9828ms 9.07% std::__new_allocator::allocate (inline) 2775ms 2.56% 22.71% 9714ms 8.96% boost::numeric::ublas::indexing_vector_assign 1341ms 1.24% 23.95% 9277ms 8.56% std::_Rb_tree::_M_erase 0 0% 23.95% 9265ms 8.55% std::allocator_traits::allocate (inline) 0 0% 23.95% 9240ms 8.53% std::_Rb_tree::_M_create_node (inline) 790ms 0.73% 24.68% 9034ms 8.34% VertexMesh::ElementIncludesPoint 374ms 0.35% 25.02% 8941ms 8.25% VertexMesh::GetNextEdgeGradientOfElementAtNode 25ms 0.023% 25.05% 8803ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 982ms 0.91% 25.95% 8629ms 7.96% operator new 0 0% 25.95% 8627ms 7.96% std::_Rb_tree::_M_get_node (inline) 82ms 0.076% 26.03% 8535ms 7.88% Cell::GetMutationState 187ms 0.17% 26.20% 8466ms 7.81% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.20% 8308ms 7.67% std::_Rb_tree::_M_drop_node (inline) 530ms 0.49% 26.69% 8219ms 7.58% VertexMesh::GetCentroidOfElement 0 0% 26.69% 8113ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 206ms 0.19% 26.88% 8079ms 7.45% std::__new_allocator::deallocate (inline) 0 0% 26.88% 8050ms 7.43% std::allocator_traits::deallocate (inline) 0 0% 26.88% 7998ms 7.38% std::_Rb_tree::_M_put_node (inline) 0 0% 26.88% 7995ms 7.38% std::set::~set (inline) 3360ms 3.10% 29.98% 7988ms 7.37% __GI___libc_free 2953ms 2.72% 32.71% 7432ms 6.86% __GI___libc_malloc 7ms 0.0065% 32.71% 7384ms 6.81% MutableVertexMesh::RemoveDeletedNodesAndElements 444ms 0.41% 33.12% 7305ms 6.74% std::map::operator[] (partial-inline) 1352ms 1.25% 34.37% 7185ms 6.63% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 140ms 0.13% 34.50% 6651ms 6.14% std::_Rb_tree::_Rb_tree (partial-inline) 122ms 0.11% 34.61% 6374ms 5.88% SimpleWntCellCycleModel::GetWntLevel 6303ms 5.82% 40.43% 6303ms 5.82% boost::numeric::ublas::c_vector::operator() 11ms 0.01% 40.44% 6266ms 5.78% std::set::set (inline) 664ms 0.61% 41.05% 6264ms 5.78% std::_Rb_tree::_M_copy (inline) 6240ms 5.76% 46.81% 6240ms 5.76% __strcmp_avx2 132ms 0.12% 46.93% 6168ms 5.69% WntConcentration::GetWntLevel 2411ms 2.22% 49.15% 5950ms 5.49% std::_Rb_tree::_M_lower_bound (inline) 0 0% 49.15% 5507ms 5.08% std::set::insert (inline) 2626ms 2.42% 51.58% 5412ms 4.99% __cxxabiv1::__si_class_type_info::__do_dyncast 722ms 0.67% 52.24% 5326ms 4.91% std::_Rb_tree::_M_clone_node (inline) 25ms 0.023% 52.27% 5174ms 4.77% MutableVertexMesh::RemoveDeletedNodes 36ms 0.033% 52.30% 5025ms 4.64% EdgeHelper::RemoveDeletedEdges 1440ms 1.33% 53.63% 4790ms 4.42% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.63% 4789ms 4.42% std::_Rb_tree::lower_bound (inline) 0 0% 53.63% 4789ms 4.42% std::map::lower_bound (inline) 36ms 0.033% 53.66% 4777ms 4.41% EdgeHelper::UpdateEdgesMapKey 46ms 0.042% 53.70% 4752ms 4.38% std::set_intersection (inline) 298ms 0.27% 53.98% 4706ms 4.34% std::__set_intersection 189ms 0.17% 54.15% 4641ms 4.28% MutableElement::ResetIndex 533ms 0.49% 54.65% 4633ms 4.28% std::_Rb_tree::_M_insert_ (inline) 4275ms 3.94% 58.59% 4616ms 4.26% _int_free 0 0% 58.59% 4572ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 4100ms 3.78% 62.37% 4100ms 3.78% boost::numeric::ublas::same_impl_ex 33ms 0.03% 62.40% 3996ms 3.69% Cell::GetCellProliferativeType 105ms 0.097% 62.50% 3923ms 3.62% AbstractCellPopulation::GetCellUsingLocationIndex 67ms 0.062% 62.56% 3673ms 3.39% AbstractCellProperty::IsType (inline) 7ms 0.0065% 62.57% 3544ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.57% 3366ms 3.11% std::insert_iterator::operator= (inline) 40ms 0.037% 62.61% 3143ms 2.90% Cell::SetCellProliferativeType 790ms 0.73% 63.33% 3076ms 2.84% AbstractElement::GetNodeLocation 2ms 0.0018% 63.34% 2980ms 2.75% std::_Rb_tree::_M_insert_unique_ (inline) 2058ms 1.90% 65.24% 2923ms 2.70% _int_malloc 2912ms 2.69% 67.92% 2912ms 2.69% std::_Rb_tree::_S_right (inline) 39ms 0.036% 67.96% 2878ms 2.66% std::_Rb_tree::erase 634ms 0.59% 68.54% 2870ms 2.65% boost::numeric::ublas::vector_binary::size (inline) 441ms 0.41% 68.95% 2819ms 2.60% std::_Rb_tree_const_iterator::operator++ (inline) 50ms 0.046% 69.00% 2629ms 2.43% CellPropertyCollection::HasProperty 724ms 0.67% 69.66% 2615ms 2.41% AbstractCellProperty::IsSame 292ms 0.27% 69.93% 2563ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 7ms 0.0065% 69.94% 2527ms 2.33% std::_Rb_tree::_M_insert_unique 0 0% 69.94% 2519ms 2.32% Cell::HasCellProperty (inline) 0 0% 69.94% 2438ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 108ms 0.1% 70.04% 2410ms 2.22% VertexMesh::GetVolumeOfElement 0 0% 70.04% 2399ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0018% 70.04% 2319ms 2.14% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 70.04% 2312ms 2.13% AbstractCellPopulation::WriteResultsToFiles 28ms 0.026% 70.07% 2308ms 2.13% Cell::GetCellData 212ms 0.2% 70.26% 2279ms 2.10% AbstractCellPopulation::Iterator::IsRealCell (inline) 85ms 0.078% 70.34% 2227ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2206ms 2.04% 72.38% 2206ms 2.04% std::_Rb_tree_increment 2ms 0.0018% 72.38% 2147ms 1.98% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.38% 2147ms 1.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 31ms 0.029% 72.41% 2028ms 1.87% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00092% 72.41% 1908ms 1.76% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.41% 1898ms 1.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 70ms 0.065% 72.47% 1894ms 1.75% MutableVertexMesh::CheckForSwapsFromShortEdges 412ms 0.38% 72.85% 1891ms 1.74% std::type_info::operator== (inline) 1246ms 1.15% 74.00% 1849ms 1.71% std::_Rb_tree::equal_range (inline) 24ms 0.022% 74.03% 1747ms 1.61% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.03% 1706ms 1.57% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.023% 74.05% 1650ms 1.52% VertexMesh::GetSurfaceAreaOfElement 152ms 0.14% 74.19% 1631ms 1.50% boost::numeric::ublas::vector_reference::operator() (inline) 37ms 0.034% 74.22% 1563ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 73ms 0.067% 74.29% 1542ms 1.42% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 70ms 0.065% 74.36% 1515ms 1.40% Node::RemoveElement 0 0% 74.36% 1499ms 1.38% boost::numeric::ublas::vector_binary::operator() (inline) 142ms 0.13% 74.49% 1455ms 1.34% CellPropertyCollection::AddProperty 18ms 0.017% 74.50% 1451ms 1.34% std::set::erase (inline) 1ms 0.00092% 74.50% 1374ms 1.27% tcache_get (inline) 1373ms 1.27% 75.77% 1373ms 1.27% tcache_get_n (inline) 0 0% 75.77% 1290ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 75.77% 1246ms 1.15% boost::numeric::ublas::norm_2 (inline) 536ms 0.49% 76.27% 1239ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 84ms 0.078% 76.34% 1197ms 1.10% std::less::operator() (inline) 23ms 0.021% 76.36% 1188ms 1.10% boost::numeric::ublas::detail::expression_type_check (inline) 95ms 0.088% 76.45% 1159ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 173ms 0.16% 76.61% 1158ms 1.07% boost::numeric::ublas::detail::equals 1146ms 1.06% 77.67% 1146ms 1.06% [libchaste_cell_based.so] 100ms 0.092% 77.76% 1140ms 1.05% std::_Rb_tree::find (inline) 0 0% 77.76% 1127ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1127ms 1.04% 78.80% 1127ms 1.04% std::_Rb_tree_insert_and_rebalance 925ms 0.85% 79.66% 1113ms 1.03% std::operator< (inline) 13ms 0.012% 79.67% 1073ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1058ms 0.98% 80.64% 1058ms 0.98% Node::rGetLocation 27ms 0.025% 80.67% 1003ms 0.93% CellPropertyRegistry::Get 0 0% 80.67% 1002ms 0.92% std::_Rb_tree::clear (inline) 8ms 0.0074% 80.68% 988ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 987ms 0.91% 81.59% 987ms 0.91% [libchaste_mesh.so] 0 0% 81.59% 983ms 0.91% std::map::clear (inline) 982ms 0.91% 82.49% 982ms 0.91% std::vector::size (inline) 157ms 0.14% 82.64% 972ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 82.64% 972ms 0.9% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.64% 967ms 0.89% std::map::find (inline) 356ms 0.33% 82.97% 915ms 0.84% Edge::GetMapIndex 0 0% 82.97% 901ms 0.83% boost::numeric::ublas::norm_inf (inline) 483ms 0.45% 83.41% 901ms 0.83% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 83.41% 842ms 0.78% VertexMeshWriter::MakeVtkMesh 110ms 0.1% 83.51% 830ms 0.77% MutableElement::GetNodeLocalIndex 0 0% 83.51% 821ms 0.76% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 83.51% 817ms 0.75% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 83.52% 817ms 0.75% boost::numeric::ublas::c_vector::swap (inline) 27ms 0.025% 83.54% 816ms 0.75% MutableElement::RegisterWithEdges (inline) 63ms 0.058% 83.60% 813ms 0.75% std::swap_ranges (inline) 171ms 0.16% 83.76% 805ms 0.74% boost::shared_ptr::shared_ptr (inline) 36ms 0.033% 83.79% 803ms 0.74% Edge::AddElement 799ms 0.74% 84.53% 803ms 0.74% boost::detail::sp_counted_base::release 104ms 0.096% 84.62% 761ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 751ms 0.69% 85.32% 751ms 0.69% Node::GetIndex 0 0% 85.32% 750ms 0.69% std::iter_swap (inline) 750ms 0.69% 86.01% 750ms 0.69% std::swap (inline) 481ms 0.44% 86.45% 745ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 98ms 0.09% 86.54% 673ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.54% 673ms 0.62% std::allocator_traits::construct (inline) 1ms 0.00092% 86.54% 637ms 0.59% std::_Vector_base::_M_allocate (inline) 604ms 0.56% 87.10% 634ms 0.59% boost::detail::shared_count::shared_count (inline) 626ms 0.58% 87.68% 626ms 0.58% [libstdc++.so.6.0.33] 0 0% 87.68% 622ms 0.57% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.027% 87.71% 622ms 0.57% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.71% 613ms 0.57% std::_Rb_tree::_M_construct_node (inline) 40ms 0.037% 87.74% 607ms 0.56% MutableElement::RegisterWithNodes (inline) 0 0% 87.74% 602ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.74% 601ms 0.55% vtkPolygon::New 2ms 0.0018% 87.75% 601ms 0.55% vtkPolygon::vtkPolygon 594ms 0.55% 88.29% 594ms 0.55% operator delete 27ms 0.025% 88.32% 590ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.32% 590ms 0.54% boost::numeric::ublas::vector::vector (inline) 24ms 0.022% 88.34% 562ms 0.52% Node::AddElement 558ms 0.51% 88.86% 558ms 0.51% boost::shared_ptr::operator-> (inline)