File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 76151ms, 88.83% of 85730ms total Dropped 1087 nodes (cum <= 428.65ms) flat flat% sum% cum cum% 0 0% 0% 85441ms 99.66% __libc_start_call_main 0 0% 0% 85441ms 99.66% __libc_start_main_impl 0 0% 0% 85441ms 99.66% _start 0 0% 0% 85422ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 85422ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 85422ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 85422ms 99.64% main 0 0% 0% 85375ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 85375ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 85375ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0023% 0.0023% 85369ms 99.58% AbstractCellBasedSimulation::Solve 13ms 0.015% 0.017% 44027ms 51.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 10ms 0.012% 0.029% 41365ms 48.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 128ms 0.15% 0.18% 40140ms 46.82% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0023% 0.18% 30814ms 35.94% AbstractCellBasedSimulation::UpdateCellPopulation 233ms 0.27% 0.45% 30767ms 35.89% NagaiHondaForce::AddForceContribution 6ms 0.007% 0.46% 19024ms 22.19% VertexBasedCellPopulation::Update 1ms 0.0012% 0.46% 18886ms 22.03% MutableVertexMesh::ReMesh 11427ms 13.33% 13.79% 18073ms 21.08% Cylindrical2dVertexMesh::GetVectorFromAtoB 61ms 0.071% 13.86% 13808ms 16.11% Cell::ReadyToDivide 48ms 0.056% 13.92% 12738ms 14.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 267ms 0.31% 14.23% 10913ms 12.73% NagaiHondaForce::GetAdhesionParameter 81ms 0.094% 14.32% 10903ms 12.72% CellPropertyCollection::GetPropertiesType (inline) 105ms 0.12% 14.45% 10894ms 12.71% SimpleWntCellCycleModel::UpdateCellCyclePhase 391ms 0.46% 14.90% 10829ms 12.63% boost::numeric::ublas::c_vector::c_vector (partial-inline) 213ms 0.25% 15.15% 9673ms 11.28% boost::numeric::ublas::vector_assign (inline) 2707ms 3.16% 18.31% 9274ms 10.82% __dynamic_cast 99ms 0.12% 18.42% 9221ms 10.76% MutableVertexMesh::CheckForIntersections 23ms 0.027% 18.45% 9161ms 10.69% AbstractCellProperty::IsSubType (inline) 69ms 0.08% 18.53% 8900ms 10.38% VertexBasedCellPopulation::GetDampingConstant 62ms 0.072% 18.60% 8463ms 9.87% AbstractTargetAreaModifier::UpdateTargetAreas 35ms 0.041% 18.64% 8388ms 9.78% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 30ms 0.035% 18.68% 8069ms 9.41% AbstractCellBasedSimulation::DoCellBirth 1019ms 1.19% 19.87% 7786ms 9.08% std::__new_allocator::allocate (inline) 0 0% 19.87% 7416ms 8.65% std::_Rb_tree::_M_create_node (inline) 0 0% 19.87% 7362ms 8.59% std::allocator_traits::allocate (inline) 2239ms 2.61% 22.48% 7332ms 8.55% boost::numeric::ublas::indexing_vector_assign 254ms 0.3% 22.77% 7181ms 8.38% VertexMesh::GetNextEdgeGradientOfElementAtNode 591ms 0.69% 23.46% 6827ms 7.96% operator new 0 0% 23.46% 6771ms 7.90% std::_Rb_tree::_M_get_node (inline) 1013ms 1.18% 24.65% 6726ms 7.85% std::_Rb_tree::_M_erase 78ms 0.091% 24.74% 6720ms 7.84% Cell::GetMutationState 25ms 0.029% 24.77% 6718ms 7.84% VertexBasedCellPopulation::GetLocationOfCellCentre 634ms 0.74% 25.51% 6701ms 7.82% VertexMesh::ElementIncludesPoint 0 0% 25.51% 6523ms 7.61% std::_Rb_tree::_Alloc_node::operator() (inline) 403ms 0.47% 25.98% 6361ms 7.42% VertexMesh::GetCentroidOfElement 15ms 0.017% 25.99% 6300ms 7.35% MutableVertexMesh::RemoveDeletedNodesAndElements 2278ms 2.66% 28.65% 6077ms 7.09% __GI___libc_malloc 177ms 0.21% 28.86% 6013ms 7.01% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.86% 6010ms 7.01% std::_Rb_tree::_M_drop_node (inline) 412ms 0.48% 29.34% 5941ms 6.93% std::map::operator[] (partial-inline) 163ms 0.19% 29.53% 5882ms 6.86% std::__new_allocator::deallocate (inline) 0 0% 29.53% 5870ms 6.85% std::allocator_traits::deallocate (inline) 1174ms 1.37% 30.90% 5806ms 6.77% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 30.90% 5786ms 6.75% std::_Rb_tree::_M_put_node (inline) 0 0% 30.90% 5719ms 6.67% std::set::~set (inline) 127ms 0.15% 31.05% 5692ms 6.64% std::_Rb_tree::_Rb_tree (partial-inline) 1790ms 2.09% 33.13% 5501ms 6.42% __GI___libc_free 5433ms 6.34% 39.47% 5433ms 6.34% __strcmp_evex 589ms 0.69% 40.16% 5366ms 6.26% std::_Rb_tree::_M_copy (inline) 14ms 0.016% 40.17% 5195ms 6.06% std::set::set (inline) 80ms 0.093% 40.27% 4825ms 5.63% SimpleWntCellCycleModel::GetWntLevel 142ms 0.17% 40.43% 4685ms 5.46% WntConcentration::GetWntLevel 4663ms 5.44% 45.87% 4663ms 5.44% boost::numeric::ublas::c_vector::operator() 1975ms 2.30% 48.18% 4663ms 5.44% std::_Rb_tree::_M_lower_bound (inline) 657ms 0.77% 48.94% 4573ms 5.33% std::_Rb_tree::_M_clone_node (inline) 14ms 0.016% 48.96% 4305ms 5.02% MutableVertexMesh::RemoveDeletedNodes 2262ms 2.64% 51.60% 4192ms 4.89% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.036% 51.63% 4154ms 4.85% EdgeHelper::RemoveDeletedEdges 0 0% 51.63% 4117ms 4.80% std::set::insert (inline) 1537ms 1.79% 53.43% 4062ms 4.74% boost::numeric::ublas::c_vector::operator[] (inline) 27ms 0.031% 53.46% 3890ms 4.54% EdgeHelper::UpdateEdgesMapKey 186ms 0.22% 53.67% 3829ms 4.47% MutableElement::ResetIndex 0 0% 53.67% 3788ms 4.42% std::_Rb_tree::lower_bound (inline) 0 0% 53.67% 3788ms 4.42% std::map::lower_bound (inline) 2ms 0.0023% 53.68% 3712ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 3328ms 3.88% 57.56% 3694ms 4.31% _int_free 445ms 0.52% 58.08% 3456ms 4.03% std::_Rb_tree::_M_insert_ (inline) 118ms 0.14% 58.22% 3439ms 4.01% AbstractCellPopulation::GetCellUsingLocationIndex 101ms 0.12% 58.33% 3260ms 3.80% std::set_intersection (inline) 190ms 0.22% 58.55% 3159ms 3.68% std::__set_intersection 22ms 0.026% 58.58% 3153ms 3.68% Cell::GetCellProliferativeType 34ms 0.04% 58.62% 3137ms 3.66% AbstractCellProperty::IsType (inline) 2894ms 3.38% 62.00% 2894ms 3.38% boost::numeric::ublas::same_impl_ex 6ms 0.007% 62.00% 2775ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1763ms 2.06% 64.06% 2622ms 3.06% _int_malloc 31ms 0.036% 64.10% 2504ms 2.92% Cell::SetCellProliferativeType 56ms 0.065% 64.16% 2493ms 2.91% std::_Rb_tree::erase 0 0% 64.16% 2414ms 2.82% std::insert_iterator::operator= (inline) 718ms 0.84% 65.00% 2338ms 2.73% AbstractElement::GetNodeLocation 553ms 0.65% 65.64% 2288ms 2.67% AbstractCellProperty::IsSame 2262ms 2.64% 68.28% 2262ms 2.64% std::_Rb_tree::_S_right (inline) 25ms 0.029% 68.31% 2249ms 2.62% CellPropertyCollection::HasProperty 0 0% 68.31% 2189ms 2.55% Cell::HasCellProperty (inline) 5ms 0.0058% 68.32% 2134ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 26ms 0.03% 68.35% 2092ms 2.44% Cell::GetCellData 0 0% 68.35% 2066ms 2.41% boost::numeric::ublas::c_vector::operator-= (inline) 164ms 0.19% 68.54% 2052ms 2.39% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.0012% 68.54% 2026ms 2.36% AbstractCellPopulation::WriteResultsToFiles 497ms 0.58% 69.12% 1993ms 2.32% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.12% 1983ms 2.31% std::_Rb_tree::_M_insert_unique 0 0% 69.12% 1975ms 2.30% boost::numeric::ublas::c_vector::assign (inline) 184ms 0.21% 69.33% 1890ms 2.20% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0012% 69.34% 1789ms 2.09% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.34% 1789ms 2.09% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 44ms 0.051% 69.39% 1782ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 60ms 0.07% 69.46% 1776ms 2.07% VertexMesh::GetVolumeOfElement 4ms 0.0047% 69.46% 1769ms 2.06% AbstractCellPopulation::Iterator::operator++ (inline) 150ms 0.17% 69.64% 1764ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 334ms 0.39% 70.03% 1735ms 2.02% std::type_info::operator== (inline) 39ms 0.045% 70.07% 1705ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 1131ms 1.32% 71.39% 1681ms 1.96% std::_Rb_tree::equal_range (inline) 0 0% 71.39% 1658ms 1.93% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.39% 1649ms 1.92% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1526ms 1.78% 73.17% 1526ms 1.78% std::_Rb_tree_increment 0 0% 73.17% 1493ms 1.74% VertexMeshWriter::WriteVtkUsingMesh 60ms 0.07% 73.24% 1463ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 15ms 0.017% 73.26% 1372ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 23ms 0.027% 73.28% 1270ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 66ms 0.077% 73.36% 1208ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 24ms 0.028% 73.39% 1194ms 1.39% VertexMesh::GetSurfaceAreaOfElement 40ms 0.047% 73.44% 1174ms 1.37% Node::RemoveElement 98ms 0.11% 73.55% 1166ms 1.36% CellPropertyCollection::AddProperty 7ms 0.0082% 73.56% 1136ms 1.33% std::set::erase (inline) 0 0% 73.56% 1079ms 1.26% boost::numeric::ublas::norm_2 (inline) 477ms 0.56% 74.12% 1072ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 58ms 0.068% 74.18% 1059ms 1.24% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.0035% 74.19% 1058ms 1.23% OffLatticeSimulation::ApplyBoundaries 1031ms 1.20% 75.39% 1031ms 1.20% [libchaste_cell_based.so] 0 0% 75.39% 1026ms 1.20% tcache_get (inline) 1026ms 1.20% 76.59% 1026ms 1.20% tcache_get_n (inline) 0 0% 76.59% 1022ms 1.19% boost::numeric::ublas::vector_binary::operator() (inline) 55ms 0.064% 76.65% 1009ms 1.18% std::less::operator() (inline) 775ms 0.9% 77.55% 954ms 1.11% std::operator< (inline) 53ms 0.062% 77.62% 920ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 24ms 0.028% 77.64% 919ms 1.07% CellPropertyRegistry::Get 13ms 0.015% 77.66% 912ms 1.06% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 7ms 0.0082% 77.67% 910ms 1.06% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 77.67% 893ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.67% 892ms 1.04% std::_Rb_tree::clear (inline) 74ms 0.086% 77.75% 889ms 1.04% std::_Rb_tree::find (inline) 6ms 0.007% 77.76% 886ms 1.03% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 77.76% 878ms 1.02% std::map::clear (inline) 0 0% 77.76% 875ms 1.02% boost::numeric::ublas::c_vector::assign_temporary (inline) 15ms 0.017% 77.78% 875ms 1.02% boost::numeric::ublas::c_vector::swap (inline) 141ms 0.16% 77.94% 864ms 1.01% boost::numeric::ublas::detail::equals 57ms 0.066% 78.01% 860ms 1.00% std::swap_ranges (inline) 838ms 0.98% 78.99% 838ms 0.98% std::_Rb_tree_insert_and_rebalance 0 0% 78.99% 803ms 0.94% std::iter_swap (inline) 803ms 0.94% 79.92% 803ms 0.94% std::swap (inline) 764ms 0.89% 80.81% 764ms 0.89% Node::rGetLocation 0 0% 80.81% 757ms 0.88% std::map::find (inline) 79ms 0.092% 80.91% 743ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 80.91% 743ms 0.87% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.91% 710ms 0.83% boost::numeric::ublas::norm_inf (inline) 326ms 0.38% 81.29% 710ms 0.83% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 81.29% 700ms 0.82% VertexMeshWriter::MakeVtkMesh 227ms 0.26% 81.55% 683ms 0.8% std::__new_allocator::construct (inline) 0 0% 81.55% 683ms 0.8% std::allocator_traits::construct (inline) 670ms 0.78% 82.33% 670ms 0.78% std::vector::size (inline) 362ms 0.42% 82.76% 663ms 0.77% Edge::GetMapIndex 0 0% 82.76% 645ms 0.75% std::_Rb_tree::_M_construct_node (inline) 627ms 0.73% 83.49% 644ms 0.75% boost::detail::sp_counted_base::release 69ms 0.08% 83.57% 620ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 12ms 0.014% 83.58% 609ms 0.71% AbstractNumericalMethod::DetectStepSizeExceptions 90ms 0.1% 83.69% 597ms 0.7% VertexBasedCellPopulation::CheckForStepSizeException 321ms 0.37% 84.06% 593ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.06% 590ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 18ms 0.021% 84.08% 590ms 0.69% Edge::AddElement 150ms 0.17% 84.26% 590ms 0.69% boost::shared_ptr::shared_ptr (inline) 0 0% 84.26% 589ms 0.69% std::_Vector_base::_M_allocate (inline) 10ms 0.012% 84.27% 585ms 0.68% MutableElement::RegisterWithEdges (inline) 581ms 0.68% 84.95% 581ms 0.68% [libchaste_mesh.so] 0 0% 84.95% 581ms 0.68% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 523ms 0.61% 85.56% 523ms 0.61% [libstdc++.so.6.0.33] 0 0% 85.56% 521ms 0.61% std::map::map (inline) 98ms 0.11% 85.67% 515ms 0.6% MutableElement::GetNodeLocalIndex 0 0% 85.67% 511ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.022% 85.69% 511ms 0.6% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.69% 494ms 0.58% vtkPolygon::New 0 0% 85.69% 494ms 0.58% vtkPolygon::vtkPolygon 5ms 0.0058% 85.70% 484ms 0.56% std::vector::_M_default_append (inline) 480ms 0.56% 86.26% 480ms 0.56% Node::GetIndex 26ms 0.03% 86.29% 455ms 0.53% MutableElement::RegisterWithNodes (inline) 455ms 0.53% 86.82% 455ms 0.53% tcache_put (inline) 67ms 0.078% 86.90% 449ms 0.52% std::_Rb_tree::_M_upper_bound (inline) 447ms 0.52% 87.42% 447ms 0.52% boost::shared_ptr::operator-> (inline) 19ms 0.022% 87.44% 443ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.44% 443ms 0.52% boost::numeric::ublas::vector::vector (inline) 315ms 0.37% 87.81% 441ms 0.51% malloc_consolidate 415ms 0.48% 88.29% 440ms 0.51% boost::detail::shared_count::shared_count (inline) 433ms 0.51% 88.80% 433ms 0.51% operator delete 2ms 0.0023% 88.80% 431ms 0.5% VertexElementMap::VertexElementMap 13ms 0.015% 88.81% 429ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate 10ms 0.012% 88.83% 429ms 0.5% Cylindrical2dVertexMesh::GetMeshForVtk 0 0% 88.83% 429ms 0.5% std::vector::resize (inline)