File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 56214ms, 88.37% of 63612ms total Dropped 1043 nodes (cum <= 318.06ms) flat flat% sum% cum cum% 0 0% 0% 63319ms 99.54% __libc_start_call_main 0 0% 0% 63319ms 99.54% __libc_start_main_impl 0 0% 0% 63319ms 99.54% _start 0 0% 0% 63304ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63304ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63304ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63304ms 99.52% main 0 0% 0% 63269ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63269ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63269ms 99.46% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 63264ms 99.45% AbstractCellBasedSimulation::Solve 9ms 0.014% 0.014% 33022ms 51.91% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.019% 0.033% 30820ms 48.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 44ms 0.069% 0.1% 30033ms 47.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 141ms 0.22% 0.32% 22928ms 36.04% NagaiHondaForce::AddForceContribution 0 0% 0.32% 22396ms 35.21% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.32% 13580ms 21.35% VertexBasedCellPopulation::Update 0 0% 0.32% 13482ms 21.19% MutableVertexMesh::ReMesh 6623ms 10.41% 10.74% 11619ms 18.27% Cylindrical2dVertexMesh::GetVectorFromAtoB 25ms 0.039% 10.77% 10267ms 16.14% Cell::ReadyToDivide 18ms 0.028% 10.80% 9619ms 15.12% AbstractPhaseBasedCellCycleModel::ReadyToDivide 60ms 0.094% 10.90% 9260ms 14.56% NagaiHondaForce::GetAdhesionParameter 28ms 0.044% 10.94% 8353ms 13.13% SimpleWntCellCycleModel::UpdateCellCyclePhase 213ms 0.33% 11.28% 7920ms 12.45% boost::numeric::ublas::c_vector::c_vector (partial-inline) 62ms 0.097% 11.37% 7491ms 11.78% CellPropertyCollection::GetPropertiesType (inline) 586ms 0.92% 12.29% 7133ms 11.21% std::__new_allocator::allocate (inline) 211ms 0.33% 12.63% 6970ms 10.96% boost::numeric::ublas::vector_assign (inline) 36ms 0.057% 12.68% 6902ms 10.85% VertexBasedCellPopulation::GetDampingConstant 0 0% 12.68% 6848ms 10.77% std::allocator_traits::allocate (inline) 0 0% 12.68% 6682ms 10.50% std::_Rb_tree::_M_create_node (inline) 679ms 1.07% 13.75% 6635ms 10.43% operator new 66ms 0.1% 13.85% 6494ms 10.21% MutableVertexMesh::CheckForIntersections 0 0% 13.85% 6455ms 10.15% std::_Rb_tree::_M_get_node (inline) 1554ms 2.44% 16.30% 6216ms 9.77% __dynamic_cast 40ms 0.063% 16.36% 6181ms 9.72% AbstractCellProperty::IsSubType (inline) 25ms 0.039% 16.40% 6172ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 7ms 0.011% 16.41% 6134ms 9.64% AbstractCellBasedSimulation::DoCellBirth 20ms 0.031% 16.44% 6101ms 9.59% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 610ms 0.96% 17.40% 5979ms 9.40% std::_Rb_tree::_M_erase 0 0% 17.40% 5868ms 9.22% std::_Rb_tree::_Alloc_node::operator() (inline) 2572ms 4.04% 21.44% 5831ms 9.17% __GI___libc_malloc 0 0% 21.44% 5815ms 9.14% std::_Rb_tree::_M_drop_node (inline) 292ms 0.46% 21.90% 5688ms 8.94% std::_Rb_tree::~_Rb_tree (inline) 0 0% 21.90% 5366ms 8.44% std::set::~set (inline) 1575ms 2.48% 24.38% 5157ms 8.11% boost::numeric::ublas::indexing_vector_assign 90ms 0.14% 24.52% 5075ms 7.98% std::__new_allocator::deallocate (inline) 0 0% 24.52% 5075ms 7.98% std::allocator_traits::deallocate (inline) 0 0% 24.52% 5031ms 7.91% std::_Rb_tree::_M_put_node (inline) 41ms 0.064% 24.58% 4941ms 7.77% Cell::GetMutationState 224ms 0.35% 24.94% 4931ms 7.75% VertexMesh::GetNextEdgeGradientOfElementAtNode 257ms 0.4% 25.34% 4779ms 7.51% std::map::operator[] (partial-inline) 898ms 1.41% 26.75% 4701ms 7.39% __GI___libc_free 27ms 0.042% 26.80% 4645ms 7.30% VertexBasedCellPopulation::GetLocationOfCellCentre 508ms 0.8% 27.59% 4603ms 7.24% VertexMesh::ElementIncludesPoint 5ms 0.0079% 27.60% 4548ms 7.15% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 27.60% 4377ms 6.88% std::set::insert (inline) 341ms 0.54% 28.14% 4336ms 6.82% VertexMesh::GetCentroidOfElement 844ms 1.33% 29.46% 4057ms 6.38% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 99ms 0.16% 29.62% 3993ms 6.28% std::_Rb_tree::_Rb_tree (partial-inline) 582ms 0.91% 30.54% 3925ms 6.17% std::_Rb_tree::_M_insert_ (inline) 428ms 0.67% 31.21% 3793ms 5.96% std::_Rb_tree::_M_copy (inline) 3580ms 5.63% 36.84% 3777ms 5.94% _int_free 3ms 0.0047% 36.84% 3734ms 5.87% std::set::set (inline) 3683ms 5.79% 42.63% 3683ms 5.79% boost::numeric::ublas::c_vector::operator() 1593ms 2.50% 45.13% 3583ms 5.63% std::_Rb_tree::_M_lower_bound (inline) 92ms 0.14% 45.28% 3496ms 5.50% SimpleWntCellCycleModel::GetWntLevel 84ms 0.13% 45.41% 3445ms 5.42% std::set_intersection (inline) 3409ms 5.36% 50.77% 3409ms 5.36% __strcmp_evex 152ms 0.24% 51.01% 3361ms 5.28% std::__set_intersection 88ms 0.14% 51.15% 3330ms 5.23% WntConcentration::GetWntLevel 1958ms 3.08% 54.23% 3270ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.028% 54.25% 3208ms 5.04% MutableVertexMesh::RemoveDeletedNodes 423ms 0.66% 54.92% 3203ms 5.04% std::_Rb_tree::_M_clone_node (inline) 25ms 0.039% 54.96% 3098ms 4.87% EdgeHelper::RemoveDeletedEdges 0 0% 54.96% 3075ms 4.83% std::_Rb_tree::lower_bound (inline) 0 0% 54.96% 3075ms 4.83% std::map::lower_bound (inline) 27ms 0.042% 55.00% 2939ms 4.62% EdgeHelper::UpdateEdgesMapKey 87ms 0.14% 55.14% 2936ms 4.62% AbstractCellPopulation::GetCellUsingLocationIndex 788ms 1.24% 56.38% 2908ms 4.57% boost::numeric::ublas::c_vector::operator[] (inline) 85ms 0.13% 56.51% 2739ms 4.31% MutableElement::ResetIndex 0 0% 56.51% 2675ms 4.21% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 56.51% 2642ms 4.15% std::insert_iterator::operator= (inline) 44ms 0.069% 56.58% 2633ms 4.14% Cell::GetCellProliferativeType 1943ms 3.05% 59.63% 2493ms 3.92% _int_malloc 13ms 0.02% 59.65% 2488ms 3.91% std::_Rb_tree::_M_insert_unique_ (inline) 2425ms 3.81% 63.47% 2425ms 3.81% boost::numeric::ublas::same_impl_ex 103ms 0.16% 63.63% 2309ms 3.63% boost::detail::shared_count::~shared_count (inline) 0 0% 63.63% 2309ms 3.63% boost::shared_ptr::~shared_ptr (inline) 2168ms 3.41% 67.04% 2180ms 3.43% boost::detail::sp_counted_base::release 69ms 0.11% 67.14% 2170ms 3.41% Cell::SetCellProliferativeType 59ms 0.093% 67.24% 2094ms 3.29% AbstractCellProperty::IsType (inline) 28ms 0.044% 67.28% 2021ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 67.28% 1889ms 2.97% std::_Rb_tree::_M_insert_unique (inline) 478ms 0.75% 68.03% 1761ms 2.77% AbstractElement::GetNodeLocation 0 0% 68.03% 1668ms 2.62% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.03% 1626ms 2.56% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.0047% 68.04% 1625ms 2.55% AbstractCellPopulation::Iterator::operator++ (inline) 293ms 0.46% 68.50% 1625ms 2.55% boost::numeric::ublas::vector_binary::size (inline) 116ms 0.18% 68.68% 1624ms 2.55% AbstractCellPopulation::Iterator::IsRealCell 32ms 0.05% 68.73% 1594ms 2.51% std::_Rb_tree::erase 1592ms 2.50% 71.23% 1592ms 2.50% std::_Rb_tree::_S_right (inline) 136ms 0.21% 71.45% 1554ms 2.44% VertexMesh::GetAreaGradientOfElementAtNode 22ms 0.035% 71.48% 1538ms 2.42% CellPropertyCollection::HasProperty 0 0% 71.48% 1498ms 2.35% Cell::HasCellProperty (inline) 317ms 0.5% 71.98% 1451ms 2.28% AbstractCellProperty::IsSame 18ms 0.028% 72.01% 1431ms 2.25% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0031% 72.01% 1407ms 2.21% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.01% 1407ms 2.21% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.0094% 72.02% 1391ms 2.19% Cell::GetCellData 1ms 0.0016% 72.02% 1385ms 2.18% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0063% 72.03% 1373ms 2.16% VertexBasedCellPopulation::WriteCellVtkResultsToFile 259ms 0.41% 72.44% 1334ms 2.10% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.44% 1251ms 1.97% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.041% 72.48% 1237ms 1.94% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.0079% 72.48% 1213ms 1.91% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 72.48% 1155ms 1.82% boost::numeric::ublas::c_vector::operator-= (inline) 139ms 0.22% 72.70% 1134ms 1.78% std::type_info::operator== (inline) 70ms 0.11% 72.81% 1122ms 1.76% VertexMesh::GetVolumeOfElement 97ms 0.15% 72.97% 1095ms 1.72% CellPropertyCollection::AddProperty 180ms 0.28% 73.25% 1043ms 1.64% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 31ms 0.049% 73.30% 1008ms 1.58% MutableVertexMesh::CheckForSwapsFromShortEdges 49ms 0.077% 73.37% 984ms 1.55% boost::numeric::ublas::vector_reference::operator() (inline) 915ms 1.44% 74.81% 915ms 1.44% std::_Rb_tree_increment 905ms 1.42% 76.24% 905ms 1.42% [libchaste_cell_based.so] 0 0% 76.24% 885ms 1.39% boost::numeric::ublas::norm_2 (inline) 1ms 0.0016% 76.24% 883ms 1.39% OffLatticeSimulation::ApplyBoundaries 16ms 0.025% 76.26% 880ms 1.38% VertexMesh::GetSurfaceAreaOfElement 362ms 0.57% 76.83% 878ms 1.38% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 29ms 0.046% 76.88% 868ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 67ms 0.11% 76.98% 855ms 1.34% std::_Rb_tree::_M_erase_aux (partial-inline) 29ms 0.046% 77.03% 833ms 1.31% Node::RemoveElement 0 0% 77.03% 814ms 1.28% std::_Rb_tree::_Auto_node::_Auto_node (inline) 533ms 0.84% 77.87% 813ms 1.28% std::_Rb_tree::equal_range (inline) 0 0% 77.87% 811ms 1.27% CellPropertyCollection::~CellPropertyCollection (inline) 808ms 1.27% 79.14% 808ms 1.27% [libchaste_mesh.so] 4ms 0.0063% 79.14% 805ms 1.27% std::set::erase (inline) 0 0% 79.14% 787ms 1.24% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.14% 787ms 1.24% std::__new_allocator::destroy (inline) 0 0% 79.14% 787ms 1.24% std::allocator_traits::destroy (inline) 32ms 0.05% 79.19% 767ms 1.21% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 19ms 0.03% 79.22% 720ms 1.13% CellPropertyRegistry::Get 0 0% 79.22% 710ms 1.12% boost::numeric::ublas::vector_binary::operator() (inline) 35ms 0.055% 79.28% 690ms 1.08% std::less::operator() (inline) 555ms 0.87% 80.15% 655ms 1.03% std::operator< (inline) 646ms 1.02% 81.17% 646ms 1.02% [libstdc++.so.6.0.33] 631ms 0.99% 82.16% 631ms 0.99% std::_Rb_tree_insert_and_rebalance 13ms 0.02% 82.18% 629ms 0.99% MutableElement::RegisterWithEdges (inline) 9ms 0.014% 82.19% 629ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 7ms 0.011% 82.20% 625ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.038% 82.24% 623ms 0.98% Edge::AddElement 1ms 0.0016% 82.24% 610ms 0.96% tcache_get (inline) 609ms 0.96% 83.20% 609ms 0.96% tcache_get_n (inline) 56ms 0.088% 83.29% 608ms 0.96% boost::numeric::ublas::detail::equals 1ms 0.0016% 83.29% 592ms 0.93% std::_Rb_tree::clear (inline) 2ms 0.0031% 83.29% 586ms 0.92% VertexMeshWriter::MakeVtkMesh 0 0% 83.29% 579ms 0.91% std::map::clear (inline) 0 0% 83.29% 562ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.017% 83.31% 562ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 505ms 0.79% 84.10% 557ms 0.88% CellPropertyCollection::GetProperty 101ms 0.16% 84.26% 551ms 0.87% std::swap_ranges (inline) 47ms 0.074% 84.34% 537ms 0.84% std::_Rb_tree::find (inline) 0 0% 84.34% 523ms 0.82% boost::numeric::ublas::norm_inf (inline) 216ms 0.34% 84.68% 523ms 0.82% boost::numeric::ublas::vector_norm_inf::apply (inline) 494ms 0.78% 85.45% 494ms 0.78% std::vector::size (inline) 49ms 0.077% 85.53% 487ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.53% 450ms 0.71% std::iter_swap (inline) 450ms 0.71% 86.24% 450ms 0.71% std::swap (inline) 1ms 0.0016% 86.24% 447ms 0.7% std::map::find (inline) 233ms 0.37% 86.60% 443ms 0.7% Edge::GetMapIndex 82ms 0.13% 86.73% 443ms 0.7% MutableElement::GetNodeLocalIndex 238ms 0.37% 87.11% 439ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 87.11% 425ms 0.67% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.11% 416ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 11ms 0.017% 87.13% 416ms 0.65% std::_Rb_tree::_M_insert_node (inline) 16ms 0.025% 87.15% 414ms 0.65% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 87.15% 409ms 0.64% vtkPolygon::New 0 0% 87.15% 409ms 0.64% vtkPolygon::vtkPolygon 75ms 0.12% 87.27% 398ms 0.63% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 87.27% 386ms 0.61% std::_Vector_base::_M_allocate (inline) 10ms 0.016% 87.28% 367ms 0.58% MutableElement::RegisterWithNodes (inline) 5ms 0.0079% 87.29% 363ms 0.57% Cylindrical2dVertexMesh::GetMeshForVtk 22ms 0.035% 87.33% 353ms 0.55% Node::AddElement 340ms 0.53% 87.86% 340ms 0.53% Node::rGetLocation 0 0% 87.86% 323ms 0.51% std::map::~map (inline) 0 0% 87.86% 321ms 0.5% vtkCell::vtkCell 320ms 0.5% 88.36% 320ms 0.5% Node::GetIndex 4ms 0.0063% 88.37% 320ms 0.5% std::vector::_M_default_append (inline)