File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95748ms, 88.20% of 108557ms total Dropped 1140 nodes (cum <= 542.78ms) flat flat% sum% cum cum% 0 0% 0% 108205ms 99.68% __libc_start_call_main 0 0% 0% 108205ms 99.68% __libc_start_main_impl 0 0% 0% 108205ms 99.68% _start 0 0% 0% 108183ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108183ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108183ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108183ms 99.66% main 0 0% 0% 108140ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108140ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108140ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00092% 0.00092% 108131ms 99.61% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.016% 56272ms 51.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.029% 53049ms 48.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 135ms 0.12% 0.15% 51906ms 47.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 313ms 0.29% 0.44% 40013ms 36.86% NagaiHondaForce::AddForceContribution 0 0% 0.44% 38835ms 35.77% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.44% 23809ms 21.93% VertexBasedCellPopulation::Update 2ms 0.0018% 0.45% 23657ms 21.79% MutableVertexMesh::ReMesh 14855ms 13.68% 14.13% 23562ms 21.70% Cylindrical2dVertexMesh::GetVectorFromAtoB 101ms 0.093% 14.22% 17744ms 16.35% Cell::ReadyToDivide 66ms 0.061% 14.28% 16426ms 15.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 322ms 0.3% 14.58% 14428ms 13.29% NagaiHondaForce::GetAdhesionParameter 467ms 0.43% 15.01% 14117ms 13.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 132ms 0.12% 15.13% 14013ms 12.91% SimpleWntCellCycleModel::UpdateCellCyclePhase 108ms 0.099% 15.23% 13314ms 12.26% CellPropertyCollection::GetPropertiesType (inline) 347ms 0.32% 15.55% 12641ms 11.64% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.68% 11902ms 10.96% MutableVertexMesh::CheckForIntersections 3521ms 3.24% 18.92% 11370ms 10.47% __dynamic_cast 54ms 0.05% 18.97% 11362ms 10.47% VertexBasedCellPopulation::GetDampingConstant 64ms 0.059% 19.03% 11271ms 10.38% AbstractCellProperty::IsSubType (inline) 57ms 0.053% 19.08% 10518ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 40ms 0.037% 19.12% 10446ms 9.62% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.027% 19.14% 10302ms 9.49% AbstractCellBasedSimulation::DoCellBirth 1221ms 1.12% 20.27% 9793ms 9.02% std::__new_allocator::allocate (inline) 2889ms 2.66% 22.93% 9556ms 8.80% boost::numeric::ublas::indexing_vector_assign 333ms 0.31% 23.24% 9406ms 8.66% VertexMesh::GetNextEdgeGradientOfElementAtNode 1340ms 1.23% 24.47% 9324ms 8.59% std::_Rb_tree::_M_erase 0 0% 24.47% 9251ms 8.52% std::_Rb_tree::_M_create_node (inline) 0 0% 24.47% 9226ms 8.50% std::allocator_traits::allocate (inline) 36ms 0.033% 24.51% 8820ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 775ms 0.71% 25.22% 8621ms 7.94% operator new 821ms 0.76% 25.98% 8565ms 7.89% VertexMesh::ElementIncludesPoint 0 0% 25.98% 8536ms 7.86% std::_Rb_tree::_M_get_node (inline) 210ms 0.19% 26.17% 8477ms 7.81% std::_Rb_tree::~_Rb_tree (inline) 84ms 0.077% 26.25% 8453ms 7.79% Cell::GetMutationState 443ms 0.41% 26.65% 8401ms 7.74% VertexMesh::GetCentroidOfElement 0 0% 26.65% 8296ms 7.64% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.65% 8172ms 7.53% std::_Rb_tree::_Alloc_node::operator() (inline) 242ms 0.22% 26.88% 8039ms 7.41% std::__new_allocator::deallocate (inline) 0 0% 26.88% 8031ms 7.40% std::allocator_traits::deallocate (inline) 0 0% 26.88% 8029ms 7.40% std::set::~set (inline) 0 0% 26.88% 7979ms 7.35% std::_Rb_tree::_M_put_node (inline) 2913ms 2.68% 29.56% 7641ms 7.04% __GI___libc_malloc 2132ms 1.96% 31.52% 7599ms 7.00% __GI___libc_free 18ms 0.017% 31.54% 7539ms 6.94% MutableVertexMesh::RemoveDeletedNodesAndElements 1493ms 1.38% 32.92% 7485ms 6.89% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 493ms 0.45% 33.37% 7314ms 6.74% std::map::operator[] (partial-inline) 149ms 0.14% 33.51% 7051ms 6.50% std::_Rb_tree::_Rb_tree (partial-inline) 729ms 0.67% 34.18% 6657ms 6.13% std::_Rb_tree::_M_copy (inline) 30ms 0.028% 34.21% 6550ms 6.03% std::set::set (inline) 162ms 0.15% 34.36% 6343ms 5.84% SimpleWntCellCycleModel::GetWntLevel 6173ms 5.69% 40.04% 6173ms 5.69% boost::numeric::ublas::c_vector::operator() 6115ms 5.63% 45.68% 6115ms 5.63% __strcmp_avx2 172ms 0.16% 45.83% 6090ms 5.61% WntConcentration::GetWntLevel 2454ms 2.26% 48.09% 5768ms 5.31% std::_Rb_tree::_M_lower_bound (inline) 882ms 0.81% 48.91% 5704ms 5.25% std::_Rb_tree::_M_clone_node (inline) 4876ms 4.49% 53.40% 5444ms 5.01% _int_free 1943ms 1.79% 55.19% 5307ms 4.89% boost::numeric::ublas::c_vector::operator[] (inline) 2880ms 2.65% 57.84% 5295ms 4.88% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.018% 57.86% 5164ms 4.76% MutableVertexMesh::RemoveDeletedNodes 0 0% 57.86% 5145ms 4.74% std::set::insert (inline) 31ms 0.029% 57.89% 4955ms 4.56% EdgeHelper::RemoveDeletedEdges 0 0% 57.89% 4747ms 4.37% std::_Rb_tree::lower_bound (inline) 0 0% 57.89% 4747ms 4.37% std::map::lower_bound (inline) 0 0% 57.89% 4714ms 4.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 38ms 0.035% 57.92% 4653ms 4.29% EdgeHelper::UpdateEdgesMapKey 210ms 0.19% 58.12% 4641ms 4.28% MutableElement::ResetIndex 135ms 0.12% 58.24% 4368ms 4.02% AbstractCellPopulation::GetCellUsingLocationIndex 467ms 0.43% 58.67% 4310ms 3.97% std::_Rb_tree::_M_insert_ (inline) 117ms 0.11% 58.78% 4231ms 3.90% std::set_intersection (inline) 38ms 0.035% 58.81% 4122ms 3.80% Cell::GetCellProliferativeType 190ms 0.18% 58.99% 4114ms 3.79% std::__set_intersection 3782ms 3.48% 62.47% 3782ms 3.48% boost::numeric::ublas::same_impl_ex 58ms 0.053% 62.53% 3692ms 3.40% AbstractCellProperty::IsType (inline) 23ms 0.021% 62.55% 3627ms 3.34% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 68ms 0.063% 62.61% 3283ms 3.02% Cell::SetCellProliferativeType 0 0% 62.61% 3123ms 2.88% std::insert_iterator::operator= (inline) 907ms 0.84% 63.45% 3113ms 2.87% AbstractElement::GetNodeLocation 2146ms 1.98% 65.42% 3092ms 2.85% _int_malloc 59ms 0.054% 65.48% 2940ms 2.71% std::_Rb_tree::erase 6ms 0.0055% 65.48% 2770ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 2761ms 2.54% 68.03% 2761ms 2.54% std::_Rb_tree::_S_right (inline) 241ms 0.22% 68.25% 2689ms 2.48% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.25% 2647ms 2.44% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.25% 2579ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 705ms 0.65% 68.90% 2570ms 2.37% AbstractCellProperty::IsSame 25ms 0.023% 68.92% 2533ms 2.33% CellPropertyCollection::HasProperty 566ms 0.52% 69.44% 2508ms 2.31% boost::numeric::ublas::vector_binary::size (inline) 256ms 0.24% 69.68% 2500ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.68% 2472ms 2.28% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.68% 2441ms 2.25% Cell::HasCellProperty (inline) 1ms 0.00092% 69.68% 2375ms 2.19% std::_Rb_tree::_M_insert_unique 68ms 0.063% 69.74% 2331ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 21ms 0.019% 69.76% 2288ms 2.11% Cell::GetCellData 65ms 0.06% 69.82% 2275ms 2.10% VertexMesh::GetVolumeOfElement 3ms 0.0028% 69.82% 2122ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 175ms 0.16% 69.98% 2111ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.98% 2040ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.98% 2032ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 30ms 0.028% 70.01% 2027ms 1.87% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0037% 70.01% 2000ms 1.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.01% 2000ms 1.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1983ms 1.83% 71.84% 1983ms 1.83% std::_Rb_tree_increment 1296ms 1.19% 73.04% 1929ms 1.78% std::_Rb_tree::equal_range (inline) 70ms 0.064% 73.10% 1886ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 475ms 0.44% 73.54% 1865ms 1.72% std::type_info::operator== (inline) 3ms 0.0028% 73.54% 1838ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 47ms 0.043% 73.58% 1614ms 1.49% VertexMesh::GetSurfaceAreaOfElement 29ms 0.027% 73.61% 1595ms 1.47% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 48ms 0.044% 73.65% 1531ms 1.41% Node::RemoveElement 11ms 0.01% 73.66% 1484ms 1.37% std::set::erase (inline) 39ms 0.036% 73.70% 1444ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.70% 1442ms 1.33% tcache_get (inline) 1442ms 1.33% 75.03% 1442ms 1.33% tcache_get_n (inline) 68ms 0.063% 75.09% 1415ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 77ms 0.071% 75.16% 1391ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 1369ms 1.26% 76.42% 1369ms 1.26% [libchaste_cell_based.so] 0 0% 76.42% 1352ms 1.25% boost::numeric::ublas::vector_binary::operator() (inline) 152ms 0.14% 76.56% 1338ms 1.23% CellPropertyCollection::AddProperty 0 0% 76.56% 1288ms 1.19% boost::numeric::ublas::norm_2 (inline) 588ms 0.54% 77.11% 1265ms 1.17% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 77.11% 1242ms 1.14% OffLatticeSimulation::ApplyBoundaries 83ms 0.076% 77.18% 1218ms 1.12% std::less::operator() (inline) 81ms 0.075% 77.26% 1157ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 22ms 0.02% 77.28% 1138ms 1.05% CellPropertyRegistry::Get 917ms 0.84% 78.12% 1135ms 1.05% std::operator< (inline) 0 0% 78.12% 1079ms 0.99% std::_Rb_tree::_Auto_node::_Auto_node (inline) 19ms 0.018% 78.14% 1075ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.14% 1069ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 13ms 0.012% 78.15% 1069ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 1ms 0.00092% 78.15% 1062ms 0.98% std::_Rb_tree::clear (inline) 5ms 0.0046% 78.16% 1056ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 92ms 0.085% 78.24% 1056ms 0.97% std::swap_ranges (inline) 95ms 0.088% 78.33% 1043ms 0.96% std::_Rb_tree::find (inline) 0 0% 78.33% 1040ms 0.96% std::map::clear (inline) 18ms 0.017% 78.35% 1029ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 123ms 0.11% 78.46% 1026ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 78.46% 1026ms 0.95% boost::shared_ptr::~shared_ptr (inline) 1021ms 0.94% 79.40% 1021ms 0.94% std::_Rb_tree_insert_and_rebalance 212ms 0.2% 79.60% 1000ms 0.92% boost::numeric::ublas::detail::equals 0 0% 79.60% 964ms 0.89% std::iter_swap (inline) 964ms 0.89% 80.48% 964ms 0.89% std::swap (inline) 962ms 0.89% 81.37% 962ms 0.89% Node::rGetLocation 902ms 0.83% 82.20% 902ms 0.83% [libchaste_mesh.so] 0 0% 82.20% 874ms 0.81% std::map::find (inline) 0 0% 82.20% 869ms 0.8% VertexMeshWriter::MakeVtkMesh 825ms 0.76% 82.96% 869ms 0.8% boost::detail::sp_counted_base::release 863ms 0.79% 83.76% 863ms 0.79% std::vector::size (inline) 166ms 0.15% 83.91% 783ms 0.72% boost::shared_ptr::shared_ptr (inline) 0 0% 83.91% 782ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 226ms 0.21% 84.12% 780ms 0.72% std::__new_allocator::construct (inline) 0 0% 84.12% 780ms 0.72% std::allocator_traits::construct (inline) 105ms 0.097% 84.21% 778ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 26ms 0.024% 84.24% 748ms 0.69% Edge::AddElement 17ms 0.016% 84.25% 743ms 0.68% MutableElement::RegisterWithEdges (inline) 130ms 0.12% 84.37% 736ms 0.68% MutableElement::GetNodeLocalIndex 377ms 0.35% 84.72% 722ms 0.67% Edge::GetMapIndex 423ms 0.39% 85.11% 716ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.11% 715ms 0.66% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.11% 713ms 0.66% boost::numeric::ublas::norm_inf (inline) 423ms 0.39% 85.50% 713ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.00092% 85.50% 686ms 0.63% std::_Vector_base::_M_allocate (inline) 0 0% 85.50% 664ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 652ms 0.6% 86.10% 652ms 0.6% tcache_put (inline) 0 0% 86.10% 633ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 35ms 0.032% 86.13% 633ms 0.58% std::_Rb_tree::_M_insert_node (inline) 45ms 0.041% 86.18% 619ms 0.57% MutableElement::RegisterWithNodes (inline) 0 0% 86.18% 619ms 0.57% vtkPolygon::New 2ms 0.0018% 86.18% 617ms 0.57% vtkPolygon::vtkPolygon 583ms 0.54% 86.71% 616ms 0.57% boost::detail::shared_count::shared_count (inline) 604ms 0.56% 87.27% 604ms 0.56% [libstdc++.so.6.0.33] 35ms 0.032% 87.30% 602ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.30% 602ms 0.55% boost::numeric::ublas::vector::vector (inline) 331ms 0.3% 87.61% 595ms 0.55% CellPropertyCollection::GetProperty 581ms 0.54% 88.14% 581ms 0.54% Node::GetIndex 31ms 0.029% 88.17% 574ms 0.53% Node::AddElement 7ms 0.0064% 88.18% 565ms 0.52% std::vector::_M_default_append (inline) 25ms 0.023% 88.20% 546ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate