File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17268ms, 84.12% of 20529ms total Dropped 753 nodes (cum <= 102.64ms) flat flat% sum% cum cum% 0 0% 0% 20487ms 99.80% __libc_start_call_main 0 0% 0% 20487ms 99.80% __libc_start_main_impl 0 0% 0% 20487ms 99.80% _start 0 0% 0% 20468ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20468ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20468ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20468ms 99.70% main 0 0% 0% 20433ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20433ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20433ms 99.53% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20406ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 15999ms 77.93% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0097% 0.0097% 10796ms 52.59% AbstractCellBasedSimulation::DoCellBirth 6ms 0.029% 0.039% 10720ms 52.22% Cell::ReadyToDivide 10ms 0.049% 0.088% 10654ms 51.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.088% 10506ms 51.18% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.049% 0.14% 10495ms 51.12% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.14% 10484ms 51.07% CellCycleModelOdeHandler::SolveOdeToTime 60ms 0.29% 0.43% 10320ms 50.27% AbstractOneStepIvpOdeSolver::InternalSolve 1045ms 5.09% 5.52% 9418ms 45.88% RungeKutta4IvpOdeSolver::CalculateNextYValue 3922ms 19.10% 24.62% 8162ms 39.76% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 24.62% 5072ms 24.71% MeshBasedCellPopulation::Update 202ms 0.98% 25.61% 4271ms 20.80% AbstractCellProperty::IsType (inline) 3ms 0.015% 25.62% 3896ms 18.98% Cylindrical2dMesh::ReMesh 536ms 2.61% 28.23% 3050ms 14.86% AbstractCellProperty::IsSame 903ms 4.40% 32.63% 2514ms 12.25% std::type_info::operator== (inline) 1ms 0.0049% 32.64% 2481ms 12.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 32.64% 2169ms 10.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.049% 32.69% 2122ms 10.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 32.69% 2085ms 10.16% MutableMesh::ReMesh 0 0% 32.69% 1923ms 9.37% AbstractCellPopulation::WriteResultsToFiles 795ms 3.87% 36.56% 1839ms 8.96% std::_Rb_tree::_M_lower_bound (inline) 160ms 0.78% 37.34% 1709ms 8.32% TetrahedralMesh::EdgeIterator::operator++ 1596ms 7.77% 45.11% 1596ms 7.77% __strcmp_avx2 69ms 0.34% 45.45% 1414ms 6.89% std::_Rb_tree::find (inline) 0 0% 45.45% 1151ms 5.61% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.019% 45.47% 1109ms 5.40% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 47ms 0.23% 45.70% 1086ms 5.29% operator new 16ms 0.078% 45.77% 1058ms 5.15% TetrahedralMesh::ImportFromMesher 244ms 1.19% 46.96% 1023ms 4.98% __GI___libc_malloc 11ms 0.054% 47.02% 1016ms 4.95% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.044% 47.06% 993ms 4.84% std::set::insert (inline) 19ms 0.093% 47.15% 984ms 4.79% std::_Rb_tree::_M_insert_unique 31ms 0.15% 47.30% 950ms 4.63% std::__new_allocator::allocate (inline) 0 0% 47.30% 945ms 4.60% std::allocator_traits::allocate (inline) 0 0% 47.30% 879ms 4.28% std::set::count (inline) 0 0% 47.30% 787ms 3.83% triangulate 722ms 3.52% 50.82% 728ms 3.55% WntCellCycleOdeSystem::CalculateStoppingEvent 1ms 0.0049% 50.83% 720ms 3.51% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 50.83% 714ms 3.48% delaunay 5ms 0.024% 50.85% 714ms 3.48% divconqdelaunay 6ms 0.029% 50.88% 702ms 3.42% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 426ms 2.08% 52.95% 696ms 3.39% _int_malloc 52ms 0.25% 53.21% 680ms 3.31% std::map::operator[] (partial-inline) 21ms 0.1% 53.31% 672ms 3.27% std::less::operator() (inline) 665ms 3.24% 56.55% 665ms 3.24% std::_Rb_tree::_S_right (inline) 3ms 0.015% 56.56% 664ms 3.23% CellPopulationElementWriter::Visit 651ms 3.17% 59.74% 651ms 3.17% std::operator< (inline) 198ms 0.96% 60.70% 624ms 3.04% __dynamic_cast 0 0% 60.70% 618ms 3.01% std::_Rb_tree::_M_create_node (inline) 22ms 0.11% 60.81% 607ms 2.96% std::_Rb_tree::_M_insert_ (inline) 26ms 0.13% 60.93% 593ms 2.89% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.058% 60.99% 590ms 2.87% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 60.99% 585ms 2.85% std::_Rb_tree::_M_get_node (inline) 0 0% 60.99% 558ms 2.72% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.0097% 61.00% 542ms 2.64% MeshBasedCellPopulation::AcceptCellWriter 0 0% 61.00% 542ms 2.64% std::_Rb_tree::lower_bound (inline) 0 0% 61.00% 542ms 2.64% std::map::lower_bound (inline) 3ms 0.015% 61.02% 531ms 2.59% CellPropertyCollection::GetPropertiesType (inline) 0 0% 61.02% 531ms 2.59% std::map::find (inline) 5ms 0.024% 61.04% 528ms 2.57% Element::Element 9ms 0.044% 61.08% 522ms 2.54% MutableMesh::ReIndex 72ms 0.35% 61.44% 503ms 2.45% std::ostream::_M_insert 0 0% 61.44% 503ms 2.45% std::ostream::operator<< (inline) 8ms 0.039% 61.47% 486ms 2.37% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.044% 61.52% 480ms 2.34% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.049% 61.57% 473ms 2.30% Element::RegisterWithNodes (inline) 3ms 0.015% 61.58% 460ms 2.24% Node::AddElement 2ms 0.0097% 61.59% 455ms 2.22% AbstractCellProperty::IsSubType (inline) 314ms 1.53% 63.12% 453ms 2.21% AbstractCellMutationState::AbstractCellMutationState 146ms 0.71% 63.83% 451ms 2.20% __GI___libc_free 120ms 0.58% 64.42% 387ms 1.89% std::_Rb_tree::_M_erase 15ms 0.073% 64.49% 378ms 1.84% divconqrecurse 15ms 0.073% 64.56% 366ms 1.78% std::__new_allocator::deallocate (inline) 16ms 0.078% 64.64% 365ms 1.78% Node::RemoveElement 4ms 0.019% 64.66% 363ms 1.77% std::set::erase (inline) 8ms 0.039% 64.70% 362ms 1.76% std::_Rb_tree::erase 2ms 0.0097% 64.71% 362ms 1.76% std::_Vector_base::_M_allocate (inline) 0 0% 64.71% 360ms 1.75% std::allocator_traits::deallocate (inline) 141ms 0.69% 65.40% 358ms 1.74% std::_Rb_tree::_M_get_insert_unique_pos 118ms 0.57% 65.97% 355ms 1.73% mergehulls 22ms 0.11% 66.08% 351ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 0 0% 66.08% 337ms 1.64% std::_Rb_tree::_M_drop_node (inline) 8ms 0.039% 66.12% 336ms 1.64% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 24ms 0.12% 66.23% 336ms 1.64% Element::ResetIndex 138ms 0.67% 66.91% 314ms 1.53% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0049% 66.91% 313ms 1.52% NodeLocationWriter::Visit 0 0% 66.91% 312ms 1.52% std::set::~set (inline) 249ms 1.21% 68.12% 304ms 1.48% _int_free 0 0% 68.12% 300ms 1.46% std::_Rb_tree::_M_put_node (inline) 7ms 0.034% 68.16% 292ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.039% 68.20% 292ms 1.42% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.019% 68.22% 289ms 1.41% Cell::GetMutationState 5ms 0.024% 68.24% 288ms 1.40% Cell::GetCellProliferativeType 22ms 0.11% 68.35% 282ms 1.37% std::num_put::_M_insert_float 16ms 0.078% 68.43% 270ms 1.32% std::_Rb_tree::_Rb_tree (partial-inline) 267ms 1.30% 69.73% 267ms 1.30% std::type_info::name (inline) 261ms 1.27% 71.00% 265ms 1.29% std::vector::operator[] (inline) 0 0% 71.00% 263ms 1.28% AbstractCellPopulation::Iterator::operator++ (inline) 33ms 0.16% 71.16% 262ms 1.28% AbstractCellPopulation::Iterator::IsRealCell (inline) 12ms 0.058% 71.22% 254ms 1.24% AbstractTetrahedralElement::CalculateJacobian 249ms 1.21% 72.43% 249ms 1.21% [libchaste_cell_based.so] 11ms 0.054% 72.48% 248ms 1.21% std::vector::push_back (inline) 4ms 0.019% 72.50% 243ms 1.18% std::set::set (inline) 3ms 0.015% 72.52% 231ms 1.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 12ms 0.058% 72.58% 231ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 15ms 0.073% 72.65% 227ms 1.11% std::vector::_M_realloc_insert 17ms 0.083% 72.73% 226ms 1.10% std::_Rb_tree::_M_erase_aux (inline) 21ms 0.1% 72.83% 225ms 1.10% std::_Rb_tree::_M_copy (inline) 60ms 0.29% 73.13% 224ms 1.09% ApcOneHitCellMutationState::ApcOneHitCellMutationState 13ms 0.063% 73.19% 223ms 1.09% std::__cxx11::collate::do_transform 0 0% 73.19% 222ms 1.08% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 73.20% 217ms 1.06% alternateaxes 205ms 1% 74.20% 213ms 1.04% vertexmedian 32ms 0.16% 74.36% 211ms 1.03% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.0097% 74.37% 207ms 1.01% ___vsnprintf 0 0% 74.37% 205ms 1% __vsnprintf_internal (inline) 1ms 0.0049% 74.37% 204ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.1% 74.48% 203ms 0.99% __printf_buffer 63ms 0.31% 74.78% 201ms 0.98% std::_Rb_tree::_M_clone_node (inline) 28ms 0.14% 74.92% 197ms 0.96% AbstractTetrahedralElement::RefreshJacobian 89ms 0.43% 75.35% 196ms 0.95% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.044% 75.40% 195ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 189ms 0.92% 76.32% 189ms 0.92% Node::GetIndex 12ms 0.058% 76.37% 187ms 0.91% Element::MarkAsDeleted 0 0% 76.37% 186ms 0.91% OffLatticeSimulation::ApplyBoundaries 0 0% 76.37% 184ms 0.9% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 76.37% 184ms 0.9% MeshBasedCellPopulation::GetDampingConstant 177ms 0.86% 77.24% 177ms 0.86% std::_Rb_tree_insert_and_rebalance 12ms 0.058% 77.30% 173ms 0.84% TetrahedralMesh::Clear 135ms 0.66% 77.95% 171ms 0.83% malloc_consolidate 1ms 0.0049% 77.96% 166ms 0.81% __printf_fp_spec (inline) 8ms 0.039% 78.00% 165ms 0.8% __printf_fp_l_buffer 5ms 0.024% 78.02% 164ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 120ms 0.58% 78.61% 156ms 0.76% AbstractElement::GetNodeGlobalIndex 1ms 0.0049% 78.61% 151ms 0.74% CellProliferativeTypesWriter::VisitCell 72ms 0.35% 78.96% 149ms 0.73% __printf_fp_buffer_1 1ms 0.0049% 78.97% 146ms 0.71% boost::numeric::ublas::vector_assign (inline) 57ms 0.28% 79.24% 145ms 0.71% AbstractElement::GetNodeLocation 142ms 0.69% 79.94% 142ms 0.69% incircle 93ms 0.45% 80.39% 136ms 0.66% std::_Rb_tree::equal_range (inline) 51ms 0.25% 80.64% 134ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 80.64% 134ms 0.65% Cell::HasCellProperty (inline) 2ms 0.0097% 80.65% 133ms 0.65% CellPropertyCollection::HasProperty 2ms 0.0097% 80.66% 133ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 132ms 0.64% 81.30% 132ms 0.64% std::vector::size (inline) 132ms 0.64% 81.94% 132ms 0.64% unlink_chunk 0 0% 81.94% 131ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.034% 81.98% 130ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.034% 82.01% 130ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.015% 82.03% 128ms 0.62% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.0049% 82.03% 124ms 0.6% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.03% 121ms 0.59% AbstractCellBasedWriter::OpenOutputFileForAppend 23ms 0.11% 82.14% 121ms 0.59% TetrahedralMesh::EdgesEnd 1ms 0.0049% 82.15% 119ms 0.58% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 82.15% 119ms 0.58% OutputFileHandler::OpenOutputFile 3ms 0.015% 82.16% 118ms 0.57% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 115ms 0.56% 82.72% 115ms 0.56% AbstractElement::IsDeleted 37ms 0.18% 82.90% 114ms 0.56% boost::numeric::ublas::indexing_vector_assign 1ms 0.0049% 82.91% 112ms 0.55% Cell::SetCellProliferativeType 62ms 0.3% 83.21% 112ms 0.55% Cylindrical2dMesh::GetVectorFromAtoB 53ms 0.26% 83.47% 111ms 0.54% std::__ostream_insert 0 0% 83.47% 107ms 0.52% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 14ms 0.068% 83.54% 107ms 0.52% boost::detail::shared_count::~shared_count (inline) 0 0% 83.54% 107ms 0.52% boost::shared_ptr::~shared_ptr (inline) 102ms 0.5% 84.03% 107ms 0.52% vertexsort 17ms 0.083% 84.12% 106ms 0.52% std::num_put::_M_insert_int