File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17025ms, 84.50% of 20148ms total Dropped 789 nodes (cum <= 100.74ms) flat flat% sum% cum cum% 0 0% 0% 20103ms 99.78% __libc_start_call_main 0 0% 0% 20103ms 99.78% __libc_start_main_impl 0 0% 0% 20103ms 99.78% _start 0 0% 0% 20085ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20085ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20085ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20085ms 99.69% main 0 0% 0% 20046ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20046ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20046ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.005% 0.005% 20019ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0.005% 15557ms 77.21% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.005% 10197ms 50.61% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.025% 10100ms 50.13% Cell::ReadyToDivide 3ms 0.015% 0.04% 10019ms 49.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.045% 9892ms 49.10% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.074% 0.12% 9886ms 49.07% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.12% 9868ms 48.98% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.35% 0.47% 9702ms 48.15% AbstractOneStepIvpOdeSolver::InternalSolve 887ms 4.40% 4.87% 8873ms 44.04% RungeKutta4IvpOdeSolver::CalculateNextYValue 3664ms 18.19% 23.06% 7767ms 38.55% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.06% 5218ms 25.90% MeshBasedCellPopulation::Update 191ms 0.95% 24.01% 4155ms 20.62% AbstractCellProperty::IsType (inline) 8ms 0.04% 24.05% 4021ms 19.96% Cylindrical2dMesh::ReMesh 565ms 2.80% 26.86% 2942ms 14.60% AbstractCellProperty::IsSame 0 0% 26.86% 2510ms 12.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 441ms 2.19% 29.05% 2377ms 11.80% std::type_info::operator== (inline) 0 0% 29.05% 2201ms 10.92% MutableMesh::ReMesh 0 0% 29.05% 2189ms 10.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.06% 29.10% 2136ms 10.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.10% 1944ms 9.65% AbstractCellPopulation::WriteResultsToFiles 1870ms 9.28% 38.39% 1870ms 9.28% __strcmp_avx2 827ms 4.10% 42.49% 1858ms 9.22% std::_Rb_tree::_M_lower_bound (inline) 165ms 0.82% 43.31% 1681ms 8.34% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.33% 43.64% 1396ms 6.93% std::_Rb_tree::find (inline) 0 0% 43.64% 1156ms 5.74% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 43.65% 1121ms 5.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 26ms 0.13% 43.78% 1117ms 5.54% TetrahedralMesh::ImportFromMesher 49ms 0.24% 44.02% 1035ms 5.14% operator new 13ms 0.065% 44.09% 1020ms 5.06% MeshBasedCellPopulation::SpringIterator::operator++ 225ms 1.12% 45.21% 977ms 4.85% __GI___libc_malloc 5ms 0.025% 45.23% 969ms 4.81% std::set::insert (inline) 21ms 0.1% 45.33% 964ms 4.78% std::_Rb_tree::_M_insert_unique 51ms 0.25% 45.59% 932ms 4.63% std::__new_allocator::allocate (inline) 0 0% 45.59% 929ms 4.61% std::allocator_traits::allocate (inline) 0 0% 45.59% 867ms 4.30% std::set::count (inline) 0 0% 45.59% 816ms 4.05% triangulate 0 0% 45.59% 743ms 3.69% delaunay 6ms 0.03% 45.62% 742ms 3.68% divconqdelaunay 1ms 0.005% 45.62% 700ms 3.47% AbstractTwoBodyInteractionForce::AddForceContribution 48ms 0.24% 45.86% 699ms 3.47% std::map::operator[] (partial-inline) 3ms 0.015% 45.88% 683ms 3.39% CellPopulationElementWriter::Visit 3ms 0.015% 45.89% 681ms 3.38% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 394ms 1.96% 47.85% 679ms 3.37% _int_malloc 17ms 0.084% 47.93% 660ms 3.28% std::less::operator() (inline) 649ms 3.22% 51.15% 649ms 3.22% std::_Rb_tree::_S_right (inline) 643ms 3.19% 54.34% 643ms 3.19% std::operator< (inline) 625ms 3.10% 57.44% 635ms 3.15% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 57.44% 619ms 3.07% std::_Rb_tree::_M_create_node (inline) 30ms 0.15% 57.59% 615ms 3.05% std::_Rb_tree::_M_insert_ (inline) 177ms 0.88% 58.47% 603ms 2.99% __dynamic_cast 0 0% 58.47% 595ms 2.95% std::_Rb_tree::_M_get_node (inline) 29ms 0.14% 58.62% 589ms 2.92% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.045% 58.66% 572ms 2.84% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.66% 565ms 2.80% std::_Rb_tree::lower_bound (inline) 0 0% 58.66% 565ms 2.80% std::map::lower_bound (inline) 0 0% 58.66% 559ms 2.77% std::_Rb_tree::_Alloc_node::operator() (inline) 18ms 0.089% 58.75% 547ms 2.71% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 58.78% 536ms 2.66% MeshBasedCellPopulation::AcceptCellWriter 9ms 0.045% 58.82% 532ms 2.64% MutableMesh::ReIndex 0 0% 58.82% 524ms 2.60% std::map::find (inline) 2ms 0.0099% 58.83% 522ms 2.59% Element::Element 0 0% 58.83% 506ms 2.51% std::ostream::operator<< (inline) 65ms 0.32% 59.15% 504ms 2.50% std::ostream::_M_insert 5ms 0.025% 59.18% 501ms 2.49% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.045% 59.22% 473ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.045% 59.27% 451ms 2.24% Element::RegisterWithNodes (inline) 7ms 0.035% 59.30% 446ms 2.21% Node::AddElement 293ms 1.45% 60.76% 445ms 2.21% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 60.77% 431ms 2.14% AbstractCellProperty::IsSubType (inline) 165ms 0.82% 61.59% 429ms 2.13% __GI___libc_free 20ms 0.099% 61.69% 389ms 1.93% divconqrecurse 15ms 0.074% 61.76% 361ms 1.79% Node::RemoveElement 100ms 0.5% 62.26% 359ms 1.78% mergehulls 6ms 0.03% 62.29% 359ms 1.78% std::_Rb_tree::erase 1ms 0.005% 62.29% 358ms 1.78% std::set::erase (inline) 108ms 0.54% 62.83% 341ms 1.69% std::_Rb_tree::_M_erase 338ms 1.68% 64.51% 338ms 1.68% std::type_info::name (inline) 3ms 0.015% 64.52% 337ms 1.67% std::_Vector_base::_M_allocate (inline) 19ms 0.094% 64.62% 335ms 1.66% std::__new_allocator::deallocate (inline) 0 0% 64.62% 333ms 1.65% std::allocator_traits::deallocate (inline) 32ms 0.16% 64.78% 332ms 1.65% Element::ResetIndex 121ms 0.6% 65.38% 328ms 1.63% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.015% 65.39% 325ms 1.61% NodeLocationWriter::Visit 11ms 0.055% 65.45% 320ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 4ms 0.02% 65.47% 317ms 1.57% Cell::GetMutationState 47ms 0.23% 65.70% 309ms 1.53% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.70% 309ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 28ms 0.14% 65.84% 309ms 1.53% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.025% 65.86% 307ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 65.86% 301ms 1.49% std::_Rb_tree::_M_drop_node (inline) 128ms 0.64% 66.50% 299ms 1.48% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.12% 66.62% 292ms 1.45% std::num_put::_M_insert_float 0 0% 66.62% 286ms 1.42% std::set::~set (inline) 1ms 0.005% 66.62% 284ms 1.41% Cell::GetCellProliferativeType 1ms 0.005% 66.63% 270ms 1.34% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.04% 66.67% 269ms 1.34% std::_Rb_tree::_Rb_tree (partial-inline) 262ms 1.30% 67.97% 267ms 1.33% std::vector::operator[] (inline) 209ms 1.04% 69.00% 264ms 1.31% _int_free 10ms 0.05% 69.05% 263ms 1.31% std::vector::push_back (inline) 15ms 0.074% 69.13% 260ms 1.29% AbstractTetrahedralElement::CalculateJacobian 0 0% 69.13% 260ms 1.29% std::_Rb_tree::_M_put_node (inline) 10ms 0.05% 69.18% 255ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 251ms 1.25% 70.42% 251ms 1.25% [libchaste_cell_based.so] 0 0% 70.42% 245ms 1.22% std::set::set (inline) 13ms 0.065% 70.49% 245ms 1.22% std::vector::_M_realloc_insert 3ms 0.015% 70.50% 244ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.03% 70.53% 237ms 1.18% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.015% 70.55% 233ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.045% 70.59% 231ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.02% 70.61% 228ms 1.13% std::__cxx11::collate::do_transform 69ms 0.34% 70.95% 226ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 70.97% 226ms 1.12% MeshBasedCellPopulation::GetDampingConstant 20ms 0.099% 71.07% 223ms 1.11% std::_Rb_tree::_M_copy (inline) 2ms 0.0099% 71.08% 222ms 1.10% AbstractCentreBasedCellPopulation::GetDampingConstant 26ms 0.13% 71.21% 216ms 1.07% TetrahedralMesh::Clear 0 0% 71.21% 216ms 1.07% ___vsnprintf 0 0% 71.21% 216ms 1.07% __vsnprintf_internal (inline) 33ms 0.16% 71.38% 210ms 1.04% __printf_buffer 1ms 0.005% 71.38% 209ms 1.04% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 71.40% 209ms 1.04% alternateaxes 26ms 0.13% 71.53% 207ms 1.03% AbstractTetrahedralElement::RefreshJacobian 199ms 0.99% 72.51% 206ms 1.02% vertexmedian 70ms 0.35% 72.86% 203ms 1.01% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.045% 72.91% 202ms 1.00% AbstractTetrahedralElement::CalculateInverseJacobian 70ms 0.35% 73.25% 200ms 0.99% std::_Rb_tree::_M_clone_node (inline) 37ms 0.18% 73.44% 194ms 0.96% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 16ms 0.079% 73.52% 190ms 0.94% Element::MarkAsDeleted 137ms 0.68% 74.20% 187ms 0.93% AbstractElement::GetNodeGlobalIndex 68ms 0.34% 74.53% 171ms 0.85% AbstractElement::GetNodeLocation 127ms 0.63% 75.16% 171ms 0.85% malloc_consolidate 7ms 0.035% 75.20% 166ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 166ms 0.82% 76.02% 166ms 0.82% Node::GetIndex 13ms 0.065% 76.09% 165ms 0.82% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 2ms 0.0099% 76.10% 164ms 0.81% __printf_fp_l_buffer 0 0% 76.10% 164ms 0.81% __printf_fp_spec (inline) 163ms 0.81% 76.91% 163ms 0.81% std::_Rb_tree_insert_and_rebalance 160ms 0.79% 77.70% 160ms 0.79% incircle 7ms 0.035% 77.73% 155ms 0.77% CellPropertyCollection::HasProperty 2ms 0.0099% 77.74% 155ms 0.77% boost::numeric::ublas::vector_assign (inline) 0 0% 77.74% 153ms 0.76% Cell::HasCellProperty (inline) 1ms 0.005% 77.75% 152ms 0.75% CellProliferativeTypesWriter::VisitCell 82ms 0.41% 78.16% 152ms 0.75% __printf_fp_buffer_1 149ms 0.74% 78.90% 149ms 0.74% unlink_chunk 144ms 0.71% 79.61% 144ms 0.71% std::vector::size (inline) 0 0% 79.61% 141ms 0.7% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.05% 79.66% 138ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 71ms 0.35% 80.01% 137ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.01% 137ms 0.68% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 47ms 0.23% 80.25% 136ms 0.68% boost::numeric::ublas::indexing_vector_assign 34ms 0.17% 80.41% 135ms 0.67% TetrahedralMesh::EdgesEnd (partial-inline) 90ms 0.45% 80.86% 133ms 0.66% std::_Rb_tree::equal_range (inline) 5ms 0.025% 80.89% 131ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 119ms 0.59% 81.48% 131ms 0.65% vertexsort 10ms 0.05% 81.53% 129ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.02% 81.55% 128ms 0.64% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 14ms 0.069% 81.62% 125ms 0.62% Node::~Node 38ms 0.19% 81.80% 122ms 0.61% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 36ms 0.18% 81.98% 122ms 0.61% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 11ms 0.055% 82.04% 122ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 82.04% 122ms 0.61% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0099% 82.05% 121ms 0.6% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.0099% 82.06% 114ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 22ms 0.11% 82.17% 111ms 0.55% std::num_put::_M_insert_int 1ms 0.005% 82.17% 110ms 0.55% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.17% 108ms 0.54% Cell::SetCellProliferativeType 0 0% 82.17% 107ms 0.53% OutputFileHandler::OpenOutputFile 106ms 0.53% 82.70% 106ms 0.53% AbstractCellProperty::~AbstractCellProperty 106ms 0.53% 83.22% 106ms 0.53% AbstractElement::IsDeleted 53ms 0.26% 83.49% 106ms 0.53% std::__ostream_insert 102ms 0.51% 83.99% 105ms 0.52% boost::detail::sp_counted_base::release 102ms 0.51% 84.50% 102ms 0.51% std::_Rb_tree_rebalance_for_erase