File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16493ms, 82.64% of 19958ms total Dropped 766 nodes (cum <= 99.79ms) flat flat% sum% cum cum% 0 0% 0% 19913ms 99.77% __libc_start_call_main 0 0% 0% 19913ms 99.77% __libc_start_main_impl 0 0% 0% 19913ms 99.77% _start 0 0% 0% 19894ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19894ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19894ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19894ms 99.68% main 0 0% 0% 19855ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19855ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19855ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19830ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15365ms 76.99% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 10125ms 50.73% AbstractCellBasedSimulation::DoCellBirth 0 0% 0.015% 10027ms 50.24% Cell::ReadyToDivide 4ms 0.02% 0.035% 9976ms 49.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.05% 9840ms 49.30% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.05% 0.1% 9832ms 49.26% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.11% 9822ms 49.21% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.4% 0.5% 9651ms 48.36% AbstractOneStepIvpOdeSolver::InternalSolve 852ms 4.27% 4.77% 8817ms 44.18% RungeKutta4IvpOdeSolver::CalculateNextYValue 3691ms 18.49% 23.26% 7774ms 38.95% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.26% 5130ms 25.70% MeshBasedCellPopulation::Update 201ms 1.01% 24.27% 4120ms 20.64% AbstractCellProperty::IsType (inline) 7ms 0.035% 24.31% 3948ms 19.78% Cylindrical2dMesh::ReMesh 568ms 2.85% 27.15% 2849ms 14.27% AbstractCellProperty::IsSame 0 0% 27.15% 2502ms 12.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 388ms 1.94% 29.10% 2281ms 11.43% std::type_info::operator== (inline) 0 0% 29.10% 2188ms 10.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.10% 2140ms 10.72% MutableMesh::ReMesh 6ms 0.03% 29.13% 2139ms 10.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.005% 29.13% 1958ms 9.81% AbstractCellPopulation::WriteResultsToFiles 786ms 3.94% 33.07% 1886ms 9.45% std::_Rb_tree::_M_lower_bound (inline) 1853ms 9.28% 42.35% 1853ms 9.28% __strcmp_avx2 163ms 0.82% 43.17% 1696ms 8.50% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.31% 43.48% 1416ms 7.09% std::_Rb_tree::find (inline) 0 0% 43.48% 1143ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 43.52% 1137ms 5.70% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 39ms 0.2% 43.71% 1072ms 5.37% operator new 18ms 0.09% 43.80% 1064ms 5.33% TetrahedralMesh::ImportFromMesher 20ms 0.1% 43.90% 1033ms 5.18% MeshBasedCellPopulation::SpringIterator::operator++ 245ms 1.23% 45.13% 1020ms 5.11% __GI___libc_malloc 6ms 0.03% 45.16% 959ms 4.81% std::set::insert (inline) 19ms 0.095% 45.26% 953ms 4.78% std::_Rb_tree::_M_insert_unique 33ms 0.17% 45.42% 932ms 4.67% std::__new_allocator::allocate (inline) 0 0% 45.42% 922ms 4.62% std::allocator_traits::allocate (inline) 0 0% 45.42% 852ms 4.27% std::set::count (inline) 1ms 0.005% 45.43% 802ms 4.02% triangulate 0 0% 45.43% 726ms 3.64% delaunay 4ms 0.02% 45.45% 725ms 3.63% divconqdelaunay 6ms 0.03% 45.48% 721ms 3.61% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 64ms 0.32% 45.80% 710ms 3.56% std::map::operator[] (partial-inline) 704ms 3.53% 49.32% 704ms 3.53% std::_Rb_tree::_S_right (inline) 1ms 0.005% 49.33% 696ms 3.49% AbstractTwoBodyInteractionForce::AddForceContribution 396ms 1.98% 51.31% 695ms 3.48% _int_malloc 10ms 0.05% 51.36% 675ms 3.38% CellPopulationElementWriter::Visit 11ms 0.055% 51.42% 657ms 3.29% std::less::operator() (inline) 646ms 3.24% 54.65% 646ms 3.24% std::operator< (inline) 611ms 3.06% 57.72% 621ms 3.11% WntCellCycleOdeSystem::CalculateStoppingEvent 171ms 0.86% 58.57% 608ms 3.05% __dynamic_cast 0 0% 58.57% 600ms 3.01% std::_Rb_tree::_M_create_node (inline) 22ms 0.11% 58.68% 587ms 2.94% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.68% 576ms 2.89% std::_Rb_tree::_M_get_node (inline) 25ms 0.13% 58.81% 572ms 2.87% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.015% 58.82% 568ms 2.85% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.82% 561ms 2.81% std::map::find (inline) 0 0% 58.82% 560ms 2.81% std::_Rb_tree::lower_bound (inline) 0 0% 58.82% 560ms 2.81% std::map::lower_bound (inline) 23ms 0.12% 58.94% 552ms 2.77% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.94% 538ms 2.70% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.055% 58.99% 535ms 2.68% Element::Element 13ms 0.065% 59.06% 524ms 2.63% MutableMesh::ReIndex 3ms 0.015% 59.07% 520ms 2.61% CellPropertyCollection::GetPropertiesType (inline) 13ms 0.065% 59.14% 484ms 2.43% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.04% 59.18% 483ms 2.42% Cylindrical2dMesh::ReconstructCylindricalMesh 346ms 1.73% 60.91% 482ms 2.42% AbstractCellMutationState::AbstractCellMutationState 9ms 0.045% 60.96% 473ms 2.37% Element::RegisterWithNodes (inline) 4ms 0.02% 60.98% 464ms 2.32% std::ostream::operator<< (inline) 13ms 0.065% 61.04% 463ms 2.32% Node::AddElement 70ms 0.35% 61.39% 460ms 2.30% std::ostream::_M_insert 148ms 0.74% 62.14% 429ms 2.15% __GI___libc_free 5ms 0.025% 62.16% 428ms 2.14% AbstractCellProperty::IsSubType (inline) 16ms 0.08% 62.24% 375ms 1.88% Node::RemoveElement 1ms 0.005% 62.25% 375ms 1.88% std::set::erase (inline) 4ms 0.02% 62.27% 374ms 1.87% std::_Rb_tree::erase 20ms 0.1% 62.37% 369ms 1.85% divconqrecurse 111ms 0.56% 62.92% 364ms 1.82% std::_Rb_tree::_M_erase 28ms 0.14% 63.06% 352ms 1.76% Element::ResetIndex 4ms 0.02% 63.08% 350ms 1.75% std::_Vector_base::_M_allocate (inline) 132ms 0.66% 63.74% 347ms 1.74% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.07% 63.81% 346ms 1.73% std::__new_allocator::deallocate (inline) 0 0% 63.81% 342ms 1.71% std::allocator_traits::deallocate (inline) 111ms 0.56% 64.37% 341ms 1.71% mergehulls 0 0% 64.37% 331ms 1.66% std::_Rb_tree::_M_drop_node (inline) 18ms 0.09% 64.46% 326ms 1.63% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.035% 64.50% 320ms 1.60% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.02% 64.52% 309ms 1.55% NodeLocationWriter::Visit 149ms 0.75% 65.26% 308ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.035% 65.30% 304ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 301ms 1.51% 66.81% 301ms 1.51% std::type_info::name (inline) 0 0% 66.81% 292ms 1.46% std::_Rb_tree::_M_put_node (inline) 0 0% 66.81% 289ms 1.45% std::set::~set (inline) 1ms 0.005% 66.81% 287ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 66.82% 286ms 1.43% Cell::GetCellProliferativeType 228ms 1.14% 67.96% 281ms 1.41% _int_free 1ms 0.005% 67.97% 276ms 1.38% AbstractCellPopulation::Iterator::operator++ (inline) 30ms 0.15% 68.12% 272ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.12% 272ms 1.36% Cell::GetMutationState 22ms 0.11% 68.23% 263ms 1.32% std::num_put::_M_insert_float 6ms 0.03% 68.26% 253ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.015% 68.27% 253ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 16ms 0.08% 68.35% 244ms 1.22% AbstractTetrahedralElement::CalculateJacobian 9ms 0.045% 68.40% 243ms 1.22% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.01% 68.41% 240ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.065% 68.47% 238ms 1.19% std::vector::push_back (inline) 18ms 0.09% 68.56% 227ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 227ms 1.14% 69.70% 227ms 1.14% std::vector::operator[] (inline) 73ms 0.37% 70.07% 226ms 1.13% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.005% 70.07% 221ms 1.11% alternateaxes 1ms 0.005% 70.08% 220ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 70.08% 219ms 1.10% std::set::set (inline) 206ms 1.03% 71.11% 219ms 1.10% vertexmedian 216ms 1.08% 72.20% 216ms 1.08% [libchaste_cell_based.so] 51ms 0.26% 72.45% 215ms 1.08% ApcOneHitCellMutationState::ApcOneHitCellMutationState 15ms 0.075% 72.53% 212ms 1.06% std::vector::_M_realloc_insert 40ms 0.2% 72.73% 208ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 8ms 0.04% 72.77% 205ms 1.03% AbstractTetrahedralElement::CalculateInverseJacobian 23ms 0.12% 72.88% 204ms 1.02% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 72.89% 200ms 1.00% std::__cxx11::collate::do_transform 2ms 0.01% 72.90% 195ms 0.98% ___vsnprintf 0 0% 72.90% 193ms 0.97% __vsnprintf_internal (inline) 24ms 0.12% 73.02% 191ms 0.96% __printf_buffer 0 0% 73.02% 190ms 0.95% OffLatticeSimulation::ApplyBoundaries 0 0% 73.02% 189ms 0.95% MeshBasedCellPopulation::GetDampingConstant 0 0% 73.02% 188ms 0.94% AbstractCentreBasedCellPopulation::GetDampingConstant 146ms 0.73% 73.75% 187ms 0.94% malloc_consolidate 186ms 0.93% 74.69% 186ms 0.93% Node::GetIndex 143ms 0.72% 75.40% 184ms 0.92% AbstractElement::GetNodeGlobalIndex 17ms 0.085% 75.49% 183ms 0.92% TetrahedralMesh::Clear 20ms 0.1% 75.59% 182ms 0.91% AbstractTetrahedralElement::RefreshJacobian 61ms 0.31% 75.89% 180ms 0.9% std::_Rb_tree::_M_clone_node (inline) 14ms 0.07% 75.96% 176ms 0.88% Element::MarkAsDeleted 1ms 0.005% 75.97% 158ms 0.79% __printf_fp_spec (inline) 158ms 0.79% 76.76% 158ms 0.79% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 76.79% 157ms 0.79% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.035% 76.83% 157ms 0.79% __printf_fp_l_buffer 1ms 0.005% 76.83% 156ms 0.78% boost::numeric::ublas::vector_assign (inline) 5ms 0.025% 76.86% 151ms 0.76% CellProliferativeTypesWriter::VisitCell 98ms 0.49% 77.35% 150ms 0.75% std::_Rb_tree::equal_range (inline) 74ms 0.37% 77.72% 145ms 0.73% __printf_fp_buffer_1 49ms 0.25% 77.96% 143ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 143ms 0.72% 78.68% 143ms 0.72% incircle 7ms 0.035% 78.72% 142ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 48ms 0.24% 78.96% 141ms 0.71% AbstractElement::GetNodeLocation 7ms 0.035% 78.99% 139ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 137ms 0.69% 79.68% 137ms 0.69% unlink_chunk 2ms 0.01% 79.69% 136ms 0.68% CellPropertyCollection::HasProperty 0 0% 79.69% 135ms 0.68% Cell::HasCellProperty (inline) 5ms 0.025% 79.71% 133ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 79.71% 128ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 16ms 0.08% 79.79% 125ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.02% 79.81% 124ms 0.62% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 79.81% 123ms 0.62% OutputFileHandler::OpenOutputFile 123ms 0.62% 80.43% 123ms 0.62% std::vector::size (inline) 24ms 0.12% 80.55% 122ms 0.61% TetrahedralMesh::EdgesEnd 109ms 0.55% 81.10% 120ms 0.6% vertexsort 6ms 0.03% 81.13% 118ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 11ms 0.055% 81.18% 118ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 81.18% 118ms 0.59% boost::shared_ptr::~shared_ptr (inline) 37ms 0.19% 81.37% 114ms 0.57% boost::numeric::ublas::indexing_vector_assign 0 0% 81.37% 112ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 38ms 0.19% 81.56% 112ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 42ms 0.21% 81.77% 111ms 0.56% std::__ostream_insert 0 0% 81.77% 110ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.035% 81.80% 107ms 0.54% Cell::SetCellProliferativeType 1ms 0.005% 81.81% 105ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.01% 81.82% 104ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 63ms 0.32% 82.13% 104ms 0.52% Cylindrical2dMesh::GetVectorFromAtoB 101ms 0.51% 82.64% 102ms 0.51% boost::detail::sp_counted_base::release