File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 14173ms, 86.04% of 16472ms total Dropped 727 nodes (cum <= 82.36ms) flat flat% sum% cum cum% 0 0% 0% 16435ms 99.78% __libc_start_call_main 0 0% 0% 16435ms 99.78% __libc_start_main_impl 0 0% 0% 16435ms 99.78% _start 0 0% 0% 16415ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16415ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16415ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16415ms 99.65% main 0 0% 0% 16384ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16384ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16384ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16364ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 12512ms 75.96% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0061% 0.0061% 7766ms 47.15% AbstractCellBasedSimulation::DoCellBirth 7ms 0.042% 0.049% 7687ms 46.67% Cell::ReadyToDivide 3ms 0.018% 0.067% 7634ms 46.35% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.067% 7506ms 45.57% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.061% 0.13% 7500ms 45.53% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.012% 0.14% 7486ms 45.45% CellCycleModelOdeHandler::SolveOdeToTime 45ms 0.27% 0.41% 7355ms 44.65% AbstractOneStepIvpOdeSolver::InternalSolve 764ms 4.64% 5.05% 6611ms 40.13% RungeKutta4IvpOdeSolver::CalculateNextYValue 2960ms 17.97% 23.02% 5577ms 33.86% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0061% 23.03% 4645ms 28.20% MeshBasedCellPopulation::Update 1ms 0.0061% 23.03% 3520ms 21.37% Cylindrical2dMesh::ReMesh 308ms 1.87% 24.90% 2724ms 16.54% AbstractCellProperty::IsType (inline) 0 0% 24.90% 2251ms 13.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.90% 1937ms 11.76% MutableMesh::ReMesh 0 0% 24.90% 1935ms 11.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.018% 24.92% 1903ms 11.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 770ms 4.67% 29.60% 1658ms 10.07% std::_Rb_tree::_M_lower_bound (inline) 0 0% 29.60% 1599ms 9.71% AbstractCellPopulation::WriteResultsToFiles 138ms 0.84% 30.43% 1564ms 9.49% TetrahedralMesh::EdgeIterator::operator++ 53ms 0.32% 30.76% 1297ms 7.87% std::_Rb_tree::find (inline) 0 0% 30.76% 1089ms 6.61% MeshBasedCellPopulation::UpdateNodePairs 142ms 0.86% 31.62% 1074ms 6.52% AbstractCellProperty::IsSame 54ms 0.33% 31.95% 1062ms 6.45% operator new 1ms 0.0061% 31.95% 1029ms 6.25% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 376ms 2.28% 34.23% 989ms 6.00% __GI___libc_malloc 20ms 0.12% 34.36% 965ms 5.86% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.067% 34.42% 965ms 5.86% TetrahedralMesh::ImportFromMesher 10ms 0.061% 34.48% 960ms 5.83% std::set::insert (inline) 18ms 0.11% 34.59% 950ms 5.77% std::_Rb_tree::_M_insert_unique 16ms 0.097% 34.69% 932ms 5.66% std::type_info::operator== (inline) 19ms 0.12% 34.80% 914ms 5.55% std::__new_allocator::allocate (inline) 912ms 5.54% 40.34% 912ms 5.54% __strcmp_evex 0 0% 40.34% 906ms 5.50% std::allocator_traits::allocate (inline) 830ms 5.04% 45.38% 830ms 5.04% [libchaste_cell_based.so] 0 0% 45.38% 812ms 4.93% std::set::count (inline) 1ms 0.0061% 45.39% 747ms 4.53% triangulate 0 0% 45.39% 679ms 4.12% delaunay 1ms 0.0061% 45.39% 679ms 4.12% divconqdelaunay 14ms 0.085% 45.48% 655ms 3.98% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 50ms 0.3% 45.78% 619ms 3.76% std::_Rb_tree::_M_insert_ (inline) 0 0% 45.78% 618ms 3.75% std::_Rb_tree::_M_create_node (inline) 0 0% 45.78% 608ms 3.69% std::_Rb_tree::_M_get_node (inline) 2ms 0.012% 45.79% 606ms 3.68% AbstractTwoBodyInteractionForce::AddForceContribution 43ms 0.26% 46.05% 578ms 3.51% std::map::operator[] (partial-inline) 560ms 3.40% 49.45% 560ms 3.40% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 49.45% 558ms 3.39% std::_Rb_tree::_Alloc_node::operator() (inline) 543ms 3.30% 52.75% 543ms 3.30% std::_Rb_tree::_S_right (inline) 26ms 0.16% 52.91% 536ms 3.25% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.067% 52.97% 535ms 3.25% CellPopulationElementWriter::Visit 303ms 1.84% 54.81% 530ms 3.22% _int_malloc 43ms 0.26% 55.08% 518ms 3.14% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.085% 55.16% 511ms 3.10% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.018% 55.18% 503ms 3.05% Element::Element 10ms 0.061% 55.24% 501ms 3.04% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.036% 55.28% 494ms 3.00% Element::RegisterWithNodes (inline) 134ms 0.81% 56.09% 491ms 2.98% __dynamic_cast 3ms 0.018% 56.11% 487ms 2.96% CellPropertyCollection::GetPropertiesType (inline) 25ms 0.15% 56.26% 487ms 2.96% Node::AddElement 0 0% 56.26% 483ms 2.93% std::map::find (inline) 249ms 1.51% 57.77% 475ms 2.88% AbstractCellMutationState::AbstractCellMutationState 9ms 0.055% 57.83% 455ms 2.76% std::less::operator() (inline) 0 0% 57.83% 454ms 2.76% std::_Rb_tree::lower_bound (inline) 0 0% 57.83% 454ms 2.76% std::map::lower_bound (inline) 446ms 2.71% 60.53% 446ms 2.71% std::operator< (inline) 10ms 0.061% 60.59% 414ms 2.51% MutableMesh::ReIndex 102ms 0.62% 61.21% 412ms 2.50% __GI___libc_free 11ms 0.067% 61.28% 388ms 2.36% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.28% 376ms 2.28% std::ostream::operator<< (inline) 42ms 0.25% 61.53% 375ms 2.28% std::ostream::_M_insert 1ms 0.0061% 61.54% 372ms 2.26% AbstractCellProperty::IsSubType (inline) 0 0% 61.54% 364ms 2.21% std::_Rb_tree::_M_drop_node (inline) 49ms 0.3% 61.84% 363ms 2.20% std::_Rb_tree::~_Rb_tree (inline) 355ms 2.16% 63.99% 355ms 2.16% [libchaste_crypt.so] 13ms 0.079% 64.07% 355ms 2.16% divconqrecurse 61ms 0.37% 64.44% 351ms 2.13% std::_Rb_tree::_M_erase 8ms 0.049% 64.49% 343ms 2.08% std::_Rb_tree::erase 11ms 0.067% 64.56% 342ms 2.08% Node::RemoveElement 0 0% 64.56% 342ms 2.08% std::set::erase (inline) 0 0% 64.56% 341ms 2.07% std::set::~set (inline) 9ms 0.055% 64.61% 338ms 2.05% std::__new_allocator::deallocate (inline) 0 0% 64.61% 334ms 2.03% std::allocator_traits::deallocate (inline) 112ms 0.68% 65.29% 332ms 2.02% mergehulls 124ms 0.75% 66.05% 313ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 271ms 1.65% 67.69% 305ms 1.85% _int_free 0 0% 67.69% 298ms 1.81% std::_Vector_base::_M_allocate (inline) 0 0% 67.69% 295ms 1.79% std::_Rb_tree::_M_put_node (inline) 3ms 0.018% 67.71% 286ms 1.74% Cell::GetMutationState 1ms 0.0061% 67.71% 283ms 1.72% AbstractCellPopulation::Iterator::operator++ (inline) 18ms 0.11% 67.82% 281ms 1.71% Element::ResetIndex 32ms 0.19% 68.02% 277ms 1.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.012% 68.03% 267ms 1.62% Cell::GetCellProliferativeType 261ms 1.58% 69.62% 266ms 1.61% std::vector::operator[] (inline) 2ms 0.012% 69.63% 261ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 17ms 0.1% 69.73% 259ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.036% 69.77% 254ms 1.54% boost::detail::shared_count::~shared_count (inline) 0 0% 69.77% 254ms 1.54% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0061% 69.77% 253ms 1.54% NodeLocationWriter::Visit 114ms 0.69% 70.47% 252ms 1.53% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.055% 70.52% 251ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0061% 70.53% 249ms 1.51% ApcOneHitCellMutationState::ApcOneHitCellMutationState 243ms 1.48% 72.00% 244ms 1.48% boost::detail::sp_counted_base::release 12ms 0.073% 72.07% 241ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.018% 72.09% 240ms 1.46% std::set::set (inline) 0 0% 72.09% 238ms 1.44% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 27ms 0.16% 72.26% 234ms 1.42% std::num_put::_M_insert_float 224ms 1.36% 73.62% 224ms 1.36% [libchaste_mesh.so] 23ms 0.14% 73.76% 219ms 1.33% std::_Rb_tree::_M_copy (inline) 9ms 0.055% 73.81% 215ms 1.31% std::vector::push_back (inline) 8ms 0.049% 73.86% 213ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 73.86% 212ms 1.29% OffLatticeSimulation::ApplyBoundaries 23ms 0.14% 74.00% 211ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0061% 74.00% 211ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.042% 74.05% 209ms 1.27% alternateaxes 13ms 0.079% 74.13% 206ms 1.25% Element::MarkAsDeleted 0 0% 74.13% 204ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 9ms 0.055% 74.18% 204ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0061% 74.19% 201ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 185ms 1.12% 75.31% 201ms 1.22% vertexmedian 8ms 0.049% 75.36% 196ms 1.19% std::vector::_M_realloc_insert 11ms 0.067% 75.42% 194ms 1.18% AbstractTetrahedralElement::CalculateJacobian 77ms 0.47% 75.89% 191ms 1.16% std::_Rb_tree::_M_clone_node (inline) 6ms 0.036% 75.93% 186ms 1.13% std::__cxx11::collate::do_transform 7ms 0.042% 75.97% 184ms 1.12% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 75.97% 184ms 1.12% MeshBasedCellPopulation::GetDampingConstant 3ms 0.018% 75.99% 182ms 1.10% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0061% 76.00% 170ms 1.03% ___vsnprintf 0 0% 76.00% 169ms 1.03% __vsnprintf_internal (inline) 11ms 0.067% 76.06% 167ms 1.01% __printf_buffer 1ms 0.0061% 76.07% 147ms 0.89% __printf_fp_l_buffer 0 0% 76.07% 147ms 0.89% __printf_fp_spec (inline) 23ms 0.14% 76.21% 146ms 0.89% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.0061% 76.21% 145ms 0.88% TetrahedralMesh::Clear 104ms 0.63% 76.85% 144ms 0.87% malloc_consolidate 143ms 0.87% 77.71% 143ms 0.87% std::_Rb_tree::_S_left (inline) 141ms 0.86% 78.57% 141ms 0.86% std::vector::size (inline) 58ms 0.35% 78.92% 140ms 0.85% AbstractElement::GetNodeGlobalIndex 60ms 0.36% 79.29% 140ms 0.85% __printf_fp_buffer_1 137ms 0.83% 80.12% 137ms 0.83% incircle 0 0% 80.12% 132ms 0.8% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 76ms 0.46% 80.58% 131ms 0.8% std::_Rb_tree::equal_range (inline) 16ms 0.097% 80.68% 130ms 0.79% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.68% 130ms 0.79% CellProliferativeTypesWriter::VisitCell 130ms 0.79% 81.47% 130ms 0.79% std::_Rb_tree_insert_and_rebalance 129ms 0.78% 82.25% 129ms 0.78% AbstractCellProperty::AbstractCellProperty 6ms 0.036% 82.29% 128ms 0.78% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 2ms 0.012% 82.30% 127ms 0.77% boost::numeric::ublas::vector_assign (inline) 0 0% 82.30% 122ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.03% 82.33% 121ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.012% 82.34% 114ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 114ms 0.69% 83.03% 114ms 0.69% std::type_info::name (inline) 3ms 0.018% 83.05% 113ms 0.69% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 8ms 0.049% 83.10% 113ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 16ms 0.097% 83.20% 111ms 0.67% TetrahedralMesh::EdgesEnd (partial-inline) 98ms 0.59% 83.79% 109ms 0.66% vertexsort 0 0% 83.79% 106ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 83.79% 104ms 0.63% Cell::HasCellProperty (inline) 0 0% 83.79% 104ms 0.63% CellPropertyCollection::HasProperty 0 0% 83.79% 101ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.018% 83.81% 99ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 3ms 0.018% 83.83% 99ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 34ms 0.21% 84.03% 97ms 0.59% AbstractElement::GetNodeLocation 6ms 0.036% 84.07% 97ms 0.59% Cell::SetCellProliferativeType 0 0% 84.07% 97ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 17ms 0.1% 84.17% 95ms 0.58% MeshBasedCellPopulation::SpringIterator::SpringIterator 47ms 0.29% 84.46% 94ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 93ms 0.56% 85.02% 93ms 0.56% unlink_chunk 21ms 0.13% 85.15% 90ms 0.55% boost::numeric::ublas::indexing_vector_assign 0 0% 85.15% 87ms 0.53% Node::~Node 4ms 0.024% 85.17% 87ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 60ms 0.36% 85.54% 85ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 83ms 0.5% 86.04% 83ms 0.5% std::_Rb_tree_increment