File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16876ms, 84.03% of 20084ms total Dropped 779 nodes (cum <= 100.42ms) flat flat% sum% cum cum% 0 0% 0% 20040ms 99.78% __libc_start_call_main 0 0% 0% 20040ms 99.78% __libc_start_main_impl 0 0% 0% 20040ms 99.78% _start 0 0% 0% 20022ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20022ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20022ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20022ms 99.69% main 0 0% 0% 19983ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19983ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19983ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19955ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15497ms 77.16% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10157ms 50.57% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.015% 10068ms 50.13% Cell::ReadyToDivide 0 0% 0.015% 10010ms 49.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.02% 9893ms 49.26% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.05% 0.07% 9880ms 49.19% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.08% 9865ms 49.12% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.37% 0.45% 9680ms 48.20% AbstractOneStepIvpOdeSolver::InternalSolve 883ms 4.40% 4.85% 8842ms 44.03% RungeKutta4IvpOdeSolver::CalculateNextYValue 3560ms 17.73% 22.58% 7734ms 38.51% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.58% 5215ms 25.97% MeshBasedCellPopulation::Update 164ms 0.82% 23.39% 4185ms 20.84% AbstractCellProperty::IsType (inline) 4ms 0.02% 23.41% 4031ms 20.07% Cylindrical2dMesh::ReMesh 555ms 2.76% 26.18% 2946ms 14.67% AbstractCellProperty::IsSame 0 0% 26.18% 2484ms 12.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 433ms 2.16% 28.33% 2391ms 11.90% std::type_info::operator== (inline) 2ms 0.01% 28.34% 2162ms 10.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.01% 28.35% 2157ms 10.74% MutableMesh::ReMesh 14ms 0.07% 28.42% 2111ms 10.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.42% 1966ms 9.79% AbstractCellPopulation::WriteResultsToFiles 830ms 4.13% 32.55% 1926ms 9.59% std::_Rb_tree::_M_lower_bound (inline) 1857ms 9.25% 41.80% 1857ms 9.25% __strcmp_avx2 163ms 0.81% 42.61% 1682ms 8.37% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.31% 42.92% 1460ms 7.27% std::_Rb_tree::find (inline) 1ms 0.005% 42.92% 1142ms 5.69% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 42.96% 1125ms 5.60% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.08% 43.04% 1124ms 5.60% TetrahedralMesh::ImportFromMesher 51ms 0.25% 43.29% 1073ms 5.34% operator new 13ms 0.065% 43.36% 1020ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 237ms 1.18% 44.54% 1012ms 5.04% __GI___libc_malloc 16ms 0.08% 44.62% 966ms 4.81% std::set::insert (inline) 20ms 0.1% 44.72% 950ms 4.73% std::_Rb_tree::_M_insert_unique 40ms 0.2% 44.92% 924ms 4.60% std::__new_allocator::allocate (inline) 0 0% 44.92% 919ms 4.58% std::allocator_traits::allocate (inline) 0 0% 44.92% 888ms 4.42% std::set::count (inline) 0 0% 44.92% 791ms 3.94% triangulate 0 0% 44.92% 736ms 3.66% delaunay 2ms 0.01% 44.93% 735ms 3.66% divconqdelaunay 3ms 0.015% 44.94% 723ms 3.60% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 4ms 0.02% 44.96% 712ms 3.55% AbstractTwoBodyInteractionForce::AddForceContribution 58ms 0.29% 45.25% 712ms 3.55% std::map::operator[] (partial-inline) 419ms 2.09% 47.34% 709ms 3.53% _int_malloc 701ms 3.49% 50.83% 701ms 3.49% std::_Rb_tree::_S_right (inline) 8ms 0.04% 50.87% 666ms 3.32% CellPopulationElementWriter::Visit 20ms 0.1% 50.97% 659ms 3.28% std::less::operator() (inline) 639ms 3.18% 54.15% 646ms 3.22% WntCellCycleOdeSystem::CalculateStoppingEvent 639ms 3.18% 57.33% 639ms 3.18% std::operator< (inline) 183ms 0.91% 58.24% 613ms 3.05% __dynamic_cast 21ms 0.1% 58.34% 600ms 2.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.34% 600ms 2.99% std::_Rb_tree::_M_create_node (inline) 7ms 0.035% 58.38% 581ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.13% 58.51% 576ms 2.87% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.51% 574ms 2.86% std::_Rb_tree::_M_get_node (inline) 0 0% 58.51% 572ms 2.85% std::map::find (inline) 0 0% 58.51% 554ms 2.76% std::_Rb_tree::lower_bound (inline) 0 0% 58.51% 554ms 2.76% std::map::lower_bound (inline) 10ms 0.05% 58.56% 551ms 2.74% CellPropertyCollection::GetPropertiesType (inline) 18ms 0.09% 58.65% 550ms 2.74% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.65% 539ms 2.68% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.045% 58.70% 538ms 2.68% Element::Element 9ms 0.045% 58.74% 533ms 2.65% MutableMesh::ReIndex 11ms 0.055% 58.80% 502ms 2.50% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.055% 58.85% 496ms 2.47% Element::RegisterWithNodes (inline) 57ms 0.28% 59.14% 486ms 2.42% std::ostream::_M_insert 0 0% 59.14% 486ms 2.42% std::ostream::operator<< (inline) 9ms 0.045% 59.18% 485ms 2.41% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.045% 59.23% 485ms 2.41% Node::AddElement 325ms 1.62% 60.84% 480ms 2.39% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 60.86% 449ms 2.24% AbstractCellProperty::IsSubType (inline) 162ms 0.81% 61.67% 437ms 2.18% __GI___libc_free 111ms 0.55% 62.22% 386ms 1.92% std::_Rb_tree::_M_erase 3ms 0.015% 62.23% 382ms 1.90% std::set::erase (inline) 6ms 0.03% 62.26% 379ms 1.89% std::_Rb_tree::erase 12ms 0.06% 62.32% 375ms 1.87% Node::RemoveElement 13ms 0.065% 62.39% 370ms 1.84% std::__new_allocator::deallocate (inline) 0 0% 62.39% 368ms 1.83% std::allocator_traits::deallocate (inline) 14ms 0.07% 62.46% 365ms 1.82% divconqrecurse 29ms 0.14% 62.60% 358ms 1.78% Element::ResetIndex 139ms 0.69% 63.29% 354ms 1.76% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.01% 63.30% 347ms 1.73% std::_Vector_base::_M_allocate (inline) 23ms 0.11% 63.42% 339ms 1.69% std::_Rb_tree::~_Rb_tree (inline) 97ms 0.48% 63.90% 338ms 1.68% mergehulls 335ms 1.67% 65.57% 335ms 1.67% std::type_info::name (inline) 11ms 0.055% 65.62% 330ms 1.64% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 65.62% 329ms 1.64% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 65.63% 322ms 1.60% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 65.63% 316ms 1.57% std::set::~set (inline) 3ms 0.015% 65.65% 310ms 1.54% Cell::GetCellProliferativeType 0 0% 65.65% 305ms 1.52% NodeLocationWriter::Visit 156ms 0.78% 66.43% 303ms 1.51% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 66.44% 301ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.44% 296ms 1.47% std::_Rb_tree::_M_put_node (inline) 29ms 0.14% 66.58% 295ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 279ms 1.39% 67.97% 279ms 1.39% std::vector::operator[] (inline) 3ms 0.015% 67.98% 274ms 1.36% Cell::GetMutationState 220ms 1.10% 69.08% 273ms 1.36% _int_free 17ms 0.085% 69.16% 273ms 1.36% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.03% 69.19% 270ms 1.34% LegacyCellProliferativeTypesWriter::VisitCell 25ms 0.12% 69.32% 266ms 1.32% std::num_put::_M_insert_float 261ms 1.30% 70.62% 261ms 1.30% [libchaste_cell_based.so] 13ms 0.065% 70.68% 252ms 1.25% std::vector::push_back (inline) 1ms 0.005% 70.69% 249ms 1.24% std::set::set (inline) 4ms 0.02% 70.71% 242ms 1.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 11ms 0.055% 70.76% 241ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.005% 70.77% 238ms 1.19% alternateaxes 23ms 0.11% 70.88% 237ms 1.18% std::_Rb_tree::_M_erase_aux (inline) 223ms 1.11% 71.99% 237ms 1.18% vertexmedian 14ms 0.07% 72.06% 234ms 1.17% std::vector::_M_realloc_insert 15ms 0.075% 72.14% 228ms 1.14% AbstractTetrahedralElement::CalculateJacobian 3ms 0.015% 72.15% 227ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 72.16% 224ms 1.12% TetrahedralMesh::RefreshJacobianCachedData 44ms 0.22% 72.38% 223ms 1.11% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 65ms 0.32% 72.70% 221ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 20ms 0.1% 72.80% 220ms 1.10% std::_Rb_tree::_M_copy (inline) 63ms 0.31% 73.12% 210ms 1.05% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.07% 73.19% 204ms 1.02% TetrahedralMesh::Clear 4ms 0.02% 73.21% 204ms 1.02% std::__cxx11::collate::do_transform 61ms 0.3% 73.51% 198ms 0.99% std::_Rb_tree::_M_clone_node (inline) 0 0% 73.51% 196ms 0.98% ___vsnprintf 0 0% 73.51% 196ms 0.98% __vsnprintf_internal (inline) 0 0% 73.51% 195ms 0.97% OffLatticeSimulation::ApplyBoundaries 1ms 0.005% 73.52% 194ms 0.97% MeshBasedCellPopulation::GetDampingConstant 0 0% 73.52% 193ms 0.96% AbstractCentreBasedCellPopulation::GetDampingConstant 27ms 0.13% 73.65% 191ms 0.95% __printf_buffer 10ms 0.05% 73.70% 184ms 0.92% AbstractTetrahedralElement::CalculateInverseJacobian 141ms 0.7% 74.40% 181ms 0.9% AbstractElement::GetNodeGlobalIndex 22ms 0.11% 74.51% 180ms 0.9% AbstractTetrahedralElement::RefreshJacobian 16ms 0.08% 74.59% 180ms 0.9% Element::MarkAsDeleted 127ms 0.63% 75.22% 174ms 0.87% malloc_consolidate 5ms 0.025% 75.25% 173ms 0.86% CellProliferativeTypesWriter::VisitCell 168ms 0.84% 76.09% 168ms 0.84% std::_Rb_tree_insert_and_rebalance 161ms 0.8% 76.89% 161ms 0.8% Node::GetIndex 3ms 0.015% 76.90% 160ms 0.8% boost::numeric::ublas::vector_assign (inline) 3ms 0.015% 76.92% 157ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.005% 76.92% 156ms 0.78% __printf_fp_spec (inline) 156ms 0.78% 77.70% 156ms 0.78% unlink_chunk 6ms 0.03% 77.73% 155ms 0.77% __printf_fp_l_buffer 4ms 0.02% 77.75% 151ms 0.75% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 147ms 0.73% 78.48% 147ms 0.73% incircle 7ms 0.035% 78.52% 144ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 94ms 0.47% 78.98% 144ms 0.72% std::_Rb_tree::equal_range (inline) 0 0% 78.98% 142ms 0.71% AbstractCellBasedWriter::OpenOutputFileForAppend 86ms 0.43% 79.41% 142ms 0.71% Cylindrical2dMesh::GetVectorFromAtoB 54ms 0.27% 79.68% 140ms 0.7% AbstractElement::GetNodeLocation 1ms 0.005% 79.69% 140ms 0.7% OutputFileHandler::OpenOutputFile 62ms 0.31% 79.99% 139ms 0.69% __printf_fp_buffer_1 39ms 0.19% 80.19% 138ms 0.69% boost::numeric::ublas::indexing_vector_assign 48ms 0.24% 80.43% 136ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 9ms 0.045% 80.47% 135ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.04% 80.51% 133ms 0.66% CellPropertyCollection::HasProperty 43ms 0.21% 80.73% 132ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 80.73% 132ms 0.66% Cell::HasCellProperty (inline) 1ms 0.005% 80.73% 125ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 80.73% 124ms 0.62% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 3ms 0.015% 80.75% 124ms 0.62% MeshBasedCellPopulation::SpringsEnd (inline) 115ms 0.57% 81.32% 124ms 0.62% vertexsort 122ms 0.61% 81.93% 122ms 0.61% AbstractElement::IsDeleted 10ms 0.05% 81.98% 121ms 0.6% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.015% 81.99% 120ms 0.6% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.16% 82.15% 117ms 0.58% TetrahedralMesh::EdgesEnd (partial-inline) 117ms 0.58% 82.73% 117ms 0.58% std::vector::size (inline) 12ms 0.06% 82.79% 113ms 0.56% boost::detail::shared_count::~shared_count (inline) 0 0% 82.79% 113ms 0.56% boost::shared_ptr::~shared_ptr (inline) 22ms 0.11% 82.90% 113ms 0.56% std::num_put::_M_insert_int 10ms 0.05% 82.95% 110ms 0.55% Node::~Node 2ms 0.01% 82.96% 108ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 107ms 0.53% 83.49% 107ms 0.53% AbstractCellProperty::~AbstractCellProperty 3ms 0.015% 83.51% 107ms 0.53% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 3ms 0.015% 83.52% 106ms 0.53% CellLocationIndexWriter::VisitCell 101ms 0.5% 84.03% 101ms 0.5% boost::shared_ptr::operator-> (inline)