File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16715ms, 84.30% of 19828ms total Dropped 818 nodes (cum <= 99.14ms) flat flat% sum% cum cum% 0 0% 0% 19781ms 99.76% __libc_start_call_main 0 0% 0% 19781ms 99.76% __libc_start_main_impl 0 0% 0% 19781ms 99.76% _start 0 0% 0% 19762ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19762ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19762ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19762ms 99.67% main 0 0% 0% 19718ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19718ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19718ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 2ms 0.01% 0.01% 19690ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0.01% 15238ms 76.85% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.02% 9981ms 50.34% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.03% 9884ms 49.85% Cell::ReadyToDivide 4ms 0.02% 0.05% 9819ms 49.52% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.02% 0.071% 9679ms 48.81% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.081% 0.15% 9665ms 48.74% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.16% 9646ms 48.65% CellCycleModelOdeHandler::SolveOdeToTime 78ms 0.39% 0.55% 9486ms 47.84% AbstractOneStepIvpOdeSolver::InternalSolve 864ms 4.36% 4.91% 8728ms 44.02% RungeKutta4IvpOdeSolver::CalculateNextYValue 3628ms 18.30% 23.21% 7653ms 38.60% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.22% 5158ms 26.01% MeshBasedCellPopulation::Update 84ms 0.42% 23.64% 4064ms 20.50% AbstractCellProperty::IsType (inline) 7ms 0.035% 23.68% 3969ms 20.02% Cylindrical2dMesh::ReMesh 597ms 3.01% 26.69% 2813ms 14.19% AbstractCellProperty::IsSame 0 0% 26.69% 2458ms 12.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 403ms 2.03% 28.72% 2216ms 11.18% std::type_info::operator== (inline) 0 0% 28.72% 2159ms 10.89% MutableMesh::ReMesh 1ms 0.005% 28.73% 2149ms 10.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.05% 28.78% 2099ms 10.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.78% 1981ms 9.99% AbstractCellPopulation::WriteResultsToFiles 781ms 3.94% 32.72% 1829ms 9.22% std::_Rb_tree::_M_lower_bound (inline) 1770ms 8.93% 41.64% 1770ms 8.93% __strcmp_avx2 168ms 0.85% 42.49% 1673ms 8.44% TetrahedralMesh::EdgeIterator::operator++ 57ms 0.29% 42.78% 1387ms 7.00% std::_Rb_tree::find (inline) 0 0% 42.78% 1141ms 5.75% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 42.79% 1135ms 5.72% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.071% 42.86% 1098ms 5.54% TetrahedralMesh::ImportFromMesher 43ms 0.22% 43.08% 1018ms 5.13% operator new 11ms 0.055% 43.14% 994ms 5.01% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.035% 43.17% 990ms 4.99% std::set::insert (inline) 26ms 0.13% 43.30% 983ms 4.96% std::_Rb_tree::_M_insert_unique 226ms 1.14% 44.44% 968ms 4.88% __GI___libc_malloc 59ms 0.3% 44.74% 906ms 4.57% std::__new_allocator::allocate (inline) 0 0% 44.74% 899ms 4.53% std::allocator_traits::allocate (inline) 0 0% 44.74% 837ms 4.22% std::set::count (inline) 4ms 0.02% 44.76% 814ms 4.11% triangulate 0 0% 44.76% 739ms 3.73% delaunay 2ms 0.01% 44.77% 739ms 3.73% divconqdelaunay 1ms 0.005% 44.78% 738ms 3.72% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 690ms 3.48% 48.25% 690ms 3.48% std::_Rb_tree::_S_right (inline) 6ms 0.03% 48.29% 675ms 3.40% CellPopulationElementWriter::Visit 51ms 0.26% 48.54% 672ms 3.39% std::map::operator[] (partial-inline) 362ms 1.83% 50.37% 667ms 3.36% _int_malloc 4ms 0.02% 50.39% 646ms 3.26% AbstractTwoBodyInteractionForce::AddForceContribution 21ms 0.11% 50.49% 645ms 3.25% std::less::operator() (inline) 624ms 3.15% 53.64% 624ms 3.15% std::operator< (inline) 0 0% 53.64% 606ms 3.06% std::_Rb_tree::_M_create_node (inline) 24ms 0.12% 53.76% 587ms 2.96% std::_Rb_tree::_M_insert_ (inline) 181ms 0.91% 54.68% 584ms 2.95% __dynamic_cast 0 0% 54.68% 576ms 2.90% std::_Rb_tree::_M_get_node (inline) 566ms 2.85% 57.53% 575ms 2.90% WntCellCycleOdeSystem::CalculateStoppingEvent 6ms 0.03% 57.56% 573ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 20ms 0.1% 57.66% 571ms 2.88% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 57.68% 555ms 2.80% CellPropertyCollection::GetPropertiesType (inline) 0 0% 57.68% 553ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 31ms 0.16% 57.84% 547ms 2.76% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 7ms 0.035% 57.87% 544ms 2.74% Element::Element 0 0% 57.87% 540ms 2.72% std::map::find (inline) 10ms 0.05% 57.92% 537ms 2.71% MutableMesh::ReIndex 0 0% 57.92% 533ms 2.69% std::_Rb_tree::lower_bound (inline) 0 0% 57.92% 533ms 2.69% std::map::lower_bound (inline) 4ms 0.02% 57.94% 502ms 2.53% Cylindrical2dMesh::ReconstructCylindricalMesh 13ms 0.066% 58.01% 489ms 2.47% Element::RegisterWithNodes (inline) 2ms 0.01% 58.02% 489ms 2.47% std::ostream::operator<< (inline) 73ms 0.37% 58.39% 487ms 2.46% std::ostream::_M_insert 14ms 0.071% 58.46% 478ms 2.41% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.045% 58.50% 475ms 2.40% Node::AddElement 313ms 1.58% 60.08% 462ms 2.33% AbstractCellMutationState::AbstractCellMutationState 4ms 0.02% 60.10% 445ms 2.24% AbstractCellProperty::IsSubType (inline) 147ms 0.74% 60.84% 418ms 2.11% __GI___libc_free 14ms 0.071% 60.91% 388ms 1.96% std::_Rb_tree::erase 0 0% 60.91% 387ms 1.95% std::set::erase (inline) 10ms 0.05% 60.96% 383ms 1.93% Node::RemoveElement 137ms 0.69% 61.66% 382ms 1.93% std::_Rb_tree::_M_erase 151ms 0.76% 62.42% 371ms 1.87% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.071% 62.49% 366ms 1.85% divconqrecurse 14ms 0.071% 62.56% 362ms 1.83% std::__new_allocator::deallocate (inline) 28ms 0.14% 62.70% 358ms 1.81% std::_Rb_tree::~_Rb_tree (inline) 0 0% 62.70% 357ms 1.80% std::allocator_traits::deallocate (inline) 34ms 0.17% 62.87% 346ms 1.75% Element::ResetIndex 109ms 0.55% 63.42% 342ms 1.72% mergehulls 0 0% 63.42% 338ms 1.70% std::set::~set (inline) 13ms 0.066% 63.49% 331ms 1.67% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.01% 63.50% 325ms 1.64% std::_Vector_base::_M_allocate (inline) 4ms 0.02% 63.52% 319ms 1.61% Cell::GetMutationState 4ms 0.02% 63.54% 310ms 1.56% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 63.54% 308ms 1.55% std::_Rb_tree::_M_drop_node (inline) 307ms 1.55% 65.08% 307ms 1.55% std::type_info::name (inline) 1ms 0.005% 65.09% 301ms 1.52% NodeLocationWriter::Visit 6ms 0.03% 65.12% 296ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 137ms 0.69% 65.81% 290ms 1.46% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 65.83% 279ms 1.41% Cell::GetCellProliferativeType 0 0% 65.83% 274ms 1.38% std::_Rb_tree::_M_put_node (inline) 15ms 0.076% 65.90% 271ms 1.37% std::_Rb_tree::_Rb_tree 218ms 1.10% 67.00% 270ms 1.36% _int_free 0 0% 67.00% 268ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 36ms 0.18% 67.18% 266ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 18ms 0.091% 67.27% 265ms 1.34% AbstractTetrahedralElement::CalculateJacobian 18ms 0.091% 67.36% 261ms 1.32% std::num_put::_M_insert_float 7ms 0.035% 67.40% 257ms 1.30% std::vector::push_back (inline) 3ms 0.015% 67.41% 255ms 1.29% std::set::set (inline) 247ms 1.25% 68.66% 247ms 1.25% std::vector::operator[] (inline) 10ms 0.05% 68.71% 238ms 1.20% std::vector::_M_realloc_insert 2ms 0.01% 68.72% 230ms 1.16% alternateaxes 60ms 0.3% 69.02% 229ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 213ms 1.07% 70.10% 228ms 1.15% vertexmedian 1ms 0.005% 70.10% 227ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.04% 70.14% 226ms 1.14% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.076% 70.22% 223ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 17ms 0.086% 70.30% 219ms 1.10% std::_Rb_tree::_M_copy (inline) 8ms 0.04% 70.34% 218ms 1.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 38ms 0.19% 70.54% 216ms 1.09% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 212ms 1.07% 71.61% 212ms 1.07% [libchaste_cell_based.so] 0 0% 71.61% 208ms 1.05% MeshBasedCellPopulation::GetDampingConstant 4ms 0.02% 71.63% 208ms 1.05% std::__cxx11::collate::do_transform 1ms 0.005% 71.63% 207ms 1.04% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 71.64% 204ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.64% 199ms 1.00% OffLatticeSimulation::ApplyBoundaries 54ms 0.27% 71.91% 199ms 1.00% std::_Rb_tree::_M_clone_node (inline) 14ms 0.071% 71.98% 198ms 1% Element::MarkAsDeleted 3ms 0.015% 72.00% 197ms 0.99% ___vsnprintf 136ms 0.69% 72.69% 197ms 0.99% malloc_consolidate 6ms 0.03% 72.72% 194ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 72.72% 194ms 0.98% __vsnprintf_internal (inline) 29ms 0.15% 72.86% 193ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 18ms 0.091% 72.95% 189ms 0.95% TetrahedralMesh::Clear 21ms 0.11% 73.06% 189ms 0.95% __printf_buffer 15ms 0.076% 73.13% 188ms 0.95% AbstractTetrahedralElement::RefreshJacobian 133ms 0.67% 73.80% 168ms 0.85% AbstractElement::GetNodeGlobalIndex 167ms 0.84% 74.65% 167ms 0.84% std::_Rb_tree_insert_and_rebalance 109ms 0.55% 75.20% 162ms 0.82% std::_Rb_tree::equal_range (inline) 66ms 0.33% 75.53% 158ms 0.8% AbstractElement::GetNodeLocation 158ms 0.8% 76.33% 158ms 0.8% unlink_chunk 5ms 0.025% 76.35% 155ms 0.78% CellProliferativeTypesWriter::VisitCell 155ms 0.78% 77.13% 155ms 0.78% Node::GetIndex 5ms 0.025% 77.16% 155ms 0.78% boost::numeric::ublas::vector_assign (inline) 44ms 0.22% 77.38% 153ms 0.77% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.03% 77.41% 151ms 0.76% __printf_fp_l_buffer 0 0% 77.41% 151ms 0.76% __printf_fp_spec (inline) 2ms 0.01% 77.42% 150ms 0.76% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.02% 77.44% 148ms 0.75% CellPropertyCollection::HasProperty 148ms 0.75% 78.19% 148ms 0.75% incircle 33ms 0.17% 78.35% 146ms 0.74% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 78.35% 144ms 0.73% Cell::HasCellProperty (inline) 5ms 0.025% 78.38% 142ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 141ms 0.71% 79.09% 141ms 0.71% AbstractCellMutationState::~AbstractCellMutationState 68ms 0.34% 79.43% 141ms 0.71% __printf_fp_buffer_1 44ms 0.22% 79.66% 140ms 0.71% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 137ms 0.69% 80.35% 137ms 0.69% std::vector::size (inline) 6ms 0.03% 80.38% 136ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.01% 80.39% 131ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 129ms 0.65% 81.04% 129ms 0.65% AbstractCellProperty::~AbstractCellProperty 122ms 0.62% 81.65% 129ms 0.65% vertexsort 81ms 0.41% 82.06% 126ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 14ms 0.071% 82.13% 125ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 45ms 0.23% 82.36% 123ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 82.36% 122ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 5ms 0.025% 82.38% 121ms 0.61% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 82.38% 119ms 0.6% OutputFileHandler::OpenOutputFile 12ms 0.061% 82.44% 117ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.005% 82.45% 113ms 0.57% Cell::SetCellProliferativeType 42ms 0.21% 82.66% 113ms 0.57% boost::numeric::ublas::indexing_vector_assign 9ms 0.045% 82.71% 112ms 0.56% Node::~Node 110ms 0.55% 83.26% 110ms 0.55% std::_Rb_tree_increment 0 0% 83.26% 109ms 0.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 28ms 0.14% 83.40% 106ms 0.53% std::num_put::_M_insert_int 105ms 0.53% 83.93% 105ms 0.53% AbstractElement::IsDeleted 70ms 0.35% 84.28% 105ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 3ms 0.015% 84.30% 100ms 0.5% CryptSimulationBoundaryCondition::ImposeBoundaryCondition