File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16688ms, 84.97% of 19639ms total Dropped 763 nodes (cum <= 98.19ms) flat flat% sum% cum cum% 0 0% 0% 19593ms 99.77% __libc_start_call_main 0 0% 0% 19593ms 99.77% __libc_start_main_impl 0 0% 0% 19593ms 99.77% _start 0 0% 0% 19572ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19572ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19572ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19572ms 99.66% main 0 0% 0% 19536ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19536ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19536ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19507ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 15137ms 77.08% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9947ms 50.65% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.036% 9870ms 50.26% Cell::ReadyToDivide 3ms 0.015% 0.051% 9796ms 49.88% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.051% 9660ms 49.19% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.087% 9656ms 49.17% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.092% 9647ms 49.12% CellCycleModelOdeHandler::SolveOdeToTime 65ms 0.33% 0.42% 9480ms 48.27% AbstractOneStepIvpOdeSolver::InternalSolve 828ms 4.22% 4.64% 8665ms 44.12% RungeKutta4IvpOdeSolver::CalculateNextYValue 3613ms 18.40% 23.04% 7622ms 38.81% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 23.04% 5069ms 25.81% MeshBasedCellPopulation::Update 104ms 0.53% 23.57% 4060ms 20.67% AbstractCellProperty::IsType (inline) 4ms 0.02% 23.59% 3888ms 19.80% Cylindrical2dMesh::ReMesh 565ms 2.88% 26.47% 2837ms 14.45% AbstractCellProperty::IsSame 2ms 0.01% 26.48% 2443ms 12.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 398ms 2.03% 28.50% 2272ms 11.57% std::type_info::operator== (inline) 1ms 0.0051% 28.51% 2131ms 10.85% MutableMesh::ReMesh 0 0% 28.51% 2121ms 10.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 28.56% 2073ms 10.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.56% 1921ms 9.78% AbstractCellPopulation::WriteResultsToFiles 827ms 4.21% 32.77% 1882ms 9.58% std::_Rb_tree::_M_lower_bound (inline) 1803ms 9.18% 41.95% 1803ms 9.18% __strcmp_avx2 139ms 0.71% 42.66% 1673ms 8.52% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.31% 42.97% 1445ms 7.36% std::_Rb_tree::find (inline) 1ms 0.0051% 42.97% 1143ms 5.82% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 42.99% 1111ms 5.66% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 46ms 0.23% 43.22% 1072ms 5.46% operator new 11ms 0.056% 43.28% 1058ms 5.39% TetrahedralMesh::ImportFromMesher 13ms 0.066% 43.34% 1019ms 5.19% MeshBasedCellPopulation::SpringIterator::operator++ 241ms 1.23% 44.57% 1013ms 5.16% __GI___libc_malloc 9ms 0.046% 44.62% 974ms 4.96% std::set::insert (inline) 16ms 0.081% 44.70% 965ms 4.91% std::_Rb_tree::_M_insert_unique 51ms 0.26% 44.96% 937ms 4.77% std::__new_allocator::allocate (inline) 0 0% 44.96% 929ms 4.73% std::allocator_traits::allocate (inline) 0 0% 44.96% 852ms 4.34% std::set::count (inline) 1ms 0.0051% 44.96% 839ms 4.27% triangulate 0 0% 44.96% 756ms 3.85% delaunay 5ms 0.025% 44.99% 755ms 3.84% divconqdelaunay 4ms 0.02% 45.01% 711ms 3.62% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 391ms 1.99% 47.00% 686ms 3.49% _int_malloc 670ms 3.41% 50.41% 670ms 3.41% std::_Rb_tree::_S_right (inline) 52ms 0.26% 50.67% 665ms 3.39% std::map::operator[] (partial-inline) 1ms 0.0051% 50.68% 658ms 3.35% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.087% 50.77% 658ms 3.35% std::less::operator() (inline) 641ms 3.26% 54.03% 641ms 3.26% std::operator< (inline) 5ms 0.025% 54.06% 639ms 3.25% CellPopulationElementWriter::Visit 613ms 3.12% 57.18% 626ms 3.19% WntCellCycleOdeSystem::CalculateStoppingEvent 28ms 0.14% 57.32% 606ms 3.09% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.32% 600ms 3.06% std::_Rb_tree::_M_create_node (inline) 0 0% 57.32% 588ms 2.99% std::map::find (inline) 173ms 0.88% 58.20% 587ms 2.99% __dynamic_cast 9ms 0.046% 58.25% 579ms 2.95% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.02% 58.27% 571ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.27% 570ms 2.90% std::_Rb_tree::_M_get_node (inline) 0 0% 58.27% 552ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.046% 58.31% 546ms 2.78% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.046% 58.36% 540ms 2.75% Cylindrical2dMesh::ReconstructCylindricalMesh 30ms 0.15% 58.51% 532ms 2.71% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 58.51% 532ms 2.71% std::_Rb_tree::lower_bound (inline) 0 0% 58.51% 532ms 2.71% std::map::lower_bound (inline) 5ms 0.025% 58.54% 522ms 2.66% Element::Element 7ms 0.036% 58.57% 486ms 2.47% MutableMesh::ReIndex 336ms 1.71% 60.28% 478ms 2.43% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 60.30% 472ms 2.40% std::ostream::operator<< (inline) 63ms 0.32% 60.62% 468ms 2.38% std::ostream::_M_insert 16ms 0.081% 60.70% 458ms 2.33% Element::RegisterWithNodes (inline) 0 0% 60.70% 455ms 2.32% AbstractCellProperty::IsSubType (inline) 5ms 0.025% 60.73% 452ms 2.30% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.041% 60.77% 442ms 2.25% Node::AddElement 149ms 0.76% 61.53% 412ms 2.10% __GI___libc_free 9ms 0.046% 61.57% 404ms 2.06% divconqrecurse 93ms 0.47% 62.04% 379ms 1.93% mergehulls 17ms 0.087% 62.13% 363ms 1.85% Node::RemoveElement 1ms 0.0051% 62.14% 360ms 1.83% std::_Vector_base::_M_allocate (inline) 5ms 0.025% 62.16% 356ms 1.81% std::_Rb_tree::erase 2ms 0.01% 62.17% 356ms 1.81% std::set::erase (inline) 133ms 0.68% 62.85% 343ms 1.75% std::_Rb_tree::_M_get_insert_unique_pos 341ms 1.74% 64.59% 341ms 1.74% std::type_info::name (inline) 7ms 0.036% 64.62% 331ms 1.69% std::__new_allocator::deallocate (inline) 102ms 0.52% 65.14% 329ms 1.68% std::_Rb_tree::_M_erase 0 0% 65.14% 325ms 1.65% std::allocator_traits::deallocate (inline) 40ms 0.2% 65.34% 322ms 1.64% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 65.35% 321ms 1.63% NodeLocationWriter::Visit 18ms 0.092% 65.45% 319ms 1.62% Element::ResetIndex 7ms 0.036% 65.48% 315ms 1.60% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 4ms 0.02% 65.50% 313ms 1.59% Cell::GetCellProliferativeType 5ms 0.025% 65.53% 307ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 65.53% 305ms 1.55% Cell::GetMutationState 147ms 0.75% 66.28% 305ms 1.55% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.28% 291ms 1.48% std::set::~set (inline) 8ms 0.041% 66.32% 284ms 1.45% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.32% 278ms 1.42% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0051% 66.33% 276ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 16ms 0.081% 66.41% 273ms 1.39% std::num_put::_M_insert_float 28ms 0.14% 66.55% 272ms 1.38% AbstractCellPopulation::Iterator::IsRealCell (inline) 16ms 0.081% 66.63% 266ms 1.35% std::_Rb_tree::_Rb_tree (partial-inline) 202ms 1.03% 67.66% 263ms 1.34% _int_free 9ms 0.046% 67.71% 260ms 1.32% std::vector::push_back (inline) 0 0% 67.71% 255ms 1.30% std::_Rb_tree::_M_put_node (inline) 251ms 1.28% 68.99% 253ms 1.29% std::vector::operator[] (inline) 3ms 0.015% 69.00% 243ms 1.24% std::set::set (inline) 16ms 0.081% 69.08% 243ms 1.24% std::vector::_M_realloc_insert 6ms 0.031% 69.11% 240ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.02% 69.13% 235ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 20ms 0.1% 69.23% 226ms 1.15% AbstractTetrahedralElement::CalculateJacobian 56ms 0.29% 69.52% 226ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 40ms 0.2% 69.72% 223ms 1.14% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 69.74% 220ms 1.12% alternateaxes 199ms 1.01% 70.75% 217ms 1.10% vertexmedian 3ms 0.015% 70.77% 215ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.77% 214ms 1.09% TetrahedralMesh::RefreshJacobianCachedData 24ms 0.12% 70.89% 214ms 1.09% std::_Rb_tree::_M_copy (inline) 10ms 0.051% 70.94% 211ms 1.07% std::_Rb_tree::_M_erase_aux (inline) 0 0% 70.94% 208ms 1.06% OffLatticeSimulation::ApplyBoundaries 7ms 0.036% 70.98% 208ms 1.06% std::__cxx11::collate::do_transform 159ms 0.81% 71.79% 205ms 1.04% AbstractElement::GetNodeGlobalIndex 0 0% 71.79% 200ms 1.02% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.79% 200ms 1.02% MeshBasedCellPopulation::GetDampingConstant 4ms 0.02% 71.81% 198ms 1.01% ___vsnprintf 197ms 1.00% 72.81% 197ms 1.00% [libchaste_cell_based.so] 43ms 0.22% 73.03% 196ms 1% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 16ms 0.081% 73.11% 196ms 1% Element::MarkAsDeleted 1ms 0.0051% 73.11% 194ms 0.99% __vsnprintf_internal (inline) 15ms 0.076% 73.19% 190ms 0.97% __printf_buffer 58ms 0.3% 73.49% 189ms 0.96% std::_Rb_tree::_M_clone_node (inline) 137ms 0.7% 74.18% 182ms 0.93% malloc_consolidate 10ms 0.051% 74.23% 180ms 0.92% AbstractTetrahedralElement::CalculateInverseJacobian 180ms 0.92% 75.15% 180ms 0.92% std::_Rb_tree_insert_and_rebalance 5ms 0.025% 75.18% 179ms 0.91% CellProliferativeTypesWriter::VisitCell 172ms 0.88% 76.05% 172ms 0.88% incircle 2ms 0.01% 76.06% 170ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 164ms 0.84% 76.90% 164ms 0.84% Node::GetIndex 24ms 0.12% 77.02% 162ms 0.82% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 77.04% 155ms 0.79% __printf_fp_l_buffer 0 0% 77.04% 155ms 0.79% __printf_fp_spec (inline) 155ms 0.79% 77.82% 155ms 0.79% std::vector::size (inline) 3ms 0.015% 77.84% 150ms 0.76% boost::numeric::ublas::vector_assign (inline) 89ms 0.45% 78.29% 150ms 0.76% std::_Rb_tree::equal_range (inline) 150ms 0.76% 79.06% 150ms 0.76% unlink_chunk 72ms 0.37% 79.42% 146ms 0.74% __printf_fp_buffer_1 10ms 0.051% 79.47% 145ms 0.74% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 79.49% 144ms 0.73% CellPropertyCollection::HasProperty 18ms 0.092% 79.58% 143ms 0.73% TetrahedralMesh::Clear 0 0% 79.58% 141ms 0.72% Cell::HasCellProperty (inline) 5ms 0.025% 79.61% 136ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 13ms 0.066% 79.67% 134ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 22ms 0.11% 79.79% 132ms 0.67% TetrahedralMesh::EdgesEnd (partial-inline) 7ms 0.036% 79.82% 130ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 43ms 0.22% 80.04% 128ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 47ms 0.24% 80.28% 125ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 80.28% 125ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 52ms 0.26% 80.54% 121ms 0.62% std::__ostream_insert 58ms 0.3% 80.84% 120ms 0.61% AbstractElement::GetNodeLocation 0 0% 80.84% 119ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 112ms 0.57% 81.41% 119ms 0.61% vertexsort 118ms 0.6% 82.01% 118ms 0.6% AbstractCellProperty::~AbstractCellProperty 67ms 0.34% 82.35% 115ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 82.35% 115ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 115ms 0.59% 82.94% 115ms 0.59% std::_Rb_tree_increment 31ms 0.16% 83.09% 114ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 113ms 0.58% 83.67% 113ms 0.58% AbstractCellMutationState::~AbstractCellMutationState 1ms 0.0051% 83.68% 112ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 38ms 0.19% 83.87% 112ms 0.57% boost::numeric::ublas::indexing_vector_assign 4ms 0.02% 83.89% 109ms 0.56% Cell::SetCellProliferativeType 106ms 0.54% 84.43% 106ms 0.54% counterclockwise 104ms 0.53% 84.96% 104ms 0.53% std::_Rb_tree_rebalance_for_erase 0 0% 84.96% 103ms 0.52% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 84.96% 103ms 0.52% OutputFileHandler::OpenOutputFile 2ms 0.01% 84.97% 101ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0051% 84.97% 100ms 0.51% std::operator<< (inline)