File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16787ms, 84.52% of 19861ms total Dropped 760 nodes (cum <= 99.31ms) flat flat% sum% cum cum% 0 0% 0% 19817ms 99.78% __libc_start_call_main 0 0% 0% 19817ms 99.78% __libc_start_main_impl 0 0% 0% 19817ms 99.78% _start 0 0% 0% 19798ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19798ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19798ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19798ms 99.68% main 0 0% 0% 19764ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19764ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19764ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19737ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 15361ms 77.34% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10142ms 51.06% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.02% 10059ms 50.65% Cell::ReadyToDivide 6ms 0.03% 0.05% 9986ms 50.28% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.05% 9857ms 49.63% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.096% 9853ms 49.61% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.096% 9840ms 49.54% CellCycleModelOdeHandler::SolveOdeToTime 97ms 0.49% 0.58% 9679ms 48.73% AbstractOneStepIvpOdeSolver::InternalSolve 918ms 4.62% 5.21% 8839ms 44.50% RungeKutta4IvpOdeSolver::CalculateNextYValue 3635ms 18.30% 23.51% 7690ms 38.72% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.51% 5099ms 25.67% MeshBasedCellPopulation::Update 182ms 0.92% 24.43% 4129ms 20.79% AbstractCellProperty::IsType (inline) 4ms 0.02% 24.45% 3911ms 19.69% Cylindrical2dMesh::ReMesh 556ms 2.80% 27.25% 2822ms 14.21% AbstractCellProperty::IsSame 0 0% 27.25% 2457ms 12.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 403ms 2.03% 29.28% 2266ms 11.41% std::type_info::operator== (inline) 1ms 0.005% 29.28% 2161ms 10.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.28% 2131ms 10.73% MutableMesh::ReMesh 7ms 0.035% 29.32% 2122ms 10.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.32% 1914ms 9.64% AbstractCellPopulation::WriteResultsToFiles 1855ms 9.34% 38.66% 1855ms 9.34% __strcmp_avx2 726ms 3.66% 42.31% 1761ms 8.87% std::_Rb_tree::_M_lower_bound (inline) 165ms 0.83% 43.14% 1716ms 8.64% TetrahedralMesh::EdgeIterator::operator++ 51ms 0.26% 43.40% 1328ms 6.69% std::_Rb_tree::find (inline) 0 0% 43.40% 1151ms 5.80% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.43% 1124ms 5.66% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 54ms 0.27% 43.70% 1068ms 5.38% operator new 17ms 0.086% 43.78% 1067ms 5.37% TetrahedralMesh::ImportFromMesher 11ms 0.055% 43.84% 1021ms 5.14% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.03% 43.87% 1008ms 5.08% std::set::insert (inline) 233ms 1.17% 45.04% 1005ms 5.06% __GI___libc_malloc 23ms 0.12% 45.16% 1001ms 5.04% std::_Rb_tree::_M_insert_unique 40ms 0.2% 45.36% 929ms 4.68% std::__new_allocator::allocate (inline) 0 0% 45.36% 926ms 4.66% std::allocator_traits::allocate (inline) 0 0% 45.36% 847ms 4.26% std::set::count (inline) 1ms 0.005% 45.37% 803ms 4.04% triangulate 0 0% 45.37% 733ms 3.69% delaunay 3ms 0.015% 45.38% 733ms 3.69% divconqdelaunay 0 0% 45.38% 698ms 3.51% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.035% 45.42% 693ms 3.49% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 388ms 1.95% 47.37% 692ms 3.48% _int_malloc 24ms 0.12% 47.49% 680ms 3.42% std::less::operator() (inline) 7ms 0.035% 47.53% 656ms 3.30% CellPopulationElementWriter::Visit 656ms 3.30% 50.83% 656ms 3.30% std::operator< (inline) 54ms 0.27% 51.10% 653ms 3.29% std::map::operator[] (partial-inline) 635ms 3.20% 54.30% 635ms 3.20% std::_Rb_tree::_S_right (inline) 33ms 0.17% 54.46% 615ms 3.10% std::_Rb_tree::_M_insert_ (inline) 182ms 0.92% 55.38% 613ms 3.09% __dynamic_cast 587ms 2.96% 58.34% 600ms 3.02% WntCellCycleOdeSystem::CalculateStoppingEvent 23ms 0.12% 58.45% 594ms 2.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.45% 590ms 2.97% std::_Rb_tree::_M_create_node (inline) 0 0% 58.45% 561ms 2.82% std::_Rb_tree::_M_get_node (inline) 0 0% 58.45% 547ms 2.75% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.015% 58.47% 545ms 2.74% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.11% 58.58% 536ms 2.70% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 58.60% 532ms 2.68% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.04% 58.64% 526ms 2.65% Element::Element 0 0% 58.64% 518ms 2.61% std::_Rb_tree::lower_bound (inline) 0 0% 58.64% 518ms 2.61% std::map::lower_bound (inline) 377ms 1.90% 60.54% 517ms 2.60% AbstractCellMutationState::AbstractCellMutationState 7ms 0.035% 60.57% 502ms 2.53% MutableMesh::ReIndex 8ms 0.04% 60.61% 484ms 2.44% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.05% 60.66% 478ms 2.41% Element::RegisterWithNodes (inline) 0 0% 60.66% 476ms 2.40% std::map::find (inline) 1ms 0.005% 60.67% 471ms 2.37% std::ostream::operator<< (inline) 16ms 0.081% 60.75% 470ms 2.37% Cylindrical2dMesh::CorrectNonPeriodicMesh 56ms 0.28% 61.03% 470ms 2.37% std::ostream::_M_insert 11ms 0.055% 61.08% 464ms 2.34% Node::AddElement 2ms 0.01% 61.09% 442ms 2.23% AbstractCellProperty::IsSubType (inline) 153ms 0.77% 61.86% 441ms 2.22% __GI___libc_free 16ms 0.081% 61.95% 368ms 1.85% divconqrecurse 0 0% 61.95% 365ms 1.84% std::_Vector_base::_M_allocate (inline) 125ms 0.63% 62.57% 363ms 1.83% std::_Rb_tree::_M_get_insert_unique_pos 110ms 0.55% 63.13% 356ms 1.79% std::_Rb_tree::_M_erase 8ms 0.04% 63.17% 356ms 1.79% std::_Rb_tree::erase 5ms 0.025% 63.19% 355ms 1.79% std::__new_allocator::deallocate (inline) 0 0% 63.19% 355ms 1.79% std::set::erase (inline) 7ms 0.035% 63.23% 347ms 1.75% Node::RemoveElement 0 0% 63.23% 346ms 1.74% std::allocator_traits::deallocate (inline) 95ms 0.48% 63.71% 340ms 1.71% mergehulls 149ms 0.75% 64.46% 331ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 23ms 0.12% 64.57% 329ms 1.66% std::_Rb_tree::~_Rb_tree (inline) 24ms 0.12% 64.69% 326ms 1.64% Element::ResetIndex 0 0% 64.69% 322ms 1.62% std::_Rb_tree::_M_drop_node (inline) 1ms 0.005% 64.70% 318ms 1.60% NodeLocationWriter::Visit 0 0% 64.70% 303ms 1.53% std::set::~set (inline) 9ms 0.045% 64.74% 295ms 1.49% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.03% 64.78% 292ms 1.47% LegacyCellProliferativeTypesWriter::VisitCell 237ms 1.19% 65.97% 287ms 1.45% _int_free 7ms 0.035% 66.00% 283ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.005% 66.01% 283ms 1.42% Cell::GetMutationState 0 0% 66.01% 283ms 1.42% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 66.03% 279ms 1.40% Cell::GetCellProliferativeType 13ms 0.065% 66.09% 279ms 1.40% std::vector::push_back (inline) 16ms 0.081% 66.17% 275ms 1.38% std::num_put::_M_insert_float 270ms 1.36% 67.53% 270ms 1.36% std::type_info::name (inline) 263ms 1.32% 68.86% 264ms 1.33% std::vector::operator[] (inline) 0 0% 68.86% 259ms 1.30% AbstractCellPopulation::Iterator::operator++ (inline) 32ms 0.16% 69.02% 258ms 1.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 13ms 0.065% 69.09% 254ms 1.28% std::_Rb_tree::_Rb_tree (partial-inline) 19ms 0.096% 69.18% 253ms 1.27% std::vector::_M_realloc_insert 5ms 0.025% 69.21% 251ms 1.26% alternateaxes 231ms 1.16% 70.37% 246ms 1.24% vertexmedian 62ms 0.31% 70.68% 245ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 56ms 0.28% 70.96% 242ms 1.22% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 70.96% 241ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.025% 70.99% 240ms 1.21% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.076% 71.06% 234ms 1.18% AbstractTetrahedralElement::CalculateJacobian 6ms 0.03% 71.09% 233ms 1.17% std::__cxx11::collate::do_transform 4ms 0.02% 71.11% 230ms 1.16% std::set::set (inline) 7ms 0.035% 71.15% 228ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 13ms 0.065% 71.21% 227ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.005% 71.22% 218ms 1.10% ___vsnprintf 72ms 0.36% 71.58% 217ms 1.09% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 71.58% 217ms 1.09% __vsnprintf_internal (inline) 21ms 0.11% 71.69% 212ms 1.07% std::_Rb_tree::_M_copy (inline) 38ms 0.19% 71.88% 210ms 1.06% __printf_buffer 13ms 0.065% 71.95% 203ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 202ms 1.02% 72.96% 202ms 1.02% [libchaste_cell_based.so] 147ms 0.74% 73.70% 200ms 1.01% malloc_consolidate 154ms 0.78% 74.48% 199ms 1.00% AbstractElement::GetNodeGlobalIndex 7ms 0.035% 74.51% 198ms 1% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 74.52% 195ms 0.98% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 74.53% 194ms 0.98% AbstractCentreBasedCellPopulation::GetDampingConstant 61ms 0.31% 74.84% 190ms 0.96% std::_Rb_tree::_M_clone_node (inline) 9ms 0.045% 74.88% 187ms 0.94% Element::MarkAsDeleted 187ms 0.94% 75.82% 187ms 0.94% Node::GetIndex 28ms 0.14% 75.96% 185ms 0.93% AbstractTetrahedralElement::RefreshJacobian 184ms 0.93% 76.89% 184ms 0.93% std::_Rb_tree_insert_and_rebalance 0 0% 76.89% 180ms 0.91% OffLatticeSimulation::ApplyBoundaries 25ms 0.13% 77.02% 179ms 0.9% TetrahedralMesh::Clear 157ms 0.79% 77.81% 157ms 0.79% incircle 3ms 0.015% 77.82% 154ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 77.83% 153ms 0.77% __printf_fp_spec (inline) 4ms 0.02% 77.85% 151ms 0.76% __printf_fp_l_buffer 1ms 0.005% 77.86% 150ms 0.76% CellProliferativeTypesWriter::VisitCell 3ms 0.015% 77.87% 148ms 0.75% CellPropertyCollection::HasProperty 30ms 0.15% 78.02% 147ms 0.74% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 78.02% 146ms 0.74% Cell::HasCellProperty (inline) 141ms 0.71% 78.73% 141ms 0.71% unlink_chunk 140ms 0.7% 79.44% 140ms 0.7% std::vector::size (inline) 57ms 0.29% 79.72% 139ms 0.7% AbstractElement::GetNodeLocation 10ms 0.05% 79.77% 139ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 75ms 0.38% 80.15% 137ms 0.69% __printf_fp_buffer_1 4ms 0.02% 80.17% 134ms 0.67% boost::numeric::ublas::vector_assign (inline) 6ms 0.03% 80.20% 131ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.035% 80.24% 131ms 0.66% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 20ms 0.1% 80.34% 130ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 81ms 0.41% 80.75% 130ms 0.65% std::_Rb_tree::equal_range (inline) 40ms 0.2% 80.95% 128ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.005% 80.95% 120ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 80.95% 120ms 0.6% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 49ms 0.25% 81.20% 120ms 0.6% std::__ostream_insert 118ms 0.59% 81.79% 118ms 0.59% AbstractElement::IsDeleted 74ms 0.37% 82.17% 117ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 82.17% 117ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 8ms 0.04% 82.21% 117ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.05% 82.26% 116ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 82.26% 116ms 0.58% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.26% 115ms 0.58% AbstractCellBasedWriter::OpenOutputFileForAppend 37ms 0.19% 82.44% 115ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.005% 82.45% 115ms 0.58% OutputFileHandler::OpenOutputFile 104ms 0.52% 82.97% 105ms 0.53% boost::detail::sp_counted_base::release 104ms 0.52% 83.50% 104ms 0.52% AbstractCellMutationState::~AbstractCellMutationState 25ms 0.13% 83.62% 102ms 0.51% boost::numeric::ublas::indexing_vector_assign 15ms 0.076% 83.70% 102ms 0.51% std::num_put::_M_insert_int 93ms 0.47% 84.16% 102ms 0.51% vertexsort 67ms 0.34% 84.50% 101ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 4ms 0.02% 84.52% 101ms 0.51% std::operator<< (inline)