File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16648ms, 83.78% of 19872ms total Dropped 736 nodes (cum <= 99.36ms) flat flat% sum% cum cum% 0 0% 0% 19828ms 99.78% __libc_start_call_main 0 0% 0% 19828ms 99.78% __libc_start_main_impl 0 0% 0% 19828ms 99.78% _start 0 0% 0% 19805ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19805ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19805ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19805ms 99.66% main 0 0% 0% 19769ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19769ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19769ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19744ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15344ms 77.21% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10168ms 51.17% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.03% 10070ms 50.67% Cell::ReadyToDivide 3ms 0.015% 0.045% 10018ms 50.41% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.055% 9879ms 49.71% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.1% 9868ms 49.66% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.12% 9857ms 49.60% CellCycleModelOdeHandler::SolveOdeToTime 62ms 0.31% 0.43% 9694ms 48.78% AbstractOneStepIvpOdeSolver::InternalSolve 875ms 4.40% 4.83% 8905ms 44.81% RungeKutta4IvpOdeSolver::CalculateNextYValue 3676ms 18.50% 23.33% 7833ms 39.42% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.33% 5078ms 25.55% MeshBasedCellPopulation::Update 175ms 0.88% 24.21% 4160ms 20.93% AbstractCellProperty::IsType (inline) 8ms 0.04% 24.26% 3887ms 19.56% Cylindrical2dMesh::ReMesh 569ms 2.86% 27.12% 2917ms 14.68% AbstractCellProperty::IsSame 0 0% 27.12% 2443ms 12.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 423ms 2.13% 29.25% 2348ms 11.82% std::type_info::operator== (inline) 0 0% 29.25% 2120ms 10.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.25% 2119ms 10.66% MutableMesh::ReMesh 9ms 0.045% 29.29% 2073ms 10.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.29% 1951ms 9.82% AbstractCellPopulation::WriteResultsToFiles 1892ms 9.52% 38.81% 1892ms 9.52% __strcmp_avx2 789ms 3.97% 42.78% 1812ms 9.12% std::_Rb_tree::_M_lower_bound (inline) 150ms 0.75% 43.54% 1639ms 8.25% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.34% 43.88% 1343ms 6.76% std::_Rb_tree::find (inline) 1ms 0.005% 43.88% 1147ms 5.77% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.91% 1136ms 5.72% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 19ms 0.096% 44.00% 1065ms 5.36% TetrahedralMesh::ImportFromMesher 46ms 0.23% 44.23% 1030ms 5.18% operator new 9ms 0.045% 44.28% 1009ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 259ms 1.30% 45.58% 978ms 4.92% __GI___libc_malloc 8ms 0.04% 45.62% 969ms 4.88% std::set::insert (inline) 17ms 0.086% 45.71% 960ms 4.83% std::_Rb_tree::_M_insert_unique 40ms 0.2% 45.91% 905ms 4.55% std::__new_allocator::allocate (inline) 0 0% 45.91% 896ms 4.51% std::allocator_traits::allocate (inline) 0 0% 45.91% 829ms 4.17% std::set::count (inline) 2ms 0.01% 45.92% 812ms 4.09% triangulate 0 0% 45.92% 740ms 3.72% delaunay 3ms 0.015% 45.93% 739ms 3.72% divconqdelaunay 5ms 0.025% 45.96% 727ms 3.66% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 42ms 0.21% 46.17% 682ms 3.43% std::map::operator[] (partial-inline) 1ms 0.005% 46.18% 679ms 3.42% AbstractTwoBodyInteractionForce::AddForceContribution 670ms 3.37% 49.55% 670ms 3.37% std::_Rb_tree::_S_right (inline) 5ms 0.025% 49.57% 667ms 3.36% CellPopulationElementWriter::Visit 373ms 1.88% 51.45% 640ms 3.22% _int_malloc 161ms 0.81% 52.26% 631ms 3.18% __dynamic_cast 18ms 0.091% 52.35% 611ms 3.07% std::less::operator() (inline) 0 0% 52.35% 605ms 3.04% std::_Rb_tree::_M_create_node (inline) 597ms 3.00% 55.35% 601ms 3.02% WntCellCycleOdeSystem::CalculateStoppingEvent 19ms 0.096% 55.45% 597ms 3.00% std::_Rb_tree::_M_insert_ (inline) 593ms 2.98% 58.43% 593ms 2.98% std::operator< (inline) 21ms 0.11% 58.54% 580ms 2.92% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.54% 574ms 2.89% std::_Rb_tree::_M_get_node (inline) 3ms 0.015% 58.55% 569ms 2.86% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.025% 58.58% 561ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.58% 555ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 58.58% 555ms 2.79% std::map::lower_bound (inline) 0 0% 58.58% 554ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.03% 58.61% 541ms 2.72% Element::Element 16ms 0.081% 58.69% 536ms 2.70% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.69% 510ms 2.57% std::map::find (inline) 353ms 1.78% 60.47% 500ms 2.52% AbstractCellMutationState::AbstractCellMutationState 10ms 0.05% 60.52% 499ms 2.51% MutableMesh::ReIndex 16ms 0.081% 60.60% 488ms 2.46% Cylindrical2dMesh::CorrectNonPeriodicMesh 6ms 0.03% 60.63% 487ms 2.45% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.005% 60.63% 487ms 2.45% std::ostream::operator<< (inline) 69ms 0.35% 60.98% 486ms 2.45% std::ostream::_M_insert 11ms 0.055% 61.04% 474ms 2.39% Element::RegisterWithNodes (inline) 3ms 0.015% 61.05% 470ms 2.37% AbstractCellProperty::IsSubType (inline) 181ms 0.91% 61.96% 470ms 2.37% __GI___libc_free 8ms 0.04% 62.00% 461ms 2.32% Node::AddElement 7ms 0.035% 62.04% 398ms 2.00% std::_Rb_tree::erase 0 0% 62.04% 397ms 2.00% std::set::erase (inline) 9ms 0.045% 62.08% 391ms 1.97% Node::RemoveElement 11ms 0.055% 62.14% 388ms 1.95% std::__new_allocator::deallocate (inline) 0 0% 62.14% 382ms 1.92% std::allocator_traits::deallocate (inline) 105ms 0.53% 62.67% 365ms 1.84% std::_Rb_tree::_M_erase 13ms 0.065% 62.73% 351ms 1.77% divconqrecurse 0 0% 62.73% 349ms 1.76% std::_Rb_tree::_M_drop_node (inline) 146ms 0.73% 63.47% 347ms 1.75% std::_Rb_tree::_M_get_insert_unique_pos 159ms 0.8% 64.27% 340ms 1.71% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.091% 64.36% 334ms 1.68% Element::ResetIndex 94ms 0.47% 64.83% 334ms 1.68% mergehulls 27ms 0.14% 64.97% 334ms 1.68% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 64.98% 324ms 1.63% std::_Vector_base::_M_allocate (inline) 4ms 0.02% 65.00% 321ms 1.62% Cell::GetCellProliferativeType 321ms 1.62% 66.61% 321ms 1.62% std::type_info::name (inline) 8ms 0.04% 66.65% 318ms 1.60% NodeLocationWriter::Visit 0 0% 66.65% 317ms 1.60% std::_Rb_tree::_M_put_node (inline) 6ms 0.03% 66.68% 307ms 1.54% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 66.68% 306ms 1.54% std::set::~set (inline) 6ms 0.03% 66.71% 294ms 1.48% Cell::GetMutationState 235ms 1.18% 67.89% 288ms 1.45% _int_free 5ms 0.025% 67.92% 272ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.015% 67.93% 272ms 1.37% LegacyCellProliferativeTypesWriter::VisitCell 15ms 0.075% 68.01% 269ms 1.35% std::num_put::_M_insert_float 0 0% 68.01% 267ms 1.34% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.18% 68.19% 266ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 8ms 0.04% 68.23% 265ms 1.33% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.01% 68.24% 258ms 1.30% alternateaxes 16ms 0.081% 68.32% 257ms 1.29% AbstractTetrahedralElement::CalculateJacobian 241ms 1.21% 69.53% 254ms 1.28% vertexmedian 13ms 0.065% 69.60% 248ms 1.25% std::_Rb_tree::_M_erase_aux (inline) 15ms 0.075% 69.67% 247ms 1.24% std::vector::push_back (inline) 55ms 0.28% 69.95% 242ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 3ms 0.015% 69.96% 235ms 1.18% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.005% 69.97% 235ms 1.18% std::set::set (inline) 234ms 1.18% 71.15% 234ms 1.18% [libchaste_cell_based.so] 29ms 0.15% 71.29% 228ms 1.15% std::_Rb_tree::_M_copy (inline) 224ms 1.13% 72.42% 225ms 1.13% std::vector::operator[] (inline) 0 0% 72.42% 219ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.01% 72.43% 219ms 1.10% std::__cxx11::collate::do_transform 11ms 0.055% 72.48% 218ms 1.10% std::vector::_M_realloc_insert 2ms 0.01% 72.49% 214ms 1.08% ___vsnprintf 65ms 0.33% 72.82% 213ms 1.07% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 72.82% 212ms 1.07% __vsnprintf_internal (inline) 9ms 0.045% 72.87% 210ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 18ms 0.091% 72.96% 210ms 1.06% __printf_buffer 43ms 0.22% 73.17% 209ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 11ms 0.055% 73.23% 207ms 1.04% Element::MarkAsDeleted 2ms 0.01% 73.24% 204ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 23ms 0.12% 73.35% 201ms 1.01% AbstractTetrahedralElement::RefreshJacobian 11ms 0.055% 73.41% 200ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 61ms 0.31% 73.72% 197ms 0.99% std::_Rb_tree::_M_clone_node (inline) 0 0% 73.72% 192ms 0.97% OffLatticeSimulation::ApplyBoundaries 187ms 0.94% 74.66% 187ms 0.94% Node::GetIndex 1ms 0.005% 74.66% 184ms 0.93% CellProliferativeTypesWriter::VisitCell 2ms 0.01% 74.67% 182ms 0.92% __printf_fp_l_buffer 0 0% 74.67% 182ms 0.92% __printf_fp_spec (inline) 15ms 0.075% 74.75% 176ms 0.89% TetrahedralMesh::Clear 5ms 0.025% 74.77% 175ms 0.88% AbstractTetrahedralElement::AbstractTetrahedralElement 124ms 0.62% 75.40% 175ms 0.88% malloc_consolidate 127ms 0.64% 76.04% 173ms 0.87% AbstractElement::GetNodeGlobalIndex 6ms 0.03% 76.07% 173ms 0.87% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 84ms 0.42% 76.49% 173ms 0.87% __printf_fp_buffer_1 172ms 0.87% 77.36% 172ms 0.87% std::_Rb_tree_insert_and_rebalance 3ms 0.015% 77.37% 169ms 0.85% MeshBasedCellPopulation::GetDampingConstant 0 0% 77.37% 166ms 0.84% AbstractCentreBasedCellPopulation::GetDampingConstant 57ms 0.29% 77.66% 157ms 0.79% AbstractElement::GetNodeLocation 95ms 0.48% 78.14% 154ms 0.77% std::_Rb_tree::equal_range (inline) 5ms 0.025% 78.16% 150ms 0.75% boost::numeric::ublas::vector_assign (inline) 141ms 0.71% 78.87% 141ms 0.71% unlink_chunk 79ms 0.4% 79.27% 140ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 3ms 0.015% 79.28% 139ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 29ms 0.15% 79.43% 137ms 0.69% TetrahedralMesh::EdgesEnd (partial-inline) 137ms 0.69% 80.12% 137ms 0.69% incircle 1ms 0.005% 80.12% 131ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.025% 80.15% 130ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.04% 80.19% 129ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 126ms 0.63% 80.82% 126ms 0.63% std::vector::size (inline) 0 0% 80.82% 123ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.82% 122ms 0.61% OutputFileHandler::OpenOutputFile 8ms 0.04% 80.86% 119ms 0.6% MeshBasedCellPopulation::SpringsEnd (inline) 31ms 0.16% 81.02% 118ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 11ms 0.055% 81.07% 118ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 81.07% 118ms 0.59% boost::shared_ptr::~shared_ptr (inline) 110ms 0.55% 81.63% 117ms 0.59% vertexsort 40ms 0.2% 81.83% 116ms 0.58% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 31ms 0.16% 81.98% 115ms 0.58% boost::numeric::ublas::indexing_vector_assign 0 0% 81.98% 114ms 0.57% Cell::SetCellProliferativeType 5ms 0.025% 82.01% 114ms 0.57% CellPropertyCollection::HasProperty 1ms 0.005% 82.01% 113ms 0.57% Cell::HasCellProperty (inline) 1ms 0.005% 82.02% 111ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 30ms 0.15% 82.17% 108ms 0.54% std::num_put::_M_insert_int 42ms 0.21% 82.38% 106ms 0.53% std::__ostream_insert 105ms 0.53% 82.91% 105ms 0.53% boost::detail::sp_counted_base::release 2ms 0.01% 82.92% 103ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 103ms 0.52% 83.44% 103ms 0.52% boost::shared_ptr::operator-> (inline) 67ms 0.34% 83.78% 101ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator