File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16424ms, 83.74% of 19612ms total Dropped 763 nodes (cum <= 98.06ms) flat flat% sum% cum cum% 0 0% 0% 19567ms 99.77% __libc_start_call_main 0 0% 0% 19567ms 99.77% __libc_start_main_impl 0 0% 0% 19567ms 99.77% _start 0 0% 0% 19548ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19548ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19548ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19548ms 99.67% main 0 0% 0% 19515ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19515ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19515ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19488ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 15226ms 77.64% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 10002ms 51.00% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.015% 9928ms 50.62% Cell::ReadyToDivide 4ms 0.02% 0.036% 9891ms 50.43% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.046% 9758ms 49.76% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.1% 0.15% 9745ms 49.69% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.16% 9721ms 49.57% CellCycleModelOdeHandler::SolveOdeToTime 57ms 0.29% 0.45% 9577ms 48.83% AbstractOneStepIvpOdeSolver::InternalSolve 867ms 4.42% 4.87% 8749ms 44.61% RungeKutta4IvpOdeSolver::CalculateNextYValue 3344ms 17.05% 21.92% 7681ms 39.16% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 21.93% 5103ms 26.02% MeshBasedCellPopulation::Update 203ms 1.04% 22.97% 4366ms 22.26% AbstractCellProperty::IsType (inline) 6ms 0.031% 23.00% 3933ms 20.05% Cylindrical2dMesh::ReMesh 546ms 2.78% 25.78% 3103ms 15.82% AbstractCellProperty::IsSame 428ms 2.18% 27.96% 2557ms 13.04% std::type_info::operator== (inline) 0 0% 27.96% 2485ms 12.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.01% 27.97% 2168ms 11.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.061% 28.03% 2132ms 10.87% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.03% 2098ms 10.70% MutableMesh::ReMesh 2082ms 10.62% 38.65% 2082ms 10.62% __strcmp_avx2 823ms 4.20% 42.85% 1825ms 9.31% std::_Rb_tree::_M_lower_bound (inline) 0 0% 42.85% 1775ms 9.05% AbstractCellPopulation::WriteResultsToFiles 145ms 0.74% 43.59% 1679ms 8.56% TetrahedralMesh::EdgeIterator::operator++ 63ms 0.32% 43.91% 1379ms 7.03% std::_Rb_tree::find (inline) 2ms 0.01% 43.92% 1138ms 5.80% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 43.96% 1112ms 5.67% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 21ms 0.11% 44.07% 1061ms 5.41% TetrahedralMesh::ImportFromMesher 49ms 0.25% 44.32% 1039ms 5.30% operator new 13ms 0.066% 44.39% 1028ms 5.24% MeshBasedCellPopulation::SpringIterator::operator++ 228ms 1.16% 45.55% 984ms 5.02% __GI___libc_malloc 5ms 0.025% 45.57% 983ms 5.01% std::set::insert (inline) 31ms 0.16% 45.73% 978ms 4.99% std::_Rb_tree::_M_insert_unique 40ms 0.2% 45.94% 899ms 4.58% std::__new_allocator::allocate (inline) 0 0% 45.94% 891ms 4.54% std::allocator_traits::allocate (inline) 0 0% 45.94% 837ms 4.27% std::set::count (inline) 2ms 0.01% 45.95% 793ms 4.04% triangulate 1ms 0.0051% 45.95% 710ms 3.62% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.046% 46.00% 708ms 3.61% CellPopulationElementWriter::Visit 0 0% 46.00% 707ms 3.60% delaunay 2ms 0.01% 46.01% 706ms 3.60% divconqdelaunay 4ms 0.02% 46.03% 694ms 3.54% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 413ms 2.11% 48.13% 681ms 3.47% _int_malloc 53ms 0.27% 48.40% 678ms 3.46% std::map::operator[] (partial-inline) 640ms 3.26% 51.67% 640ms 3.26% std::_Rb_tree::_S_right (inline) 628ms 3.20% 54.87% 636ms 3.24% WntCellCycleOdeSystem::CalculateStoppingEvent 15ms 0.076% 54.95% 623ms 3.18% std::less::operator() (inline) 30ms 0.15% 55.10% 608ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 608ms 3.10% 58.20% 608ms 3.10% std::operator< (inline) 32ms 0.16% 58.36% 603ms 3.07% std::_Rb_tree::_M_insert_ (inline) 168ms 0.86% 59.22% 597ms 3.04% __dynamic_cast 0 0% 59.22% 595ms 3.03% std::_Rb_tree::_M_create_node (inline) 0 0% 59.22% 574ms 2.93% std::_Rb_tree::_M_get_node (inline) 7ms 0.036% 59.25% 562ms 2.87% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.041% 59.30% 546ms 2.78% Element::Element 0 0% 59.30% 546ms 2.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 59.30% 537ms 2.74% std::map::find (inline) 18ms 0.092% 59.39% 536ms 2.73% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.056% 59.44% 535ms 2.73% MutableMesh::ReIndex 0 0% 59.44% 531ms 2.71% std::_Rb_tree::lower_bound (inline) 0 0% 59.44% 531ms 2.71% std::map::lower_bound (inline) 10ms 0.051% 59.49% 525ms 2.68% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.046% 59.54% 507ms 2.59% Cylindrical2dMesh::ReconstructCylindricalMesh 359ms 1.83% 61.37% 497ms 2.53% AbstractCellMutationState::AbstractCellMutationState 8ms 0.041% 61.41% 492ms 2.51% Element::RegisterWithNodes (inline) 11ms 0.056% 61.47% 489ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.061% 61.53% 479ms 2.44% Node::AddElement 1ms 0.0051% 61.53% 433ms 2.21% AbstractCellProperty::IsSubType (inline) 149ms 0.76% 62.29% 433ms 2.21% __GI___libc_free 14ms 0.071% 62.36% 386ms 1.97% Node::RemoveElement 9ms 0.046% 62.41% 384ms 1.96% std::_Rb_tree::erase 0 0% 62.41% 381ms 1.94% std::set::erase (inline) 15ms 0.076% 62.49% 366ms 1.87% divconqrecurse 111ms 0.57% 63.05% 363ms 1.85% std::_Rb_tree::_M_erase 136ms 0.69% 63.75% 344ms 1.75% std::_Rb_tree::_M_get_insert_unique_pos 92ms 0.47% 64.22% 343ms 1.75% mergehulls 21ms 0.11% 64.32% 339ms 1.73% std::__new_allocator::deallocate (inline) 7ms 0.036% 64.36% 335ms 1.71% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.36% 332ms 1.69% std::allocator_traits::deallocate (inline) 25ms 0.13% 64.49% 328ms 1.67% Element::ResetIndex 17ms 0.087% 64.57% 318ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 0 0% 64.57% 317ms 1.62% std::_Vector_base::_M_allocate (inline) 0 0% 64.57% 311ms 1.59% std::_Rb_tree::_M_drop_node (inline) 155ms 0.79% 65.36% 309ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 8ms 0.041% 65.40% 304ms 1.55% Cell::GetCellProliferativeType 301ms 1.53% 66.94% 301ms 1.53% std::type_info::name (inline) 0 0% 66.94% 299ms 1.52% std::set::~set (inline) 9ms 0.046% 66.98% 290ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 215ms 1.10% 68.08% 284ms 1.45% _int_free 1ms 0.0051% 68.09% 280ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 36ms 0.18% 68.27% 274ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.01% 68.28% 266ms 1.36% Cell::GetMutationState 0 0% 68.28% 262ms 1.34% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 68.30% 259ms 1.32% LegacyCellProliferativeTypesWriter::VisitCell 18ms 0.092% 68.39% 255ms 1.30% std::vector::push_back (inline) 14ms 0.071% 68.46% 252ms 1.28% AbstractTetrahedralElement::CalculateJacobian 16ms 0.082% 68.54% 246ms 1.25% std::_Rb_tree::_Rb_tree (partial-inline) 22ms 0.11% 68.66% 236ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 5ms 0.025% 68.68% 233ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 79ms 0.4% 69.09% 232ms 1.18% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 229ms 1.17% 70.25% 229ms 1.17% [libchaste_cell_based.so] 227ms 1.16% 71.41% 228ms 1.16% std::vector::operator[] (inline) 14ms 0.071% 71.48% 227ms 1.16% std::vector::_M_realloc_insert 2ms 0.01% 71.49% 221ms 1.13% std::set::set (inline) 36ms 0.18% 71.68% 220ms 1.12% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.01% 71.69% 219ms 1.12% std::ostream::operator<< (inline) 0 0% 71.69% 216ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 71.70% 216ms 1.10% alternateaxes 48ms 0.24% 71.95% 215ms 1.10% std::ostream::_M_insert 204ms 1.04% 72.99% 212ms 1.08% vertexmedian 12ms 0.061% 73.05% 209ms 1.07% Element::MarkAsDeleted 4ms 0.02% 73.07% 208ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 73.08% 205ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 51ms 0.26% 73.34% 205ms 1.05% ApcOneHitCellMutationState::ApcOneHitCellMutationState 14ms 0.071% 73.41% 205ms 1.05% std::_Rb_tree::_M_copy (inline) 1ms 0.0051% 73.42% 199ms 1.01% OffLatticeSimulation::ApplyBoundaries 149ms 0.76% 74.18% 196ms 1% AbstractElement::GetNodeGlobalIndex 7ms 0.036% 74.21% 192ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 190ms 0.97% 75.18% 190ms 0.97% std::_Rb_tree_insert_and_rebalance 52ms 0.27% 75.45% 189ms 0.96% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0051% 75.45% 186ms 0.95% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.45% 186ms 0.95% MeshBasedCellPopulation::GetDampingConstant 23ms 0.12% 75.57% 183ms 0.93% AbstractTetrahedralElement::RefreshJacobian 171ms 0.87% 76.44% 171ms 0.87% Node::GetIndex 120ms 0.61% 77.05% 171ms 0.87% malloc_consolidate 3ms 0.015% 77.07% 169ms 0.86% CellProliferativeTypesWriter::VisitCell 8ms 0.041% 77.11% 161ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.076% 77.19% 154ms 0.79% TetrahedralMesh::Clear 153ms 0.78% 77.97% 153ms 0.78% unlink_chunk 4ms 0.02% 77.99% 150ms 0.76% boost::numeric::ublas::vector_assign (inline) 149ms 0.76% 78.75% 149ms 0.76% incircle 96ms 0.49% 79.24% 145ms 0.74% std::_Rb_tree::equal_range (inline) 69ms 0.35% 79.59% 144ms 0.73% AbstractElement::GetNodeLocation 1ms 0.0051% 79.59% 135ms 0.69% NodeLocationWriter::Visit 85ms 0.43% 80.03% 134ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 15ms 0.076% 80.10% 134ms 0.68% boost::detail::shared_count::~shared_count (inline) 0 0% 80.10% 134ms 0.68% boost::shared_ptr::~shared_ptr (inline) 8ms 0.041% 80.14% 132ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.046% 80.19% 129ms 0.66% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 47ms 0.24% 80.43% 128ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 32ms 0.16% 80.59% 128ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 80.59% 127ms 0.65% AbstractCellBasedWriter::WriteDoubleAndSpace (inline) 6ms 0.031% 80.62% 125ms 0.64% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 125ms 0.64% 81.26% 125ms 0.64% std::vector::size (inline) 3ms 0.015% 81.28% 123ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 81.28% 120ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.02% 81.30% 118ms 0.6% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 106ms 0.54% 81.84% 117ms 0.6% vertexsort 114ms 0.58% 82.42% 116ms 0.59% boost::detail::sp_counted_base::release 3ms 0.015% 82.43% 114ms 0.58% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 27ms 0.14% 82.57% 114ms 0.58% std::num_put::_M_insert_int 40ms 0.2% 82.78% 113ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.025% 82.80% 111ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 33ms 0.17% 82.97% 111ms 0.57% boost::numeric::ublas::indexing_vector_assign 41ms 0.21% 83.18% 111ms 0.57% std::__ostream_insert 0 0% 83.18% 108ms 0.55% AbstractCellBasedWriter::WriteDouble (inline) 1ms 0.0051% 83.18% 108ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 104ms 0.53% 83.71% 104ms 0.53% AbstractElement::IsDeleted 5ms 0.025% 83.74% 103ms 0.53% Cell::SetCellProliferativeType 0 0% 83.74% 100ms 0.51% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0051% 83.74% 100ms 0.51% CellPropertyCollection::HasProperty (partial-inline) 0 0% 83.74% 99ms 0.5% OutputFileHandler::OpenOutputFile