File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16674ms, 84.62% of 19704ms total Dropped 773 nodes (cum <= 98.52ms) flat flat% sum% cum cum% 0 0% 0% 19657ms 99.76% __libc_start_call_main 0 0% 0% 19657ms 99.76% __libc_start_main_impl 0 0% 0% 19657ms 99.76% _start 0 0% 0% 19636ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19636ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19636ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19636ms 99.65% main 0 0% 0% 19602ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19602ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19602ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19576ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15162ms 76.95% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 9929ms 50.39% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.025% 9844ms 49.96% Cell::ReadyToDivide 5ms 0.025% 0.051% 9776ms 49.61% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.061% 9618ms 48.81% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.061% 0.12% 9609ms 48.77% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.12% 9594ms 48.69% CellCycleModelOdeHandler::SolveOdeToTime 85ms 0.43% 0.55% 9451ms 47.96% AbstractOneStepIvpOdeSolver::InternalSolve 898ms 4.56% 5.11% 8620ms 43.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 3544ms 17.99% 23.10% 7526ms 38.20% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.10% 5118ms 25.97% MeshBasedCellPopulation::Update 91ms 0.46% 23.56% 4044ms 20.52% AbstractCellProperty::IsType (inline) 4ms 0.02% 23.58% 3951ms 20.05% Cylindrical2dMesh::ReMesh 508ms 2.58% 26.16% 2817ms 14.30% AbstractCellProperty::IsSame 0 0% 26.16% 2453ms 12.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 432ms 2.19% 28.35% 2309ms 11.72% std::type_info::operator== (inline) 0 0% 28.35% 2121ms 10.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.35% 2099ms 10.65% MutableMesh::ReMesh 7ms 0.036% 28.39% 2059ms 10.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.39% 1957ms 9.93% AbstractCellPopulation::WriteResultsToFiles 818ms 4.15% 32.54% 1879ms 9.54% std::_Rb_tree::_M_lower_bound (inline) 1817ms 9.22% 41.76% 1817ms 9.22% __strcmp_avx2 162ms 0.82% 42.58% 1705ms 8.65% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.33% 42.92% 1438ms 7.30% std::_Rb_tree::find (inline) 2ms 0.01% 42.93% 1135ms 5.76% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 42.95% 1121ms 5.69% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 56ms 0.28% 43.23% 1099ms 5.58% operator new 18ms 0.091% 43.32% 1077ms 5.47% TetrahedralMesh::ImportFromMesher 241ms 1.22% 44.54% 1031ms 5.23% __GI___libc_malloc 8ms 0.041% 44.58% 999ms 5.07% std::set::insert (inline) 9ms 0.046% 44.63% 996ms 5.05% MeshBasedCellPopulation::SpringIterator::operator++ 19ms 0.096% 44.73% 991ms 5.03% std::_Rb_tree::_M_insert_unique 34ms 0.17% 44.90% 959ms 4.87% std::__new_allocator::allocate (inline) 0 0% 44.90% 950ms 4.82% std::allocator_traits::allocate (inline) 0 0% 44.90% 868ms 4.41% std::set::count (inline) 1ms 0.0051% 44.90% 794ms 4.03% triangulate 4ms 0.02% 44.92% 726ms 3.68% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.92% 711ms 3.61% delaunay 2ms 0.01% 44.94% 711ms 3.61% divconqdelaunay 402ms 2.04% 46.98% 702ms 3.56% _int_malloc 51ms 0.26% 47.23% 670ms 3.40% std::map::operator[] (partial-inline) 6ms 0.03% 47.26% 668ms 3.39% CellPopulationElementWriter::Visit 662ms 3.36% 50.62% 662ms 3.36% std::_Rb_tree::_S_right (inline) 0 0% 50.62% 651ms 3.30% AbstractTwoBodyInteractionForce::AddForceContribution 22ms 0.11% 50.74% 649ms 3.29% std::less::operator() (inline) 30ms 0.15% 50.89% 631ms 3.20% std::_Rb_tree::_M_insert_ (inline) 627ms 3.18% 54.07% 627ms 3.18% std::operator< (inline) 0 0% 54.07% 626ms 3.18% std::_Rb_tree::_M_create_node (inline) 602ms 3.06% 57.13% 617ms 3.13% WntCellCycleOdeSystem::CalculateStoppingEvent 175ms 0.89% 58.01% 602ms 3.06% __dynamic_cast 0 0% 58.01% 589ms 2.99% std::_Rb_tree::_M_get_node (inline) 1ms 0.0051% 58.02% 572ms 2.90% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.02% 570ms 2.89% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.02% 562ms 2.85% std::map::find (inline) 22ms 0.11% 58.13% 560ms 2.84% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.015% 58.15% 553ms 2.81% CellPropertyCollection::GetPropertiesType (inline) 25ms 0.13% 58.27% 543ms 2.76% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 2ms 0.01% 58.28% 542ms 2.75% Element::Element 12ms 0.061% 58.34% 534ms 2.71% MutableMesh::ReIndex 0 0% 58.34% 529ms 2.68% std::_Rb_tree::lower_bound (inline) 0 0% 58.34% 529ms 2.68% std::map::lower_bound (inline) 15ms 0.076% 58.42% 511ms 2.59% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.066% 58.49% 510ms 2.59% Element::RegisterWithNodes (inline) 14ms 0.071% 58.56% 494ms 2.51% Node::AddElement 65ms 0.33% 58.89% 491ms 2.49% std::ostream::_M_insert 0 0% 58.89% 491ms 2.49% std::ostream::operator<< (inline) 12ms 0.061% 58.95% 481ms 2.44% Cylindrical2dMesh::ReconstructCylindricalMesh 318ms 1.61% 60.56% 465ms 2.36% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 60.58% 448ms 2.27% AbstractCellProperty::IsSubType (inline) 150ms 0.76% 61.34% 423ms 2.15% __GI___libc_free 8ms 0.041% 61.38% 378ms 1.92% std::_Rb_tree::erase 0 0% 61.38% 378ms 1.92% std::set::erase (inline) 15ms 0.076% 61.45% 377ms 1.91% Node::RemoveElement 24ms 0.12% 61.58% 372ms 1.89% Element::ResetIndex 364ms 1.85% 63.42% 364ms 1.85% std::type_info::name (inline) 2ms 0.01% 63.43% 363ms 1.84% std::_Vector_base::_M_allocate (inline) 111ms 0.56% 64.00% 362ms 1.84% std::_Rb_tree::_M_erase 12ms 0.061% 64.06% 357ms 1.81% std::__new_allocator::deallocate (inline) 0 0% 64.06% 353ms 1.79% std::allocator_traits::deallocate (inline) 9ms 0.046% 64.10% 344ms 1.75% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 138ms 0.7% 64.80% 342ms 1.74% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 64.80% 337ms 1.71% std::_Rb_tree::_M_drop_node (inline) 25ms 0.13% 64.93% 330ms 1.67% std::_Rb_tree::~_Rb_tree (inline) 11ms 0.056% 64.99% 321ms 1.63% divconqrecurse 3ms 0.015% 65.00% 315ms 1.60% Cell::GetCellProliferativeType 3ms 0.015% 65.02% 315ms 1.60% NodeLocationWriter::Visit 126ms 0.64% 65.66% 310ms 1.57% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0051% 65.66% 304ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 87ms 0.44% 66.10% 303ms 1.54% mergehulls 0 0% 66.10% 300ms 1.52% std::set::~set (inline) 8ms 0.041% 66.14% 299ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 66.15% 296ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 29ms 0.15% 66.30% 293ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.30% 293ms 1.49% std::_Rb_tree::_M_put_node (inline) 22ms 0.11% 66.41% 280ms 1.42% std::_Rb_tree::_Rb_tree (partial-inline) 13ms 0.066% 66.48% 275ms 1.40% std::num_put::_M_insert_float 223ms 1.13% 67.61% 273ms 1.39% _int_free 1ms 0.0051% 67.62% 272ms 1.38% Cell::GetMutationState 16ms 0.081% 67.70% 265ms 1.34% std::vector::push_back (inline) 5ms 0.025% 67.72% 257ms 1.30% alternateaxes 2ms 0.01% 67.73% 254ms 1.29% std::set::set (inline) 8ms 0.041% 67.77% 253ms 1.28% AbstractTetrahedralElement::CalculateJacobian 238ms 1.21% 68.98% 251ms 1.27% vertexmedian 13ms 0.066% 69.05% 243ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 241ms 1.22% 70.27% 242ms 1.23% std::vector::operator[] (inline) 24ms 0.12% 70.39% 239ms 1.21% std::vector::_M_realloc_insert 51ms 0.26% 70.65% 232ms 1.18% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 4ms 0.02% 70.67% 230ms 1.17% std::__cxx11::collate::do_transform 9ms 0.046% 70.72% 229ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.046% 70.76% 228ms 1.16% std::_Rb_tree::_M_erase_aux (inline) 28ms 0.14% 70.90% 226ms 1.15% std::_Rb_tree::_M_copy (inline) 53ms 0.27% 71.17% 223ms 1.13% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 71.19% 221ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 71.20% 220ms 1.12% ___vsnprintf 0 0% 71.20% 218ms 1.11% __vsnprintf_internal (inline) 25ms 0.13% 71.33% 215ms 1.09% __printf_buffer 2ms 0.01% 71.34% 208ms 1.06% TetrahedralMesh::RefreshJacobianCachedData 0 0% 71.34% 202ms 1.03% OffLatticeSimulation::ApplyBoundaries 20ms 0.1% 71.44% 199ms 1.01% AbstractTetrahedralElement::RefreshJacobian 45ms 0.23% 71.67% 198ms 1.00% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 197ms 1% 72.67% 197ms 1% [libchaste_cell_based.so] 152ms 0.77% 73.44% 195ms 0.99% AbstractElement::GetNodeGlobalIndex 62ms 0.31% 73.76% 195ms 0.99% std::_Rb_tree::_M_clone_node (inline) 12ms 0.061% 73.82% 187ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0051% 73.82% 186ms 0.94% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 73.83% 185ms 0.94% AbstractCentreBasedCellPopulation::GetDampingConstant 181ms 0.92% 74.75% 181ms 0.92% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 74.78% 174ms 0.88% Element::MarkAsDeleted 134ms 0.68% 75.46% 173ms 0.88% malloc_consolidate 170ms 0.86% 76.32% 170ms 0.86% Node::GetIndex 6ms 0.03% 76.35% 168ms 0.85% __printf_fp_l_buffer 0 0% 76.35% 168ms 0.85% __printf_fp_spec (inline) 5ms 0.025% 76.38% 165ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 19ms 0.096% 76.47% 165ms 0.84% TetrahedralMesh::Clear 58ms 0.29% 76.77% 159ms 0.81% AbstractElement::GetNodeLocation 5ms 0.025% 76.79% 156ms 0.79% CellPropertyCollection::HasProperty 75ms 0.38% 77.17% 153ms 0.78% __printf_fp_buffer_1 1ms 0.0051% 77.18% 152ms 0.77% CellProliferativeTypesWriter::VisitCell 0 0% 77.18% 150ms 0.76% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 95ms 0.48% 77.66% 149ms 0.76% std::_Rb_tree::equal_range (inline) 0 0% 77.66% 147ms 0.75% Cell::HasCellProperty (inline) 3ms 0.015% 77.67% 146ms 0.74% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 144ms 0.73% 78.41% 144ms 0.73% incircle 4ms 0.02% 78.43% 137ms 0.7% boost::numeric::ublas::vector_assign (inline) 1ms 0.0051% 78.43% 136ms 0.69% Cell::SetCellProliferativeType 134ms 0.68% 79.11% 134ms 0.68% unlink_chunk 39ms 0.2% 79.31% 130ms 0.66% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 79.31% 127ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 126ms 0.64% 79.95% 126ms 0.64% AbstractCellProperty::~AbstractCellProperty 0 0% 79.95% 126ms 0.64% OutputFileHandler::OpenOutputFile 124ms 0.63% 80.58% 124ms 0.63% AbstractCellMutationState::~AbstractCellMutationState 39ms 0.2% 80.78% 123ms 0.62% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 37ms 0.19% 80.96% 122ms 0.62% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 4ms 0.02% 80.98% 119ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 10ms 0.051% 81.03% 118ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.036% 81.07% 117ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 81.07% 117ms 0.59% boost::shared_ptr::~shared_ptr (inline) 29ms 0.15% 81.22% 116ms 0.59% TetrahedralMesh::EdgesEnd 107ms 0.54% 81.76% 116ms 0.59% vertexsort 4ms 0.02% 81.78% 114ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 114ms 0.58% 82.36% 114ms 0.58% std::vector::size (inline) 3ms 0.015% 82.37% 113ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 82.37% 112ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 82.37% 111ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0051% 82.38% 110ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 29ms 0.15% 82.53% 109ms 0.55% std::num_put::_M_insert_int 107ms 0.54% 83.07% 107ms 0.54% boost::detail::sp_counted_base::release 60ms 0.3% 83.37% 102ms 0.52% Cylindrical2dMesh::GetVectorFromAtoB 102ms 0.52% 83.89% 102ms 0.52% std::_Rb_tree_rebalance_for_erase 101ms 0.51% 84.40% 101ms 0.51% [libchaste_mesh.so] 43ms 0.22% 84.62% 101ms 0.51% std::__ostream_insert