File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16841ms, 85.12% of 19786ms total Dropped 730 nodes (cum <= 98.93ms) flat flat% sum% cum cum% 0 0% 0% 19742ms 99.78% __libc_start_call_main 0 0% 0% 19742ms 99.78% __libc_start_main_impl 0 0% 0% 19742ms 99.78% _start 0 0% 0% 19723ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19723ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19723ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19723ms 99.68% main 0 0% 0% 19686ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19686ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19686ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19660ms 99.36% AbstractCellBasedSimulation::Solve 2ms 0.01% 0.01% 15267ms 77.16% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.025% 10099ms 51.04% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0051% 0.03% 10015ms 50.62% Cell::ReadyToDivide 3ms 0.015% 0.045% 9954ms 50.31% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.056% 9818ms 49.62% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.066% 0.12% 9812ms 49.59% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.14% 9795ms 49.50% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.34% 0.48% 9631ms 48.68% AbstractOneStepIvpOdeSolver::InternalSolve 887ms 4.48% 4.96% 8840ms 44.68% RungeKutta4IvpOdeSolver::CalculateNextYValue 3672ms 18.56% 23.52% 7726ms 39.05% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 23.52% 5058ms 25.56% MeshBasedCellPopulation::Update 153ms 0.77% 24.29% 4104ms 20.74% AbstractCellProperty::IsType (inline) 6ms 0.03% 24.33% 3889ms 19.66% Cylindrical2dMesh::ReMesh 516ms 2.61% 26.93% 2828ms 14.29% AbstractCellProperty::IsSame 2ms 0.01% 26.94% 2445ms 12.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 396ms 2.00% 28.94% 2312ms 11.69% std::type_info::operator== (inline) 1ms 0.0051% 28.95% 2129ms 10.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.95% 2099ms 10.61% MutableMesh::ReMesh 6ms 0.03% 28.98% 2088ms 10.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.98% 1942ms 9.82% AbstractCellPopulation::WriteResultsToFiles 795ms 4.02% 33.00% 1866ms 9.43% std::_Rb_tree::_M_lower_bound (inline) 1845ms 9.32% 42.32% 1845ms 9.32% __strcmp_avx2 131ms 0.66% 42.98% 1670ms 8.44% TetrahedralMesh::EdgeIterator::operator++ 78ms 0.39% 43.38% 1417ms 7.16% std::_Rb_tree::find (inline) 1ms 0.0051% 43.38% 1130ms 5.71% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 43.41% 1114ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 24ms 0.12% 43.54% 1060ms 5.36% TetrahedralMesh::ImportFromMesher 50ms 0.25% 43.79% 1026ms 5.19% operator new 2ms 0.01% 43.80% 1016ms 5.13% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.061% 43.86% 1009ms 5.10% std::set::insert (inline) 13ms 0.066% 43.92% 997ms 5.04% std::_Rb_tree::_M_insert_unique 219ms 1.11% 45.03% 970ms 4.90% __GI___libc_malloc 34ms 0.17% 45.20% 896ms 4.53% std::__new_allocator::allocate (inline) 0 0% 45.20% 891ms 4.50% std::allocator_traits::allocate (inline) 0 0% 45.20% 863ms 4.36% std::set::count (inline) 1ms 0.0051% 45.21% 798ms 4.03% triangulate 0 0% 45.21% 725ms 3.66% delaunay 2ms 0.01% 45.22% 724ms 3.66% divconqdelaunay 2ms 0.01% 45.23% 713ms 3.60% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 694ms 3.51% 48.74% 694ms 3.51% std::_Rb_tree::_S_right (inline) 64ms 0.32% 49.06% 693ms 3.50% std::map::operator[] (partial-inline) 1ms 0.0051% 49.06% 686ms 3.47% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.025% 49.09% 675ms 3.41% CellPopulationElementWriter::Visit 386ms 1.95% 51.04% 674ms 3.41% _int_malloc 25ms 0.13% 51.17% 666ms 3.37% std::less::operator() (inline) 641ms 3.24% 54.41% 641ms 3.24% std::operator< (inline) 27ms 0.14% 54.54% 615ms 3.11% std::_Rb_tree::_M_insert_ (inline) 0 0% 54.54% 602ms 3.04% std::_Rb_tree::_M_create_node (inline) 585ms 2.96% 57.50% 597ms 3.02% WntCellCycleOdeSystem::CalculateStoppingEvent 177ms 0.89% 58.39% 580ms 2.93% __dynamic_cast 29ms 0.15% 58.54% 578ms 2.92% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 16ms 0.081% 58.62% 571ms 2.89% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.62% 569ms 2.88% std::_Rb_tree::_M_get_node (inline) 2ms 0.01% 58.63% 565ms 2.86% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.02% 58.65% 554ms 2.80% Element::Element 0 0% 58.65% 553ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.65% 552ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 58.65% 552ms 2.79% std::map::find (inline) 0 0% 58.65% 552ms 2.79% std::map::lower_bound (inline) 7ms 0.035% 58.69% 535ms 2.70% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.04% 58.73% 535ms 2.70% MutableMesh::ReIndex 2ms 0.01% 58.74% 527ms 2.66% std::ostream::operator<< (inline) 79ms 0.4% 59.14% 524ms 2.65% std::ostream::_M_insert 9ms 0.045% 59.18% 500ms 2.53% Cylindrical2dMesh::ReconstructCylindricalMesh 338ms 1.71% 60.89% 496ms 2.51% AbstractCellMutationState::AbstractCellMutationState 4ms 0.02% 60.91% 493ms 2.49% Element::RegisterWithNodes (inline) 8ms 0.04% 60.95% 482ms 2.44% Node::AddElement 12ms 0.061% 61.01% 477ms 2.41% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.01% 435ms 2.20% AbstractCellProperty::IsSubType (inline) 144ms 0.73% 61.74% 399ms 2.02% __GI___libc_free 5ms 0.025% 61.77% 394ms 1.99% std::_Rb_tree::erase 0 0% 61.77% 394ms 1.99% std::set::erase (inline) 10ms 0.051% 61.82% 390ms 1.97% Node::RemoveElement 132ms 0.67% 62.48% 369ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.071% 62.55% 362ms 1.83% divconqrecurse 18ms 0.091% 62.65% 354ms 1.79% Element::ResetIndex 13ms 0.066% 62.71% 342ms 1.73% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 94ms 0.48% 63.19% 341ms 1.72% std::_Rb_tree::_M_erase 102ms 0.52% 63.70% 339ms 1.71% mergehulls 9ms 0.045% 63.75% 327ms 1.65% std::__new_allocator::deallocate (inline) 4ms 0.02% 63.77% 326ms 1.65% std::_Vector_base::_M_allocate (inline) 1ms 0.0051% 63.77% 325ms 1.64% NodeLocationWriter::Visit 0 0% 63.77% 323ms 1.63% std::allocator_traits::deallocate (inline) 26ms 0.13% 63.90% 319ms 1.61% std::_Rb_tree::~_Rb_tree (inline) 0 0% 63.90% 313ms 1.58% std::_Rb_tree::_M_drop_node (inline) 311ms 1.57% 65.48% 311ms 1.57% std::type_info::name (inline) 10ms 0.051% 65.53% 306ms 1.55% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 65.54% 306ms 1.55% Cell::GetMutationState 0 0% 65.54% 297ms 1.50% std::set::~set (inline) 14ms 0.071% 65.61% 296ms 1.50% std::num_put::_M_insert_float 135ms 0.68% 66.29% 286ms 1.45% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 66.30% 283ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 66.31% 282ms 1.43% LegacyCellProliferativeTypesWriter::VisitCell 32ms 0.16% 66.48% 281ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 20ms 0.1% 66.58% 271ms 1.37% AbstractTetrahedralElement::CalculateJacobian 266ms 1.34% 67.92% 267ms 1.35% std::vector::operator[] (inline) 5ms 0.025% 67.95% 265ms 1.34% Cell::GetCellProliferativeType 0 0% 67.95% 262ms 1.32% std::_Rb_tree::_M_put_node (inline) 9ms 0.045% 67.99% 259ms 1.31% std::vector::push_back (inline) 209ms 1.06% 69.05% 254ms 1.28% _int_free 5ms 0.025% 69.07% 253ms 1.28% std::_Rb_tree::_Rb_tree (partial-inline) 252ms 1.27% 70.35% 252ms 1.27% [libchaste_cell_based.so] 11ms 0.056% 70.40% 245ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.071% 70.47% 243ms 1.23% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.03% 70.50% 240ms 1.21% std::__cxx11::collate::do_transform 22ms 0.11% 70.62% 240ms 1.21% std::vector::_M_realloc_insert 48ms 0.24% 70.86% 239ms 1.21% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.025% 70.88% 237ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 55ms 0.28% 71.16% 234ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 71.16% 230ms 1.16% ___vsnprintf 0 0% 71.16% 230ms 1.16% __vsnprintf_internal (inline) 28ms 0.14% 71.30% 228ms 1.15% __printf_buffer 2ms 0.01% 71.31% 226ms 1.14% std::set::set (inline) 21ms 0.11% 71.42% 222ms 1.12% std::_Rb_tree::_M_copy (inline) 1ms 0.0051% 71.42% 218ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 71.44% 216ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 71.46% 215ms 1.09% alternateaxes 197ms 1% 72.46% 210ms 1.06% vertexmedian 26ms 0.13% 72.59% 208ms 1.05% AbstractTetrahedralElement::RefreshJacobian 9ms 0.045% 72.63% 200ms 1.01% Element::MarkAsDeleted 0 0% 72.63% 199ms 1.01% OffLatticeSimulation::ApplyBoundaries 63ms 0.32% 72.95% 199ms 1.01% std::_Rb_tree::_M_clone_node (inline) 2ms 0.01% 72.96% 197ms 1% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 72.97% 195ms 0.99% AbstractCentreBasedCellPopulation::GetDampingConstant 72ms 0.36% 73.33% 192ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 139ms 0.7% 74.04% 185ms 0.94% AbstractElement::GetNodeGlobalIndex 1ms 0.0051% 74.04% 184ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0051% 74.05% 183ms 0.92% __printf_fp_spec (inline) 8ms 0.04% 74.09% 182ms 0.92% __printf_fp_l_buffer 182ms 0.92% 75.01% 182ms 0.92% std::_Rb_tree_insert_and_rebalance 12ms 0.061% 75.07% 178ms 0.9% AbstractTetrahedralElement::CalculateInverseJacobian 176ms 0.89% 75.96% 176ms 0.89% Node::GetIndex 125ms 0.63% 76.59% 171ms 0.86% malloc_consolidate 74ms 0.37% 76.96% 170ms 0.86% __printf_fp_buffer_1 19ms 0.096% 77.06% 164ms 0.83% TetrahedralMesh::Clear 74ms 0.37% 77.43% 163ms 0.82% AbstractElement::GetNodeLocation 3ms 0.015% 77.45% 160ms 0.81% boost::numeric::ublas::vector_assign (inline) 100ms 0.51% 77.95% 155ms 0.78% std::_Rb_tree::equal_range (inline) 4ms 0.02% 77.97% 150ms 0.76% CellProliferativeTypesWriter::VisitCell 39ms 0.2% 78.17% 146ms 0.74% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 144ms 0.73% 78.90% 144ms 0.73% incircle 7ms 0.035% 78.93% 143ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.0051% 78.94% 141ms 0.71% CellPropertyCollection::HasProperty 6ms 0.03% 78.97% 141ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 78.97% 139ms 0.7% Cell::HasCellProperty (inline) 129ms 0.65% 79.62% 139ms 0.7% vertexsort 14ms 0.071% 79.69% 138ms 0.7% boost::detail::shared_count::~shared_count (inline) 0 0% 79.69% 138ms 0.7% boost::shared_ptr::~shared_ptr (inline) 10ms 0.051% 79.74% 136ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 136ms 0.69% 80.43% 136ms 0.69% std::vector::size (inline) 136ms 0.69% 81.12% 136ms 0.69% unlink_chunk 39ms 0.2% 81.32% 135ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 12ms 0.061% 81.38% 134ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.03% 81.41% 131ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.01% 81.42% 130ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 74ms 0.37% 81.79% 129ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 35ms 0.18% 81.97% 127ms 0.64% boost::numeric::ublas::indexing_vector_assign 122ms 0.62% 82.58% 122ms 0.62% boost::detail::sp_counted_base::release 116ms 0.59% 83.17% 116ms 0.59% AbstractCellProperty::~AbstractCellProperty 112ms 0.57% 83.74% 112ms 0.57% AbstractCellMutationState::~AbstractCellMutationState 0 0% 83.74% 112ms 0.57% Cell::SetCellProliferativeType 31ms 0.16% 83.89% 112ms 0.57% TetrahedralMesh::EdgesEnd 4ms 0.02% 83.91% 111ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 83.91% 107ms 0.54% AbstractCellBasedWriter::OpenOutputFileForAppend 24ms 0.12% 84.03% 107ms 0.54% std::num_put::_M_insert_int 0 0% 84.03% 106ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 84.04% 106ms 0.54% CellLocationIndexWriter::VisitCell 0 0% 84.04% 106ms 0.54% OutputFileHandler::OpenOutputFile 0 0% 84.04% 102ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 102ms 0.52% 84.56% 102ms 0.52% std::_Rb_tree_rebalance_for_erase 11ms 0.056% 84.62% 99ms 0.5% std::_Rb_tree_const_iterator::operator++ (inline) 99ms 0.5% 85.12% 99ms 0.5% std::_Rb_tree_increment