File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16874ms, 85.13% of 19821ms total Dropped 782 nodes (cum <= 99.11ms) flat flat% sum% cum cum% 0 0% 0% 19771ms 99.75% __libc_start_call_main 0 0% 0% 19771ms 99.75% __libc_start_main_impl 0 0% 0% 19771ms 99.75% _start 0 0% 0% 19748ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19748ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19748ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19748ms 99.63% main 0 0% 0% 19709ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19709ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19709ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19683ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 15046ms 75.91% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9512ms 47.99% AbstractCellBasedSimulation::DoCellBirth 16ms 0.081% 0.081% 9398ms 47.41% Cell::ReadyToDivide 5ms 0.025% 0.11% 9281ms 46.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.11% 9143ms 46.13% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.05% 0.16% 9138ms 46.10% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.18% 9127ms 46.05% CellCycleModelOdeHandler::SolveOdeToTime 71ms 0.36% 0.53% 8958ms 45.19% AbstractOneStepIvpOdeSolver::InternalSolve 986ms 4.97% 5.51% 8075ms 40.74% RungeKutta4IvpOdeSolver::CalculateNextYValue 2666ms 13.45% 18.96% 6904ms 34.83% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 18.96% 5414ms 27.31% MeshBasedCellPopulation::Update 47ms 0.24% 19.20% 4258ms 21.48% AbstractCellProperty::IsType (inline) 7ms 0.035% 19.23% 4214ms 21.26% Cylindrical2dMesh::ReMesh 374ms 1.89% 21.12% 2908ms 14.67% AbstractCellProperty::IsSame 0 0% 21.12% 2549ms 12.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 405ms 2.04% 23.16% 2534ms 12.78% std::type_info::operator== (inline) 1ms 0.005% 23.17% 2289ms 11.55% MutableMesh::ReMesh 0 0% 23.17% 2228ms 11.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.055% 23.22% 2178ms 10.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 2091ms 10.55% 33.77% 2091ms 10.55% __strcmp_avx2 1ms 0.005% 33.78% 2083ms 10.51% AbstractCellPopulation::WriteResultsToFiles 856ms 4.32% 38.10% 1817ms 9.17% std::_Rb_tree::_M_lower_bound (inline) 206ms 1.04% 39.14% 1680ms 8.48% TetrahedralMesh::EdgeIterator::operator++ 97ms 0.49% 39.62% 1380ms 6.96% std::_Rb_tree::find (inline) 2ms 0.01% 39.63% 1158ms 5.84% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 39.66% 1155ms 5.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.076% 39.74% 1145ms 5.78% TetrahedralMesh::ImportFromMesher 49ms 0.25% 39.98% 1067ms 5.38% operator new 6ms 0.03% 40.01% 1032ms 5.21% MeshBasedCellPopulation::SpringIterator::operator++ 225ms 1.14% 41.15% 1008ms 5.09% __GI___libc_malloc 53ms 0.27% 41.42% 942ms 4.75% std::__new_allocator::allocate (inline) 10ms 0.05% 41.47% 937ms 4.73% std::set::insert (inline) 0 0% 41.47% 933ms 4.71% std::allocator_traits::allocate (inline) 15ms 0.076% 41.54% 927ms 4.68% std::_Rb_tree::_M_insert_unique 1ms 0.005% 41.55% 873ms 4.40% triangulate 0 0% 41.55% 824ms 4.16% std::set::count (inline) 6ms 0.03% 41.58% 800ms 4.04% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.005% 41.58% 787ms 3.97% delaunay 2ms 0.01% 41.59% 784ms 3.96% divconqdelaunay 64ms 0.32% 41.92% 728ms 3.67% std::map::operator[] (partial-inline) 8ms 0.04% 41.96% 716ms 3.61% CellPopulationElementWriter::Visit 388ms 1.96% 43.91% 701ms 3.54% _int_malloc 2ms 0.01% 43.92% 699ms 3.53% AbstractTwoBodyInteractionForce::AddForceContribution 699ms 3.53% 47.45% 699ms 3.53% WntCellCycleOdeSystem::CalculateStoppingEvent 206ms 1.04% 48.49% 662ms 3.34% __dynamic_cast 655ms 3.30% 51.79% 655ms 3.30% std::_Rb_tree::_S_right (inline) 5ms 0.025% 51.82% 654ms 3.30% MeshBasedCellPopulation::AcceptCellWriter 33ms 0.17% 51.99% 618ms 3.12% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 51.99% 617ms 3.11% std::_Rb_tree::_M_create_node (inline) 6ms 0.03% 52.02% 611ms 3.08% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.05% 52.07% 584ms 2.95% std::less::operator() (inline) 14ms 0.071% 52.14% 581ms 2.93% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.14% 575ms 2.90% std::_Rb_tree::_M_get_node (inline) 574ms 2.90% 55.03% 574ms 2.90% std::operator< (inline) 10ms 0.05% 55.08% 555ms 2.80% MutableMesh::ReIndex 32ms 0.16% 55.24% 553ms 2.79% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.24% 553ms 2.79% std::map::find (inline) 0 0% 55.24% 551ms 2.78% std::_Rb_tree::lower_bound (inline) 0 0% 55.24% 551ms 2.78% std::map::lower_bound (inline) 4ms 0.02% 55.26% 546ms 2.75% Element::Element 0 0% 55.26% 541ms 2.73% std::_Rb_tree::_Alloc_node::operator() (inline) 15ms 0.076% 55.34% 521ms 2.63% Cylindrical2dMesh::CorrectNonPeriodicMesh 165ms 0.83% 56.17% 517ms 2.61% __GI___libc_free 1ms 0.005% 56.18% 509ms 2.57% AbstractCellProperty::IsSubType (inline) 0 0% 56.18% 488ms 2.46% std::ostream::operator<< (inline) 90ms 0.45% 56.63% 487ms 2.46% std::ostream::_M_insert 9ms 0.045% 56.68% 483ms 2.44% Element::RegisterWithNodes (inline) 13ms 0.066% 56.74% 472ms 2.38% Cylindrical2dMesh::ReconstructCylindricalMesh 15ms 0.076% 56.82% 467ms 2.36% Node::AddElement 290ms 1.46% 58.28% 436ms 2.20% AbstractCellMutationState::AbstractCellMutationState 116ms 0.59% 58.87% 427ms 2.15% std::_Rb_tree::_M_erase 12ms 0.061% 58.93% 427ms 2.15% std::__new_allocator::deallocate (inline) 0 0% 58.93% 425ms 2.14% std::allocator_traits::deallocate (inline) 0 0% 58.93% 391ms 1.97% std::_Rb_tree::_M_drop_node (inline) 7ms 0.035% 58.96% 389ms 1.96% std::_Rb_tree::erase 2ms 0.01% 58.97% 389ms 1.96% std::set::erase (inline) 7ms 0.035% 59.01% 379ms 1.91% Node::RemoveElement 23ms 0.12% 59.12% 378ms 1.91% std::_Rb_tree::~_Rb_tree (inline) 134ms 0.68% 59.80% 360ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 59.80% 358ms 1.81% std::_Vector_base::_M_allocate (inline) 0 0% 59.80% 356ms 1.80% std::_Rb_tree::_M_put_node (inline) 0 0% 59.80% 354ms 1.79% std::set::~set (inline) 277ms 1.40% 61.20% 348ms 1.76% _int_free 4ms 0.02% 61.22% 346ms 1.75% LegacyCellProliferativeTypesWriter::VisitCell 21ms 0.11% 61.32% 342ms 1.73% Element::ResetIndex 9ms 0.045% 61.37% 342ms 1.73% divconqrecurse 337ms 1.70% 63.07% 337ms 1.70% [libchaste_cell_based.so] 4ms 0.02% 63.09% 329ms 1.66% Cell::GetCellProliferativeType 2ms 0.01% 63.10% 328ms 1.65% Cell::GetMutationState 90ms 0.45% 63.55% 327ms 1.65% mergehulls 327ms 1.65% 65.20% 327ms 1.65% std::type_info::name (inline) 5ms 0.025% 65.23% 320ms 1.61% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.03% 65.26% 311ms 1.57% AbstractCellPopulation::GetLocationIndexUsingCell 141ms 0.71% 65.97% 300ms 1.51% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 65.99% 293ms 1.48% alternateaxes 272ms 1.37% 67.36% 288ms 1.45% vertexmedian 14ms 0.071% 67.43% 286ms 1.44% std::vector::push_back (inline) 1ms 0.005% 67.44% 281ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 40ms 0.2% 67.64% 280ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 276ms 1.39% 69.03% 279ms 1.41% std::vector::operator[] (inline) 0 0% 69.03% 275ms 1.39% NodeLocationWriter::Visit 15ms 0.076% 69.11% 269ms 1.36% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.11% 69.21% 267ms 1.35% std::vector::_M_realloc_insert 12ms 0.061% 69.28% 261ms 1.32% std::_Rb_tree::_M_erase_aux (inline) 99ms 0.5% 69.77% 259ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.035% 69.81% 253ms 1.28% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.071% 69.88% 245ms 1.24% std::num_put::_M_insert_float 2ms 0.01% 69.89% 244ms 1.23% std::set::set (inline) 14ms 0.071% 69.96% 243ms 1.23% AbstractTetrahedralElement::CalculateJacobian 15ms 0.076% 70.04% 242ms 1.22% TetrahedralMesh::Clear 0 0% 70.04% 234ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 14ms 0.071% 70.11% 230ms 1.16% std::_Rb_tree::_M_copy (inline) 88ms 0.44% 70.55% 229ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 8ms 0.04% 70.59% 227ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 70.60% 225ms 1.14% MeshBasedCellPopulation::GetDampingConstant 56ms 0.28% 70.88% 224ms 1.13% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.005% 70.89% 222ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.90% 214ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 63ms 0.32% 71.22% 212ms 1.07% std::_Rb_tree::_M_clone_node (inline) 6ms 0.03% 71.25% 209ms 1.05% std::__cxx11::collate::do_transform 11ms 0.055% 71.30% 207ms 1.04% Element::MarkAsDeleted 3ms 0.015% 71.32% 206ms 1.04% CellPropertyCollection::HasProperty 147ms 0.74% 72.06% 206ms 1.04% malloc_consolidate 146ms 0.74% 72.80% 205ms 1.03% AbstractElement::GetNodeGlobalIndex 0 0% 72.80% 205ms 1.03% Cell::HasCellProperty (inline) 6ms 0.03% 72.83% 199ms 1.00% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 72.84% 198ms 1% ___vsnprintf 0 0% 72.84% 196ms 0.99% __vsnprintf_internal (inline) 31ms 0.16% 72.99% 194ms 0.98% __printf_buffer 22ms 0.11% 73.10% 189ms 0.95% AbstractTetrahedralElement::RefreshJacobian 0 0% 73.10% 189ms 0.95% OffLatticeSimulation::ApplyBoundaries 181ms 0.91% 74.02% 181ms 0.91% [libchaste_crypt.so] 5ms 0.025% 74.04% 180ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 74.05% 177ms 0.89% CellProliferativeTypesWriter::VisitCell 170ms 0.86% 74.91% 170ms 0.86% Node::GetIndex 4ms 0.02% 74.93% 167ms 0.84% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 162ms 0.82% 75.75% 162ms 0.82% std::vector::size (inline) 158ms 0.8% 76.55% 158ms 0.8% unlink_chunk 2ms 0.01% 76.56% 157ms 0.79% __printf_fp_l_buffer 0 0% 76.56% 157ms 0.79% __printf_fp_spec (inline) 60ms 0.3% 76.86% 156ms 0.79% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 64ms 0.32% 77.18% 154ms 0.78% AbstractElement::GetNodeLocation 154ms 0.78% 77.96% 154ms 0.78% incircle 28ms 0.14% 78.10% 153ms 0.77% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.015% 78.11% 152ms 0.77% boost::numeric::ublas::vector_assign (inline) 9ms 0.045% 78.16% 151ms 0.76% Node::~Node 79ms 0.4% 78.56% 148ms 0.75% __printf_fp_buffer_1 145ms 0.73% 79.29% 145ms 0.73% std::_Rb_tree_insert_and_rebalance 1ms 0.005% 79.29% 144ms 0.73% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 79.29% 143ms 0.72% OutputFileHandler::OpenOutputFile 13ms 0.066% 79.36% 140ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 85ms 0.43% 79.79% 137ms 0.69% std::_Rb_tree::equal_range (inline) 45ms 0.23% 80.02% 136ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 129ms 0.65% 80.67% 136ms 0.69% vertexsort 82ms 0.41% 81.08% 133ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.04% 81.12% 133ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.035% 81.16% 132ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.005% 81.16% 129ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 81.16% 125ms 0.63% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 121ms 0.61% 81.77% 121ms 0.61% std::_Rb_tree_increment 34ms 0.17% 81.94% 119ms 0.6% boost::numeric::ublas::indexing_vector_assign 33ms 0.17% 82.11% 118ms 0.6% std::__ostream_insert 0 0% 82.11% 117ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.005% 82.11% 116ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 75ms 0.38% 82.49% 115ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 7ms 0.035% 82.53% 115ms 0.58% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.01% 82.54% 114ms 0.58% Cell::SetCellProliferativeType 13ms 0.066% 82.60% 113ms 0.57% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 5ms 0.025% 82.63% 113ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 108ms 0.54% 83.17% 108ms 0.54% boost::shared_ptr::operator-> (inline) 25ms 0.13% 83.30% 106ms 0.53% std::num_put::_M_insert_int 105ms 0.53% 83.83% 105ms 0.53% AbstractCellProperty::AbstractCellProperty 103ms 0.52% 84.35% 103ms 0.52% std::_Rb_tree_rebalance_for_erase 101ms 0.51% 84.86% 101ms 0.51% AbstractElement::IsDeleted 3ms 0.015% 84.87% 101ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 47ms 0.24% 85.11% 101ms 0.51% boost::shared_ptr::shared_ptr (inline) 4ms 0.02% 85.13% 100ms 0.5% Cylindrical2dMesh::CreateMirrorNodes