File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16711ms, 84.85% of 19694ms total Dropped 808 nodes (cum <= 98.47ms) flat flat% sum% cum cum% 0 0% 0% 19647ms 99.76% __libc_start_call_main 0 0% 0% 19647ms 99.76% __libc_start_main_impl 0 0% 0% 19647ms 99.76% _start 0 0% 0% 19626ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19626ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19626ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19626ms 99.65% main 0 0% 0% 19577ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19577ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19577ms 99.41% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19549ms 99.26% AbstractCellBasedSimulation::Solve 1ms 0.0051% 0.0051% 14941ms 75.87% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 9423ms 47.85% AbstractCellBasedSimulation::DoCellBirth 10ms 0.051% 0.066% 9338ms 47.42% Cell::ReadyToDivide 5ms 0.025% 0.091% 9247ms 46.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.096% 9079ms 46.10% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.051% 0.15% 9070ms 46.05% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.16% 9053ms 45.97% CellCycleModelOdeHandler::SolveOdeToTime 78ms 0.4% 0.55% 8886ms 45.12% AbstractOneStepIvpOdeSolver::InternalSolve 990ms 5.03% 5.58% 7923ms 40.23% RungeKutta4IvpOdeSolver::CalculateNextYValue 2409ms 12.23% 17.81% 6742ms 34.23% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 17.81% 5392ms 27.38% MeshBasedCellPopulation::Update 57ms 0.29% 18.10% 4329ms 21.98% AbstractCellProperty::IsType (inline) 6ms 0.03% 18.13% 4167ms 21.16% Cylindrical2dMesh::ReMesh 333ms 1.69% 19.82% 2949ms 14.97% AbstractCellProperty::IsSame 281ms 1.43% 21.25% 2616ms 13.28% std::type_info::operator== (inline) 1ms 0.0051% 21.26% 2570ms 13.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 2388ms 12.13% 33.38% 2388ms 12.13% __strcmp_avx2 0 0% 33.38% 2259ms 11.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 33.38% 2257ms 11.46% MutableMesh::ReMesh 17ms 0.086% 33.47% 2203ms 11.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 33.47% 2034ms 10.33% AbstractCellPopulation::WriteResultsToFiles 800ms 4.06% 37.53% 1930ms 9.80% std::_Rb_tree::_M_lower_bound (inline) 169ms 0.86% 38.39% 1690ms 8.58% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.3% 38.69% 1413ms 7.17% std::_Rb_tree::find (inline) 2ms 0.01% 38.70% 1187ms 6.03% MeshBasedCellPopulation::UpdateNodePairs 24ms 0.12% 38.82% 1151ms 5.84% TetrahedralMesh::ImportFromMesher 4ms 0.02% 38.84% 1145ms 5.81% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 39ms 0.2% 39.04% 1065ms 5.41% operator new 12ms 0.061% 39.10% 1037ms 5.27% MeshBasedCellPopulation::SpringIterator::operator++ 244ms 1.24% 40.34% 1021ms 5.18% __GI___libc_malloc 13ms 0.066% 40.41% 964ms 4.89% std::set::insert (inline) 7ms 0.036% 40.44% 950ms 4.82% std::_Rb_tree::_M_insert_unique 33ms 0.17% 40.61% 921ms 4.68% std::__new_allocator::allocate (inline) 0 0% 40.61% 918ms 4.66% std::allocator_traits::allocate (inline) 0 0% 40.61% 865ms 4.39% std::set::count (inline) 1ms 0.0051% 40.62% 857ms 4.35% triangulate 0 0% 40.62% 781ms 3.97% delaunay 3ms 0.015% 40.63% 781ms 3.97% divconqdelaunay 57ms 0.29% 40.92% 757ms 3.84% std::map::operator[] (partial-inline) 5ms 0.025% 40.95% 741ms 3.76% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 737ms 3.74% 44.69% 737ms 3.74% std::_Rb_tree::_S_right (inline) 732ms 3.72% 48.41% 732ms 3.72% WntCellCycleOdeSystem::CalculateStoppingEvent 9ms 0.046% 48.45% 711ms 3.61% CellPopulationElementWriter::Visit 3ms 0.015% 48.47% 706ms 3.58% AbstractTwoBodyInteractionForce::AddForceContribution 20ms 0.1% 48.57% 704ms 3.57% std::less::operator() (inline) 684ms 3.47% 52.04% 684ms 3.47% std::operator< (inline) 229ms 1.16% 53.20% 680ms 3.45% __dynamic_cast 376ms 1.91% 55.11% 676ms 3.43% _int_malloc 13ms 0.066% 55.18% 634ms 3.22% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.036% 55.21% 621ms 3.15% CellPropertyCollection::GetPropertiesType (inline) 25ms 0.13% 55.34% 608ms 3.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 55.34% 591ms 3.00% std::_Rb_tree::lower_bound (inline) 0 0% 55.34% 591ms 3.00% std::map::lower_bound (inline) 5ms 0.025% 55.37% 590ms 3.00% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.37% 580ms 2.95% std::_Rb_tree::_M_create_node (inline) 11ms 0.056% 55.42% 578ms 2.93% MutableMesh::ReIndex 30ms 0.15% 55.58% 556ms 2.82% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.58% 553ms 2.81% std::_Rb_tree::_M_get_node (inline) 0 0% 55.58% 540ms 2.74% std::map::find (inline) 9ms 0.046% 55.62% 538ms 2.73% Element::Element 13ms 0.066% 55.69% 522ms 2.65% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 55.69% 512ms 2.60% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0051% 55.69% 509ms 2.58% AbstractCellProperty::IsSubType (inline) 150ms 0.76% 56.45% 498ms 2.53% __GI___libc_free 12ms 0.061% 56.51% 484ms 2.46% Element::RegisterWithNodes (inline) 7ms 0.036% 56.55% 467ms 2.37% Node::AddElement 1ms 0.0051% 56.56% 462ms 2.35% std::ostream::operator<< (inline) 57ms 0.29% 56.84% 461ms 2.34% std::ostream::_M_insert 304ms 1.54% 58.39% 445ms 2.26% AbstractCellMutationState::AbstractCellMutationState 11ms 0.056% 58.44% 444ms 2.25% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.061% 58.51% 410ms 2.08% std::__new_allocator::deallocate (inline) 113ms 0.57% 59.08% 408ms 2.07% std::_Rb_tree::_M_erase 0 0% 59.08% 407ms 2.07% std::allocator_traits::deallocate (inline) 39ms 0.2% 59.28% 403ms 2.05% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.036% 59.31% 395ms 2.01% std::_Rb_tree::erase 1ms 0.0051% 59.32% 393ms 2.00% std::set::erase (inline) 11ms 0.056% 59.37% 389ms 1.98% Node::RemoveElement 136ms 0.69% 60.06% 388ms 1.97% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 60.06% 387ms 1.97% std::set::~set (inline) 0 0% 60.06% 370ms 1.88% std::_Rb_tree::_M_drop_node (inline) 25ms 0.13% 60.19% 367ms 1.86% Element::ResetIndex 19ms 0.096% 60.29% 367ms 1.86% divconqrecurse 1ms 0.0051% 60.29% 366ms 1.86% std::_Vector_base::_M_allocate (inline) 279ms 1.42% 61.71% 346ms 1.76% _int_free 3ms 0.015% 61.72% 344ms 1.75% Cell::GetCellProliferativeType 4ms 0.02% 61.74% 339ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 335ms 1.70% 63.45% 335ms 1.70% [libchaste_cell_based.so] 97ms 0.49% 63.94% 334ms 1.70% mergehulls 0 0% 63.94% 332ms 1.69% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 63.96% 330ms 1.68% Cell::GetMutationState 157ms 0.8% 64.76% 318ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 64.77% 311ms 1.58% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 64.77% 304ms 1.54% NodeLocationWriter::Visit 0 0% 64.77% 296ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 289ms 1.47% 66.24% 293ms 1.49% std::vector::operator[] (inline) 17ms 0.086% 66.32% 290ms 1.47% std::vector::push_back (inline) 39ms 0.2% 66.52% 288ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 66.54% 281ms 1.43% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 66.55% 278ms 1.41% alternateaxes 16ms 0.081% 66.63% 278ms 1.41% std::_Rb_tree::_Rb_tree 259ms 1.32% 67.94% 274ms 1.39% vertexmedian 3ms 0.015% 67.96% 269ms 1.37% std::set::set (inline) 20ms 0.1% 68.06% 265ms 1.35% std::vector::_M_realloc_insert 8ms 0.041% 68.10% 263ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.051% 68.15% 256ms 1.30% std::num_put::_M_insert_float 64ms 0.32% 68.48% 255ms 1.29% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.01% 68.49% 249ms 1.26% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 68.50% 247ms 1.25% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.046% 68.55% 243ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 14ms 0.071% 68.62% 242ms 1.23% AbstractTetrahedralElement::CalculateJacobian 11ms 0.056% 68.68% 234ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 96ms 0.49% 69.16% 233ms 1.18% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 13ms 0.066% 69.23% 231ms 1.17% TetrahedralMesh::Clear 79ms 0.4% 69.63% 230ms 1.17% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 18ms 0.091% 69.72% 228ms 1.16% std::_Rb_tree::_M_copy (inline) 1ms 0.0051% 69.73% 222ms 1.13% OffLatticeSimulation::ApplyBoundaries 4ms 0.02% 69.75% 220ms 1.12% std::__cxx11::collate::do_transform 0 0% 69.75% 217ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 69.75% 214ms 1.09% ___vsnprintf 0 0% 69.75% 214ms 1.09% __vsnprintf_internal (inline) 29ms 0.15% 69.89% 213ms 1.08% __printf_buffer 0 0% 69.89% 210ms 1.07% TetrahedralMesh::RefreshJacobianCachedData 205ms 1.04% 70.94% 205ms 1.04% std::type_info::name (inline) 76ms 0.39% 71.32% 204ms 1.04% std::_Rb_tree::_M_clone_node (inline) 149ms 0.76% 72.08% 200ms 1.02% malloc_consolidate 153ms 0.78% 72.85% 197ms 1.00% AbstractElement::GetNodeGlobalIndex 4ms 0.02% 72.87% 194ms 0.99% CellProliferativeTypesWriter::VisitCell 14ms 0.071% 72.95% 192ms 0.97% Element::MarkAsDeleted 9ms 0.046% 72.99% 187ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 27ms 0.14% 73.13% 183ms 0.93% AbstractTetrahedralElement::RefreshJacobian 2ms 0.01% 73.14% 172ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.02% 73.16% 172ms 0.87% __printf_fp_l_buffer 0 0% 73.16% 172ms 0.87% __printf_fp_spec (inline) 2ms 0.01% 73.17% 171ms 0.87% CellPropertyCollection::HasProperty 0 0% 73.17% 167ms 0.85% Cell::HasCellProperty (inline) 7ms 0.036% 73.21% 164ms 0.83% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 79ms 0.4% 73.61% 164ms 0.83% __printf_fp_buffer_1 161ms 0.82% 74.42% 161ms 0.82% Node::GetIndex 102ms 0.52% 74.94% 161ms 0.82% std::_Rb_tree::equal_range (inline) 157ms 0.8% 75.74% 157ms 0.8% std::_Rb_tree_insert_and_rebalance 4ms 0.02% 75.76% 154ms 0.78% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 151ms 0.77% 76.53% 151ms 0.77% incircle 49ms 0.25% 76.77% 150ms 0.76% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 56ms 0.28% 77.06% 149ms 0.76% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 145ms 0.74% 77.80% 145ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 11ms 0.056% 77.85% 145ms 0.74% Node::~Node 144ms 0.73% 78.58% 144ms 0.73% [libchaste_crypt.so] 1ms 0.0051% 78.59% 143ms 0.73% boost::numeric::ublas::vector_assign (inline) 61ms 0.31% 78.90% 140ms 0.71% AbstractElement::GetNodeLocation 4ms 0.02% 78.92% 139ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 33ms 0.17% 79.09% 136ms 0.69% TetrahedralMesh::EdgesEnd (partial-inline) 134ms 0.68% 79.77% 134ms 0.68% unlink_chunk 13ms 0.066% 79.83% 132ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 44ms 0.22% 80.05% 131ms 0.67% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 130ms 0.66% 80.71% 130ms 0.66% std::vector::size (inline) 3ms 0.015% 80.73% 128ms 0.65% Cell::SetCellProliferativeType 5ms 0.025% 80.76% 127ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.76% 126ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 126ms 0.64% 81.40% 126ms 0.64% std::_Rb_tree_increment 74ms 0.38% 81.77% 125ms 0.63% TimeStepper::AdvanceOneTimeStep 110ms 0.56% 82.33% 125ms 0.63% vertexsort 3ms 0.015% 82.34% 124ms 0.63% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 69ms 0.35% 82.70% 124ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 82.70% 123ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 82.70% 123ms 0.62% OutputFileHandler::OpenOutputFile 10ms 0.051% 82.75% 123ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 12ms 0.061% 82.81% 119ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 82.81% 119ms 0.6% boost::shared_ptr::~shared_ptr (inline) 38ms 0.19% 83.00% 118ms 0.6% std::__ostream_insert 9ms 0.046% 83.05% 116ms 0.59% Cylindrical2dMesh::CreateMirrorNodes 2ms 0.01% 83.06% 116ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 25ms 0.13% 83.18% 110ms 0.56% boost::numeric::ublas::indexing_vector_assign 1ms 0.0051% 83.19% 109ms 0.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.025% 83.21% 109ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 106ms 0.54% 83.75% 106ms 0.54% TetrahedralMesh::EdgeIterator::operator!= 25ms 0.13% 83.88% 102ms 0.52% std::num_put::_M_insert_int 100ms 0.51% 84.39% 100ms 0.51% [libchaste_mesh.so] 92ms 0.47% 84.85% 100ms 0.51% boost::detail::sp_counted_base::release