File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16626ms, 84.31% of 19721ms total Dropped 765 nodes (cum <= 98.61ms) flat flat% sum% cum cum% 0 0% 0% 19674ms 99.76% __libc_start_call_main 0 0% 0% 19674ms 99.76% __libc_start_main_impl 0 0% 0% 19674ms 99.76% _start 0 0% 0% 19650ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19650ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19650ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19650ms 99.64% main 0 0% 0% 19609ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19609ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19609ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19582ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 14986ms 75.99% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9512ms 48.23% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.041% 9421ms 47.77% Cell::ReadyToDivide 5ms 0.025% 0.066% 9334ms 47.33% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.066% 9178ms 46.54% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.046% 0.11% 9176ms 46.53% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.13% 9163ms 46.46% CellCycleModelOdeHandler::SolveOdeToTime 84ms 0.43% 0.56% 8998ms 45.63% AbstractOneStepIvpOdeSolver::InternalSolve 1032ms 5.23% 5.79% 8043ms 40.78% RungeKutta4IvpOdeSolver::CalculateNextYValue 2839ms 14.40% 20.19% 6833ms 34.65% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.19% 5368ms 27.22% MeshBasedCellPopulation::Update 5ms 0.025% 20.21% 4152ms 21.05% Cylindrical2dMesh::ReMesh 76ms 0.39% 20.60% 4047ms 20.52% AbstractCellProperty::IsType (inline) 429ms 2.18% 22.77% 2619ms 13.28% AbstractCellProperty::IsSame 0 0% 22.77% 2551ms 12.94% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.77% 2242ms 11.37% MutableMesh::ReMesh 294ms 1.49% 24.26% 2190ms 11.10% std::type_info::operator== (inline) 0 0% 24.26% 2181ms 11.06% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.046% 24.31% 2131ms 10.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 2047ms 10.38% 34.69% 2047ms 10.38% __strcmp_avx2 0 0% 34.69% 2040ms 10.34% AbstractCellPopulation::WriteResultsToFiles 825ms 4.18% 38.87% 1873ms 9.50% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.8% 39.67% 1686ms 8.55% TetrahedralMesh::EdgeIterator::operator++ 85ms 0.43% 40.10% 1441ms 7.31% std::_Rb_tree::find (inline) 1ms 0.0051% 40.11% 1181ms 5.99% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 40.12% 1168ms 5.92% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.061% 40.19% 1128ms 5.72% TetrahedralMesh::ImportFromMesher 41ms 0.21% 40.39% 1091ms 5.53% operator new 245ms 1.24% 41.64% 1034ms 5.24% __GI___libc_malloc 13ms 0.066% 41.70% 1020ms 5.17% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.056% 41.76% 1007ms 5.11% std::set::insert (inline) 12ms 0.061% 41.82% 997ms 5.06% std::_Rb_tree::_M_insert_unique 37ms 0.19% 42.01% 949ms 4.81% std::__new_allocator::allocate (inline) 0 0% 42.01% 944ms 4.79% std::allocator_traits::allocate (inline) 1ms 0.0051% 42.01% 879ms 4.46% triangulate 0 0% 42.01% 844ms 4.28% std::set::count (inline) 0 0% 42.01% 800ms 4.06% delaunay 5ms 0.025% 42.04% 800ms 4.06% divconqdelaunay 4ms 0.02% 42.06% 784ms 3.98% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 747ms 3.79% 45.84% 747ms 3.79% WntCellCycleOdeSystem::CalculateStoppingEvent 78ms 0.4% 46.24% 711ms 3.61% std::map::operator[] (partial-inline) 399ms 2.02% 48.26% 710ms 3.60% _int_malloc 690ms 3.50% 51.76% 690ms 3.50% std::_Rb_tree::_S_right (inline) 4ms 0.02% 51.78% 662ms 3.36% CellPopulationElementWriter::Visit 2ms 0.01% 51.79% 660ms 3.35% AbstractTwoBodyInteractionForce::AddForceContribution 204ms 1.03% 52.83% 643ms 3.26% __dynamic_cast 5ms 0.025% 52.85% 638ms 3.24% MeshBasedCellPopulation::AcceptCellWriter 21ms 0.11% 52.96% 636ms 3.22% std::less::operator() (inline) 0 0% 52.96% 622ms 3.15% std::_Rb_tree::_M_create_node (inline) 10ms 0.051% 53.01% 618ms 3.13% CellPropertyCollection::GetPropertiesType (inline) 615ms 3.12% 56.13% 615ms 3.12% std::operator< (inline) 0 0% 56.13% 593ms 3.01% std::_Rb_tree::_M_get_node (inline) 34ms 0.17% 56.30% 593ms 3.01% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.30% 593ms 3.01% std::map::find (inline) 29ms 0.15% 56.45% 562ms 2.85% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.046% 56.49% 561ms 2.84% Element::Element 27ms 0.14% 56.63% 555ms 2.81% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 56.63% 553ms 2.80% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.061% 56.69% 552ms 2.80% MutableMesh::ReIndex 0 0% 56.69% 529ms 2.68% std::_Rb_tree::lower_bound (inline) 0 0% 56.69% 529ms 2.68% std::map::lower_bound (inline) 18ms 0.091% 56.78% 513ms 2.60% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 56.78% 502ms 2.55% AbstractCellProperty::IsSubType (inline) 12ms 0.061% 56.84% 500ms 2.54% Cylindrical2dMesh::ReconstructCylindricalMesh 68ms 0.34% 57.19% 494ms 2.50% std::ostream::_M_insert 0 0% 57.19% 494ms 2.50% std::ostream::operator<< (inline) 8ms 0.041% 57.23% 487ms 2.47% Element::RegisterWithNodes (inline) 8ms 0.041% 57.27% 480ms 2.43% Node::AddElement 297ms 1.51% 58.77% 461ms 2.34% AbstractCellMutationState::AbstractCellMutationState 143ms 0.73% 59.50% 460ms 2.33% __GI___libc_free 11ms 0.056% 59.56% 417ms 2.11% std::_Rb_tree::erase 0 0% 59.56% 416ms 2.11% std::set::erase (inline) 131ms 0.66% 60.22% 408ms 2.07% std::_Rb_tree::_M_erase 12ms 0.061% 60.28% 403ms 2.04% Node::RemoveElement 139ms 0.7% 60.99% 392ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos 23ms 0.12% 61.10% 388ms 1.97% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.051% 61.15% 385ms 1.95% std::__new_allocator::deallocate (inline) 22ms 0.11% 61.26% 384ms 1.95% Element::ResetIndex 384ms 1.95% 63.21% 384ms 1.95% [libchaste_cell_based.so] 0 0% 63.21% 382ms 1.94% std::allocator_traits::deallocate (inline) 14ms 0.071% 63.28% 376ms 1.91% divconqrecurse 111ms 0.56% 63.85% 354ms 1.80% mergehulls 0 0% 63.85% 354ms 1.80% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 63.86% 354ms 1.80% std::_Vector_base::_M_allocate (inline) 0 0% 63.86% 354ms 1.80% std::set::~set (inline) 3ms 0.015% 63.88% 343ms 1.74% Cell::GetCellProliferativeType 8ms 0.041% 63.92% 334ms 1.69% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.03% 63.95% 330ms 1.67% AbstractCellPopulation::GetLocationIndexUsingCell 261ms 1.32% 65.27% 317ms 1.61% _int_free 143ms 0.73% 66.00% 316ms 1.60% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.00% 316ms 1.60% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 66.02% 315ms 1.60% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.02% 312ms 1.58% Cell::GetMutationState 0 0% 66.02% 307ms 1.56% NodeLocationWriter::Visit 0 0% 66.02% 304ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 36ms 0.18% 66.20% 303ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.02% 66.22% 283ms 1.44% alternateaxes 250ms 1.27% 67.49% 279ms 1.41% vertexmedian 23ms 0.12% 67.60% 277ms 1.40% std::num_put::_M_insert_float 12ms 0.061% 67.66% 270ms 1.37% std::_Rb_tree::_Rb_tree (partial-inline) 20ms 0.1% 67.77% 256ms 1.30% AbstractTetrahedralElement::CalculateJacobian 76ms 0.39% 68.15% 255ms 1.29% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.056% 68.21% 254ms 1.29% std::vector::push_back (inline) 250ms 1.27% 69.47% 252ms 1.28% std::vector::operator[] (inline) 13ms 0.066% 69.54% 251ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.025% 69.57% 248ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.086% 69.65% 248ms 1.26% std::_Rb_tree::_M_erase_aux (inline) 56ms 0.28% 69.94% 241ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 69.96% 241ms 1.22% std::set::set (inline) 17ms 0.086% 70.04% 236ms 1.20% std::vector::_M_realloc_insert 93ms 0.47% 70.51% 229ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 70.51% 228ms 1.16% OffLatticeSimulation::ApplyBoundaries 8ms 0.041% 70.55% 227ms 1.15% std::__cxx11::collate::do_transform 25ms 0.13% 70.68% 226ms 1.15% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 70.69% 224ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.015% 70.71% 221ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 70.71% 221ms 1.12% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.72% 215ms 1.09% ___vsnprintf 16ms 0.081% 70.80% 213ms 1.08% TetrahedralMesh::Clear 0 0% 70.80% 213ms 1.08% TetrahedralMesh::RefreshJacobianCachedData 0 0% 70.80% 213ms 1.08% __vsnprintf_internal (inline) 19ms 0.096% 70.89% 211ms 1.07% __printf_buffer 7ms 0.035% 70.93% 199ms 1.01% CellPropertyCollection::HasProperty 63ms 0.32% 71.25% 197ms 1% std::_Rb_tree::_M_clone_node (inline) 144ms 0.73% 71.98% 193ms 0.98% AbstractElement::GetNodeGlobalIndex 26ms 0.13% 72.11% 192ms 0.97% AbstractTetrahedralElement::RefreshJacobian 0 0% 72.11% 192ms 0.97% Cell::HasCellProperty (inline) 8ms 0.041% 72.15% 189ms 0.96% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.035% 72.19% 187ms 0.95% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 136ms 0.69% 72.88% 184ms 0.93% malloc_consolidate 12ms 0.061% 72.94% 183ms 0.93% Element::MarkAsDeleted 3ms 0.015% 72.95% 182ms 0.92% CellProliferativeTypesWriter::VisitCell 6ms 0.03% 72.98% 182ms 0.92% __printf_fp_l_buffer 0 0% 72.98% 182ms 0.92% __printf_fp_spec (inline) 7ms 0.035% 73.02% 181ms 0.92% AbstractTetrahedralElement::AbstractTetrahedralElement 171ms 0.87% 73.89% 171ms 0.87% Node::GetIndex 74ms 0.38% 74.26% 170ms 0.86% __printf_fp_buffer_1 119ms 0.6% 74.86% 169ms 0.86% std::_Rb_tree::equal_range (inline) 165ms 0.84% 75.70% 165ms 0.84% [libchaste_crypt.so] 49ms 0.25% 75.95% 158ms 0.8% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 158ms 0.8% 76.75% 158ms 0.8% unlink_chunk 15ms 0.076% 76.83% 154ms 0.78% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 154ms 0.78% 77.61% 154ms 0.78% incircle 56ms 0.28% 77.89% 153ms 0.78% AbstractElement::GetNodeLocation 0 0% 77.89% 150ms 0.76% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 150ms 0.76% 78.65% 150ms 0.76% std::_Rb_tree_insert_and_rebalance 149ms 0.76% 79.41% 149ms 0.76% std::vector::size (inline) 97ms 0.49% 79.90% 143ms 0.73% Cylindrical2dMesh::GetVectorFromAtoB 6ms 0.03% 79.93% 141ms 0.71% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.03% 79.96% 140ms 0.71% Node::~Node 23ms 0.12% 80.08% 140ms 0.71% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0051% 80.08% 137ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.08% 135ms 0.68% OutputFileHandler::OpenOutputFile 2ms 0.01% 80.09% 135ms 0.68% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 47ms 0.24% 80.33% 134ms 0.68% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 133ms 0.67% 81.01% 133ms 0.67% std::type_info::name (inline) 121ms 0.61% 81.62% 131ms 0.66% vertexsort 1ms 0.0051% 81.62% 129ms 0.65% boost::numeric::ublas::vector_assign (inline) 4ms 0.02% 81.64% 128ms 0.65% Cell::SetCellProliferativeType 1ms 0.0051% 81.65% 124ms 0.63% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.025% 81.67% 116ms 0.59% Cylindrical2dMesh::CreateMirrorNodes 14ms 0.071% 81.75% 116ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 81.75% 116ms 0.59% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0051% 81.75% 115ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 72ms 0.37% 82.12% 115ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0051% 82.12% 113ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 10ms 0.051% 82.17% 112ms 0.57% boost::numeric::ublas::c_vector::c_vector (inline) 106ms 0.54% 82.71% 106ms 0.54% std::_Rb_tree_increment 0 0% 82.71% 105ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 18ms 0.091% 82.80% 105ms 0.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.025% 82.83% 104ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 19ms 0.096% 82.92% 104ms 0.53% std::num_put::_M_insert_int 103ms 0.52% 83.44% 103ms 0.52% AbstractCellProperty::AbstractCellProperty 6ms 0.03% 83.47% 103ms 0.52% CellLocationIndexWriter::VisitCell 3ms 0.015% 83.49% 101ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.51% 84.00% 101ms 0.51% std::_Rb_tree_rebalance_for_erase 31ms 0.16% 84.16% 101ms 0.51% std::__ostream_insert 3ms 0.015% 84.17% 100ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 26ms 0.13% 84.31% 99ms 0.5% boost::numeric::ublas::indexing_vector_assign