File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16322ms, 84.21% of 19383ms total Dropped 746 nodes (cum <= 96.92ms) flat flat% sum% cum cum% 0 0% 0% 19339ms 99.77% __libc_start_call_main 0 0% 0% 19339ms 99.77% __libc_start_main_impl 0 0% 0% 19339ms 99.77% _start 0 0% 0% 19318ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19318ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19318ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19318ms 99.66% main 0 0% 0% 19278ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19278ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19278ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19251ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 14680ms 75.74% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0052% 0.0052% 9262ms 47.78% AbstractCellBasedSimulation::DoCellBirth 6ms 0.031% 0.036% 9163ms 47.27% Cell::ReadyToDivide 3ms 0.015% 0.052% 9090ms 46.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.052% 8945ms 46.15% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 18ms 0.093% 0.14% 8941ms 46.13% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.15% 8920ms 46.02% CellCycleModelOdeHandler::SolveOdeToTime 51ms 0.26% 0.42% 8758ms 45.18% AbstractOneStepIvpOdeSolver::InternalSolve 996ms 5.14% 5.56% 7878ms 40.64% RungeKutta4IvpOdeSolver::CalculateNextYValue 2842ms 14.66% 20.22% 6687ms 34.50% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.22% 5309ms 27.39% MeshBasedCellPopulation::Update 5ms 0.026% 20.24% 4112ms 21.21% Cylindrical2dMesh::ReMesh 68ms 0.35% 20.60% 3858ms 19.90% AbstractCellProperty::IsType (inline) 2ms 0.01% 20.61% 2566ms 13.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 329ms 1.70% 22.30% 2460ms 12.69% AbstractCellProperty::IsSame 0 0% 22.30% 2242ms 11.57% MutableMesh::ReMesh 0 0% 22.30% 2232ms 11.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.062% 22.36% 2186ms 11.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 223ms 1.15% 23.52% 2131ms 10.99% std::type_info::operator== (inline) 2034ms 10.49% 34.01% 2034ms 10.49% __strcmp_avx2 1ms 0.0052% 34.01% 1999ms 10.31% AbstractCellPopulation::WriteResultsToFiles 829ms 4.28% 38.29% 1895ms 9.78% std::_Rb_tree::_M_lower_bound (inline) 163ms 0.84% 39.13% 1667ms 8.60% TetrahedralMesh::EdgeIterator::operator++ 71ms 0.37% 39.50% 1408ms 7.26% std::_Rb_tree::find (inline) 2ms 0.01% 39.51% 1158ms 5.97% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.021% 39.53% 1139ms 5.88% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.088% 39.62% 1122ms 5.79% TetrahedralMesh::ImportFromMesher 53ms 0.27% 39.89% 1069ms 5.52% operator new 12ms 0.062% 39.95% 1007ms 5.20% MeshBasedCellPopulation::SpringIterator::operator++ 239ms 1.23% 41.19% 1002ms 5.17% __GI___libc_malloc 13ms 0.067% 41.25% 987ms 5.09% std::set::insert (inline) 13ms 0.067% 41.32% 974ms 5.03% std::_Rb_tree::_M_insert_unique 49ms 0.25% 41.57% 934ms 4.82% std::__new_allocator::allocate (inline) 0 0% 41.57% 928ms 4.79% std::allocator_traits::allocate (inline) 1ms 0.0052% 41.58% 885ms 4.57% triangulate 0 0% 41.58% 821ms 4.24% std::set::count (inline) 0 0% 41.58% 792ms 4.09% delaunay 0 0% 41.58% 792ms 4.09% divconqdelaunay 3ms 0.015% 41.59% 767ms 3.96% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 746ms 3.85% 45.44% 746ms 3.85% std::_Rb_tree::_S_right (inline) 1ms 0.0052% 45.45% 745ms 3.84% AbstractTwoBodyInteractionForce::AddForceContribution 60ms 0.31% 45.76% 716ms 3.69% std::map::operator[] (partial-inline) 4ms 0.021% 45.78% 713ms 3.68% CellPopulationElementWriter::Visit 703ms 3.63% 49.40% 703ms 3.63% WntCellCycleOdeSystem::CalculateStoppingEvent 357ms 1.84% 51.25% 672ms 3.47% _int_malloc 188ms 0.97% 52.22% 651ms 3.36% __dynamic_cast 16ms 0.083% 52.30% 642ms 3.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.041% 52.34% 618ms 3.19% MeshBasedCellPopulation::AcceptCellWriter 21ms 0.11% 52.45% 605ms 3.12% AbstractCellPopulation::GetCellUsingLocationIndex 22ms 0.11% 52.56% 603ms 3.11% std::less::operator() (inline) 0 0% 52.56% 601ms 3.10% std::_Rb_tree::_M_create_node (inline) 10ms 0.052% 52.61% 586ms 3.02% CellPropertyCollection::GetPropertiesType (inline) 0 0% 52.61% 584ms 3.01% std::map::find (inline) 581ms 3.00% 55.61% 581ms 3.00% std::operator< (inline) 7ms 0.036% 55.65% 574ms 2.96% Element::Element 0 0% 55.65% 572ms 2.95% std::_Rb_tree::_M_get_node (inline) 34ms 0.18% 55.82% 570ms 2.94% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.82% 567ms 2.93% std::_Rb_tree::lower_bound (inline) 0 0% 55.82% 567ms 2.93% std::map::lower_bound (inline) 0 0% 55.82% 548ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 15ms 0.077% 55.90% 542ms 2.80% MutableMesh::ReIndex 9ms 0.046% 55.95% 523ms 2.70% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.036% 55.98% 493ms 2.54% Element::RegisterWithNodes (inline) 11ms 0.057% 56.04% 485ms 2.50% Node::AddElement 13ms 0.067% 56.11% 482ms 2.49% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 56.11% 477ms 2.46% std::ostream::operator<< (inline) 77ms 0.4% 56.50% 476ms 2.46% std::ostream::_M_insert 0 0% 56.50% 470ms 2.42% AbstractCellProperty::IsSubType (inline) 295ms 1.52% 58.03% 449ms 2.32% AbstractCellMutationState::AbstractCellMutationState 124ms 0.64% 58.66% 410ms 2.12% __GI___libc_free 122ms 0.63% 59.29% 392ms 2.02% std::_Rb_tree::_M_erase 149ms 0.77% 60.06% 391ms 2.02% std::_Rb_tree::_M_get_insert_unique_pos 15ms 0.077% 60.14% 375ms 1.93% divconqrecurse 17ms 0.088% 60.23% 370ms 1.91% std::_Rb_tree::~_Rb_tree (inline) 12ms 0.062% 60.29% 360ms 1.86% std::_Rb_tree::erase 0 0% 60.29% 359ms 1.85% std::set::erase (inline) 17ms 0.088% 60.38% 357ms 1.84% Node::RemoveElement 1ms 0.0052% 60.38% 357ms 1.84% std::_Vector_base::_M_allocate (inline) 87ms 0.45% 60.83% 356ms 1.84% mergehulls 9ms 0.046% 60.88% 347ms 1.79% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 60.88% 347ms 1.79% std::set::~set (inline) 20ms 0.1% 60.98% 345ms 1.78% Element::ResetIndex 11ms 0.057% 61.04% 335ms 1.73% std::__new_allocator::deallocate (inline) 161ms 0.83% 61.87% 332ms 1.71% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.87% 331ms 1.71% std::allocator_traits::deallocate (inline) 0 0% 61.87% 326ms 1.68% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0052% 61.87% 325ms 1.68% Cell::GetCellProliferativeType 9ms 0.046% 61.92% 321ms 1.66% AbstractCellPopulation::GetLocationIndexUsingCell 316ms 1.63% 63.55% 316ms 1.63% [libchaste_cell_based.so] 2ms 0.01% 63.56% 312ms 1.61% Cell::GetMutationState 4ms 0.021% 63.58% 311ms 1.60% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 63.58% 303ms 1.56% AbstractCellPopulation::Iterator::operator++ (inline) 38ms 0.2% 63.78% 302ms 1.56% AbstractCellPopulation::Iterator::IsRealCell (inline) 284ms 1.47% 65.24% 287ms 1.48% std::vector::operator[] (inline) 236ms 1.22% 66.46% 286ms 1.48% _int_free 11ms 0.057% 66.52% 286ms 1.48% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0052% 66.52% 283ms 1.46% NodeLocationWriter::Visit 0 0% 66.52% 283ms 1.46% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 66.53% 265ms 1.37% alternateaxes 253ms 1.31% 67.84% 263ms 1.36% vertexmedian 4ms 0.021% 67.86% 261ms 1.35% std::set::set (inline) 98ms 0.51% 68.36% 255ms 1.32% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 13ms 0.067% 68.43% 249ms 1.28% std::vector::push_back (inline) 7ms 0.036% 68.47% 248ms 1.28% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.1% 68.57% 247ms 1.27% AbstractTetrahedralElement::CalculateJacobian 16ms 0.083% 68.65% 245ms 1.26% std::num_put::_M_insert_float 103ms 0.53% 69.18% 240ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 23ms 0.12% 69.30% 238ms 1.23% std::_Rb_tree::_M_copy (inline) 6ms 0.031% 69.33% 235ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 69.34% 234ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 51ms 0.26% 69.61% 234ms 1.21% ApcOneHitCellMutationState::ApcOneHitCellMutationState 26ms 0.13% 69.74% 231ms 1.19% std::vector::_M_realloc_insert 14ms 0.072% 69.81% 216ms 1.11% std::_Rb_tree::_M_erase_aux (inline) 173ms 0.89% 70.71% 215ms 1.11% AbstractElement::GetNodeGlobalIndex 0 0% 70.71% 215ms 1.11% OffLatticeSimulation::ApplyBoundaries 1ms 0.0052% 70.71% 215ms 1.11% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.026% 70.74% 210ms 1.08% std::__cxx11::collate::do_transform 0 0% 70.74% 207ms 1.07% MeshBasedCellPopulation::GetDampingConstant 63ms 0.33% 71.06% 207ms 1.07% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.06% 206ms 1.06% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0052% 71.07% 203ms 1.05% ___vsnprintf 0 0% 71.07% 202ms 1.04% __vsnprintf_internal (inline) 16ms 0.083% 71.15% 201ms 1.04% __printf_buffer 5ms 0.026% 71.18% 200ms 1.03% AbstractTetrahedralElement::AbstractTetrahedralElement 13ms 0.067% 71.24% 199ms 1.03% TetrahedralMesh::Clear 146ms 0.75% 72.00% 198ms 1.02% malloc_consolidate 10ms 0.052% 72.05% 188ms 0.97% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.062% 72.11% 186ms 0.96% Element::MarkAsDeleted 29ms 0.15% 72.26% 184ms 0.95% AbstractTetrahedralElement::RefreshJacobian 5ms 0.026% 72.28% 179ms 0.92% __printf_fp_l_buffer 0 0% 72.28% 179ms 0.92% __printf_fp_spec (inline) 3ms 0.015% 72.30% 176ms 0.91% CellProliferativeTypesWriter::VisitCell 173ms 0.89% 73.19% 173ms 0.89% incircle 83ms 0.43% 73.62% 170ms 0.88% __printf_fp_buffer_1 165ms 0.85% 74.47% 165ms 0.85% [libchaste_crypt.so] 4ms 0.021% 74.49% 164ms 0.85% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 74.49% 159ms 0.82% Cell::HasCellProperty (inline) 4ms 0.021% 74.51% 159ms 0.82% CellPropertyCollection::HasProperty 155ms 0.8% 75.31% 155ms 0.8% std::type_info::name (inline) 154ms 0.79% 76.11% 154ms 0.79% Node::GetIndex 153ms 0.79% 76.90% 153ms 0.79% unlink_chunk 52ms 0.27% 77.17% 147ms 0.76% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 83ms 0.43% 77.59% 146ms 0.75% Cylindrical2dMesh::GetVectorFromAtoB 143ms 0.74% 78.33% 143ms 0.74% std::_Rb_tree_insert_and_rebalance 127ms 0.66% 78.99% 143ms 0.74% vertexsort 142ms 0.73% 79.72% 142ms 0.73% AbstractCellMutationState::~AbstractCellMutationState 86ms 0.44% 80.16% 139ms 0.72% std::_Rb_tree::equal_range (inline) 54ms 0.28% 80.44% 138ms 0.71% AbstractElement::GetNodeLocation 6ms 0.031% 80.47% 136ms 0.7% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.0052% 80.48% 136ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 136ms 0.7% 81.18% 136ms 0.7% std::vector::size (inline) 52ms 0.27% 81.45% 135ms 0.7% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0052% 81.45% 135ms 0.7% boost::numeric::ublas::vector_assign (inline) 41ms 0.21% 81.66% 133ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 9ms 0.046% 81.71% 133ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 23ms 0.12% 81.83% 130ms 0.67% TetrahedralMesh::EdgesEnd 8ms 0.041% 81.87% 126ms 0.65% Node::~Node 30ms 0.15% 82.03% 125ms 0.64% std::__ostream_insert 13ms 0.067% 82.09% 120ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 18ms 0.093% 82.19% 116ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 82.19% 116ms 0.6% boost::shared_ptr::~shared_ptr (inline) 115ms 0.59% 82.78% 115ms 0.59% std::_Rb_tree_increment 1ms 0.0052% 82.78% 113ms 0.58% Cell::SetCellProliferativeType 8ms 0.041% 82.83% 113ms 0.58% std::_Rb_tree_const_iterator::operator++ (inline) 30ms 0.15% 82.98% 111ms 0.57% std::num_put::_M_insert_int 109ms 0.56% 83.54% 109ms 0.56% AbstractElement::IsDeleted 0 0% 83.54% 108ms 0.56% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 33ms 0.17% 83.71% 108ms 0.56% boost::numeric::ublas::indexing_vector_assign 0 0% 83.71% 107ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 83.73% 107ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 13ms 0.067% 83.80% 105ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 76ms 0.39% 84.19% 102ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 4ms 0.021% 84.21% 98ms 0.51% std::operator<< (inline)