File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16626ms, 84.69% of 19631ms total Dropped 755 nodes (cum <= 98.16ms) flat flat% sum% cum cum% 0 0% 0% 19588ms 99.78% __libc_start_call_main 0 0% 0% 19588ms 99.78% __libc_start_main_impl 0 0% 0% 19588ms 99.78% _start 0 0% 0% 19571ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19571ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19571ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19571ms 99.69% main 0 0% 0% 19532ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19532ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19532ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19506ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15205ms 77.45% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 10098ms 51.44% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.031% 10031ms 51.10% Cell::ReadyToDivide 7ms 0.036% 0.066% 9965ms 50.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.082% 9841ms 50.13% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.082% 0.16% 9834ms 50.09% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.17% 9817ms 50.01% CellCycleModelOdeHandler::SolveOdeToTime 81ms 0.41% 0.58% 9643ms 49.12% AbstractOneStepIvpOdeSolver::InternalSolve 869ms 4.43% 5.01% 8797ms 44.81% RungeKutta4IvpOdeSolver::CalculateNextYValue 3364ms 17.14% 22.14% 7714ms 39.29% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 22.15% 4995ms 25.44% MeshBasedCellPopulation::Update 158ms 0.8% 22.96% 4343ms 22.12% AbstractCellProperty::IsType (inline) 13ms 0.066% 23.02% 3815ms 19.43% Cylindrical2dMesh::ReMesh 598ms 3.05% 26.07% 3117ms 15.88% AbstractCellProperty::IsSame 354ms 1.80% 27.87% 2519ms 12.83% std::type_info::operator== (inline) 2ms 0.01% 27.88% 2400ms 12.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 2160ms 11.00% 38.89% 2160ms 11.00% __strcmp_avx2 0 0% 38.89% 2132ms 10.86% MutableMesh::ReMesh 2ms 0.01% 38.90% 2118ms 10.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.056% 38.95% 2065ms 10.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 38.95% 1896ms 9.66% AbstractCellPopulation::WriteResultsToFiles 816ms 4.16% 43.11% 1785ms 9.09% std::_Rb_tree::_M_lower_bound (inline) 150ms 0.76% 43.87% 1630ms 8.30% TetrahedralMesh::EdgeIterator::operator++ 71ms 0.36% 44.24% 1316ms 6.70% std::_Rb_tree::find (inline) 1ms 0.0051% 44.24% 1145ms 5.83% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 44.26% 1062ms 5.41% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.071% 44.33% 1029ms 5.24% TetrahedralMesh::ImportFromMesher 14ms 0.071% 44.40% 998ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 38ms 0.19% 44.60% 973ms 4.96% operator new 7ms 0.036% 44.63% 972ms 4.95% std::set::insert (inline) 25ms 0.13% 44.76% 965ms 4.92% std::_Rb_tree::_M_insert_unique 222ms 1.13% 45.89% 926ms 4.72% __GI___libc_malloc 36ms 0.18% 46.08% 857ms 4.37% std::__new_allocator::allocate (inline) 0 0% 46.08% 846ms 4.31% std::allocator_traits::allocate (inline) 0 0% 46.08% 845ms 4.30% triangulate 0 0% 46.08% 806ms 4.11% std::set::count (inline) 0 0% 46.08% 775ms 3.95% delaunay 3ms 0.015% 46.09% 773ms 3.94% divconqdelaunay 2ms 0.01% 46.10% 713ms 3.63% AbstractTwoBodyInteractionForce::AddForceContribution 44ms 0.22% 46.32% 690ms 3.51% std::map::operator[] (partial-inline) 3ms 0.015% 46.34% 688ms 3.50% CellPopulationElementWriter::Visit 4ms 0.02% 46.36% 666ms 3.39% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 640ms 3.26% 49.62% 651ms 3.32% WntCellCycleOdeSystem::CalculateStoppingEvent 166ms 0.85% 50.47% 648ms 3.30% __dynamic_cast 25ms 0.13% 50.59% 614ms 3.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 613ms 3.12% 53.72% 613ms 3.12% std::_Rb_tree::_S_right (inline) 27ms 0.14% 53.85% 613ms 3.12% std::less::operator() (inline) 346ms 1.76% 55.62% 612ms 3.12% _int_malloc 586ms 2.99% 58.60% 586ms 2.99% std::operator< (inline) 0 0% 58.60% 567ms 2.89% std::_Rb_tree::lower_bound (inline) 0 0% 58.60% 567ms 2.89% std::map::lower_bound (inline) 25ms 0.13% 58.73% 565ms 2.88% std::_Rb_tree::_M_insert_ (inline) 19ms 0.097% 58.83% 564ms 2.87% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.83% 564ms 2.87% std::_Rb_tree::_M_create_node (inline) 2ms 0.01% 58.84% 555ms 2.83% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.031% 58.87% 542ms 2.76% Element::Element 0 0% 58.87% 535ms 2.73% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.87% 529ms 2.69% std::_Rb_tree::_M_get_node (inline) 358ms 1.82% 60.69% 518ms 2.64% AbstractCellMutationState::AbstractCellMutationState 0 0% 60.69% 513ms 2.61% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 60.69% 508ms 2.59% std::map::find (inline) 1ms 0.0051% 60.69% 508ms 2.59% std::ostream::operator<< (inline) 77ms 0.39% 61.09% 507ms 2.58% std::ostream::_M_insert 12ms 0.061% 61.15% 502ms 2.56% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.051% 61.20% 465ms 2.37% MutableMesh::ReIndex 3ms 0.015% 61.21% 459ms 2.34% AbstractCellProperty::IsSubType (inline) 11ms 0.056% 61.27% 456ms 2.32% Element::RegisterWithNodes (inline) 4ms 0.02% 61.29% 445ms 2.27% Node::AddElement 9ms 0.046% 61.34% 410ms 2.09% Cylindrical2dMesh::CorrectNonPeriodicMesh 21ms 0.11% 61.44% 405ms 2.06% divconqrecurse 155ms 0.79% 62.23% 398ms 2.03% __GI___libc_free 160ms 0.82% 63.05% 375ms 1.91% std::_Rb_tree::_M_get_insert_unique_pos 104ms 0.53% 63.58% 373ms 1.90% mergehulls 178ms 0.91% 64.48% 340ms 1.73% __cxxabiv1::__si_class_type_info::__do_dyncast 97ms 0.49% 64.98% 335ms 1.71% std::_Rb_tree::_M_erase 3ms 0.015% 64.99% 333ms 1.70% std::set::erase (inline) 12ms 0.061% 65.06% 331ms 1.69% std::_Rb_tree::erase 11ms 0.056% 65.11% 330ms 1.68% std::__new_allocator::deallocate (inline) 0 0% 65.11% 326ms 1.66% std::allocator_traits::deallocate (inline) 1ms 0.0051% 65.12% 318ms 1.62% std::_Vector_base::_M_allocate (inline) 6ms 0.031% 65.15% 317ms 1.61% Node::RemoveElement 0 0% 65.15% 311ms 1.58% Cell::GetMutationState 0 0% 65.15% 307ms 1.56% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.15% 305ms 1.55% NodeLocationWriter::Visit 305ms 1.55% 66.70% 305ms 1.55% std::type_info::name (inline) 24ms 0.12% 66.82% 303ms 1.54% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.031% 66.85% 292ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 22ms 0.11% 66.97% 291ms 1.48% Element::ResetIndex 2ms 0.01% 66.98% 282ms 1.44% Cell::GetCellProliferativeType 16ms 0.082% 67.06% 276ms 1.41% AbstractTetrahedralElement::CalculateJacobian 0 0% 67.06% 274ms 1.40% std::set::~set (inline) 2ms 0.01% 67.07% 272ms 1.39% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 67.07% 272ms 1.39% std::_Rb_tree::_M_put_node (inline) 17ms 0.087% 67.15% 272ms 1.39% std::num_put::_M_insert_float 8ms 0.041% 67.19% 271ms 1.38% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 259ms 1.32% 68.51% 262ms 1.33% std::vector::operator[] (inline) 72ms 0.37% 68.88% 260ms 1.32% ApcOneHitCellMutationState::ApcOneHitCellMutationState 18ms 0.092% 68.97% 252ms 1.28% AbstractCellPopulation::Iterator::IsRealCell 0 0% 68.97% 251ms 1.28% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 68.98% 251ms 1.28% alternateaxes 234ms 1.19% 70.17% 246ms 1.25% vertexmedian 15ms 0.076% 70.25% 245ms 1.25% std::_Rb_tree::_Rb_tree 195ms 0.99% 71.24% 243ms 1.24% _int_free 242ms 1.23% 72.48% 242ms 1.23% [libchaste_cell_based.so] 10ms 0.051% 72.53% 235ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 9ms 0.046% 72.57% 233ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 72.57% 231ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0051% 72.58% 229ms 1.17% std::set::set (inline) 11ms 0.056% 72.64% 226ms 1.15% std::vector::push_back (inline) 1ms 0.0051% 72.64% 221ms 1.13% std::__cxx11::collate::do_transform 13ms 0.066% 72.71% 215ms 1.10% std::_Rb_tree::_M_erase_aux (inline) 41ms 0.21% 72.92% 214ms 1.09% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.046% 72.96% 212ms 1.08% std::vector::_M_realloc_insert 2ms 0.01% 72.97% 211ms 1.07% ___vsnprintf 2ms 0.01% 72.98% 210ms 1.07% MeshBasedCellPopulation::GetDampingConstant 0 0% 72.98% 209ms 1.06% __vsnprintf_internal (inline) 1ms 0.0051% 72.99% 207ms 1.05% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0051% 72.99% 205ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 26ms 0.13% 73.12% 205ms 1.04% AbstractTetrahedralElement::RefreshJacobian 22ms 0.11% 73.24% 203ms 1.03% __printf_buffer 21ms 0.11% 73.34% 202ms 1.03% std::_Rb_tree::_M_copy (inline) 12ms 0.061% 73.40% 201ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 149ms 0.76% 74.16% 196ms 1% AbstractElement::GetNodeGlobalIndex 6ms 0.031% 74.19% 196ms 1% AbstractTetrahedralElement::AbstractTetrahedralElement 31ms 0.16% 74.35% 189ms 0.96% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 53ms 0.27% 74.62% 180ms 0.92% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.62% 176ms 0.9% OffLatticeSimulation::ApplyBoundaries 9ms 0.046% 74.67% 175ms 0.89% Element::MarkAsDeleted 172ms 0.88% 75.54% 172ms 0.88% incircle 170ms 0.87% 76.41% 170ms 0.87% std::_Rb_tree_insert_and_rebalance 124ms 0.63% 77.04% 169ms 0.86% malloc_consolidate 1ms 0.0051% 77.05% 167ms 0.85% __printf_fp_spec (inline) 6ms 0.031% 77.08% 166ms 0.85% __printf_fp_l_buffer 2ms 0.01% 77.09% 160ms 0.82% CellProliferativeTypesWriter::VisitCell 46ms 0.23% 77.32% 157ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 154ms 0.78% 78.11% 154ms 0.78% Node::GetIndex 12ms 0.061% 78.17% 154ms 0.78% TetrahedralMesh::Clear 67ms 0.34% 78.51% 153ms 0.78% AbstractElement::GetNodeLocation 79ms 0.4% 78.91% 153ms 0.78% __printf_fp_buffer_1 6ms 0.031% 78.94% 149ms 0.76% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 78.94% 143ms 0.73% boost::numeric::ublas::vector_assign (inline) 13ms 0.066% 79.01% 141ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 79.01% 140ms 0.71% Cell::HasCellProperty (inline) 5ms 0.025% 79.03% 140ms 0.71% CellPropertyCollection::HasProperty 135ms 0.69% 79.72% 135ms 0.69% unlink_chunk 4ms 0.02% 79.74% 132ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 131ms 0.67% 80.41% 131ms 0.67% std::vector::size (inline) 47ms 0.24% 80.65% 129ms 0.66% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 44ms 0.22% 80.87% 127ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 120ms 0.61% 81.48% 120ms 0.61% boost::shared_ptr::operator-> (inline) 30ms 0.15% 81.64% 120ms 0.61% std::num_put::_M_insert_int 5ms 0.025% 81.66% 119ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 71ms 0.36% 82.02% 116ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 10ms 0.051% 82.07% 115ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 75ms 0.38% 82.46% 115ms 0.59% std::_Rb_tree::equal_range (inline) 11ms 0.056% 82.51% 114ms 0.58% boost::detail::shared_count::~shared_count (inline) 40ms 0.2% 82.72% 114ms 0.58% boost::numeric::ublas::indexing_vector_assign 0 0% 82.72% 114ms 0.58% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.72% 113ms 0.58% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.72% 112ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 82.73% 111ms 0.57% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 109ms 0.56% 83.29% 109ms 0.56% AbstractCellProperty::~AbstractCellProperty 0 0% 83.29% 109ms 0.56% OutputFileHandler::OpenOutputFile 1ms 0.0051% 83.29% 107ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 97ms 0.49% 83.79% 103ms 0.52% vertexsort 78ms 0.4% 84.18% 101ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 100ms 0.51% 84.69% 100ms 0.51% [libchaste_mesh.so]