File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16676ms, 84.16% of 19814ms total Dropped 792 nodes (cum <= 99.07ms) flat flat% sum% cum cum% 0 0% 0% 19767ms 99.76% __libc_start_call_main 0 0% 0% 19767ms 99.76% __libc_start_main_impl 0 0% 0% 19767ms 99.76% _start 0 0% 0% 19747ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19747ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19747ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19747ms 99.66% main 0 0% 0% 19708ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19708ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19708ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19682ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 15185ms 76.64% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 9978ms 50.36% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 9896ms 49.94% Cell::ReadyToDivide 4ms 0.02% 0.04% 9813ms 49.53% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.056% 9662ms 48.76% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.071% 0.13% 9649ms 48.70% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.14% 9632ms 48.61% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.38% 0.51% 9490ms 47.90% AbstractOneStepIvpOdeSolver::InternalSolve 916ms 4.62% 5.14% 8688ms 43.85% RungeKutta4IvpOdeSolver::CalculateNextYValue 3514ms 17.73% 22.87% 7548ms 38.09% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 22.88% 5102ms 25.75% MeshBasedCellPopulation::Update 84ms 0.42% 23.31% 4087ms 20.63% AbstractCellProperty::IsType (inline) 4ms 0.02% 23.33% 3943ms 19.90% Cylindrical2dMesh::ReMesh 593ms 2.99% 26.32% 2843ms 14.35% AbstractCellProperty::IsSame 1ms 0.005% 26.32% 2441ms 12.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 419ms 2.11% 28.44% 2250ms 11.36% std::type_info::operator== (inline) 0 0% 28.44% 2159ms 10.90% MutableMesh::ReMesh 0 0% 28.44% 2140ms 10.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.025% 28.46% 2091ms 10.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.46% 2052ms 10.36% AbstractCellPopulation::WriteResultsToFiles 857ms 4.33% 32.79% 1922ms 9.70% std::_Rb_tree::_M_lower_bound (inline) 1770ms 8.93% 41.72% 1770ms 8.93% __strcmp_avx2 161ms 0.81% 42.54% 1685ms 8.50% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.28% 42.82% 1398ms 7.06% std::_Rb_tree::find (inline) 7ms 0.035% 42.85% 1130ms 5.70% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.005% 42.86% 1126ms 5.68% MeshBasedCellPopulation::UpdateNodePairs 17ms 0.086% 42.94% 1082ms 5.46% TetrahedralMesh::ImportFromMesher 36ms 0.18% 43.13% 1079ms 5.45% operator new 15ms 0.076% 43.20% 1023ms 5.16% MeshBasedCellPopulation::SpringIterator::operator++ 234ms 1.18% 44.38% 1023ms 5.16% __GI___libc_malloc 10ms 0.05% 44.43% 970ms 4.90% std::set::insert (inline) 20ms 0.1% 44.53% 960ms 4.85% std::_Rb_tree::_M_insert_unique 34ms 0.17% 44.71% 939ms 4.74% std::__new_allocator::allocate (inline) 0 0% 44.71% 935ms 4.72% std::allocator_traits::allocate (inline) 0 0% 44.71% 869ms 4.39% std::set::count (inline) 0 0% 44.71% 805ms 4.06% triangulate 3ms 0.015% 44.72% 791ms 3.99% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 58ms 0.29% 45.01% 739ms 3.73% std::map::operator[] (partial-inline) 0 0% 45.01% 720ms 3.63% delaunay 3ms 0.015% 45.03% 719ms 3.63% divconqdelaunay 398ms 2.01% 47.04% 697ms 3.52% _int_malloc 1ms 0.005% 47.04% 693ms 3.50% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.035% 47.08% 688ms 3.47% CellPopulationElementWriter::Visit 672ms 3.39% 50.47% 672ms 3.39% std::_Rb_tree::_S_right (inline) 17ms 0.086% 50.56% 635ms 3.20% AbstractCellPopulation::GetCellUsingLocationIndex 27ms 0.14% 50.69% 634ms 3.20% std::_Rb_tree::_M_insert_ (inline) 8ms 0.04% 50.73% 633ms 3.19% MeshBasedCellPopulation::AcceptCellWriter 0 0% 50.73% 633ms 3.19% std::_Rb_tree::_M_create_node (inline) 14ms 0.071% 50.80% 630ms 3.18% std::less::operator() (inline) 613ms 3.09% 53.90% 625ms 3.15% WntCellCycleOdeSystem::CalculateStoppingEvent 616ms 3.11% 57.01% 616ms 3.11% std::operator< (inline) 0 0% 57.01% 600ms 3.03% std::_Rb_tree::_M_get_node (inline) 154ms 0.78% 57.78% 598ms 3.02% __dynamic_cast 31ms 0.16% 57.94% 594ms 3.00% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 57.94% 590ms 2.98% std::_Rb_tree::lower_bound (inline) 0 0% 57.94% 590ms 2.98% std::map::lower_bound (inline) 7ms 0.035% 57.97% 585ms 2.95% CellPropertyCollection::GetPropertiesType (inline) 0 0% 57.97% 570ms 2.88% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.015% 57.99% 544ms 2.75% Element::Element 0 0% 57.99% 523ms 2.64% std::map::find (inline) 13ms 0.066% 58.05% 515ms 2.60% Cylindrical2dMesh::ReconstructCylindricalMesh 7ms 0.035% 58.09% 506ms 2.55% MutableMesh::ReIndex 18ms 0.091% 58.18% 486ms 2.45% Element::RegisterWithNodes (inline) 2ms 0.01% 58.19% 480ms 2.42% std::ostream::operator<< (inline) 61ms 0.31% 58.50% 478ms 2.41% std::ostream::_M_insert 306ms 1.54% 60.04% 470ms 2.37% AbstractCellMutationState::AbstractCellMutationState 7ms 0.035% 60.08% 467ms 2.36% AbstractCellProperty::IsSubType (inline) 10ms 0.05% 60.13% 464ms 2.34% Node::AddElement 158ms 0.8% 60.93% 451ms 2.28% __GI___libc_free 9ms 0.045% 60.97% 449ms 2.27% Cylindrical2dMesh::CorrectNonPeriodicMesh 17ms 0.086% 61.06% 380ms 1.92% divconqrecurse 8ms 0.04% 61.10% 366ms 1.85% std::__new_allocator::deallocate (inline) 5ms 0.025% 61.12% 361ms 1.82% std::_Rb_tree::erase 0 0% 61.12% 361ms 1.82% std::set::erase (inline) 0 0% 61.12% 360ms 1.82% std::allocator_traits::deallocate (inline) 11ms 0.056% 61.18% 358ms 1.81% Node::RemoveElement 106ms 0.53% 61.71% 357ms 1.80% mergehulls 101ms 0.51% 62.22% 357ms 1.80% std::_Rb_tree::_M_erase 36ms 0.18% 62.41% 344ms 1.74% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.005% 62.41% 336ms 1.70% std::_Vector_base::_M_allocate (inline) 335ms 1.69% 64.10% 335ms 1.69% std::type_info::name (inline) 168ms 0.85% 64.95% 334ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 64.96% 333ms 1.68% Cell::GetCellProliferativeType 6ms 0.03% 64.99% 327ms 1.65% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 64.99% 327ms 1.65% std::_Rb_tree::_M_drop_node (inline) 32ms 0.16% 65.16% 326ms 1.65% Element::ResetIndex 0 0% 65.16% 318ms 1.60% std::set::~set (inline) 2ms 0.01% 65.17% 306ms 1.54% NodeLocationWriter::Visit 121ms 0.61% 65.78% 306ms 1.54% std::_Rb_tree::_M_get_insert_unique_pos 5ms 0.025% 65.80% 299ms 1.51% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.03% 65.83% 298ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 5ms 0.025% 65.86% 298ms 1.50% Cell::GetMutationState 235ms 1.19% 67.04% 293ms 1.48% _int_free 36ms 0.18% 67.23% 291ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.23% 286ms 1.44% std::_Rb_tree::_M_put_node (inline) 1ms 0.005% 67.23% 272ms 1.37% std::set::set (inline) 268ms 1.35% 68.58% 270ms 1.36% std::vector::operator[] (inline) 1ms 0.005% 68.59% 260ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.056% 68.64% 260ms 1.31% std::vector::push_back (inline) 34ms 0.17% 68.81% 255ms 1.29% AbstractCellPopulation::Iterator::IsRealCell (inline) 19ms 0.096% 68.91% 252ms 1.27% std::num_put::_M_insert_float 72ms 0.36% 69.27% 250ms 1.26% ApcOneHitCellMutationState::ApcOneHitCellMutationState 23ms 0.12% 69.39% 244ms 1.23% std::vector::_M_realloc_insert 1ms 0.005% 69.40% 243ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.02% 69.42% 242ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.1% 69.52% 239ms 1.21% AbstractTetrahedralElement::CalculateJacobian 23ms 0.12% 69.63% 225ms 1.14% std::_Rb_tree::_M_copy (inline) 224ms 1.13% 70.76% 224ms 1.13% [libchaste_cell_based.so] 4ms 0.02% 70.78% 219ms 1.11% alternateaxes 9ms 0.045% 70.83% 217ms 1.10% std::_Rb_tree::_M_erase_aux (inline) 203ms 1.02% 71.85% 215ms 1.09% vertexmedian 41ms 0.21% 72.06% 208ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 7ms 0.035% 72.10% 207ms 1.04% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 45ms 0.23% 72.32% 207ms 1.04% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 162ms 0.82% 73.14% 204ms 1.03% AbstractElement::GetNodeGlobalIndex 151ms 0.76% 73.90% 202ms 1.02% malloc_consolidate 14ms 0.071% 73.97% 201ms 1.01% Element::MarkAsDeleted 63ms 0.32% 74.29% 199ms 1.00% std::_Rb_tree::_M_clone_node (inline) 3ms 0.015% 74.31% 196ms 0.99% std::__cxx11::collate::do_transform 12ms 0.061% 74.37% 193ms 0.97% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 74.38% 191ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 188ms 0.95% 75.33% 188ms 0.95% std::_Rb_tree_insert_and_rebalance 0 0% 75.33% 187ms 0.94% ___vsnprintf 0 0% 75.33% 187ms 0.94% __vsnprintf_internal (inline) 27ms 0.14% 75.46% 185ms 0.93% AbstractTetrahedralElement::RefreshJacobian 16ms 0.081% 75.54% 184ms 0.93% __printf_buffer 0 0% 75.54% 177ms 0.89% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.54% 177ms 0.89% MeshBasedCellPopulation::GetDampingConstant 1ms 0.005% 75.55% 176ms 0.89% CellProliferativeTypesWriter::VisitCell 0 0% 75.55% 176ms 0.89% OffLatticeSimulation::ApplyBoundaries 22ms 0.11% 75.66% 176ms 0.89% TetrahedralMesh::Clear 3ms 0.015% 75.67% 175ms 0.88% CellPropertyCollection::HasProperty 0 0% 75.67% 173ms 0.87% Cell::HasCellProperty (inline) 167ms 0.84% 76.52% 167ms 0.84% Node::GetIndex 14ms 0.071% 76.59% 165ms 0.83% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.025% 76.61% 160ms 0.81% __printf_fp_l_buffer 0 0% 76.61% 160ms 0.81% __printf_fp_spec (inline) 155ms 0.78% 77.39% 155ms 0.78% incircle 65ms 0.33% 77.72% 148ms 0.75% __printf_fp_buffer_1 84ms 0.42% 78.15% 146ms 0.74% std::_Rb_tree::equal_range (inline) 2ms 0.01% 78.16% 145ms 0.73% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 145ms 0.73% 78.89% 145ms 0.73% std::vector::size (inline) 60ms 0.3% 79.19% 144ms 0.73% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 59ms 0.3% 79.49% 142ms 0.72% AbstractElement::GetNodeLocation 9ms 0.045% 79.53% 140ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 140ms 0.71% 80.24% 140ms 0.71% unlink_chunk 3ms 0.015% 80.26% 139ms 0.7% boost::numeric::ublas::vector_assign (inline) 46ms 0.23% 80.49% 136ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.005% 80.49% 130ms 0.66% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.005% 80.50% 130ms 0.66% Cell::SetCellProliferativeType 1ms 0.005% 80.50% 128ms 0.65% OutputFileHandler::OpenOutputFile 124ms 0.63% 81.13% 124ms 0.63% AbstractCellProperty::~AbstractCellProperty 38ms 0.19% 81.32% 124ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 8ms 0.04% 81.36% 121ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.02% 81.38% 120ms 0.61% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 119ms 0.6% 81.98% 119ms 0.6% AbstractCellMutationState::~AbstractCellMutationState 63ms 0.32% 82.30% 119ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 31ms 0.16% 82.46% 118ms 0.6% TetrahedralMesh::EdgesEnd 42ms 0.21% 82.67% 118ms 0.6% boost::numeric::ublas::indexing_vector_assign 1ms 0.005% 82.67% 117ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 32ms 0.16% 82.84% 117ms 0.59% std::num_put::_M_insert_int 47ms 0.24% 83.07% 116ms 0.59% std::__ostream_insert 112ms 0.57% 83.64% 112ms 0.57% AbstractElement::IsDeleted 96ms 0.48% 84.12% 106ms 0.53% vertexsort 6ms 0.03% 84.15% 105ms 0.53% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 84.15% 102ms 0.51% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 84.16% 100ms 0.5% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath