File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16562ms, 83.37% of 19866ms total Dropped 761 nodes (cum <= 99.33ms) flat flat% sum% cum cum% 0 0% 0% 19819ms 99.76% __libc_start_call_main 0 0% 0% 19819ms 99.76% __libc_start_main_impl 0 0% 0% 19819ms 99.76% _start 0 0% 0% 19799ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19799ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19799ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19799ms 99.66% main 0 0% 0% 19763ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19763ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19763ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19735ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 15250ms 76.76% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 9988ms 50.28% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.025% 9902ms 49.84% Cell::ReadyToDivide 8ms 0.04% 0.065% 9827ms 49.47% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.076% 9674ms 48.70% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.12% 9663ms 48.64% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.13% 9653ms 48.59% CellCycleModelOdeHandler::SolveOdeToTime 80ms 0.4% 0.53% 9452ms 47.58% AbstractOneStepIvpOdeSolver::InternalSolve 860ms 4.33% 4.86% 8617ms 43.38% RungeKutta4IvpOdeSolver::CalculateNextYValue 3610ms 18.17% 23.03% 7557ms 38.04% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.03% 5152ms 25.93% MeshBasedCellPopulation::Update 91ms 0.46% 23.49% 4004ms 20.16% AbstractCellProperty::IsType (inline) 3ms 0.015% 23.50% 3970ms 19.98% Cylindrical2dMesh::ReMesh 598ms 3.01% 26.51% 2833ms 14.26% AbstractCellProperty::IsSame 0 0% 26.51% 2443ms 12.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 454ms 2.29% 28.80% 2235ms 11.25% std::type_info::operator== (inline) 0 0% 28.80% 2161ms 10.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.80% 2133ms 10.74% MutableMesh::ReMesh 14ms 0.07% 28.87% 2110ms 10.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.01% 28.88% 2037ms 10.25% AbstractCellPopulation::WriteResultsToFiles 856ms 4.31% 33.19% 1900ms 9.56% std::_Rb_tree::_M_lower_bound (inline) 1723ms 8.67% 41.86% 1723ms 8.67% __strcmp_avx2 166ms 0.84% 42.70% 1689ms 8.50% TetrahedralMesh::EdgeIterator::operator++ 68ms 0.34% 43.04% 1416ms 7.13% std::_Rb_tree::find (inline) 1ms 0.005% 43.04% 1143ms 5.75% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 43.07% 1124ms 5.66% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 52ms 0.26% 43.34% 1117ms 5.62% operator new 13ms 0.065% 43.40% 1094ms 5.51% TetrahedralMesh::ImportFromMesher 237ms 1.19% 44.59% 1052ms 5.30% __GI___libc_malloc 5ms 0.025% 44.62% 1028ms 5.17% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.05% 44.67% 995ms 5.01% std::set::insert (inline) 24ms 0.12% 44.79% 985ms 4.96% std::_Rb_tree::_M_insert_unique 25ms 0.13% 44.92% 964ms 4.85% std::__new_allocator::allocate (inline) 0 0% 44.92% 958ms 4.82% std::allocator_traits::allocate (inline) 0 0% 44.92% 866ms 4.36% std::set::count (inline) 0 0% 44.92% 764ms 3.85% triangulate 5ms 0.025% 44.94% 763ms 3.84% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 400ms 2.01% 46.95% 726ms 3.65% _int_malloc 49ms 0.25% 47.20% 717ms 3.61% std::map::operator[] (partial-inline) 8ms 0.04% 47.24% 707ms 3.56% CellPopulationElementWriter::Visit 3ms 0.015% 47.26% 688ms 3.46% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 47.26% 683ms 3.44% delaunay 2ms 0.01% 47.27% 682ms 3.43% divconqdelaunay 675ms 3.40% 50.66% 675ms 3.40% std::_Rb_tree::_S_right (inline) 632ms 3.18% 53.85% 639ms 3.22% WntCellCycleOdeSystem::CalculateStoppingEvent 15ms 0.076% 53.92% 630ms 3.17% std::less::operator() (inline) 28ms 0.14% 54.06% 625ms 3.15% std::_Rb_tree::_M_insert_ (inline) 193ms 0.97% 55.03% 617ms 3.11% __dynamic_cast 615ms 3.10% 58.13% 615ms 3.10% std::operator< (inline) 6ms 0.03% 58.16% 612ms 3.08% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.16% 611ms 3.08% std::_Rb_tree::_M_create_node (inline) 29ms 0.15% 58.31% 593ms 2.98% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 58.33% 586ms 2.95% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.33% 583ms 2.93% std::_Rb_tree::_M_get_node (inline) 0 0% 58.33% 580ms 2.92% std::_Rb_tree::lower_bound (inline) 0 0% 58.33% 580ms 2.92% std::map::lower_bound (inline) 30ms 0.15% 58.48% 564ms 2.84% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 58.48% 555ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.48% 546ms 2.75% std::map::find (inline) 6ms 0.03% 58.51% 539ms 2.71% MutableMesh::ReIndex 7ms 0.035% 58.55% 537ms 2.70% Element::Element 2ms 0.01% 58.56% 499ms 2.51% std::ostream::operator<< (inline) 14ms 0.07% 58.63% 498ms 2.51% Cylindrical2dMesh::CorrectNonPeriodicMesh 66ms 0.33% 58.96% 496ms 2.50% std::ostream::_M_insert 2ms 0.01% 58.97% 484ms 2.44% AbstractCellProperty::IsSubType (inline) 171ms 0.86% 59.83% 480ms 2.42% __GI___libc_free 11ms 0.055% 59.89% 475ms 2.39% Cylindrical2dMesh::ReconstructCylindricalMesh 8ms 0.04% 59.93% 470ms 2.37% Element::RegisterWithNodes (inline) 6ms 0.03% 59.96% 467ms 2.35% Node::AddElement 309ms 1.56% 61.51% 443ms 2.23% AbstractCellMutationState::AbstractCellMutationState 4ms 0.02% 61.53% 379ms 1.91% std::_Vector_base::_M_allocate (inline) 11ms 0.055% 61.59% 375ms 1.89% std::__new_allocator::deallocate (inline) 5ms 0.025% 61.61% 373ms 1.88% std::_Rb_tree::erase 1ms 0.005% 61.62% 372ms 1.87% std::set::erase (inline) 0 0% 61.62% 367ms 1.85% std::allocator_traits::deallocate (inline) 11ms 0.055% 61.67% 359ms 1.81% Node::RemoveElement 112ms 0.56% 62.24% 355ms 1.79% std::_Rb_tree::_M_erase 12ms 0.06% 62.30% 353ms 1.78% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 62.30% 338ms 1.70% std::_Rb_tree::_M_drop_node (inline) 25ms 0.13% 62.42% 337ms 1.70% Element::ResetIndex 129ms 0.65% 63.07% 336ms 1.69% std::_Rb_tree::_M_get_insert_unique_pos 16ms 0.081% 63.15% 332ms 1.67% divconqrecurse 331ms 1.67% 64.82% 331ms 1.67% std::type_info::name (inline) 23ms 0.12% 64.94% 328ms 1.65% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 64.95% 324ms 1.63% Cell::GetMutationState 3ms 0.015% 64.97% 314ms 1.58% NodeLocationWriter::Visit 4ms 0.02% 64.99% 311ms 1.57% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.04% 65.03% 311ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 157ms 0.79% 65.82% 311ms 1.57% __cxxabiv1::__si_class_type_info::__do_dyncast 91ms 0.46% 66.27% 310ms 1.56% mergehulls 259ms 1.30% 67.58% 309ms 1.56% _int_free 0 0% 67.58% 306ms 1.54% std::_Rb_tree::_M_put_node (inline) 0 0% 67.58% 304ms 1.53% std::set::~set (inline) 3ms 0.015% 67.59% 302ms 1.52% Cell::GetCellProliferativeType 21ms 0.11% 67.70% 277ms 1.39% std::_Rb_tree::_Rb_tree (partial-inline) 27ms 0.14% 67.83% 277ms 1.39% std::num_put::_M_insert_float 31ms 0.16% 67.99% 269ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.99% 269ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 19ms 0.096% 68.09% 267ms 1.34% AbstractTetrahedralElement::CalculateJacobian 1ms 0.005% 68.09% 261ms 1.31% std::set::set (inline) 7ms 0.035% 68.13% 253ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.076% 68.20% 249ms 1.25% std::vector::push_back (inline) 247ms 1.24% 69.45% 248ms 1.25% std::vector::operator[] (inline) 1ms 0.005% 69.45% 246ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 16ms 0.081% 69.53% 242ms 1.22% std::_Rb_tree::_M_erase_aux (inline) 8ms 0.04% 69.57% 227ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 23ms 0.12% 69.69% 223ms 1.12% std::_Rb_tree::_M_copy (inline) 14ms 0.07% 69.76% 222ms 1.12% std::vector::_M_realloc_insert 35ms 0.18% 69.93% 216ms 1.09% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.01% 69.94% 215ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 169ms 0.85% 70.79% 214ms 1.08% malloc_consolidate 6ms 0.03% 70.82% 213ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.015% 70.84% 211ms 1.06% std::__cxx11::collate::do_transform 22ms 0.11% 70.95% 206ms 1.04% TetrahedralMesh::Clear 3ms 0.015% 70.97% 206ms 1.04% alternateaxes 19ms 0.096% 71.06% 203ms 1.02% AbstractTetrahedralElement::RefreshJacobian 0 0% 71.06% 203ms 1.02% ___vsnprintf 22ms 0.11% 71.17% 203ms 1.02% __printf_buffer 0 0% 71.17% 203ms 1.02% __vsnprintf_internal (inline) 187ms 0.94% 72.11% 202ms 1.02% vertexmedian 158ms 0.8% 72.91% 200ms 1.01% AbstractElement::GetNodeGlobalIndex 1ms 0.005% 72.91% 199ms 1.00% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 72.92% 198ms 1% AbstractCentreBasedCellPopulation::GetDampingConstant 196ms 0.99% 73.91% 196ms 0.99% std::_Rb_tree_insert_and_rebalance 59ms 0.3% 74.21% 195ms 0.98% std::_Rb_tree::_M_clone_node (inline) 52ms 0.26% 74.47% 193ms 0.97% ApcOneHitCellMutationState::ApcOneHitCellMutationState 34ms 0.17% 74.64% 191ms 0.96% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.076% 74.72% 184ms 0.93% Element::MarkAsDeleted 0 0% 74.72% 178ms 0.9% OffLatticeSimulation::ApplyBoundaries 178ms 0.9% 75.61% 178ms 0.9% [libchaste_cell_based.so] 175ms 0.88% 76.49% 175ms 0.88% Node::GetIndex 5ms 0.025% 76.52% 172ms 0.87% __printf_fp_l_buffer 0 0% 76.52% 172ms 0.87% __printf_fp_spec (inline) 2ms 0.01% 76.53% 170ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.015% 76.54% 167ms 0.84% CellProliferativeTypesWriter::VisitCell 69ms 0.35% 76.89% 162ms 0.82% AbstractElement::GetNodeLocation 4ms 0.02% 76.91% 161ms 0.81% CellPropertyCollection::HasProperty 5ms 0.025% 76.94% 161ms 0.81% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 77ms 0.39% 77.32% 160ms 0.81% __printf_fp_buffer_1 0 0% 77.32% 158ms 0.8% Cell::HasCellProperty (inline) 7ms 0.035% 77.36% 144ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 143ms 0.72% 78.08% 143ms 0.72% unlink_chunk 141ms 0.71% 78.79% 141ms 0.71% incircle 4ms 0.02% 78.81% 140ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.005% 78.81% 140ms 0.7% boost::numeric::ublas::vector_assign (inline) 94ms 0.47% 79.29% 139ms 0.7% std::_Rb_tree::equal_range (inline) 32ms 0.16% 79.45% 135ms 0.68% TetrahedralMesh::EdgesEnd (partial-inline) 126ms 0.63% 80.08% 135ms 0.68% vertexsort 45ms 0.23% 80.31% 131ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 131ms 0.66% 80.97% 131ms 0.66% std::vector::size (inline) 130ms 0.65% 81.62% 130ms 0.65% AbstractCellProperty::~AbstractCellProperty 32ms 0.16% 81.78% 130ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.03% 81.81% 127ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.04% 81.85% 121ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 119ms 0.6% 82.45% 119ms 0.6% AbstractCellMutationState::~AbstractCellMutationState 40ms 0.2% 82.65% 117ms 0.59% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 82.65% 115ms 0.58% AbstractCellBasedWriter::OpenOutputFileForAppend 16ms 0.081% 82.73% 114ms 0.57% boost::detail::shared_count::~shared_count (inline) 0 0% 82.73% 114ms 0.57% boost::shared_ptr::~shared_ptr (inline) 1ms 0.005% 82.74% 112ms 0.56% Cell::SetCellProliferativeType 0 0% 82.74% 112ms 0.56% OutputFileHandler::OpenOutputFile 23ms 0.12% 82.86% 110ms 0.55% std::num_put::_M_insert_int 29ms 0.15% 83.00% 109ms 0.55% boost::numeric::ublas::indexing_vector_assign 1ms 0.005% 83.01% 108ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 83.01% 108ms 0.54% std::vector::vector (inline) 3ms 0.015% 83.02% 105ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.05% 83.07% 104ms 0.52% Node::~Node 59ms 0.3% 83.37% 101ms 0.51% Cylindrical2dMesh::GetVectorFromAtoB