File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17056ms, 84.56% of 20171ms total Dropped 778 nodes (cum <= 100.86ms) flat flat% sum% cum cum% 0 0% 0% 20128ms 99.79% __libc_start_call_main 0 0% 0% 20128ms 99.79% __libc_start_main_impl 0 0% 0% 20128ms 99.79% _start 0 0% 0% 20109ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20109ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20109ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20109ms 99.69% main 0 0% 0% 20074ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20074ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20074ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20047ms 99.39% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15602ms 77.35% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0099% 0.015% 10410ms 51.61% AbstractCellBasedSimulation::DoCellBirth 15ms 0.074% 0.089% 10306ms 51.09% Cell::ReadyToDivide 1ms 0.005% 0.094% 10238ms 50.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.094% 10082ms 49.98% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.084% 0.18% 10077ms 49.96% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.2% 10058ms 49.86% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.39% 0.59% 9883ms 49.00% AbstractOneStepIvpOdeSolver::InternalSolve 860ms 4.26% 4.85% 9041ms 44.82% RungeKutta4IvpOdeSolver::CalculateNextYValue 3693ms 18.31% 23.16% 7953ms 39.43% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.17% 5098ms 25.27% MeshBasedCellPopulation::Update 189ms 0.94% 24.10% 4274ms 21.19% AbstractCellProperty::IsType (inline) 4ms 0.02% 24.12% 3964ms 19.65% Cylindrical2dMesh::ReMesh 749ms 3.71% 27.84% 3014ms 14.94% AbstractCellProperty::IsSame 0 0% 27.84% 2471ms 12.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 423ms 2.10% 29.93% 2265ms 11.23% std::type_info::operator== (inline) 1ms 0.005% 29.94% 2171ms 10.76% MutableMesh::ReMesh 0 0% 29.94% 2157ms 10.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.05% 29.99% 2119ms 10.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.99% 1968ms 9.76% AbstractCellPopulation::WriteResultsToFiles 1840ms 9.12% 39.11% 1840ms 9.12% __strcmp_avx2 775ms 3.84% 42.95% 1815ms 9.00% std::_Rb_tree::_M_lower_bound (inline) 169ms 0.84% 43.79% 1621ms 8.04% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.3% 44.09% 1352ms 6.70% std::_Rb_tree::find (inline) 6ms 0.03% 44.12% 1101ms 5.46% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.005% 44.12% 1094ms 5.42% MeshBasedCellPopulation::UpdateNodePairs 14ms 0.069% 44.19% 1086ms 5.38% TetrahedralMesh::ImportFromMesher 58ms 0.29% 44.48% 1035ms 5.13% operator new 12ms 0.059% 44.54% 976ms 4.84% MeshBasedCellPopulation::SpringIterator::operator++ 232ms 1.15% 45.69% 966ms 4.79% __GI___libc_malloc 7ms 0.035% 45.72% 948ms 4.70% std::set::insert (inline) 13ms 0.064% 45.79% 941ms 4.67% std::_Rb_tree::_M_insert_unique 50ms 0.25% 46.04% 909ms 4.51% std::__new_allocator::allocate (inline) 0 0% 46.04% 902ms 4.47% std::allocator_traits::allocate (inline) 0 0% 46.04% 813ms 4.03% triangulate 0 0% 46.04% 799ms 3.96% std::set::count (inline) 2ms 0.0099% 46.05% 746ms 3.70% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.0099% 46.06% 744ms 3.69% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 46.06% 740ms 3.67% delaunay 2ms 0.0099% 46.07% 740ms 3.67% divconqdelaunay 6ms 0.03% 46.10% 702ms 3.48% CellPopulationElementWriter::Visit 73ms 0.36% 46.46% 687ms 3.41% std::map::operator[] (partial-inline) 682ms 3.38% 49.84% 682ms 3.38% std::_Rb_tree::_S_right (inline) 384ms 1.90% 51.74% 665ms 3.30% _int_malloc 166ms 0.82% 52.57% 649ms 3.22% __dynamic_cast 631ms 3.13% 55.69% 641ms 3.18% WntCellCycleOdeSystem::CalculateStoppingEvent 25ms 0.12% 55.82% 624ms 3.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 18ms 0.089% 55.91% 605ms 3.00% std::less::operator() (inline) 6ms 0.03% 55.94% 600ms 2.97% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.94% 589ms 2.92% std::_Rb_tree::_M_create_node (inline) 587ms 2.91% 58.85% 587ms 2.91% std::operator< (inline) 9ms 0.045% 58.89% 585ms 2.90% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.094% 58.99% 568ms 2.82% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.99% 559ms 2.77% std::_Rb_tree::_M_get_node (inline) 0 0% 58.99% 548ms 2.72% std::map::find (inline) 17ms 0.084% 59.07% 547ms 2.71% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 59.07% 541ms 2.68% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 59.07% 540ms 2.68% std::_Rb_tree::lower_bound (inline) 0 0% 59.07% 540ms 2.68% std::map::lower_bound (inline) 8ms 0.04% 59.11% 529ms 2.62% Cylindrical2dMesh::ReconstructCylindricalMesh 4ms 0.02% 59.13% 511ms 2.53% Element::Element 12ms 0.059% 59.19% 496ms 2.46% MutableMesh::ReIndex 2ms 0.0099% 59.20% 480ms 2.38% std::ostream::operator<< (inline) 76ms 0.38% 59.58% 477ms 2.36% std::ostream::_M_insert 4ms 0.02% 59.60% 474ms 2.35% AbstractCellProperty::IsSubType (inline) 16ms 0.079% 59.67% 472ms 2.34% Cylindrical2dMesh::CorrectNonPeriodicMesh 298ms 1.48% 61.15% 463ms 2.30% AbstractCellMutationState::AbstractCellMutationState 16ms 0.079% 61.23% 444ms 2.20% Element::RegisterWithNodes (inline) 155ms 0.77% 62.00% 430ms 2.13% __GI___libc_free 13ms 0.064% 62.06% 429ms 2.13% Node::AddElement 11ms 0.055% 62.12% 398ms 1.97% std::_Rb_tree::erase 0 0% 62.12% 397ms 1.97% std::set::erase (inline) 8ms 0.04% 62.16% 388ms 1.92% Node::RemoveElement 16ms 0.079% 62.24% 373ms 1.85% divconqrecurse 102ms 0.51% 62.74% 366ms 1.81% std::_Rb_tree::_M_erase 141ms 0.7% 63.44% 360ms 1.78% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.05% 63.49% 358ms 1.77% std::__new_allocator::deallocate (inline) 159ms 0.79% 64.28% 350ms 1.74% __cxxabiv1::__si_class_type_info::__do_dyncast 98ms 0.49% 64.77% 350ms 1.74% mergehulls 0 0% 64.77% 350ms 1.74% std::allocator_traits::deallocate (inline) 19ms 0.094% 64.86% 348ms 1.73% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 64.88% 347ms 1.72% std::_Vector_base::_M_allocate (inline) 0 0% 64.88% 327ms 1.62% std::_Rb_tree::_M_drop_node (inline) 16ms 0.079% 64.96% 317ms 1.57% Element::ResetIndex 0 0% 64.96% 315ms 1.56% std::set::~set (inline) 4ms 0.02% 64.98% 314ms 1.56% Cell::GetCellProliferativeType 1ms 0.005% 64.98% 314ms 1.56% Cell::GetMutationState 7ms 0.035% 65.02% 309ms 1.53% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.005% 65.02% 309ms 1.53% NodeLocationWriter::Visit 1ms 0.005% 65.03% 303ms 1.50% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.025% 65.05% 297ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 295ms 1.46% 66.52% 295ms 1.46% std::type_info::name (inline) 1ms 0.005% 66.52% 288ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 33ms 0.16% 66.68% 287ms 1.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 283ms 1.40% 68.09% 285ms 1.41% std::vector::operator[] (inline) 0 0% 68.09% 284ms 1.41% std::_Rb_tree::_M_put_node (inline) 20ms 0.099% 68.19% 282ms 1.40% std::_Rb_tree::_Rb_tree (partial-inline) 224ms 1.11% 69.30% 273ms 1.35% _int_free 6ms 0.03% 69.33% 261ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 13ms 0.064% 69.39% 256ms 1.27% std::vector::push_back (inline) 13ms 0.064% 69.46% 255ms 1.26% std::num_put::_M_insert_float 14ms 0.069% 69.53% 252ms 1.25% AbstractTetrahedralElement::CalculateJacobian 252ms 1.25% 70.77% 252ms 1.25% [libchaste_cell_based.so] 2ms 0.0099% 70.78% 247ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.0099% 70.79% 247ms 1.22% std::set::set (inline) 8ms 0.04% 70.83% 237ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 16ms 0.079% 70.91% 235ms 1.17% std::vector::_M_realloc_insert 27ms 0.13% 71.05% 233ms 1.16% std::_Rb_tree::_M_copy (inline) 5ms 0.025% 71.07% 229ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 71.09% 229ms 1.14% alternateaxes 208ms 1.03% 72.12% 226ms 1.12% vertexmedian 65ms 0.32% 72.44% 225ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 49ms 0.24% 72.68% 224ms 1.11% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.0099% 72.69% 223ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 12ms 0.059% 72.75% 209ms 1.04% Element::MarkAsDeleted 5ms 0.025% 72.78% 208ms 1.03% std::__cxx11::collate::do_transform 62ms 0.31% 73.09% 205ms 1.02% std::_Rb_tree::_M_clone_node (inline) 32ms 0.16% 73.24% 204ms 1.01% TetrahedralMesh::Clear 78ms 0.39% 73.63% 202ms 1.00% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 10ms 0.05% 73.68% 200ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 20ms 0.099% 73.78% 200ms 0.99% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0099% 73.79% 199ms 0.99% ___vsnprintf 1ms 0.005% 73.79% 197ms 0.98% __vsnprintf_internal (inline) 26ms 0.13% 73.92% 196ms 0.97% __printf_buffer 1ms 0.005% 73.93% 186ms 0.92% OffLatticeSimulation::ApplyBoundaries 128ms 0.63% 74.56% 181ms 0.9% AbstractElement::GetNodeGlobalIndex 1ms 0.005% 74.57% 181ms 0.9% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 74.58% 180ms 0.89% AbstractCentreBasedCellPopulation::GetDampingConstant 131ms 0.65% 75.23% 178ms 0.88% malloc_consolidate 7ms 0.035% 75.27% 170ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 168ms 0.83% 76.10% 168ms 0.83% Node::GetIndex 164ms 0.81% 76.91% 164ms 0.81% std::_Rb_tree_insert_and_rebalance 60ms 0.3% 77.21% 163ms 0.81% AbstractElement::GetNodeLocation 106ms 0.53% 77.74% 161ms 0.8% std::_Rb_tree::equal_range (inline) 2ms 0.0099% 77.75% 158ms 0.78% CellProliferativeTypesWriter::VisitCell 158ms 0.78% 78.53% 158ms 0.78% incircle 1ms 0.005% 78.53% 153ms 0.76% __printf_fp_spec (inline) 5ms 0.025% 78.56% 152ms 0.75% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.03% 78.59% 152ms 0.75% __printf_fp_l_buffer 2ms 0.0099% 78.60% 146ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.025% 78.62% 142ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 142ms 0.7% 79.33% 142ms 0.7% unlink_chunk 65ms 0.32% 79.65% 140ms 0.69% __printf_fp_buffer_1 46ms 0.23% 79.88% 136ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 135ms 0.67% 80.55% 135ms 0.67% std::vector::size (inline) 7ms 0.035% 80.58% 131ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.02% 80.60% 128ms 0.63% CellPropertyCollection::HasProperty 1ms 0.005% 80.61% 126ms 0.62% boost::numeric::ublas::vector_assign (inline) 120ms 0.59% 81.20% 125ms 0.62% vertexsort 0 0% 81.20% 124ms 0.61% Cell::HasCellProperty (inline) 18ms 0.089% 81.29% 123ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 81.29% 123ms 0.61% boost::shared_ptr::~shared_ptr (inline) 36ms 0.18% 81.47% 121ms 0.6% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 78ms 0.39% 81.86% 121ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 44ms 0.22% 82.07% 121ms 0.6% std::__ostream_insert 3ms 0.015% 82.09% 117ms 0.58% Cell::SetCellProliferativeType 19ms 0.094% 82.18% 116ms 0.58% TetrahedralMesh::EdgesEnd 115ms 0.57% 82.75% 115ms 0.57% std::_Rb_tree_rebalance_for_erase 21ms 0.1% 82.86% 112ms 0.56% std::num_put::_M_insert_int 8ms 0.04% 82.90% 111ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 108ms 0.54% 83.43% 108ms 0.54% AbstractCellProperty::~AbstractCellProperty 10ms 0.05% 83.48% 108ms 0.54% Node::~Node 104ms 0.52% 84.00% 105ms 0.52% boost::detail::sp_counted_base::release 10ms 0.05% 84.05% 105ms 0.52% boost::numeric::ublas::c_vector::c_vector (inline) 103ms 0.51% 84.56% 103ms 0.51% std::_Rb_tree_increment