File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16787ms, 84.28% of 19919ms total Dropped 777 nodes (cum <= 99.59ms) flat flat% sum% cum cum% 0 0% 0% 19874ms 99.77% __libc_start_call_main 0 0% 0% 19874ms 99.77% __libc_start_main_impl 0 0% 0% 19874ms 99.77% _start 0 0% 0% 19856ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19856ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19856ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19856ms 99.68% main 0 0% 0% 19821ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19820ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19820ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19792ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15363ms 77.13% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 10155ms 50.98% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.025% 10058ms 50.49% Cell::ReadyToDivide 4ms 0.02% 0.045% 10001ms 50.21% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.05% 9859ms 49.50% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.095% 9853ms 49.47% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.095% 9839ms 49.40% CellCycleModelOdeHandler::SolveOdeToTime 71ms 0.36% 0.45% 9687ms 48.63% AbstractOneStepIvpOdeSolver::InternalSolve 915ms 4.59% 5.05% 8862ms 44.49% RungeKutta4IvpOdeSolver::CalculateNextYValue 3615ms 18.15% 23.19% 7726ms 38.79% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.19% 5111ms 25.66% MeshBasedCellPopulation::Update 185ms 0.93% 24.12% 4128ms 20.72% AbstractCellProperty::IsType (inline) 5ms 0.025% 24.15% 3942ms 19.79% Cylindrical2dMesh::ReMesh 572ms 2.87% 27.02% 2878ms 14.45% AbstractCellProperty::IsSame 0 0% 27.02% 2488ms 12.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 427ms 2.14% 29.16% 2306ms 11.58% std::type_info::operator== (inline) 1ms 0.005% 29.17% 2125ms 10.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.17% 2114ms 10.61% MutableMesh::ReMesh 15ms 0.075% 29.24% 2068ms 10.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.24% 1935ms 9.71% AbstractCellPopulation::WriteResultsToFiles 790ms 3.97% 33.21% 1833ms 9.20% std::_Rb_tree::_M_lower_bound (inline) 1822ms 9.15% 42.36% 1822ms 9.15% __strcmp_avx2 168ms 0.84% 43.20% 1686ms 8.46% TetrahedralMesh::EdgeIterator::operator++ 74ms 0.37% 43.57% 1393ms 6.99% std::_Rb_tree::find (inline) 2ms 0.01% 43.58% 1137ms 5.71% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 43.61% 1121ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 52ms 0.26% 43.87% 1092ms 5.48% operator new 16ms 0.08% 43.95% 1074ms 5.39% TetrahedralMesh::ImportFromMesher 263ms 1.32% 45.27% 1023ms 5.14% __GI___libc_malloc 14ms 0.07% 45.34% 1012ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.035% 45.38% 998ms 5.01% std::set::insert (inline) 17ms 0.085% 45.46% 991ms 4.98% std::_Rb_tree::_M_insert_unique 36ms 0.18% 45.64% 957ms 4.80% std::__new_allocator::allocate (inline) 0 0% 45.64% 949ms 4.76% std::allocator_traits::allocate (inline) 0 0% 45.64% 853ms 4.28% std::set::count (inline) 1ms 0.005% 45.65% 804ms 4.04% triangulate 4ms 0.02% 45.67% 720ms 3.61% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.67% 718ms 3.60% delaunay 2ms 0.01% 45.68% 718ms 3.60% divconqdelaunay 2ms 0.01% 45.69% 685ms 3.44% AbstractTwoBodyInteractionForce::AddForceContribution 391ms 1.96% 47.65% 682ms 3.42% _int_malloc 44ms 0.22% 47.87% 662ms 3.32% std::map::operator[] (partial-inline) 28ms 0.14% 48.01% 654ms 3.28% std::less::operator() (inline) 650ms 3.26% 51.28% 650ms 3.26% std::_Rb_tree::_S_right (inline) 7ms 0.035% 51.31% 648ms 3.25% CellPopulationElementWriter::Visit 0 0% 51.31% 644ms 3.23% std::_Rb_tree::_M_create_node (inline) 618ms 3.10% 54.42% 633ms 3.18% WntCellCycleOdeSystem::CalculateStoppingEvent 626ms 3.14% 57.56% 626ms 3.14% std::operator< (inline) 18ms 0.09% 57.65% 620ms 3.11% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.65% 610ms 3.06% std::_Rb_tree::_M_get_node (inline) 164ms 0.82% 58.47% 604ms 3.03% __dynamic_cast 5ms 0.025% 58.50% 597ms 3.00% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.50% 585ms 2.94% std::_Rb_tree::_Alloc_node::operator() (inline) 20ms 0.1% 58.60% 570ms 2.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.035% 58.63% 564ms 2.83% Element::Element 0 0% 58.63% 538ms 2.70% std::map::find (inline) 12ms 0.06% 58.69% 534ms 2.68% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.69% 530ms 2.66% std::_Rb_tree::lower_bound (inline) 0 0% 58.69% 530ms 2.66% std::map::lower_bound (inline) 13ms 0.065% 58.76% 522ms 2.62% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.05% 58.81% 520ms 2.61% MutableMesh::ReIndex 1ms 0.005% 58.81% 505ms 2.54% std::ostream::operator<< (inline) 79ms 0.4% 59.21% 504ms 2.53% std::ostream::_M_insert 7ms 0.035% 59.24% 501ms 2.52% Element::RegisterWithNodes (inline) 8ms 0.04% 59.29% 492ms 2.47% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.045% 59.33% 492ms 2.47% Node::AddElement 19ms 0.095% 59.43% 491ms 2.46% Cylindrical2dMesh::CorrectNonPeriodicMesh 330ms 1.66% 61.08% 458ms 2.30% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 61.10% 435ms 2.18% AbstractCellProperty::IsSubType (inline) 136ms 0.68% 61.78% 422ms 2.12% __GI___libc_free 15ms 0.075% 61.86% 396ms 1.99% Node::RemoveElement 7ms 0.035% 61.89% 391ms 1.96% std::_Rb_tree::erase 1ms 0.005% 61.90% 391ms 1.96% std::set::erase (inline) 35ms 0.18% 62.07% 373ms 1.87% Element::ResetIndex 19ms 0.095% 62.17% 369ms 1.85% divconqrecurse 146ms 0.73% 62.90% 354ms 1.78% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.055% 62.95% 352ms 1.77% std::__new_allocator::deallocate (inline) 0 0% 62.95% 348ms 1.75% std::allocator_traits::deallocate (inline) 84ms 0.42% 63.38% 344ms 1.73% mergehulls 95ms 0.48% 63.85% 343ms 1.72% std::_Rb_tree::_M_erase 2ms 0.01% 63.86% 341ms 1.71% std::_Vector_base::_M_allocate (inline) 10ms 0.05% 63.91% 336ms 1.69% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 19ms 0.095% 64.01% 317ms 1.59% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 64.02% 314ms 1.58% NodeLocationWriter::Visit 313ms 1.57% 65.60% 313ms 1.57% std::type_info::name (inline) 9ms 0.045% 65.64% 311ms 1.56% Cell::GetCellProliferativeType 146ms 0.73% 66.37% 311ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.37% 309ms 1.55% std::_Rb_tree::_M_drop_node (inline) 8ms 0.04% 66.41% 306ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 7ms 0.035% 66.45% 298ms 1.50% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.005% 66.45% 291ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 44ms 0.22% 66.68% 289ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.68% 288ms 1.45% std::set::~set (inline) 225ms 1.13% 67.80% 286ms 1.44% _int_free 0 0% 67.80% 275ms 1.38% std::_Rb_tree::_M_put_node (inline) 22ms 0.11% 67.92% 275ms 1.38% std::num_put::_M_insert_float 268ms 1.35% 69.26% 271ms 1.36% std::vector::operator[] (inline) 7ms 0.035% 69.30% 269ms 1.35% Cell::GetMutationState 11ms 0.055% 69.35% 266ms 1.34% std::_Rb_tree::_Rb_tree (partial-inline) 16ms 0.08% 69.43% 250ms 1.26% AbstractTetrahedralElement::CalculateJacobian 4ms 0.02% 69.45% 236ms 1.18% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.01% 69.46% 236ms 1.18% std::set::set (inline) 24ms 0.12% 69.58% 234ms 1.17% std::_Rb_tree::_M_copy (inline) 233ms 1.17% 70.75% 233ms 1.17% [libchaste_cell_based.so] 15ms 0.075% 70.83% 233ms 1.17% std::vector::push_back (inline) 7ms 0.035% 70.86% 228ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.02% 70.88% 226ms 1.13% alternateaxes 0 0% 70.88% 224ms 1.12% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 70.90% 223ms 1.12% std::__cxx11::collate::do_transform 207ms 1.04% 71.94% 222ms 1.11% vertexmedian 12ms 0.06% 72.00% 221ms 1.11% std::_Rb_tree::_M_erase_aux (inline) 68ms 0.34% 72.34% 220ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 3ms 0.015% 72.35% 218ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 48ms 0.24% 72.59% 215ms 1.08% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 72.59% 214ms 1.07% __vsnprintf_internal (inline) 0 0% 72.59% 213ms 1.07% ___vsnprintf 1ms 0.005% 72.60% 212ms 1.06% TetrahedralMesh::RefreshJacobianCachedData 24ms 0.12% 72.72% 210ms 1.05% __printf_buffer 72ms 0.36% 73.08% 209ms 1.05% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.03% 73.11% 209ms 1.05% std::vector::_M_realloc_insert 56ms 0.28% 73.39% 208ms 1.04% std::_Rb_tree::_M_clone_node (inline) 10ms 0.05% 73.44% 200ms 1.00% Element::MarkAsDeleted 142ms 0.71% 74.16% 190ms 0.95% malloc_consolidate 138ms 0.69% 74.85% 187ms 0.94% AbstractElement::GetNodeGlobalIndex 187ms 0.94% 75.79% 187ms 0.94% std::_Rb_tree_insert_and_rebalance 183ms 0.92% 76.71% 183ms 0.92% Node::GetIndex 18ms 0.09% 76.80% 181ms 0.91% AbstractTetrahedralElement::RefreshJacobian 7ms 0.035% 76.83% 173ms 0.87% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.005% 76.84% 172ms 0.86% __printf_fp_spec (inline) 7ms 0.035% 76.87% 171ms 0.86% __printf_fp_l_buffer 4ms 0.02% 76.89% 170ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 114ms 0.57% 77.46% 170ms 0.85% std::_Rb_tree::equal_range (inline) 3ms 0.015% 77.48% 166ms 0.83% CellProliferativeTypesWriter::VisitCell 1ms 0.005% 77.48% 162ms 0.81% MeshBasedCellPopulation::GetDampingConstant 17ms 0.085% 77.57% 162ms 0.81% TetrahedralMesh::Clear 1ms 0.005% 77.57% 161ms 0.81% AbstractCentreBasedCellPopulation::GetDampingConstant 160ms 0.8% 78.38% 160ms 0.8% incircle 76ms 0.38% 78.76% 155ms 0.78% __printf_fp_buffer_1 63ms 0.32% 79.08% 151ms 0.76% AbstractElement::GetNodeLocation 6ms 0.03% 79.11% 147ms 0.74% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 38ms 0.19% 79.30% 142ms 0.71% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 139ms 0.7% 79.99% 139ms 0.7% std::vector::size (inline) 136ms 0.68% 80.68% 136ms 0.68% unlink_chunk 2ms 0.01% 80.69% 133ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 44ms 0.22% 80.91% 129ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.03% 80.94% 128ms 0.64% CellPropertyCollection::HasProperty 37ms 0.19% 81.12% 127ms 0.64% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.06% 81.18% 126ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 81.18% 126ms 0.63% Cell::HasCellProperty (inline) 2ms 0.01% 81.19% 125ms 0.63% boost::numeric::ublas::vector_assign (inline) 6ms 0.03% 81.22% 125ms 0.63% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 12ms 0.06% 81.28% 123ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 62ms 0.31% 81.60% 119ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 3ms 0.015% 81.61% 118ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.005% 81.62% 115ms 0.58% Cell::SetCellProliferativeType 6ms 0.03% 81.65% 115ms 0.58% MeshBasedCellPopulation::SpringsEnd (inline) 110ms 0.55% 82.20% 110ms 0.55% AbstractElement::IsDeleted 37ms 0.19% 82.38% 110ms 0.55% std::num_put::_M_insert_int 104ms 0.52% 82.91% 110ms 0.55% vertexsort 12ms 0.06% 82.97% 109ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 82.97% 109ms 0.55% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.97% 108ms 0.54% AbstractCellBasedWriter::OpenOutputFileForAppend 108ms 0.54% 83.51% 108ms 0.54% AbstractCellMutationState::~AbstractCellMutationState 2ms 0.01% 83.52% 106ms 0.53% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 83.52% 104ms 0.52% OutputFileHandler::OpenOutputFile 50ms 0.25% 83.77% 103ms 0.52% std::__ostream_insert 101ms 0.51% 84.28% 101ms 0.51% AbstractCellProperty::~AbstractCellProperty