File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16515ms, 83.01% of 19894ms total Dropped 786 nodes (cum <= 99.47ms) flat flat% sum% cum cum% 0 0% 0% 19847ms 99.76% __libc_start_call_main 0 0% 0% 19847ms 99.76% __libc_start_main_impl 0 0% 0% 19847ms 99.76% _start 0 0% 0% 19826ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19826ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19826ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19826ms 99.66% main 0 0% 0% 19786ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19786ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19786ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19759ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 15314ms 76.98% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10148ms 51.01% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.02% 10040ms 50.47% Cell::ReadyToDivide 4ms 0.02% 0.04% 9966ms 50.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.045% 9812ms 49.32% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.075% 0.12% 9796ms 49.24% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 9778ms 49.15% CellCycleModelOdeHandler::SolveOdeToTime 82ms 0.41% 0.54% 9623ms 48.37% AbstractOneStepIvpOdeSolver::InternalSolve 896ms 4.50% 5.05% 8750ms 43.98% RungeKutta4IvpOdeSolver::CalculateNextYValue 3580ms 18.00% 23.04% 7644ms 38.42% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.05% 5056ms 25.41% MeshBasedCellPopulation::Update 170ms 0.85% 23.90% 4102ms 20.62% AbstractCellProperty::IsType (inline) 7ms 0.035% 23.94% 3942ms 19.82% Cylindrical2dMesh::ReMesh 585ms 2.94% 26.88% 2911ms 14.63% AbstractCellProperty::IsSame 0 0% 26.88% 2451ms 12.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 418ms 2.10% 28.98% 2326ms 11.69% std::type_info::operator== (inline) 2ms 0.01% 28.99% 2118ms 10.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.99% 2091ms 10.51% MutableMesh::ReMesh 11ms 0.055% 29.04% 2077ms 10.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.04% 1991ms 10.01% AbstractCellPopulation::WriteResultsToFiles 836ms 4.20% 33.25% 1892ms 9.51% std::_Rb_tree::_M_lower_bound (inline) 1861ms 9.35% 42.60% 1861ms 9.35% __strcmp_avx2 147ms 0.74% 43.34% 1643ms 8.26% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.34% 43.68% 1413ms 7.10% std::_Rb_tree::find (inline) 4ms 0.02% 43.70% 1097ms 5.51% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 51ms 0.26% 43.95% 1083ms 5.44% operator new 8ms 0.04% 43.99% 1072ms 5.39% TetrahedralMesh::ImportFromMesher 0 0% 43.99% 1068ms 5.37% MeshBasedCellPopulation::UpdateNodePairs 229ms 1.15% 45.14% 1024ms 5.15% __GI___libc_malloc 11ms 0.055% 45.20% 993ms 4.99% std::set::insert (inline) 12ms 0.06% 45.26% 982ms 4.94% std::_Rb_tree::_M_insert_unique 37ms 0.19% 45.45% 949ms 4.77% std::__new_allocator::allocate (inline) 5ms 0.025% 45.47% 946ms 4.76% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 45.47% 945ms 4.75% std::allocator_traits::allocate (inline) 0 0% 45.47% 816ms 4.10% std::set::count (inline) 0 0% 45.47% 772ms 3.88% triangulate 4ms 0.02% 45.49% 735ms 3.69% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 62ms 0.31% 45.80% 718ms 3.61% std::map::operator[] (partial-inline) 0 0% 45.80% 708ms 3.56% delaunay 1ms 0.005% 45.81% 707ms 3.55% divconqdelaunay 705ms 3.54% 49.35% 705ms 3.54% std::_Rb_tree::_S_right (inline) 410ms 2.06% 51.41% 701ms 3.52% _int_malloc 2ms 0.01% 51.42% 694ms 3.49% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.06% 51.48% 659ms 3.31% CellPopulationElementWriter::Visit 652ms 3.28% 54.76% 659ms 3.31% WntCellCycleOdeSystem::CalculateStoppingEvent 23ms 0.12% 54.88% 638ms 3.21% std::less::operator() (inline) 0 0% 54.88% 626ms 3.15% std::_Rb_tree::_M_create_node (inline) 615ms 3.09% 57.97% 615ms 3.09% std::operator< (inline) 185ms 0.93% 58.90% 613ms 3.08% __dynamic_cast 32ms 0.16% 59.06% 608ms 3.06% std::_Rb_tree::_M_insert_ (inline) 0 0% 59.06% 605ms 3.04% std::_Rb_tree::_M_get_node (inline) 0 0% 59.06% 588ms 2.96% std::map::find (inline) 3ms 0.015% 59.07% 579ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 29ms 0.15% 59.22% 575ms 2.89% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 59.22% 565ms 2.84% std::_Rb_tree::lower_bound (inline) 0 0% 59.22% 565ms 2.84% std::map::lower_bound (inline) 0 0% 59.22% 561ms 2.82% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.025% 59.24% 554ms 2.78% CellPropertyCollection::GetPropertiesType (inline) 24ms 0.12% 59.36% 547ms 2.75% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 59.39% 543ms 2.73% Element::Element 7ms 0.035% 59.42% 541ms 2.72% MutableMesh::ReIndex 9ms 0.045% 59.47% 514ms 2.58% Cylindrical2dMesh::CorrectNonPeriodicMesh 11ms 0.055% 59.53% 488ms 2.45% Cylindrical2dMesh::ReconstructCylindricalMesh 55ms 0.28% 59.80% 483ms 2.43% std::ostream::_M_insert 0 0% 59.80% 483ms 2.43% std::ostream::operator<< (inline) 7ms 0.035% 59.84% 477ms 2.40% Element::RegisterWithNodes (inline) 4ms 0.02% 59.86% 464ms 2.33% Node::AddElement 2ms 0.01% 59.87% 444ms 2.23% AbstractCellProperty::IsSubType (inline) 309ms 1.55% 61.42% 431ms 2.17% AbstractCellMutationState::AbstractCellMutationState 134ms 0.67% 62.09% 414ms 2.08% __GI___libc_free 14ms 0.07% 62.16% 385ms 1.94% std::_Rb_tree::erase 3ms 0.015% 62.18% 385ms 1.94% std::set::erase (inline) 9ms 0.045% 62.22% 375ms 1.88% Node::RemoveElement 123ms 0.62% 62.84% 362ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 34ms 0.17% 63.01% 359ms 1.80% Element::ResetIndex 12ms 0.06% 63.07% 357ms 1.79% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 63.09% 343ms 1.72% std::_Vector_base::_M_allocate (inline) 14ms 0.07% 63.16% 341ms 1.71% divconqrecurse 105ms 0.53% 63.69% 329ms 1.65% std::_Rb_tree::_M_erase 10ms 0.05% 63.74% 326ms 1.64% std::__new_allocator::deallocate (inline) 100ms 0.5% 64.24% 323ms 1.62% mergehulls 3ms 0.015% 64.26% 321ms 1.61% NodeLocationWriter::Visit 0 0% 64.26% 319ms 1.60% std::allocator_traits::deallocate (inline) 5ms 0.025% 64.28% 313ms 1.57% AbstractCellPopulation::GetLocationIndexUsingCell 313ms 1.57% 65.85% 313ms 1.57% std::type_info::name (inline) 5ms 0.025% 65.88% 311ms 1.56% Cell::GetCellProliferativeType 133ms 0.67% 66.55% 307ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.09% 66.64% 296ms 1.49% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.025% 66.66% 295ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.66% 292ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 30ms 0.15% 66.81% 291ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 66.83% 291ms 1.46% Cell::GetMutationState 0 0% 66.83% 289ms 1.45% std::_Rb_tree::_M_drop_node (inline) 25ms 0.13% 66.95% 285ms 1.43% std::num_put::_M_insert_float 237ms 1.19% 68.15% 279ms 1.40% _int_free 276ms 1.39% 69.53% 276ms 1.39% std::vector::operator[] (inline) 0 0% 69.53% 266ms 1.34% std::set::~set (inline) 17ms 0.085% 69.62% 264ms 1.33% AbstractTetrahedralElement::CalculateJacobian 12ms 0.06% 69.68% 263ms 1.32% std::vector::push_back (inline) 262ms 1.32% 71.00% 262ms 1.32% [libchaste_cell_based.so] 0 0% 71.00% 258ms 1.30% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 71.01% 257ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 13ms 0.065% 71.08% 250ms 1.26% std::_Rb_tree::_Rb_tree (partial-inline) 10ms 0.05% 71.13% 247ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 12ms 0.06% 71.19% 241ms 1.21% std::vector::_M_realloc_insert 3ms 0.015% 71.20% 239ms 1.20% alternateaxes 221ms 1.11% 72.31% 235ms 1.18% vertexmedian 5ms 0.025% 72.34% 233ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 72.34% 230ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.025% 72.36% 228ms 1.15% std::__cxx11::collate::do_transform 59ms 0.3% 72.66% 223ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.01% 72.67% 218ms 1.10% ___vsnprintf 0 0% 72.67% 216ms 1.09% __vsnprintf_internal (inline) 21ms 0.11% 72.78% 215ms 1.08% __printf_buffer 7ms 0.035% 72.81% 215ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 21ms 0.11% 72.92% 214ms 1.08% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 72.93% 214ms 1.08% std::set::set (inline) 155ms 0.78% 73.71% 211ms 1.06% AbstractElement::GetNodeGlobalIndex 11ms 0.055% 73.76% 201ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 47ms 0.24% 74.00% 199ms 1.00% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 19ms 0.096% 74.09% 196ms 0.99% AbstractTetrahedralElement::RefreshJacobian 2ms 0.01% 74.10% 192ms 0.97% MeshBasedCellPopulation::GetDampingConstant 0 0% 74.10% 190ms 0.96% AbstractCentreBasedCellPopulation::GetDampingConstant 79ms 0.4% 74.50% 190ms 0.96% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 74.50% 190ms 0.96% OffLatticeSimulation::ApplyBoundaries 46ms 0.23% 74.73% 190ms 0.96% std::_Rb_tree::_M_clone_node (inline) 124ms 0.62% 75.35% 181ms 0.91% malloc_consolidate 178ms 0.89% 76.25% 178ms 0.89% std::_Rb_tree_insert_and_rebalance 14ms 0.07% 76.32% 176ms 0.88% TetrahedralMesh::Clear 174ms 0.87% 77.19% 174ms 0.87% Node::GetIndex 11ms 0.055% 77.25% 173ms 0.87% Element::MarkAsDeleted 6ms 0.03% 77.28% 168ms 0.84% __printf_fp_l_buffer 0 0% 77.28% 168ms 0.84% __printf_fp_spec (inline) 2ms 0.01% 77.29% 164ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 114ms 0.57% 77.86% 164ms 0.82% std::_Rb_tree::equal_range (inline) 73ms 0.37% 78.23% 157ms 0.79% __printf_fp_buffer_1 76ms 0.38% 78.61% 154ms 0.77% AbstractElement::GetNodeLocation 8ms 0.04% 78.65% 154ms 0.77% CellPropertyCollection::HasProperty 151ms 0.76% 79.41% 151ms 0.76% unlink_chunk 150ms 0.75% 80.16% 150ms 0.75% std::vector::size (inline) 0 0% 80.16% 149ms 0.75% Cell::HasCellProperty (inline) 0 0% 80.16% 149ms 0.75% CellProliferativeTypesWriter::VisitCell 6ms 0.03% 80.20% 143ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 80.20% 142ms 0.71% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.20% 141ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.20% 138ms 0.69% OutputFileHandler::OpenOutputFile 135ms 0.68% 80.87% 135ms 0.68% incircle 3ms 0.015% 80.89% 133ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 6ms 0.03% 80.92% 132ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 4ms 0.02% 80.94% 130ms 0.65% boost::numeric::ublas::vector_assign (inline) 1ms 0.005% 80.94% 125ms 0.63% Cell::SetCellProliferativeType 0 0% 80.94% 121ms 0.61% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 33ms 0.17% 81.11% 121ms 0.61% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 110ms 0.55% 81.66% 119ms 0.6% vertexsort 40ms 0.2% 81.86% 115ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 69ms 0.35% 82.21% 113ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.01% 82.22% 113ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 11ms 0.055% 82.28% 113ms 0.57% boost::detail::shared_count::~shared_count (inline) 5ms 0.025% 82.30% 113ms 0.57% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.30% 113ms 0.57% boost::shared_ptr::~shared_ptr (inline) 2ms 0.01% 82.31% 110ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 21ms 0.11% 82.42% 110ms 0.55% TetrahedralMesh::EdgesEnd 0 0% 82.42% 108ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 21ms 0.11% 82.52% 102ms 0.51% boost::numeric::ublas::indexing_vector_assign 98ms 0.49% 83.01% 100ms 0.5% boost::detail::sp_counted_base::release