File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12446ms, 84.15% of 14791ms total Dropped 758 nodes (cum <= 73.95ms) flat flat% sum% cum cum% 0 0% 0% 14755ms 99.76% __libc_start_call_main 0 0% 0% 14755ms 99.76% __libc_start_main_impl 0 0% 0% 14755ms 99.76% _start 0 0% 0% 14740ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14740ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14740ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14740ms 99.66% main 0 0% 0% 14701ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14701ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14701ms 99.39% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14680ms 99.25% AbstractCellBasedSimulation::Solve 1ms 0.0068% 0.0068% 11246ms 76.03% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0068% 7137ms 48.25% AbstractCellBasedSimulation::DoCellBirth 2ms 0.014% 0.02% 7066ms 47.77% Cell::ReadyToDivide 4ms 0.027% 0.047% 7017ms 47.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0068% 0.054% 6921ms 46.79% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.054% 0.11% 6916ms 46.76% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.034% 0.14% 6903ms 46.67% CellCycleModelOdeHandler::SolveOdeToTime 49ms 0.33% 0.47% 6761ms 45.71% AbstractOneStepIvpOdeSolver::InternalSolve 811ms 5.48% 5.96% 6034ms 40.80% RungeKutta4IvpOdeSolver::CalculateNextYValue 2160ms 14.60% 20.56% 5086ms 34.39% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0068% 20.57% 4028ms 27.23% MeshBasedCellPopulation::Update 2ms 0.014% 20.58% 3069ms 20.75% Cylindrical2dMesh::ReMesh 50ms 0.34% 20.92% 2895ms 19.57% AbstractCellProperty::IsType (inline) 1ms 0.0068% 20.92% 1908ms 12.90% OffLatticeSimulation::UpdateCellLocationsAndTopology 207ms 1.40% 22.32% 1838ms 12.43% AbstractCellProperty::IsSame 0 0% 22.32% 1735ms 11.73% MutableMesh::ReMesh 1ms 0.0068% 22.33% 1681ms 11.37% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.034% 22.36% 1642ms 11.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 136ms 0.92% 23.28% 1631ms 11.03% std::type_info::operator== (inline) 1589ms 10.74% 34.03% 1589ms 10.74% __strcmp_evex 0 0% 34.03% 1521ms 10.28% AbstractCellPopulation::WriteResultsToFiles 653ms 4.41% 38.44% 1431ms 9.67% std::_Rb_tree::_M_lower_bound (inline) 141ms 0.95% 39.40% 1326ms 8.96% TetrahedralMesh::EdgeIterator::operator++ 49ms 0.33% 39.73% 1083ms 7.32% std::_Rb_tree::find (inline) 0 0% 39.73% 929ms 6.28% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.02% 39.75% 896ms 6.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.081% 39.83% 870ms 5.88% TetrahedralMesh::ImportFromMesher 7ms 0.047% 39.88% 820ms 5.54% MeshBasedCellPopulation::SpringIterator::operator++ 30ms 0.2% 40.08% 799ms 5.40% operator new 201ms 1.36% 41.44% 757ms 5.12% __GI___libc_malloc 9ms 0.061% 41.50% 724ms 4.89% std::set::insert (inline) 10ms 0.068% 41.57% 715ms 4.83% std::_Rb_tree::_M_insert_unique 22ms 0.15% 41.71% 680ms 4.60% std::__new_allocator::allocate (inline) 0 0% 41.71% 680ms 4.60% std::allocator_traits::allocate (inline) 0 0% 41.71% 670ms 4.53% std::set::count (inline) 0 0% 41.71% 657ms 4.44% triangulate 0 0% 41.71% 592ms 4.00% delaunay 3ms 0.02% 41.73% 592ms 4.00% divconqdelaunay 579ms 3.91% 45.65% 579ms 3.91% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.02% 45.67% 532ms 3.60% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.02% 45.69% 531ms 3.59% CellPopulationElementWriter::Visit 44ms 0.3% 45.99% 525ms 3.55% std::map::operator[] (partial-inline) 1ms 0.0068% 45.99% 511ms 3.45% AbstractTwoBodyInteractionForce::AddForceContribution 510ms 3.45% 49.44% 510ms 3.45% std::_Rb_tree::_S_right (inline) 136ms 0.92% 50.36% 505ms 3.41% __dynamic_cast 267ms 1.81% 52.17% 497ms 3.36% _int_malloc 14ms 0.095% 52.26% 487ms 3.29% std::less::operator() (inline) 473ms 3.20% 55.46% 473ms 3.20% std::operator< (inline) 14ms 0.095% 55.55% 451ms 3.05% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.041% 55.59% 441ms 2.98% Cylindrical2dMesh::ReconstructCylindricalMesh 4ms 0.027% 55.62% 436ms 2.95% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.62% 436ms 2.95% std::_Rb_tree::_M_create_node (inline) 21ms 0.14% 55.76% 432ms 2.92% std::_Rb_tree::_M_insert_ (inline) 4ms 0.027% 55.79% 429ms 2.90% CellPropertyCollection::GetPropertiesType (inline) 15ms 0.1% 55.89% 428ms 2.89% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.034% 55.93% 428ms 2.89% Element::Element 0 0% 55.93% 422ms 2.85% std::_Rb_tree::_M_get_node (inline) 0 0% 55.93% 413ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 55.93% 413ms 2.79% std::map::lower_bound (inline) 0 0% 55.93% 409ms 2.77% std::map::find (inline) 1ms 0.0068% 55.93% 396ms 2.68% std::ostream::operator<< (inline) 64ms 0.43% 56.37% 394ms 2.66% std::ostream::_M_insert 0 0% 56.37% 390ms 2.64% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.02% 56.39% 374ms 2.53% AbstractCellProperty::IsSubType (inline) 4ms 0.027% 56.41% 358ms 2.42% MutableMesh::ReIndex 6ms 0.041% 56.45% 353ms 2.39% Element::RegisterWithNodes (inline) 6ms 0.041% 56.49% 346ms 2.34% Node::AddElement 114ms 0.77% 57.26% 339ms 2.29% __GI___libc_free 222ms 1.50% 58.77% 338ms 2.29% AbstractCellMutationState::AbstractCellMutationState 12ms 0.081% 58.85% 309ms 2.09% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.081% 58.93% 305ms 2.06% std::_Rb_tree::erase 0 0% 58.93% 305ms 2.06% std::set::erase (inline) 9ms 0.061% 58.99% 298ms 2.01% Node::RemoveElement 9ms 0.061% 59.05% 280ms 1.89% divconqrecurse 73ms 0.49% 59.54% 278ms 1.88% std::_Rb_tree::_M_erase 98ms 0.66% 60.21% 274ms 1.85% std::_Rb_tree::_M_get_insert_unique_pos 77ms 0.52% 60.73% 266ms 1.80% mergehulls 4ms 0.027% 60.75% 262ms 1.77% std::_Vector_base::_M_allocate (inline) 7ms 0.047% 60.80% 258ms 1.74% std::__new_allocator::deallocate (inline) 0 0% 60.80% 255ms 1.72% std::allocator_traits::deallocate (inline) 137ms 0.93% 61.73% 254ms 1.72% __cxxabiv1::__si_class_type_info::__do_dyncast 17ms 0.11% 61.84% 252ms 1.70% std::_Rb_tree::~_Rb_tree (inline) 0 0% 61.84% 249ms 1.68% std::_Rb_tree::_M_drop_node (inline) 4ms 0.027% 61.87% 241ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.014% 61.88% 239ms 1.62% Cell::GetMutationState 0 0% 61.88% 237ms 1.60% std::set::~set (inline) 2ms 0.014% 61.90% 234ms 1.58% NodeLocationWriter::Visit 6ms 0.041% 61.94% 231ms 1.56% LegacyCellProliferativeTypesWriter::VisitCell 188ms 1.27% 63.21% 225ms 1.52% _int_free 222ms 1.50% 64.71% 223ms 1.51% std::vector::operator[] (inline) 19ms 0.13% 64.84% 221ms 1.49% Element::ResetIndex 0 0% 64.84% 217ms 1.47% std::_Rb_tree::_M_put_node (inline) 212ms 1.43% 66.27% 212ms 1.43% [libchaste_cell_based.so] 1ms 0.0068% 66.28% 211ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 19ms 0.13% 66.41% 207ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.41% 207ms 1.40% Cell::GetCellProliferativeType 7ms 0.047% 66.45% 203ms 1.37% std::num_put::_M_insert_float 17ms 0.11% 66.57% 201ms 1.36% std::vector::push_back (inline) 11ms 0.074% 66.64% 200ms 1.35% AbstractTetrahedralElement::CalculateJacobian 2ms 0.014% 66.66% 200ms 1.35% alternateaxes 9ms 0.061% 66.72% 199ms 1.35% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 186ms 1.26% 67.97% 197ms 1.33% vertexmedian 10ms 0.068% 68.04% 194ms 1.31% std::_Rb_tree::_Rb_tree (partial-inline) 79ms 0.53% 68.58% 189ms 1.28% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 12ms 0.081% 68.66% 189ms 1.28% std::_Rb_tree::_M_erase_aux (inline) 18ms 0.12% 68.78% 187ms 1.26% Element::MarkAsDeleted 37ms 0.25% 69.03% 185ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 71ms 0.48% 69.51% 183ms 1.24% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 4ms 0.027% 69.54% 180ms 1.22% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 4ms 0.027% 69.56% 179ms 1.21% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0068% 69.57% 179ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0068% 69.58% 179ms 1.21% std::set::set (inline) 11ms 0.074% 69.65% 177ms 1.20% std::vector::_M_realloc_insert 1ms 0.0068% 69.66% 170ms 1.15% std::__cxx11::collate::do_transform 2ms 0.014% 69.67% 167ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 9ms 0.061% 69.73% 163ms 1.10% TetrahedralMesh::Clear 2ms 0.014% 69.75% 162ms 1.10% ___vsnprintf 0 0% 69.75% 160ms 1.08% __vsnprintf_internal (inline) 11ms 0.074% 69.82% 159ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 22ms 0.15% 69.97% 158ms 1.07% std::_Rb_tree::_M_copy (inline) 16ms 0.11% 70.08% 156ms 1.05% __printf_buffer 0 0% 70.08% 154ms 1.04% MeshBasedCellPopulation::GetDampingConstant 0 0% 70.08% 153ms 1.03% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.047% 70.12% 152ms 1.03% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 70.12% 148ms 1.00% OffLatticeSimulation::ApplyBoundaries 3ms 0.02% 70.14% 147ms 0.99% AbstractTetrahedralElement::AbstractTetrahedralElement 102ms 0.69% 70.83% 144ms 0.97% malloc_consolidate 23ms 0.16% 70.99% 140ms 0.95% AbstractTetrahedralElement::RefreshJacobian 37ms 0.25% 71.24% 135ms 0.91% std::_Rb_tree::_M_clone_node (inline) 28ms 0.19% 71.43% 132ms 0.89% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0068% 71.44% 132ms 0.89% __printf_fp_spec (inline) 132ms 0.89% 72.33% 132ms 0.89% std::_Rb_tree_insert_and_rebalance 100ms 0.68% 73.00% 131ms 0.89% AbstractElement::GetNodeGlobalIndex 5ms 0.034% 73.04% 131ms 0.89% __printf_fp_l_buffer 127ms 0.86% 73.90% 127ms 0.86% incircle 56ms 0.38% 74.27% 124ms 0.84% __printf_fp_buffer_1 121ms 0.82% 75.09% 121ms 0.82% [libchaste_crypt.so] 5ms 0.034% 75.13% 114ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 112ms 0.76% 75.88% 112ms 0.76% std::type_info::name (inline) 4ms 0.027% 75.91% 110ms 0.74% MeshBasedCellPopulation::SpringsEnd (inline) 110ms 0.74% 76.65% 110ms 0.74% Node::GetIndex 110ms 0.74% 77.40% 110ms 0.74% std::vector::size (inline) 0 0% 77.40% 109ms 0.74% CellProliferativeTypesWriter::VisitCell 3ms 0.02% 77.42% 109ms 0.74% CellPropertyCollection::HasProperty 109ms 0.74% 78.16% 109ms 0.74% unlink_chunk 40ms 0.27% 78.43% 108ms 0.73% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 69ms 0.47% 78.89% 108ms 0.73% std::_Rb_tree::equal_range (inline) 42ms 0.28% 79.18% 107ms 0.72% AbstractElement::GetNodeLocation 0 0% 79.18% 105ms 0.71% Cell::HasCellProperty (inline) 104ms 0.7% 79.88% 104ms 0.7% AbstractCellMutationState::~AbstractCellMutationState 69ms 0.47% 80.35% 104ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 93ms 0.63% 80.97% 103ms 0.7% vertexsort 0 0% 80.97% 102ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 31ms 0.21% 81.18% 102ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 81.18% 100ms 0.68% OutputFileHandler::OpenOutputFile 5ms 0.034% 81.22% 98ms 0.66% Node::~Node 33ms 0.22% 81.44% 95ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.014% 81.45% 92ms 0.62% boost::numeric::ublas::vector_assign (inline) 2ms 0.014% 81.47% 91ms 0.62% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0068% 81.48% 91ms 0.62% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 66ms 0.45% 81.92% 90ms 0.61% TetrahedralMesh::EdgeIterator::EdgeIterator 14ms 0.095% 82.02% 90ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 82.02% 90ms 0.61% boost::shared_ptr::~shared_ptr (inline) 21ms 0.14% 82.16% 88ms 0.59% std::__ostream_insert 25ms 0.17% 82.33% 86ms 0.58% std::num_put::_M_insert_int 1ms 0.0068% 82.33% 81ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 9ms 0.061% 82.39% 81ms 0.55% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.39% 79ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 78ms 0.53% 82.92% 78ms 0.53% std::_Rb_tree_rebalance_for_erase 1ms 0.0068% 82.93% 76ms 0.51% Cell::SetCellProliferativeType 0 0% 82.93% 76ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 31ms 0.21% 83.14% 76ms 0.51% std::basic_filebuf::xsputn 75ms 0.51% 83.65% 75ms 0.51% AbstractCellProperty::AbstractCellProperty 74ms 0.5% 84.15% 74ms 0.5% [libchaste_mesh.so]