File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12724ms, 85.30% of 14917ms total Dropped 744 nodes (cum <= 74.58ms) flat flat% sum% cum cum% 0 0% 0% 14880ms 99.75% __libc_start_call_main 0 0% 0% 14880ms 99.75% __libc_start_main_impl 0 0% 0% 14880ms 99.75% _start 0 0% 0% 14864ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14864ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14864ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14864ms 99.64% main 0 0% 0% 14822ms 99.36% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14822ms 99.36% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14822ms 99.36% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14802ms 99.23% AbstractCellBasedSimulation::Solve 0 0% 0% 11364ms 76.18% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.027% 0.027% 7184ms 48.16% AbstractCellBasedSimulation::DoCellBirth 5ms 0.034% 0.06% 7097ms 47.58% Cell::ReadyToDivide 3ms 0.02% 0.08% 7034ms 47.15% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.08% 6925ms 46.42% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.027% 0.11% 6923ms 46.41% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.013% 0.12% 6917ms 46.37% CellCycleModelOdeHandler::SolveOdeToTime 47ms 0.32% 0.44% 6778ms 45.44% AbstractOneStepIvpOdeSolver::InternalSolve 731ms 4.90% 5.34% 6094ms 40.85% RungeKutta4IvpOdeSolver::CalculateNextYValue 2178ms 14.60% 19.94% 5218ms 34.98% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0067% 19.94% 4104ms 27.51% MeshBasedCellPopulation::Update 7ms 0.047% 19.99% 3151ms 21.12% Cylindrical2dMesh::ReMesh 45ms 0.3% 20.29% 3048ms 20.43% AbstractCellProperty::IsType (inline) 0 0% 20.29% 1914ms 12.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 248ms 1.66% 21.95% 1907ms 12.78% AbstractCellProperty::IsSame 0 0% 21.95% 1785ms 11.97% MutableMesh::ReMesh 0 0% 21.95% 1692ms 11.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.06% 22.02% 1660ms 11.13% AbstractNumericalMethod::ComputeForcesIncludingDamping 148ms 0.99% 23.01% 1659ms 11.12% std::type_info::operator== (inline) 1593ms 10.68% 33.69% 1593ms 10.68% __strcmp_evex 1ms 0.0067% 33.69% 1514ms 10.15% AbstractCellPopulation::WriteResultsToFiles 583ms 3.91% 37.60% 1367ms 9.16% std::_Rb_tree::_M_lower_bound (inline) 153ms 1.03% 38.63% 1319ms 8.84% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.23% 38.86% 1019ms 6.83% std::_Rb_tree::find (inline) 4ms 0.027% 38.89% 934ms 6.26% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.06% 38.95% 894ms 5.99% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.11% 39.06% 885ms 5.93% TetrahedralMesh::ImportFromMesher 13ms 0.087% 39.15% 821ms 5.50% MeshBasedCellPopulation::SpringIterator::operator++ 31ms 0.21% 39.36% 807ms 5.41% operator new 10ms 0.067% 39.42% 779ms 5.22% std::set::insert (inline) 194ms 1.30% 40.73% 770ms 5.16% __GI___libc_malloc 10ms 0.067% 40.79% 770ms 5.16% std::_Rb_tree::_M_insert_unique 35ms 0.23% 41.03% 705ms 4.73% std::__new_allocator::allocate (inline) 0 0% 41.03% 701ms 4.70% std::allocator_traits::allocate (inline) 0 0% 41.03% 676ms 4.53% triangulate 0 0% 41.03% 615ms 4.12% std::set::count (inline) 1ms 0.0067% 41.03% 614ms 4.12% delaunay 2ms 0.013% 41.05% 612ms 4.10% divconqdelaunay 548ms 3.67% 44.72% 548ms 3.67% WntCellCycleOdeSystem::CalculateStoppingEvent 1ms 0.0067% 44.73% 531ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.06% 44.79% 531ms 3.56% CellPopulationElementWriter::Visit 2ms 0.013% 44.80% 515ms 3.45% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 39ms 0.26% 45.06% 512ms 3.43% std::map::operator[] (partial-inline) 510ms 3.42% 48.48% 510ms 3.42% std::_Rb_tree::_S_right (inline) 274ms 1.84% 50.32% 507ms 3.40% _int_malloc 14ms 0.094% 50.41% 497ms 3.33% std::less::operator() (inline) 483ms 3.24% 53.65% 483ms 3.24% std::operator< (inline) 0 0% 53.65% 478ms 3.20% std::_Rb_tree::_M_create_node (inline) 16ms 0.11% 53.76% 472ms 3.16% AbstractCellPopulation::GetCellUsingLocationIndex 21ms 0.14% 53.90% 464ms 3.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 53.90% 461ms 3.09% std::_Rb_tree::_M_get_node (inline) 20ms 0.13% 54.03% 453ms 3.04% std::_Rb_tree::_M_insert_ (inline) 132ms 0.88% 54.92% 451ms 3.02% __dynamic_cast 7ms 0.047% 54.96% 432ms 2.90% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 54.96% 431ms 2.89% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.04% 55.00% 416ms 2.79% Element::Element 2ms 0.013% 55.02% 411ms 2.76% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.027% 55.04% 405ms 2.72% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.04% 403ms 2.70% std::_Rb_tree::lower_bound (inline) 0 0% 55.04% 403ms 2.70% std::map::lower_bound (inline) 0 0% 55.04% 402ms 2.69% std::map::find (inline) 2ms 0.013% 55.06% 383ms 2.57% std::ostream::operator<< (inline) 54ms 0.36% 55.42% 379ms 2.54% std::ostream::_M_insert 9ms 0.06% 55.48% 376ms 2.52% MutableMesh::ReIndex 6ms 0.04% 55.52% 364ms 2.44% Element::RegisterWithNodes (inline) 3ms 0.02% 55.54% 360ms 2.41% Node::AddElement 249ms 1.67% 57.21% 359ms 2.41% AbstractCellMutationState::AbstractCellMutationState 117ms 0.78% 57.99% 359ms 2.41% __GI___libc_free 0 0% 57.99% 332ms 2.23% AbstractCellProperty::IsSubType (inline) 9ms 0.06% 58.05% 317ms 2.13% Cylindrical2dMesh::CorrectNonPeriodicMesh 123ms 0.82% 58.88% 307ms 2.06% std::_Rb_tree::_M_get_insert_unique_pos 13ms 0.087% 58.97% 301ms 2.02% Node::RemoveElement 11ms 0.074% 59.04% 298ms 2.00% divconqrecurse 5ms 0.034% 59.07% 298ms 2.00% std::_Rb_tree::erase 10ms 0.067% 59.14% 298ms 2.00% std::__new_allocator::deallocate (inline) 0 0% 59.14% 298ms 2.00% std::set::erase (inline) 0 0% 59.14% 293ms 1.96% std::allocator_traits::deallocate (inline) 78ms 0.52% 59.66% 289ms 1.94% std::_Rb_tree::_M_erase 70ms 0.47% 60.13% 285ms 1.91% mergehulls 17ms 0.11% 60.25% 282ms 1.89% std::_Rb_tree::~_Rb_tree (inline) 0 0% 60.25% 274ms 1.84% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.25% 271ms 1.82% std::set::~set (inline) 0 0% 60.25% 248ms 1.66% std::_Rb_tree::_M_put_node (inline) 3ms 0.02% 60.27% 244ms 1.64% NodeLocationWriter::Visit 198ms 1.33% 61.59% 242ms 1.62% _int_free 1ms 0.0067% 61.60% 241ms 1.62% std::_Vector_base::_M_allocate (inline) 240ms 1.61% 63.21% 240ms 1.61% [libchaste_cell_based.so] 20ms 0.13% 63.34% 239ms 1.60% Element::ResetIndex 2ms 0.013% 63.36% 238ms 1.60% Cell::GetMutationState 225ms 1.51% 64.87% 229ms 1.54% std::vector::operator[] (inline) 11ms 0.074% 64.94% 226ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 122ms 0.82% 65.76% 218ms 1.46% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0067% 65.76% 214ms 1.43% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.027% 65.79% 213ms 1.43% alternateaxes 8ms 0.054% 65.84% 212ms 1.42% std::num_put::_M_insert_float 3ms 0.02% 65.86% 210ms 1.41% std::set::set (inline) 197ms 1.32% 67.19% 209ms 1.40% vertexmedian 1ms 0.0067% 67.19% 208ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 6ms 0.04% 67.23% 207ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 22ms 0.15% 67.38% 207ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.034% 67.41% 206ms 1.38% Cell::GetCellProliferativeType 7ms 0.047% 67.46% 205ms 1.37% std::vector::push_back (inline) 8ms 0.054% 67.51% 202ms 1.35% AbstractTetrahedralElement::CalculateJacobian 66ms 0.44% 67.96% 199ms 1.33% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 67.96% 199ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 57ms 0.38% 68.34% 198ms 1.33% ApcOneHitCellMutationState::ApcOneHitCellMutationState 74ms 0.5% 68.83% 194ms 1.30% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.074% 68.91% 193ms 1.29% std::vector::_M_realloc_insert 3ms 0.02% 68.93% 185ms 1.24% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 19ms 0.13% 69.06% 185ms 1.24% TetrahedralMesh::Clear 22ms 0.15% 69.20% 183ms 1.23% std::_Rb_tree::_M_copy (inline) 5ms 0.034% 69.24% 180ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.013% 69.25% 179ms 1.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.06% 69.31% 178ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 5ms 0.034% 69.34% 175ms 1.17% std::__cxx11::collate::do_transform 10ms 0.067% 69.41% 170ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.034% 69.44% 169ms 1.13% Element::MarkAsDeleted 24ms 0.16% 69.61% 161ms 1.08% AbstractTetrahedralElement::RefreshJacobian 0 0% 69.61% 159ms 1.07% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.61% 159ms 1.07% MeshBasedCellPopulation::GetDampingConstant 2ms 0.013% 69.62% 159ms 1.07% ___vsnprintf 1ms 0.0067% 69.63% 157ms 1.05% __vsnprintf_internal (inline) 19ms 0.13% 69.75% 156ms 1.05% __printf_buffer 49ms 0.33% 70.08% 156ms 1.05% std::_Rb_tree::_M_clone_node (inline) 3ms 0.02% 70.10% 150ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.10% 147ms 0.99% OffLatticeSimulation::ApplyBoundaries 33ms 0.22% 70.32% 146ms 0.98% TetrahedralMesh::EdgesEnd (partial-inline) 106ms 0.71% 71.03% 142ms 0.95% malloc_consolidate 135ms 0.91% 71.94% 135ms 0.91% incircle 97ms 0.65% 72.59% 134ms 0.9% AbstractElement::GetNodeGlobalIndex 6ms 0.04% 72.63% 131ms 0.88% __printf_fp_l_buffer 0 0% 72.63% 131ms 0.88% __printf_fp_spec (inline) 59ms 0.4% 73.02% 125ms 0.84% AbstractElement::GetNodeLocation 44ms 0.29% 73.32% 123ms 0.82% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.034% 73.35% 123ms 0.82% Node::~Node 123ms 0.82% 74.18% 123ms 0.82% unlink_chunk 2ms 0.013% 74.19% 122ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 81ms 0.54% 74.73% 121ms 0.81% std::_Rb_tree::equal_range (inline) 0 0% 74.73% 120ms 0.8% Cell::HasCellProperty (inline) 0 0% 74.73% 120ms 0.8% CellPropertyCollection::HasProperty 33ms 0.22% 74.95% 119ms 0.8% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 6ms 0.04% 74.99% 119ms 0.8% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.013% 75.01% 117ms 0.78% CellProliferativeTypesWriter::VisitCell 117ms 0.78% 75.79% 117ms 0.78% [libchaste_crypt.so] 39ms 0.26% 76.05% 114ms 0.76% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.04% 76.09% 114ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 42ms 0.28% 76.38% 114ms 0.76% __printf_fp_buffer_1 113ms 0.76% 77.13% 113ms 0.76% std::_Rb_tree_insert_and_rebalance 112ms 0.75% 77.88% 112ms 0.75% Node::GetIndex 111ms 0.74% 78.63% 111ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 7ms 0.047% 78.68% 110ms 0.74% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 78.68% 109ms 0.73% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 78.68% 109ms 0.73% OutputFileHandler::OpenOutputFile 78ms 0.52% 79.20% 108ms 0.72% TetrahedralMesh::EdgeIterator::EdgeIterator 2ms 0.013% 79.21% 107ms 0.72% boost::numeric::ublas::vector_assign (inline) 1ms 0.0067% 79.22% 105ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 105ms 0.7% 79.92% 105ms 0.7% std::vector::size (inline) 0 0% 79.92% 95ms 0.64% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 90ms 0.6% 80.53% 95ms 0.64% vertexsort 60ms 0.4% 80.93% 93ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.054% 80.98% 93ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.04% 81.02% 91ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 81.02% 91ms 0.61% boost::shared_ptr::~shared_ptr (inline) 26ms 0.17% 81.20% 88ms 0.59% std::__ostream_insert 3ms 0.02% 81.22% 86ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 86ms 0.58% 81.79% 86ms 0.58% std::type_info::name (inline) 42ms 0.28% 82.07% 82ms 0.55% boost::shared_ptr::shared_ptr (inline) 79ms 0.53% 82.60% 81ms 0.54% boost::detail::sp_counted_base::release 0 0% 82.60% 80ms 0.54% Cell::SetCellProliferativeType 45ms 0.3% 82.91% 80ms 0.54% TimeStepper::AdvanceOneTimeStep 80ms 0.54% 83.44% 80ms 0.54% std::_Rb_tree_increment 7ms 0.047% 83.49% 77ms 0.52% Cylindrical2dMesh::CreateMirrorNodes 0 0% 83.49% 77ms 0.52% std::operator<< (inline) 76ms 0.51% 84.00% 76ms 0.51% TetrahedralMesh::EdgeIterator::operator!= 76ms 0.51% 84.51% 76ms 0.51% boost::shared_ptr::operator-> (inline) 76ms 0.51% 85.02% 76ms 0.51% counterclockwise 18ms 0.12% 85.14% 76ms 0.51% std::num_put::_M_insert_int 1ms 0.0067% 85.14% 75ms 0.5% AbstractCellBasedSimulation::DoCellRemoval (inline) 19ms 0.13% 85.27% 75ms 0.5% boost::numeric::ublas::indexing_vector_assign 4ms 0.027% 85.30% 75ms 0.5% std::_Rb_tree_const_iterator::operator++ (inline)