File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16803ms, 85.13% of 19738ms total Dropped 822 nodes (cum <= 98.69ms) flat flat% sum% cum cum% 0 0% 0% 19693ms 99.77% __libc_start_call_main 0 0% 0% 19693ms 99.77% __libc_start_main_impl 0 0% 0% 19693ms 99.77% _start 0 0% 0% 19671ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19671ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19671ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19671ms 99.66% main 0 0% 0% 19627ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19627ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19627ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 2ms 0.01% 0.01% 19600ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0.01% 14901ms 75.49% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.015% 9349ms 47.37% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.03% 9260ms 46.91% Cell::ReadyToDivide 4ms 0.02% 0.051% 9180ms 46.51% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.056% 9034ms 45.77% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 25ms 0.13% 0.18% 9023ms 45.71% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.19% 8993ms 45.56% CellCycleModelOdeHandler::SolveOdeToTime 62ms 0.31% 0.5% 8808ms 44.62% AbstractOneStepIvpOdeSolver::InternalSolve 976ms 4.94% 5.45% 7846ms 39.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 2684ms 13.60% 19.04% 6692ms 33.90% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.05% 5432ms 27.52% MeshBasedCellPopulation::Update 3ms 0.015% 19.06% 4207ms 21.31% Cylindrical2dMesh::ReMesh 61ms 0.31% 19.37% 4020ms 20.37% AbstractCellProperty::IsType (inline) 367ms 1.86% 21.23% 2695ms 13.65% AbstractCellProperty::IsSame 0 0% 21.23% 2614ms 13.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 213ms 1.08% 22.31% 2328ms 11.79% std::type_info::operator== (inline) 2ms 0.01% 22.32% 2312ms 11.71% MutableMesh::ReMesh 2ms 0.01% 22.33% 2276ms 11.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 17ms 0.086% 22.42% 2219ms 11.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 2171ms 11.00% 33.42% 2171ms 11.00% __strcmp_avx2 0 0% 33.42% 2074ms 10.51% AbstractCellPopulation::WriteResultsToFiles 788ms 3.99% 37.41% 1866ms 9.45% std::_Rb_tree::_M_lower_bound (inline) 193ms 0.98% 38.39% 1726ms 8.74% TetrahedralMesh::EdgeIterator::operator++ 69ms 0.35% 38.74% 1357ms 6.88% std::_Rb_tree::find (inline) 0 0% 38.74% 1193ms 6.04% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 38.77% 1151ms 5.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 8ms 0.041% 38.81% 1150ms 5.83% TetrahedralMesh::ImportFromMesher 45ms 0.23% 39.04% 1107ms 5.61% operator new 18ms 0.091% 39.13% 1066ms 5.40% MeshBasedCellPopulation::SpringIterator::operator++ 260ms 1.32% 40.45% 1048ms 5.31% __GI___libc_malloc 13ms 0.066% 40.52% 1010ms 5.12% std::set::insert (inline) 13ms 0.066% 40.58% 997ms 5.05% std::_Rb_tree::_M_insert_unique 41ms 0.21% 40.79% 968ms 4.90% std::__new_allocator::allocate (inline) 0 0% 40.79% 962ms 4.87% std::allocator_traits::allocate (inline) 2ms 0.01% 40.80% 893ms 4.52% triangulate 0 0% 40.80% 820ms 4.15% std::set::count (inline) 0 0% 40.80% 812ms 4.11% delaunay 1ms 0.0051% 40.80% 810ms 4.10% divconqdelaunay 783ms 3.97% 44.77% 783ms 3.97% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.015% 44.79% 770ms 3.90% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 48ms 0.24% 45.03% 747ms 3.78% std::map::operator[] (partial-inline) 742ms 3.76% 48.79% 742ms 3.76% std::_Rb_tree::_S_right (inline) 0 0% 48.79% 741ms 3.75% AbstractTwoBodyInteractionForce::AddForceContribution 383ms 1.94% 50.73% 700ms 3.55% _int_malloc 7ms 0.035% 50.77% 694ms 3.52% CellPopulationElementWriter::Visit 220ms 1.11% 51.88% 671ms 3.40% __dynamic_cast 26ms 0.13% 52.01% 650ms 3.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 21ms 0.11% 52.12% 642ms 3.25% std::less::operator() (inline) 0 0% 52.12% 635ms 3.22% std::_Rb_tree::_M_create_node (inline) 20ms 0.1% 52.22% 634ms 3.21% AbstractCellPopulation::GetCellUsingLocationIndex 621ms 3.15% 55.37% 621ms 3.15% std::operator< (inline) 7ms 0.035% 55.40% 618ms 3.13% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.40% 606ms 3.07% std::_Rb_tree::lower_bound (inline) 0 0% 55.40% 606ms 3.07% std::map::lower_bound (inline) 0 0% 55.40% 603ms 3.06% std::_Rb_tree::_M_get_node (inline) 10ms 0.051% 55.45% 595ms 3.01% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.15% 55.60% 584ms 2.96% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.60% 577ms 2.92% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.046% 55.65% 573ms 2.90% Element::Element 6ms 0.03% 55.68% 543ms 2.75% MutableMesh::ReIndex 0 0% 55.68% 534ms 2.71% std::map::find (inline) 8ms 0.041% 55.72% 506ms 2.56% Cylindrical2dMesh::ReconstructCylindricalMesh 19ms 0.096% 55.82% 496ms 2.51% Element::RegisterWithNodes (inline) 2ms 0.01% 55.83% 496ms 2.51% std::ostream::operator<< (inline) 2ms 0.01% 55.84% 493ms 2.50% AbstractCellProperty::IsSubType (inline) 14ms 0.071% 55.91% 493ms 2.50% Cylindrical2dMesh::CorrectNonPeriodicMesh 72ms 0.36% 56.27% 493ms 2.50% std::ostream::_M_insert 7ms 0.035% 56.31% 468ms 2.37% Node::AddElement 134ms 0.68% 56.99% 446ms 2.26% __GI___libc_free 3ms 0.015% 57.00% 418ms 2.12% std::set::erase (inline) 11ms 0.056% 57.06% 417ms 2.11% std::_Rb_tree::erase 254ms 1.29% 58.34% 413ms 2.09% AbstractCellMutationState::AbstractCellMutationState 20ms 0.1% 58.45% 412ms 2.09% Node::RemoveElement 163ms 0.83% 59.27% 401ms 2.03% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.056% 59.33% 396ms 2.01% divconqrecurse 120ms 0.61% 59.94% 393ms 1.99% std::_Rb_tree::_M_erase 102ms 0.52% 60.45% 378ms 1.92% mergehulls 27ms 0.14% 60.59% 372ms 1.88% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 60.60% 362ms 1.83% std::_Vector_base::_M_allocate (inline) 13ms 0.066% 60.67% 359ms 1.82% std::__new_allocator::deallocate (inline) 31ms 0.16% 60.83% 354ms 1.79% Element::ResetIndex 0 0% 60.83% 352ms 1.78% std::allocator_traits::deallocate (inline) 351ms 1.78% 62.61% 351ms 1.78% [libchaste_cell_based.so] 0 0% 62.61% 345ms 1.75% std::set::~set (inline) 0 0% 62.61% 341ms 1.73% std::_Rb_tree::_M_drop_node (inline) 174ms 0.88% 63.49% 338ms 1.71% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.02% 63.51% 325ms 1.65% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 63.52% 320ms 1.62% Cell::GetCellProliferativeType 11ms 0.056% 63.58% 319ms 1.62% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 243ms 1.23% 64.81% 311ms 1.58% _int_free 9ms 0.046% 64.85% 302ms 1.53% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 64.86% 302ms 1.53% NodeLocationWriter::Visit 1ms 0.0051% 64.86% 294ms 1.49% Cell::GetMutationState 0 0% 64.86% 290ms 1.47% std::_Rb_tree::_M_put_node (inline) 0 0% 64.86% 287ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 41ms 0.21% 65.07% 285ms 1.44% AbstractCellPopulation::Iterator::IsRealCell 14ms 0.071% 65.14% 284ms 1.44% std::_Rb_tree::_Rb_tree (partial-inline) 13ms 0.066% 65.21% 281ms 1.42% std::vector::push_back (inline) 273ms 1.38% 66.59% 275ms 1.39% std::vector::operator[] (inline) 21ms 0.11% 66.70% 270ms 1.37% std::num_put::_M_insert_float 94ms 0.48% 67.17% 266ms 1.35% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 67.19% 266ms 1.35% alternateaxes 4ms 0.02% 67.21% 265ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.086% 67.30% 262ms 1.33% AbstractTetrahedralElement::CalculateJacobian 249ms 1.26% 68.56% 260ms 1.32% vertexmedian 16ms 0.081% 68.64% 259ms 1.31% std::vector::_M_realloc_insert 16ms 0.081% 68.72% 249ms 1.26% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0051% 68.73% 249ms 1.26% std::set::set (inline) 1ms 0.0051% 68.73% 242ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 22ms 0.11% 68.84% 242ms 1.23% std::_Rb_tree::_M_copy (inline) 19ms 0.096% 68.94% 232ms 1.18% Element::MarkAsDeleted 24ms 0.12% 69.06% 229ms 1.16% TetrahedralMesh::Clear 9ms 0.046% 69.11% 225ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 68ms 0.34% 69.45% 225ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 8ms 0.041% 69.49% 218ms 1.10% std::__cxx11::collate::do_transform 60ms 0.3% 69.79% 215ms 1.09% std::_Rb_tree::_M_clone_node (inline) 0 0% 69.79% 214ms 1.08% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 69.81% 208ms 1.05% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.81% 208ms 1.05% MeshBasedCellPopulation::GetDampingConstant 6ms 0.03% 69.84% 206ms 1.04% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 69.84% 206ms 1.04% ___vsnprintf 0 0% 69.84% 206ms 1.04% __vsnprintf_internal (inline) 17ms 0.086% 69.93% 204ms 1.03% __printf_buffer 4ms 0.02% 69.95% 203ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.12% 70.07% 202ms 1.02% AbstractTetrahedralElement::RefreshJacobian 158ms 0.8% 70.87% 201ms 1.02% malloc_consolidate 144ms 0.73% 71.60% 198ms 1.00% AbstractElement::GetNodeGlobalIndex 80ms 0.41% 72.00% 192ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 191ms 0.97% 72.97% 191ms 0.97% std::type_info::name (inline) 187ms 0.95% 73.92% 187ms 0.95% incircle 3ms 0.015% 73.93% 177ms 0.9% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.025% 73.96% 177ms 0.9% __printf_fp_l_buffer 0 0% 73.96% 177ms 0.9% __printf_fp_spec (inline) 80ms 0.41% 74.36% 168ms 0.85% __printf_fp_buffer_1 112ms 0.57% 74.93% 168ms 0.85% std::_Rb_tree::equal_range (inline) 166ms 0.84% 75.77% 166ms 0.84% Node::GetIndex 0 0% 75.77% 165ms 0.84% CellPropertyCollection::HasProperty 0 0% 75.77% 164ms 0.83% Cell::HasCellProperty (inline) 5ms 0.025% 75.80% 164ms 0.83% CellProliferativeTypesWriter::VisitCell 5ms 0.025% 75.82% 158ms 0.8% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 69ms 0.35% 76.17% 157ms 0.8% AbstractElement::GetNodeLocation 1ms 0.0051% 76.18% 157ms 0.8% boost::numeric::ublas::vector_assign (inline) 52ms 0.26% 76.44% 155ms 0.79% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 151ms 0.77% 77.21% 151ms 0.77% unlink_chunk 150ms 0.76% 77.97% 150ms 0.76% std::_Rb_tree_insert_and_rebalance 148ms 0.75% 78.72% 148ms 0.75% std::vector::size (inline) 0 0% 78.72% 144ms 0.73% AbstractCellBasedWriter::OpenOutputFileForAppend 141ms 0.71% 79.43% 141ms 0.71% [libchaste_crypt.so] 5ms 0.025% 79.46% 141ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 132ms 0.67% 80.12% 141ms 0.71% vertexsort 0 0% 80.12% 138ms 0.7% OutputFileHandler::OpenOutputFile 3ms 0.015% 80.14% 138ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 9ms 0.046% 80.19% 138ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 13ms 0.066% 80.25% 137ms 0.69% Node::~Node 50ms 0.25% 80.50% 136ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 90ms 0.46% 80.96% 136ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.96% 129ms 0.65% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 40ms 0.2% 81.16% 129ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 26ms 0.13% 81.29% 127ms 0.64% TetrahedralMesh::EdgesEnd (partial-inline) 125ms 0.63% 81.93% 125ms 0.63% AbstractCellMutationState::~AbstractCellMutationState 46ms 0.23% 82.16% 124ms 0.63% boost::numeric::ublas::indexing_vector_assign 8ms 0.041% 82.20% 121ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 82.20% 121ms 0.61% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.20% 119ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 82.21% 118ms 0.6% Cell::SetCellProliferativeType 3ms 0.015% 82.23% 116ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.02% 82.25% 116ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.01% 82.26% 115ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 109ms 0.55% 82.81% 109ms 0.55% TetrahedralMesh::EdgeIterator::operator!= 6ms 0.03% 82.84% 107ms 0.54% Cylindrical2dMesh::CreateMirrorNodes 36ms 0.18% 83.02% 107ms 0.54% std::__ostream_insert 104ms 0.53% 83.55% 104ms 0.53% std::_Rb_tree_increment 64ms 0.32% 83.87% 103ms 0.52% TimeStepper::AdvanceOneTimeStep 93ms 0.47% 84.34% 103ms 0.52% boost::detail::sp_counted_base::release 5ms 0.025% 84.37% 101ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 100ms 0.51% 84.88% 100ms 0.51% std::_Rb_tree_rebalance_for_erase 15ms 0.076% 84.95% 100ms 0.51% std::num_put::_M_insert_int 35ms 0.18% 85.13% 99ms 0.5% std::basic_filebuf::xsputn