File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16751ms, 83.71% of 20011ms total Dropped 776 nodes (cum <= 100.06ms) flat flat% sum% cum cum% 0 0% 0% 19965ms 99.77% __libc_start_call_main 0 0% 0% 19965ms 99.77% __libc_start_main_impl 0 0% 0% 19965ms 99.77% _start 0 0% 0% 19945ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19945ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19945ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19945ms 99.67% main 0 0% 0% 19907ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19907ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19907ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19881ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15333ms 76.62% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10023ms 50.09% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 9914ms 49.54% Cell::ReadyToDivide 6ms 0.03% 0.05% 9839ms 49.17% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.03% 0.08% 9704ms 48.49% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.1% 0.18% 9691ms 48.43% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.18% 9668ms 48.31% CellCycleModelOdeHandler::SolveOdeToTime 87ms 0.43% 0.62% 9485ms 47.40% AbstractOneStepIvpOdeSolver::InternalSolve 936ms 4.68% 5.30% 8667ms 43.31% RungeKutta4IvpOdeSolver::CalculateNextYValue 3495ms 17.47% 22.76% 7528ms 37.62% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.76% 5188ms 25.93% MeshBasedCellPopulation::Update 80ms 0.4% 23.16% 4080ms 20.39% AbstractCellProperty::IsType (inline) 7ms 0.035% 23.20% 4018ms 20.08% Cylindrical2dMesh::ReMesh 602ms 3.01% 26.21% 2858ms 14.28% AbstractCellProperty::IsSame 0 0% 26.21% 2474ms 12.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 387ms 1.93% 28.14% 2256ms 11.27% std::type_info::operator== (inline) 0 0% 28.14% 2197ms 10.98% MutableMesh::ReMesh 0 0% 28.14% 2187ms 10.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.07% 28.21% 2133ms 10.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.21% 2070ms 10.34% AbstractCellPopulation::WriteResultsToFiles 841ms 4.20% 32.41% 1827ms 9.13% std::_Rb_tree::_M_lower_bound (inline) 1790ms 8.95% 41.36% 1790ms 8.95% __strcmp_avx2 149ms 0.74% 42.10% 1683ms 8.41% TetrahedralMesh::EdgeIterator::operator++ 50ms 0.25% 42.35% 1361ms 6.80% std::_Rb_tree::find (inline) 0 0% 42.35% 1136ms 5.68% MeshBasedCellPopulation::UpdateNodePairs 18ms 0.09% 42.44% 1136ms 5.68% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 41ms 0.2% 42.65% 1124ms 5.62% operator new 16ms 0.08% 42.73% 1120ms 5.60% TetrahedralMesh::ImportFromMesher 248ms 1.24% 43.97% 1069ms 5.34% __GI___libc_malloc 5ms 0.025% 43.99% 1000ms 5.00% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.06% 44.05% 983ms 4.91% std::set::insert (inline) 16ms 0.08% 44.13% 971ms 4.85% std::_Rb_tree::_M_insert_unique 31ms 0.15% 44.29% 969ms 4.84% std::__new_allocator::allocate (inline) 0 0% 44.29% 964ms 4.82% std::allocator_traits::allocate (inline) 0 0% 44.29% 860ms 4.30% std::set::count (inline) 0 0% 44.29% 801ms 4.00% triangulate 6ms 0.03% 44.32% 770ms 3.85% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 44.33% 731ms 3.65% AbstractTwoBodyInteractionForce::AddForceContribution 433ms 2.16% 46.49% 730ms 3.65% _int_malloc 4ms 0.02% 46.51% 728ms 3.64% CellPopulationElementWriter::Visit 1ms 0.005% 46.51% 719ms 3.59% delaunay 6ms 0.03% 46.54% 717ms 3.58% divconqdelaunay 63ms 0.31% 46.86% 707ms 3.53% std::map::operator[] (partial-inline) 20ms 0.1% 46.96% 644ms 3.22% std::less::operator() (inline) 211ms 1.05% 48.01% 635ms 3.17% __dynamic_cast 0 0% 48.01% 632ms 3.16% std::_Rb_tree::_M_create_node (inline) 624ms 3.12% 51.13% 624ms 3.12% std::operator< (inline) 611ms 3.05% 54.19% 623ms 3.11% WntCellCycleOdeSystem::CalculateStoppingEvent 619ms 3.09% 57.28% 619ms 3.09% std::_Rb_tree::_S_right (inline) 2ms 0.01% 57.29% 617ms 3.08% MeshBasedCellPopulation::AcceptCellWriter 35ms 0.17% 57.46% 612ms 3.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 30ms 0.15% 57.61% 603ms 3.01% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.61% 599ms 2.99% std::_Rb_tree::_M_get_node (inline) 8ms 0.04% 57.65% 586ms 2.93% CellPropertyCollection::GetPropertiesType (inline) 0 0% 57.65% 579ms 2.89% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.07% 57.72% 561ms 2.80% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.72% 558ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 57.72% 558ms 2.79% std::map::lower_bound (inline) 8ms 0.04% 57.76% 548ms 2.74% Element::Element 4ms 0.02% 57.78% 535ms 2.67% std::ostream::operator<< (inline) 70ms 0.35% 58.13% 531ms 2.65% std::ostream::_M_insert 342ms 1.71% 59.84% 502ms 2.51% AbstractCellMutationState::AbstractCellMutationState 6ms 0.03% 59.87% 502ms 2.51% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 59.87% 499ms 2.49% std::map::find (inline) 11ms 0.055% 59.93% 498ms 2.49% MutableMesh::ReIndex 13ms 0.065% 59.99% 493ms 2.46% Element::RegisterWithNodes (inline) 3ms 0.015% 60.01% 484ms 2.42% AbstractCellProperty::IsSubType (inline) 10ms 0.05% 60.06% 478ms 2.39% Node::AddElement 24ms 0.12% 60.18% 462ms 2.31% Cylindrical2dMesh::CorrectNonPeriodicMesh 150ms 0.75% 60.93% 420ms 2.10% __GI___libc_free 14ms 0.07% 61.00% 384ms 1.92% divconqrecurse 114ms 0.57% 61.57% 374ms 1.87% std::_Rb_tree::_M_erase 22ms 0.11% 61.68% 368ms 1.84% Node::RemoveElement 1ms 0.005% 61.68% 366ms 1.83% std::_Vector_base::_M_allocate (inline) 111ms 0.55% 62.24% 362ms 1.81% mergehulls 6ms 0.03% 62.27% 359ms 1.79% std::_Rb_tree::erase 1ms 0.005% 62.27% 359ms 1.79% std::set::erase (inline) 147ms 0.73% 63.01% 352ms 1.76% std::_Rb_tree::_M_get_insert_unique_pos 32ms 0.16% 63.17% 352ms 1.76% std::_Rb_tree::~_Rb_tree (inline) 343ms 1.71% 64.88% 343ms 1.71% std::type_info::name (inline) 0 0% 64.88% 336ms 1.68% std::set::~set (inline) 9ms 0.045% 64.92% 332ms 1.66% std::__new_allocator::deallocate (inline) 6ms 0.03% 64.95% 330ms 1.65% Cell::GetCellProliferativeType 163ms 0.81% 65.77% 330ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.77% 329ms 1.64% std::allocator_traits::deallocate (inline) 3ms 0.015% 65.78% 318ms 1.59% LegacyCellProliferativeTypesWriter::VisitCell 24ms 0.12% 65.90% 304ms 1.52% Element::ResetIndex 12ms 0.06% 65.96% 303ms 1.51% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 65.96% 302ms 1.51% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 65.98% 298ms 1.49% Cell::GetMutationState 1ms 0.005% 65.98% 297ms 1.48% NodeLocationWriter::Visit 24ms 0.12% 66.10% 292ms 1.46% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.10% 279ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 56ms 0.28% 66.38% 278ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 66.40% 275ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.085% 66.48% 270ms 1.35% std::num_put::_M_insert_float 212ms 1.06% 67.54% 269ms 1.34% _int_free 0 0% 67.54% 266ms 1.33% std::_Rb_tree::_M_put_node (inline) 7ms 0.035% 67.58% 264ms 1.32% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.01% 67.59% 260ms 1.30% std::set::set (inline) 14ms 0.07% 67.66% 257ms 1.28% AbstractTetrahedralElement::CalculateJacobian 251ms 1.25% 68.91% 253ms 1.26% std::vector::operator[] (inline) 60ms 0.3% 69.21% 252ms 1.26% ApcOneHitCellMutationState::ApcOneHitCellMutationState 10ms 0.05% 69.26% 248ms 1.24% std::vector::push_back (inline) 0 0% 69.26% 246ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 16ms 0.08% 69.34% 237ms 1.18% std::vector::_M_realloc_insert 24ms 0.12% 69.46% 233ms 1.16% std::_Rb_tree::_M_copy (inline) 8ms 0.04% 69.50% 226ms 1.13% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 69.51% 224ms 1.12% alternateaxes 213ms 1.06% 70.58% 220ms 1.10% vertexmedian 10ms 0.05% 70.63% 219ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 217ms 1.08% 71.71% 217ms 1.08% [libchaste_cell_based.so] 19ms 0.095% 71.81% 216ms 1.08% TetrahedralMesh::Clear 38ms 0.19% 72.00% 214ms 1.07% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 11ms 0.055% 72.05% 214ms 1.07% Element::MarkAsDeleted 5ms 0.025% 72.08% 214ms 1.07% std::__cxx11::collate::do_transform 36ms 0.18% 72.26% 209ms 1.04% AbstractTetrahedralElement::RefreshJacobian 39ms 0.19% 72.45% 208ms 1.04% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.03% 72.48% 207ms 1.03% AbstractTetrahedralElement::CalculateInverseJacobian 51ms 0.25% 72.73% 205ms 1.02% std::_Rb_tree::_M_clone_node (inline) 3ms 0.015% 72.75% 201ms 1.00% ___vsnprintf 0 0% 72.75% 198ms 0.99% __vsnprintf_internal (inline) 31ms 0.15% 72.90% 197ms 0.98% __printf_buffer 140ms 0.7% 73.60% 193ms 0.96% malloc_consolidate 4ms 0.02% 73.62% 192ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 73.63% 190ms 0.95% CellProliferativeTypesWriter::VisitCell 2ms 0.01% 73.64% 180ms 0.9% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 73.64% 180ms 0.9% MeshBasedCellPopulation::GetDampingConstant 124ms 0.62% 74.26% 175ms 0.87% AbstractElement::GetNodeGlobalIndex 0 0% 74.26% 169ms 0.84% OffLatticeSimulation::ApplyBoundaries 4ms 0.02% 74.28% 164ms 0.82% CellPropertyCollection::HasProperty 0 0% 74.28% 161ms 0.8% Cell::HasCellProperty (inline) 67ms 0.33% 74.61% 159ms 0.79% AbstractElement::GetNodeLocation 159ms 0.79% 75.41% 159ms 0.79% std::_Rb_tree_insert_and_rebalance 157ms 0.78% 76.19% 157ms 0.78% incircle 6ms 0.03% 76.22% 156ms 0.78% __printf_fp_l_buffer 0 0% 76.22% 156ms 0.78% __printf_fp_spec (inline) 4ms 0.02% 76.24% 154ms 0.77% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.035% 76.28% 151ms 0.75% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 150ms 0.75% 77.03% 150ms 0.75% unlink_chunk 82ms 0.41% 77.44% 146ms 0.73% __printf_fp_buffer_1 24ms 0.12% 77.56% 141ms 0.7% std::num_put::_M_insert_int 12ms 0.06% 77.62% 139ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 139ms 0.69% 78.31% 139ms 0.69% Node::GetIndex 101ms 0.5% 78.82% 139ms 0.69% std::_Rb_tree::equal_range (inline) 14ms 0.07% 78.89% 137ms 0.68% Node::~Node 130ms 0.65% 79.54% 130ms 0.65% std::vector::size (inline) 0 0% 79.54% 128ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 79.54% 126ms 0.63% OutputFileHandler::OpenOutputFile 1ms 0.005% 79.54% 126ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 88ms 0.44% 79.98% 125ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 36ms 0.18% 80.16% 123ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 5ms 0.025% 80.19% 123ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.19% 122ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.005% 80.19% 121ms 0.6% boost::numeric::ublas::vector_assign (inline) 35ms 0.17% 80.37% 119ms 0.59% AbstractTetrahedralMesh::GetElement 45ms 0.22% 80.59% 119ms 0.59% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.005% 80.60% 118ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.18% 80.78% 117ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 49ms 0.24% 81.03% 117ms 0.58% std::__ostream_insert 0 0% 81.03% 114ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 112ms 0.56% 81.59% 112ms 0.56% AbstractCellMutationState::~AbstractCellMutationState 111ms 0.55% 82.14% 111ms 0.55% AbstractCellProperty::~AbstractCellProperty 109ms 0.54% 82.68% 109ms 0.54% AbstractElement::IsDeleted 0 0% 82.68% 109ms 0.54% std::vector::resize (inline) 13ms 0.065% 82.75% 108ms 0.54% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.005% 82.75% 108ms 0.54% std::vector::_M_default_append 107ms 0.53% 83.29% 107ms 0.53% std::_Rb_tree_rebalance_for_erase 1ms 0.005% 83.29% 106ms 0.53% Cell::SetCellProliferativeType 22ms 0.11% 83.40% 106ms 0.53% TetrahedralMesh::EdgesEnd 1ms 0.005% 83.41% 105ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 18ms 0.09% 83.50% 105ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 83.50% 102ms 0.51% NodeMap::NodeMap 42ms 0.21% 83.71% 101ms 0.5% std::basic_filebuf::xsputn