File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16931ms, 84.87% of 19949ms total Dropped 793 nodes (cum <= 99.75ms) flat flat% sum% cum cum% 0 0% 0% 19904ms 99.77% __libc_start_call_main 0 0% 0% 19904ms 99.77% __libc_start_main_impl 0 0% 0% 19904ms 99.77% _start 0 0% 0% 19885ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19885ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19885ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19885ms 99.68% main 0 0% 0% 19850ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19850ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19850ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19822ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15383ms 77.11% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10156ms 50.91% AbstractCellBasedSimulation::DoCellBirth 6ms 0.03% 0.03% 10062ms 50.44% Cell::ReadyToDivide 4ms 0.02% 0.05% 10000ms 50.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.055% 9865ms 49.45% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 18ms 0.09% 0.15% 9858ms 49.42% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.16% 9838ms 49.32% CellCycleModelOdeHandler::SolveOdeToTime 76ms 0.38% 0.54% 9666ms 48.45% AbstractOneStepIvpOdeSolver::InternalSolve 916ms 4.59% 5.13% 8868ms 44.45% RungeKutta4IvpOdeSolver::CalculateNextYValue 3738ms 18.74% 23.87% 7760ms 38.90% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 23.87% 5117ms 25.65% MeshBasedCellPopulation::Update 178ms 0.89% 24.76% 4046ms 20.28% AbstractCellProperty::IsType (inline) 2ms 0.01% 24.77% 3921ms 19.66% Cylindrical2dMesh::ReMesh 597ms 2.99% 27.77% 2816ms 14.12% AbstractCellProperty::IsSame 2ms 0.01% 27.78% 2490ms 12.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 409ms 2.05% 29.83% 2219ms 11.12% std::type_info::operator== (inline) 0 0% 29.83% 2164ms 10.85% MutableMesh::ReMesh 1ms 0.005% 29.83% 2162ms 10.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.055% 29.89% 2111ms 10.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.89% 1944ms 9.74% AbstractCellPopulation::WriteResultsToFiles 782ms 3.92% 33.81% 1880ms 9.42% std::_Rb_tree::_M_lower_bound (inline) 1787ms 8.96% 42.76% 1787ms 8.96% __strcmp_avx2 157ms 0.79% 43.55% 1721ms 8.63% TetrahedralMesh::EdgeIterator::operator++ 53ms 0.27% 43.82% 1401ms 7.02% std::_Rb_tree::find (inline) 0 0% 43.82% 1150ms 5.76% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.84% 1107ms 5.55% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 50ms 0.25% 44.09% 1088ms 5.45% operator new 20ms 0.1% 44.19% 1074ms 5.38% TetrahedralMesh::ImportFromMesher 14ms 0.07% 44.26% 1029ms 5.16% MeshBasedCellPopulation::SpringIterator::operator++ 219ms 1.10% 45.36% 1026ms 5.14% __GI___libc_malloc 8ms 0.04% 45.40% 1003ms 5.03% std::set::insert (inline) 24ms 0.12% 45.52% 995ms 4.99% std::_Rb_tree::_M_insert_unique 39ms 0.2% 45.72% 981ms 4.92% std::__new_allocator::allocate (inline) 0 0% 45.72% 972ms 4.87% std::allocator_traits::allocate (inline) 0 0% 45.72% 875ms 4.39% std::set::count (inline) 0 0% 45.72% 831ms 4.17% triangulate 1ms 0.005% 45.72% 754ms 3.78% delaunay 3ms 0.015% 45.74% 752ms 3.77% divconqdelaunay 3ms 0.015% 45.75% 726ms 3.64% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.02% 45.77% 716ms 3.59% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 74ms 0.37% 46.14% 715ms 3.58% std::map::operator[] (partial-inline) 402ms 2.02% 48.16% 706ms 3.54% _int_malloc 685ms 3.43% 51.59% 685ms 3.43% std::_Rb_tree::_S_right (inline) 4ms 0.02% 51.61% 680ms 3.41% CellPopulationElementWriter::Visit 0 0% 51.61% 671ms 3.36% std::_Rb_tree::_M_create_node (inline) 18ms 0.09% 51.70% 664ms 3.33% std::less::operator() (inline) 646ms 3.24% 54.94% 646ms 3.24% std::operator< (inline) 0 0% 54.94% 644ms 3.23% std::_Rb_tree::_M_get_node (inline) 28ms 0.14% 55.08% 628ms 3.15% std::_Rb_tree::_M_insert_ (inline) 14ms 0.07% 55.15% 619ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 601ms 3.01% 58.16% 611ms 3.06% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.16% 608ms 3.05% std::_Rb_tree::_Alloc_node::operator() (inline) 155ms 0.78% 58.94% 601ms 3.01% __dynamic_cast 30ms 0.15% 59.09% 585ms 2.93% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 59.12% 566ms 2.84% CellPropertyCollection::GetPropertiesType (inline) 12ms 0.06% 59.18% 558ms 2.80% Element::Element 5ms 0.025% 59.20% 557ms 2.79% MeshBasedCellPopulation::AcceptCellWriter 0 0% 59.20% 553ms 2.77% std::_Rb_tree::lower_bound (inline) 0 0% 59.20% 553ms 2.77% std::map::lower_bound (inline) 0 0% 59.20% 518ms 2.60% std::map::find (inline) 15ms 0.075% 59.28% 512ms 2.57% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.06% 59.34% 494ms 2.48% MutableMesh::ReIndex 9ms 0.045% 59.38% 486ms 2.44% Element::RegisterWithNodes (inline) 343ms 1.72% 61.10% 483ms 2.42% AbstractCellMutationState::AbstractCellMutationState 11ms 0.055% 61.16% 472ms 2.37% Node::AddElement 2ms 0.01% 61.17% 470ms 2.36% std::ostream::operator<< (inline) 66ms 0.33% 61.50% 468ms 2.35% std::ostream::_M_insert 159ms 0.8% 62.29% 455ms 2.28% __GI___libc_free 11ms 0.055% 62.35% 445ms 2.23% AbstractCellProperty::IsSubType (inline) 11ms 0.055% 62.40% 443ms 2.22% Cylindrical2dMesh::CorrectNonPeriodicMesh 122ms 0.61% 63.02% 396ms 1.99% std::_Rb_tree::_M_erase 6ms 0.03% 63.05% 369ms 1.85% std::_Rb_tree::erase 4ms 0.02% 63.07% 366ms 1.83% divconqrecurse 10ms 0.05% 63.12% 366ms 1.83% std::__new_allocator::deallocate (inline) 1ms 0.005% 63.12% 366ms 1.83% std::set::erase (inline) 0 0% 63.12% 362ms 1.81% std::allocator_traits::deallocate (inline) 12ms 0.06% 63.18% 361ms 1.81% Node::RemoveElement 19ms 0.095% 63.28% 358ms 1.79% std::_Rb_tree::~_Rb_tree (inline) 105ms 0.53% 63.80% 348ms 1.74% mergehulls 164ms 0.82% 64.62% 344ms 1.72% __cxxabiv1::__si_class_type_info::__do_dyncast 144ms 0.72% 65.35% 343ms 1.72% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 65.35% 330ms 1.65% std::_Rb_tree::_M_drop_node (inline) 1ms 0.005% 65.35% 329ms 1.65% std::_Vector_base::_M_allocate (inline) 0 0% 65.35% 322ms 1.61% std::set::~set (inline) 31ms 0.16% 65.51% 314ms 1.57% Element::ResetIndex 4ms 0.02% 65.53% 310ms 1.55% Cell::GetMutationState 8ms 0.04% 65.57% 301ms 1.51% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.005% 65.57% 300ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 65.59% 299ms 1.50% Cell::GetCellProliferativeType 4ms 0.02% 65.61% 296ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 34ms 0.17% 65.78% 296ms 1.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.01% 65.79% 296ms 1.48% NodeLocationWriter::Visit 238ms 1.19% 66.98% 296ms 1.48% _int_free 0 0% 66.98% 296ms 1.48% std::_Rb_tree::_M_put_node (inline) 1ms 0.005% 66.99% 285ms 1.43% LegacyCellProliferativeTypesWriter::VisitCell 14ms 0.07% 67.06% 269ms 1.35% std::_Rb_tree::_Rb_tree (partial-inline) 269ms 1.35% 68.40% 269ms 1.35% std::type_info::name (inline) 12ms 0.06% 68.46% 259ms 1.30% std::num_put::_M_insert_float 13ms 0.065% 68.53% 254ms 1.27% AbstractTetrahedralElement::CalculateJacobian 5ms 0.025% 68.55% 248ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 78ms 0.39% 68.95% 248ms 1.24% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.01% 68.96% 246ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 245ms 1.23% 70.18% 245ms 1.23% std::vector::operator[] (inline) 2ms 0.01% 70.19% 244ms 1.22% std::set::set (inline) 4ms 0.02% 70.21% 241ms 1.21% alternateaxes 238ms 1.19% 71.41% 238ms 1.19% [libchaste_cell_based.so] 218ms 1.09% 72.50% 236ms 1.18% vertexmedian 9ms 0.045% 72.54% 230ms 1.15% std::vector::push_back (inline) 2ms 0.01% 72.56% 228ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 72.56% 226ms 1.13% TetrahedralMesh::RefreshJacobianCachedData 25ms 0.13% 72.69% 225ms 1.13% std::_Rb_tree::_M_copy (inline) 10ms 0.05% 72.74% 222ms 1.11% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.035% 72.77% 212ms 1.06% std::__cxx11::collate::do_transform 19ms 0.095% 72.87% 210ms 1.05% std::vector::_M_realloc_insert 26ms 0.13% 73.00% 203ms 1.02% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.005% 73.00% 202ms 1.01% ___vsnprintf 0 0% 73.00% 201ms 1.01% __vsnprintf_internal (inline) 34ms 0.17% 73.17% 199ms 1% AbstractTetrahedralElement::RefreshJacobian 62ms 0.31% 73.48% 199ms 1% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 22ms 0.11% 73.59% 199ms 1% __printf_buffer 49ms 0.25% 73.84% 198ms 0.99% std::_Rb_tree::_M_clone_node (inline) 15ms 0.075% 73.91% 196ms 0.98% Element::MarkAsDeleted 0 0% 73.91% 196ms 0.98% OffLatticeSimulation::ApplyBoundaries 8ms 0.04% 73.95% 193ms 0.97% AbstractTetrahedralElement::CalculateInverseJacobian 135ms 0.68% 74.63% 189ms 0.95% malloc_consolidate 17ms 0.085% 74.72% 187ms 0.94% TetrahedralMesh::Clear 179ms 0.9% 75.61% 179ms 0.9% Node::GetIndex 1ms 0.005% 75.62% 172ms 0.86% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.62% 171ms 0.86% AbstractCentreBasedCellPopulation::GetDampingConstant 130ms 0.65% 76.27% 170ms 0.85% AbstractElement::GetNodeGlobalIndex 3ms 0.015% 76.28% 170ms 0.85% CellProliferativeTypesWriter::VisitCell 5ms 0.025% 76.31% 170ms 0.85% __printf_fp_l_buffer 0 0% 76.31% 170ms 0.85% __printf_fp_spec (inline) 5ms 0.025% 76.33% 159ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 158ms 0.79% 77.13% 158ms 0.79% unlink_chunk 67ms 0.34% 77.46% 156ms 0.78% __printf_fp_buffer_1 66ms 0.33% 77.79% 154ms 0.77% AbstractElement::GetNodeLocation 3ms 0.015% 77.81% 152ms 0.76% boost::numeric::ublas::vector_assign (inline) 152ms 0.76% 78.57% 152ms 0.76% std::_Rb_tree_insert_and_rebalance 90ms 0.45% 79.02% 151ms 0.76% std::_Rb_tree::equal_range (inline) 150ms 0.75% 79.77% 150ms 0.75% incircle 5ms 0.025% 79.80% 145ms 0.73% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 143ms 0.72% 80.52% 143ms 0.72% std::vector::size (inline) 40ms 0.2% 80.72% 138ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 80.72% 131ms 0.66% AbstractCellBasedWriter::OpenOutputFileForAppend 6ms 0.03% 80.75% 131ms 0.66% CellPropertyCollection::HasProperty 1ms 0.005% 80.75% 131ms 0.66% OutputFileHandler::OpenOutputFile 0 0% 80.75% 128ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 127ms 0.64% 81.39% 127ms 0.64% AbstractElement::IsDeleted 0 0% 81.39% 127ms 0.64% Cell::HasCellProperty (inline) 3ms 0.015% 81.40% 127ms 0.64% boost::numeric::ublas::c_vector::c_vector (inline) 117ms 0.59% 81.99% 126ms 0.63% vertexsort 7ms 0.035% 82.02% 125ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.01% 82.03% 118ms 0.59% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 82.05% 115ms 0.58% MeshBasedCellPopulation::SpringsEnd (inline) 15ms 0.075% 82.12% 115ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 82.12% 115ms 0.58% boost::shared_ptr::~shared_ptr (inline) 2ms 0.01% 82.13% 113ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 29ms 0.15% 82.28% 113ms 0.57% boost::numeric::ublas::indexing_vector_assign 3ms 0.015% 82.29% 111ms 0.56% Cell::SetCellProliferativeType 0 0% 82.29% 108ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.005% 82.30% 106ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 106ms 0.53% 82.83% 106ms 0.53% std::_Rb_tree_increment 0 0% 82.83% 105ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 61ms 0.31% 83.14% 105ms 0.53% Cylindrical2dMesh::GetVectorFromAtoB 10ms 0.05% 83.19% 105ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 16ms 0.08% 83.27% 103ms 0.52% Node::~Node 102ms 0.51% 83.78% 102ms 0.51% AbstractCellProperty::~AbstractCellProperty 19ms 0.095% 83.87% 101ms 0.51% TetrahedralMesh::EdgesEnd 101ms 0.51% 84.38% 101ms 0.51% [libchaste_mesh.so] 98ms 0.49% 84.87% 100ms 0.5% boost::detail::sp_counted_base::release