File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12824ms, 85.01% of 15085ms total Dropped 746 nodes (cum <= 75.42ms) flat flat% sum% cum cum% 0 0% 0% 15047ms 99.75% __libc_start_call_main 0 0% 0% 15047ms 99.75% __libc_start_main_impl 0 0% 0% 15047ms 99.75% _start 0 0% 0% 15031ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15031ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15031ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15031ms 99.64% main 0 0% 0% 14991ms 99.38% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14991ms 99.38% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14991ms 99.38% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14970ms 99.24% AbstractCellBasedSimulation::Solve 1ms 0.0066% 0.0066% 11422ms 75.72% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0066% 0.013% 7188ms 47.65% AbstractCellBasedSimulation::DoCellBirth 8ms 0.053% 0.066% 7111ms 47.14% Cell::ReadyToDivide 1ms 0.0066% 0.073% 7048ms 46.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.073% 6935ms 45.97% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.11% 0.19% 6925ms 45.91% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0066% 0.19% 6905ms 45.77% CellCycleModelOdeHandler::SolveOdeToTime 49ms 0.32% 0.52% 6765ms 44.85% AbstractOneStepIvpOdeSolver::InternalSolve 855ms 5.67% 6.18% 6086ms 40.34% RungeKutta4IvpOdeSolver::CalculateNextYValue 1895ms 12.56% 18.75% 5082ms 33.69% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 18.75% 4154ms 27.54% MeshBasedCellPopulation::Update 47ms 0.31% 19.06% 3195ms 21.18% AbstractCellProperty::IsType (inline) 4ms 0.027% 19.09% 3191ms 21.15% Cylindrical2dMesh::ReMesh 228ms 1.51% 20.60% 2154ms 14.28% AbstractCellProperty::IsSame 0 0% 20.60% 1962ms 13.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 195ms 1.29% 21.89% 1926ms 12.77% std::type_info::operator== (inline) 0 0% 21.89% 1797ms 11.91% MutableMesh::ReMesh 1748ms 11.59% 33.48% 1748ms 11.59% __strcmp_evex 0 0% 33.48% 1714ms 11.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.066% 33.54% 1666ms 11.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 33.54% 1584ms 10.50% AbstractCellPopulation::WriteResultsToFiles 635ms 4.21% 37.75% 1482ms 9.82% std::_Rb_tree::_M_lower_bound (inline) 129ms 0.86% 38.61% 1334ms 8.84% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.44% 39.05% 1115ms 7.39% std::_Rb_tree::find (inline) 2ms 0.013% 39.06% 938ms 6.22% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.04% 39.10% 902ms 5.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.08% 39.18% 884ms 5.86% TetrahedralMesh::ImportFromMesher 13ms 0.086% 39.26% 821ms 5.44% MeshBasedCellPopulation::SpringIterator::operator++ 33ms 0.22% 39.48% 791ms 5.24% operator new 173ms 1.15% 40.63% 749ms 4.97% __GI___libc_malloc 5ms 0.033% 40.66% 748ms 4.96% std::set::insert (inline) 9ms 0.06% 40.72% 743ms 4.93% std::_Rb_tree::_M_insert_unique 26ms 0.17% 40.89% 688ms 4.56% std::__new_allocator::allocate (inline) 2ms 0.013% 40.91% 687ms 4.55% triangulate 0 0% 40.91% 683ms 4.53% std::allocator_traits::allocate (inline) 0 0% 40.91% 664ms 4.40% std::set::count (inline) 1ms 0.0066% 40.91% 618ms 4.10% delaunay 6ms 0.04% 40.95% 617ms 4.09% divconqdelaunay 4ms 0.027% 40.98% 611ms 4.05% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 559ms 3.71% 44.69% 559ms 3.71% std::_Rb_tree::_S_right (inline) 3ms 0.02% 44.71% 551ms 3.65% CellPopulationElementWriter::Visit 45ms 0.3% 45.00% 549ms 3.64% std::map::operator[] (partial-inline) 547ms 3.63% 48.63% 547ms 3.63% WntCellCycleOdeSystem::CalculateStoppingEvent 1ms 0.0066% 48.64% 534ms 3.54% AbstractTwoBodyInteractionForce::AddForceContribution 280ms 1.86% 50.49% 512ms 3.39% _int_malloc 10ms 0.066% 50.56% 512ms 3.39% std::less::operator() (inline) 169ms 1.12% 51.68% 511ms 3.39% __dynamic_cast 502ms 3.33% 55.01% 502ms 3.33% std::operator< (inline) 14ms 0.093% 55.10% 484ms 3.21% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.04% 55.14% 478ms 3.17% MeshBasedCellPopulation::AcceptCellWriter 17ms 0.11% 55.25% 469ms 3.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 55.25% 455ms 3.02% std::_Rb_tree::lower_bound (inline) 0 0% 55.25% 455ms 3.02% std::map::lower_bound (inline) 3ms 0.02% 55.27% 451ms 2.99% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.11% 55.39% 451ms 2.99% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 55.39% 448ms 2.97% std::map::find (inline) 0 0% 55.39% 446ms 2.96% std::_Rb_tree::_M_create_node (inline) 10ms 0.066% 55.45% 440ms 2.92% Element::Element 24ms 0.16% 55.61% 434ms 2.88% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.61% 431ms 2.86% std::_Rb_tree::_M_get_node (inline) 0 0% 55.61% 413ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.013% 55.62% 387ms 2.57% AbstractCellProperty::IsSubType (inline) 9ms 0.06% 55.68% 385ms 2.55% Element::RegisterWithNodes (inline) 121ms 0.8% 56.49% 379ms 2.51% __GI___libc_free 7ms 0.046% 56.53% 378ms 2.51% MutableMesh::ReIndex 8ms 0.053% 56.59% 370ms 2.45% Node::AddElement 230ms 1.52% 58.11% 344ms 2.28% AbstractCellMutationState::AbstractCellMutationState 2ms 0.013% 58.12% 337ms 2.23% std::ostream::operator<< (inline) 61ms 0.4% 58.53% 334ms 2.21% std::ostream::_M_insert 9ms 0.06% 58.59% 333ms 2.21% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.086% 58.67% 322ms 2.13% std::__new_allocator::deallocate (inline) 0 0% 58.67% 318ms 2.11% std::allocator_traits::deallocate (inline) 7ms 0.046% 58.72% 314ms 2.08% divconqrecurse 76ms 0.5% 59.22% 309ms 2.05% std::_Rb_tree::_M_erase 0 0% 59.22% 304ms 2.02% std::_Rb_tree::_M_drop_node (inline) 23ms 0.15% 59.38% 304ms 2.02% std::_Rb_tree::~_Rb_tree (inline) 88ms 0.58% 59.96% 302ms 2.00% mergehulls 113ms 0.75% 60.71% 301ms 2.00% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.066% 60.78% 294ms 1.95% std::_Rb_tree::erase 1ms 0.0066% 60.78% 294ms 1.95% std::set::erase (inline) 10ms 0.066% 60.85% 292ms 1.94% Node::RemoveElement 0 0% 60.85% 276ms 1.83% std::set::~set (inline) 0 0% 60.85% 272ms 1.80% std::_Rb_tree::_M_put_node (inline) 222ms 1.47% 62.32% 256ms 1.70% _int_free 2ms 0.013% 62.33% 254ms 1.68% std::_Vector_base::_M_allocate (inline) 3ms 0.02% 62.35% 247ms 1.64% Cell::GetMutationState 3ms 0.02% 62.37% 238ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0066% 62.38% 235ms 1.56% Cell::GetCellProliferativeType 5ms 0.033% 62.41% 234ms 1.55% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.11% 62.52% 234ms 1.55% Element::ResetIndex 122ms 0.81% 63.33% 227ms 1.50% __cxxabiv1::__si_class_type_info::__do_dyncast 41ms 0.27% 63.60% 224ms 1.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 63.60% 224ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 215ms 1.43% 65.02% 215ms 1.43% [libchaste_cell_based.so] 3ms 0.02% 65.04% 212ms 1.41% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 211ms 1.40% 66.44% 212ms 1.41% std::vector::operator[] (inline) 0 0% 66.44% 208ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.053% 66.50% 208ms 1.38% std::vector::push_back (inline) 13ms 0.086% 66.58% 206ms 1.37% std::_Rb_tree::_Rb_tree 3ms 0.02% 66.60% 204ms 1.35% NodeLocationWriter::Visit 4ms 0.027% 66.63% 201ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.11% 66.74% 201ms 1.33% AbstractTetrahedralElement::CalculateJacobian 4ms 0.027% 66.76% 201ms 1.33% std::set::set (inline) 6ms 0.04% 66.80% 192ms 1.27% alternateaxes 189ms 1.25% 68.05% 189ms 1.25% std::type_info::name (inline) 67ms 0.44% 68.50% 187ms 1.24% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.093% 68.59% 187ms 1.24% std::vector::_M_realloc_insert 43ms 0.29% 68.88% 186ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 176ms 1.17% 70.04% 185ms 1.23% vertexmedian 15ms 0.099% 70.14% 182ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 76ms 0.5% 70.65% 179ms 1.19% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.099% 70.75% 179ms 1.19% std::num_put::_M_insert_float 13ms 0.086% 70.83% 175ms 1.16% TetrahedralMesh::Clear 9ms 0.06% 70.89% 174ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 9ms 0.06% 70.95% 173ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 18ms 0.12% 71.07% 166ms 1.10% std::_Rb_tree::_M_copy (inline) 5ms 0.033% 71.10% 162ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 10ms 0.066% 71.17% 161ms 1.07% Element::MarkAsDeleted 1ms 0.0066% 71.18% 159ms 1.05% OffLatticeSimulation::ApplyBoundaries 18ms 0.12% 71.30% 156ms 1.03% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0066% 71.30% 153ms 1.01% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0066% 71.31% 151ms 1.00% AbstractCentreBasedCellPopulation::GetDampingConstant 50ms 0.33% 71.64% 145ms 0.96% std::_Rb_tree::_M_clone_node (inline) 98ms 0.65% 72.29% 144ms 0.95% AbstractElement::GetNodeGlobalIndex 4ms 0.027% 72.32% 139ms 0.92% std::__cxx11::collate::do_transform 93ms 0.62% 72.93% 135ms 0.89% malloc_consolidate 4ms 0.027% 72.96% 134ms 0.89% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 133ms 0.88% 73.84% 133ms 0.88% std::vector::size (inline) 6ms 0.04% 73.88% 132ms 0.88% CellProliferativeTypesWriter::VisitCell 131ms 0.87% 74.75% 131ms 0.87% incircle 6ms 0.04% 74.79% 130ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 130ms 0.86% 75.65% 130ms 0.86% Node::GetIndex 1ms 0.0066% 75.66% 129ms 0.86% ___vsnprintf 0 0% 75.66% 128ms 0.85% __vsnprintf_internal (inline) 1ms 0.0066% 75.66% 127ms 0.84% CellPropertyCollection::HasProperty 12ms 0.08% 75.74% 126ms 0.84% __printf_buffer 0 0% 75.74% 125ms 0.83% Cell::HasCellProperty (inline) 2ms 0.013% 75.76% 124ms 0.82% boost::numeric::ublas::vector_assign (inline) 123ms 0.82% 76.57% 123ms 0.82% unlink_chunk 58ms 0.38% 76.96% 118ms 0.78% AbstractElement::GetNodeLocation 46ms 0.3% 77.26% 118ms 0.78% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 7ms 0.046% 77.31% 115ms 0.76% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.033% 77.34% 115ms 0.76% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 113ms 0.75% 78.09% 113ms 0.75% [libchaste_crypt.so] 72ms 0.48% 78.57% 113ms 0.75% std::_Rb_tree::equal_range (inline) 22ms 0.15% 78.71% 110ms 0.73% TetrahedralMesh::EdgesEnd 1ms 0.0066% 78.72% 107ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.013% 78.73% 105ms 0.7% __printf_fp_l_buffer 0 0% 78.73% 105ms 0.7% __printf_fp_spec (inline) 60ms 0.4% 79.13% 103ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 79.13% 101ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 79.13% 100ms 0.66% OutputFileHandler::OpenOutputFile 14ms 0.093% 79.22% 100ms 0.66% boost::detail::shared_count::~shared_count (inline) 31ms 0.21% 79.43% 100ms 0.66% boost::numeric::ublas::indexing_vector_assign 0 0% 79.43% 100ms 0.66% boost::shared_ptr::~shared_ptr (inline) 99ms 0.66% 80.09% 99ms 0.66% AbstractCellMutationState::~AbstractCellMutationState 32ms 0.21% 80.30% 98ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 8ms 0.053% 80.35% 97ms 0.64% Node::~Node 43ms 0.29% 80.64% 97ms 0.64% __printf_fp_buffer_1 96ms 0.64% 81.27% 96ms 0.64% std::_Rb_tree_insert_and_rebalance 92ms 0.61% 81.88% 95ms 0.63% vertexsort 33ms 0.22% 82.10% 93ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.027% 82.13% 92ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 82.13% 91ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0066% 82.13% 85ms 0.56% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 37ms 0.25% 82.38% 83ms 0.55% AbstractTetrahedralMesh::GetElement 1ms 0.0066% 82.39% 81ms 0.54% Cell::SetCellProliferativeType 81ms 0.54% 82.92% 81ms 0.54% std::_Rb_tree_increment 75ms 0.5% 83.42% 80ms 0.53% boost::detail::sp_counted_base::release 80ms 0.53% 83.95% 80ms 0.53% boost::shared_ptr::operator-> (inline) 4ms 0.027% 83.98% 79ms 0.52% Cylindrical2dMesh::CreateMirrorNodes 79ms 0.52% 84.50% 79ms 0.52% counterclockwise 3ms 0.02% 84.52% 78ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 53ms 0.35% 84.87% 77ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 84.87% 76ms 0.5% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 84.87% 76ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 21ms 0.14% 85.01% 76ms 0.5% std::__ostream_insert