File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12395ms, 84.58% of 14654ms total Dropped 727 nodes (cum <= 73.27ms) flat flat% sum% cum cum% 0 0% 0% 14617ms 99.75% __libc_start_call_main 0 0% 0% 14617ms 99.75% __libc_start_main_impl 0 0% 0% 14617ms 99.75% _start 0 0% 0% 14600ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14600ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14600ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14600ms 99.63% main 0 0% 0% 14561ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14561ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14561ms 99.37% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14540ms 99.22% AbstractCellBasedSimulation::Solve 0 0% 0% 11193ms 76.38% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.014% 0.014% 7181ms 49.00% AbstractCellBasedSimulation::DoCellBirth 2ms 0.014% 0.027% 7105ms 48.49% Cell::ReadyToDivide 8ms 0.055% 0.082% 7031ms 47.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0068% 0.089% 6925ms 47.26% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.068% 0.16% 6918ms 47.21% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0068% 0.16% 6901ms 47.09% CellCycleModelOdeHandler::SolveOdeToTime 46ms 0.31% 0.48% 6798ms 46.39% AbstractOneStepIvpOdeSolver::InternalSolve 795ms 5.43% 5.90% 6075ms 41.46% RungeKutta4IvpOdeSolver::CalculateNextYValue 2099ms 14.32% 20.23% 5118ms 34.93% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.23% 3921ms 26.76% MeshBasedCellPopulation::Update 58ms 0.4% 20.62% 3041ms 20.75% AbstractCellProperty::IsType (inline) 1ms 0.0068% 20.63% 3023ms 20.63% Cylindrical2dMesh::ReMesh 234ms 1.60% 22.23% 1969ms 13.44% AbstractCellProperty::IsSame 0 0% 22.23% 1858ms 12.68% OffLatticeSimulation::UpdateCellLocationsAndTopology 171ms 1.17% 23.39% 1735ms 11.84% std::type_info::operator== (inline) 1ms 0.0068% 23.40% 1719ms 11.73% MutableMesh::ReMesh 0 0% 23.40% 1603ms 10.94% ForwardEulerNumericalMethod::UpdateAllNodePositions 1586ms 10.82% 34.22% 1586ms 10.82% __strcmp_evex 6ms 0.041% 34.26% 1574ms 10.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 34.26% 1482ms 10.11% AbstractCellPopulation::WriteResultsToFiles 142ms 0.97% 35.23% 1273ms 8.69% TetrahedralMesh::EdgeIterator::operator++ 617ms 4.21% 39.44% 1262ms 8.61% std::_Rb_tree::_M_lower_bound (inline) 58ms 0.4% 39.84% 961ms 6.56% std::_Rb_tree::find (inline) 3ms 0.02% 39.86% 878ms 5.99% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 39.86% 875ms 5.97% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.034% 39.89% 830ms 5.66% TetrahedralMesh::ImportFromMesher 34ms 0.23% 40.13% 787ms 5.37% operator new 10ms 0.068% 40.19% 778ms 5.31% MeshBasedCellPopulation::SpringIterator::operator++ 210ms 1.43% 41.63% 738ms 5.04% __GI___libc_malloc 5ms 0.034% 41.66% 732ms 5.00% std::set::insert (inline) 9ms 0.061% 41.72% 727ms 4.96% std::_Rb_tree::_M_insert_unique 24ms 0.16% 41.89% 701ms 4.78% std::__new_allocator::allocate (inline) 0 0% 41.89% 698ms 4.76% std::allocator_traits::allocate (inline) 1ms 0.0068% 41.89% 657ms 4.48% triangulate 0 0% 41.89% 615ms 4.20% std::set::count (inline) 0 0% 41.89% 592ms 4.04% delaunay 1ms 0.0068% 41.90% 591ms 4.03% divconqdelaunay 579ms 3.95% 45.85% 579ms 3.95% WntCellCycleOdeSystem::CalculateStoppingEvent 6ms 0.041% 45.89% 556ms 3.79% CellPopulationElementWriter::Visit 5ms 0.034% 45.93% 504ms 3.44% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.02% 45.95% 498ms 3.40% AbstractTwoBodyInteractionForce::AddForceContribution 36ms 0.25% 46.19% 495ms 3.38% std::map::operator[] (partial-inline) 0 0% 46.19% 483ms 3.30% std::_Rb_tree::_M_create_node (inline) 259ms 1.77% 47.96% 471ms 3.21% _int_malloc 0 0% 47.96% 456ms 3.11% std::_Rb_tree::_M_get_node (inline) 25ms 0.17% 48.13% 445ms 3.04% std::_Rb_tree::_M_insert_ (inline) 141ms 0.96% 49.09% 442ms 3.02% __dynamic_cast 5ms 0.034% 49.13% 436ms 2.98% std::less::operator() (inline) 0 0% 49.13% 435ms 2.97% std::_Rb_tree::_Alloc_node::operator() (inline) 431ms 2.94% 52.07% 431ms 2.94% std::operator< (inline) 16ms 0.11% 52.18% 424ms 2.89% AbstractCellPopulation::GetCellUsingLocationIndex 16ms 0.11% 52.29% 414ms 2.83% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.0068% 52.29% 414ms 2.83% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.048% 52.34% 413ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 405ms 2.76% 55.10% 405ms 2.76% std::_Rb_tree::_S_right (inline) 5ms 0.034% 55.14% 389ms 2.65% Element::Element 0 0% 55.14% 381ms 2.60% std::_Rb_tree::lower_bound (inline) 0 0% 55.14% 381ms 2.60% std::map::lower_bound (inline) 117ms 0.8% 55.94% 379ms 2.59% __GI___libc_free 3ms 0.02% 55.96% 374ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 4ms 0.027% 55.98% 371ms 2.53% MutableMesh::ReIndex 231ms 1.58% 57.56% 354ms 2.42% AbstractCellMutationState::AbstractCellMutationState 1ms 0.0068% 57.57% 352ms 2.40% std::ostream::operator<< (inline) 46ms 0.31% 57.88% 350ms 2.39% std::ostream::_M_insert 9ms 0.061% 57.94% 342ms 2.33% Element::RegisterWithNodes (inline) 0 0% 57.94% 342ms 2.33% std::map::find (inline) 0 0% 57.94% 341ms 2.33% AbstractCellProperty::IsSubType (inline) 5ms 0.034% 57.98% 332ms 2.27% Node::AddElement 18ms 0.12% 58.10% 328ms 2.24% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.068% 58.17% 314ms 2.14% std::__new_allocator::deallocate (inline) 0 0% 58.17% 310ms 2.12% std::allocator_traits::deallocate (inline) 19ms 0.13% 58.30% 304ms 2.07% divconqrecurse 12ms 0.082% 58.38% 303ms 2.07% Node::RemoveElement 1ms 0.0068% 58.39% 303ms 2.07% std::set::erase (inline) 72ms 0.49% 58.88% 302ms 2.06% std::_Rb_tree::_M_erase 6ms 0.041% 58.92% 302ms 2.06% std::_Rb_tree::erase 0 0% 58.92% 291ms 1.99% std::_Rb_tree::_M_drop_node (inline) 78ms 0.53% 59.45% 283ms 1.93% mergehulls 20ms 0.14% 59.59% 280ms 1.91% std::_Rb_tree::~_Rb_tree (inline) 109ms 0.74% 60.33% 273ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 60.33% 266ms 1.82% std::_Rb_tree::_M_put_node (inline) 0 0% 60.33% 263ms 1.79% std::set::~set (inline) 225ms 1.54% 61.87% 262ms 1.79% _int_free 24ms 0.16% 62.03% 245ms 1.67% Element::ResetIndex 0 0% 62.03% 242ms 1.65% std::_Vector_base::_M_allocate (inline) 233ms 1.59% 63.62% 237ms 1.62% std::vector::operator[] (inline) 1ms 0.0068% 63.63% 225ms 1.54% Cell::GetCellProliferativeType 14ms 0.096% 63.72% 224ms 1.53% std::_Rb_tree::_Rb_tree (partial-inline) 223ms 1.52% 65.24% 223ms 1.52% [libchaste_cell_based.so] 15ms 0.1% 65.35% 220ms 1.50% AbstractTetrahedralElement::CalculateJacobian 2ms 0.014% 65.36% 220ms 1.50% Cell::GetMutationState 5ms 0.034% 65.40% 218ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.014% 65.41% 218ms 1.49% NodeLocationWriter::Visit 1ms 0.0068% 65.42% 217ms 1.48% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0068% 65.42% 213ms 1.45% LegacyCellProliferativeTypesWriter::VisitCell 100ms 0.68% 66.10% 212ms 1.45% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.014% 66.12% 211ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 18ms 0.12% 66.24% 210ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 19ms 0.13% 66.37% 202ms 1.38% std::_Rb_tree::_M_erase_aux (inline) 3ms 0.02% 66.39% 201ms 1.37% alternateaxes 2ms 0.014% 66.41% 199ms 1.36% std::set::set (inline) 12ms 0.082% 66.49% 197ms 1.34% std::num_put::_M_insert_float 184ms 1.26% 67.74% 197ms 1.34% vertexmedian 12ms 0.082% 67.82% 193ms 1.32% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.068% 67.89% 193ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 74ms 0.5% 68.40% 193ms 1.32% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 56ms 0.38% 68.78% 192ms 1.31% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.061% 68.84% 187ms 1.28% std::vector::push_back (inline) 13ms 0.089% 68.93% 185ms 1.26% TetrahedralMesh::Clear 8ms 0.055% 68.98% 182ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 33ms 0.23% 69.21% 182ms 1.24% AbstractTetrahedralElement::RefreshJacobian 7ms 0.048% 69.26% 182ms 1.24% Element::MarkAsDeleted 12ms 0.082% 69.34% 181ms 1.24% std::_Rb_tree::_M_copy (inline) 60ms 0.41% 69.75% 177ms 1.21% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.075% 69.82% 171ms 1.17% std::vector::_M_realloc_insert 3ms 0.02% 69.84% 168ms 1.15% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 45ms 0.31% 70.15% 166ms 1.13% std::_Rb_tree::_M_clone_node (inline) 2ms 0.014% 70.17% 159ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 7ms 0.048% 70.21% 159ms 1.09% std::__cxx11::collate::do_transform 150ms 1.02% 71.24% 150ms 1.02% std::type_info::name (inline) 2ms 0.014% 71.25% 148ms 1.01% ___vsnprintf 99ms 0.68% 71.93% 146ms 1% AbstractElement::GetNodeGlobalIndex 0 0% 71.93% 146ms 1% OffLatticeSimulation::ApplyBoundaries 0 0% 71.93% 146ms 1% __vsnprintf_internal (inline) 14ms 0.096% 72.02% 144ms 0.98% __printf_buffer 1ms 0.0068% 72.03% 141ms 0.96% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.03% 141ms 0.96% MeshBasedCellPopulation::GetDampingConstant 3ms 0.02% 72.05% 136ms 0.93% CellPropertyCollection::HasProperty 135ms 0.92% 72.97% 135ms 0.92% incircle 2ms 0.014% 72.98% 133ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 72.98% 132ms 0.9% Cell::HasCellProperty (inline) 10ms 0.068% 73.05% 128ms 0.87% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 4ms 0.027% 73.08% 126ms 0.86% __printf_fp_l_buffer 0 0% 73.08% 126ms 0.86% __printf_fp_spec (inline) 52ms 0.35% 73.43% 125ms 0.85% AbstractElement::GetNodeLocation 124ms 0.85% 74.28% 124ms 0.85% std::vector::size (inline) 88ms 0.6% 74.88% 123ms 0.84% malloc_consolidate 1ms 0.0068% 74.89% 120ms 0.82% CellProliferativeTypesWriter::VisitCell 120ms 0.82% 75.71% 120ms 0.82% std::_Rb_tree_insert_and_rebalance 34ms 0.23% 75.94% 117ms 0.8% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 24ms 0.16% 76.10% 117ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 55ms 0.38% 76.48% 115ms 0.78% __printf_fp_buffer_1 111ms 0.76% 77.23% 111ms 0.76% [libchaste_crypt.so] 1ms 0.0068% 77.24% 111ms 0.76% boost::numeric::ublas::vector_assign (inline) 109ms 0.74% 77.99% 109ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 42ms 0.29% 78.27% 108ms 0.74% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 106ms 0.72% 79.00% 106ms 0.72% Node::GetIndex 6ms 0.041% 79.04% 106ms 0.72% Node::~Node 103ms 0.7% 79.74% 103ms 0.7% unlink_chunk 28ms 0.19% 79.93% 102ms 0.7% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.0068% 79.94% 98ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 58ms 0.4% 80.33% 96ms 0.66% std::_Rb_tree::equal_range (inline) 57ms 0.39% 80.72% 95ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0068% 80.73% 93ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 9ms 0.061% 80.79% 93ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 33ms 0.23% 81.02% 91ms 0.62% std::__ostream_insert 14ms 0.096% 81.11% 90ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 81.11% 90ms 0.61% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.11% 89ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0068% 81.12% 89ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0068% 81.12% 86ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 3ms 0.02% 81.15% 85ms 0.58% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 84ms 0.57% 81.72% 84ms 0.57% [libchaste_mesh.so] 21ms 0.14% 81.86% 83ms 0.57% std::num_put::_M_insert_int 77ms 0.53% 82.39% 82ms 0.56% vertexsort 0 0% 82.39% 81ms 0.55% AbstractCellBasedWriter::OpenOutputFileForAppend 30ms 0.2% 82.59% 81ms 0.55% boost::numeric::ublas::indexing_vector_assign 1ms 0.0068% 82.60% 80ms 0.55% OutputFileHandler::OpenOutputFile 5ms 0.034% 82.63% 79ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 58ms 0.4% 83.03% 77ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 6ms 0.041% 83.07% 76ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 75ms 0.51% 83.58% 75ms 0.51% AbstractCellProperty::AbstractCellProperty 1ms 0.0068% 83.59% 75ms 0.51% Cell::SetCellProliferativeType 75ms 0.51% 84.10% 75ms 0.51% TetrahedralMesh::EdgeIterator::operator!= 71ms 0.48% 84.58% 74ms 0.5% boost::detail::sp_counted_base::release