File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 10402ms, 85.40% of 12181ms total Dropped 719 nodes (cum <= 60.91ms) flat flat% sum% cum cum% 0 0% 0% 12145ms 99.70% __libc_start_call_main 0 0% 0% 12145ms 99.70% __libc_start_main_impl 0 0% 0% 12145ms 99.70% _start 0 0% 0% 12130ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 12130ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 12130ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 12130ms 99.58% main 0 0% 0% 12089ms 99.24% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 12089ms 99.24% CxxTest::TestRunner::runTest (inline) 0 0% 0% 12089ms 99.24% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 12068ms 99.07% AbstractCellBasedSimulation::Solve 0 0% 0% 8814ms 72.36% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 4811ms 39.50% AbstractCellBasedSimulation::DoCellBirth 2ms 0.016% 0.016% 4756ms 39.04% Cell::ReadyToDivide 6ms 0.049% 0.066% 4710ms 38.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.066% 4594ms 37.71% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.049% 0.11% 4588ms 37.67% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0082% 0.12% 4580ms 37.60% CellCycleModelOdeHandler::SolveOdeToTime 41ms 0.34% 0.46% 4430ms 36.37% AbstractOneStepIvpOdeSolver::InternalSolve 1ms 0.0082% 0.47% 3912ms 32.12% MeshBasedCellPopulation::Update 778ms 6.39% 6.85% 3686ms 30.26% RungeKutta4IvpOdeSolver::CalculateNextYValue 1ms 0.0082% 6.86% 3014ms 24.74% Cylindrical2dMesh::ReMesh 2424ms 19.90% 26.76% 2770ms 22.74% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 26.76% 1734ms 14.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0082% 26.77% 1698ms 13.94% MutableMesh::ReMesh 0 0% 26.77% 1516ms 12.45% AbstractCellPopulation::WriteResultsToFiles 0 0% 26.77% 1492ms 12.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.041% 26.81% 1453ms 11.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 116ms 0.95% 27.76% 1235ms 10.14% TetrahedralMesh::EdgeIterator::operator++ 583ms 4.79% 32.55% 1222ms 10.03% std::_Rb_tree::_M_lower_bound (inline) 62ms 0.51% 33.06% 955ms 7.84% std::_Rb_tree::find (inline) 0 0% 33.06% 884ms 7.26% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.016% 33.08% 837ms 6.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.074% 33.15% 816ms 6.70% TetrahedralMesh::ImportFromMesher 12ms 0.099% 33.25% 770ms 6.32% MeshBasedCellPopulation::SpringIterator::operator++ 37ms 0.3% 33.55% 738ms 6.06% operator new 9ms 0.074% 33.63% 722ms 5.93% std::set::insert (inline) 15ms 0.12% 33.75% 713ms 5.85% std::_Rb_tree::_M_insert_unique 157ms 1.29% 35.04% 694ms 5.70% __GI___libc_malloc 1ms 0.0082% 35.05% 657ms 5.39% triangulate 19ms 0.16% 35.20% 648ms 5.32% std::__new_allocator::allocate (inline) 0 0% 35.20% 645ms 5.30% std::allocator_traits::allocate (inline) 600ms 4.93% 40.13% 600ms 4.93% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 40.13% 594ms 4.88% delaunay 1ms 0.0082% 40.14% 594ms 4.88% divconqdelaunay 0 0% 40.14% 584ms 4.79% std::set::count (inline) 0 0% 40.14% 582ms 4.78% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.016% 40.15% 553ms 4.54% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0082% 40.16% 514ms 4.22% CellPopulationElementWriter::Visit 3ms 0.025% 40.19% 492ms 4.04% AbstractCellProperty::IsSubType (inline) 126ms 1.03% 41.22% 490ms 4.02% __dynamic_cast 53ms 0.44% 41.66% 487ms 4.00% std::map::operator[] (partial-inline) 255ms 2.09% 43.75% 467ms 3.83% _int_malloc 6ms 0.049% 43.80% 466ms 3.83% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.041% 43.84% 450ms 3.69% std::less::operator() (inline) 445ms 3.65% 47.49% 445ms 3.65% std::operator< (inline) 0 0% 47.49% 430ms 3.53% std::_Rb_tree::_M_create_node (inline) 12ms 0.099% 47.59% 421ms 3.46% AbstractCellPopulation::GetCellUsingLocationIndex 26ms 0.21% 47.80% 421ms 3.46% std::_Rb_tree::_M_insert_ (inline) 5ms 0.041% 47.85% 412ms 3.38% Element::Element 0 0% 47.85% 411ms 3.37% std::_Rb_tree::_M_get_node (inline) 391ms 3.21% 51.05% 391ms 3.21% std::_Rb_tree::_S_right (inline) 19ms 0.16% 51.21% 386ms 3.17% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 51.21% 383ms 3.14% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.033% 51.24% 375ms 3.08% MutableMesh::ReIndex 1ms 0.0082% 51.25% 370ms 3.04% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 51.25% 369ms 3.03% std::map::find (inline) 0 0% 51.25% 366ms 3.00% std::ostream::operator<< (inline) 110ms 0.9% 52.15% 364ms 2.99% __GI___libc_free 55ms 0.45% 52.61% 363ms 2.98% std::ostream::_M_insert 0 0% 52.61% 360ms 2.96% std::_Rb_tree::lower_bound (inline) 0 0% 52.61% 360ms 2.96% std::map::lower_bound (inline) 5ms 0.041% 52.65% 327ms 2.68% Element::RegisterWithNodes (inline) 7ms 0.057% 52.71% 326ms 2.68% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.082% 52.79% 319ms 2.62% Node::AddElement 1ms 0.0082% 52.80% 304ms 2.50% Cell::GetMutationState 11ms 0.09% 52.89% 304ms 2.50% std::__new_allocator::deallocate (inline) 44ms 0.36% 53.25% 303ms 2.49% AbstractCellProperty::IsType (inline) 0 0% 53.25% 299ms 2.45% std::allocator_traits::deallocate (inline) 70ms 0.57% 53.82% 298ms 2.45% std::_Rb_tree::_M_erase 10ms 0.082% 53.90% 297ms 2.44% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.16% 54.06% 286ms 2.35% std::_Rb_tree::~_Rb_tree (inline) 11ms 0.09% 54.15% 285ms 2.34% std::_Rb_tree::erase 11ms 0.09% 54.24% 282ms 2.32% divconqrecurse 0 0% 54.24% 282ms 2.32% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.24% 282ms 2.32% std::set::erase (inline) 1ms 0.0082% 54.25% 279ms 2.29% Cell::GetCellProliferativeType 7ms 0.057% 54.31% 278ms 2.28% Node::RemoveElement 115ms 0.94% 55.25% 277ms 2.27% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 55.25% 266ms 2.18% std::set::~set (inline) 75ms 0.62% 55.87% 265ms 2.18% mergehulls 259ms 2.13% 57.99% 259ms 2.13% CellProperty::GetTypeId 137ms 1.12% 59.12% 257ms 2.11% __cxxabiv1::__si_class_type_info::__do_dyncast 209ms 1.72% 60.83% 254ms 2.09% _int_free 0 0% 60.83% 254ms 2.09% std::_Rb_tree::_M_put_node (inline) 2ms 0.016% 60.85% 237ms 1.95% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.016% 60.87% 236ms 1.94% std::_Vector_base::_M_allocate (inline) 21ms 0.17% 61.04% 235ms 1.93% AbstractTetrahedralElement::CalculateJacobian 231ms 1.90% 62.93% 231ms 1.90% __strcmp_evex 18ms 0.15% 63.08% 225ms 1.85% Element::ResetIndex 3ms 0.025% 63.11% 218ms 1.79% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0082% 63.11% 215ms 1.77% NodeLocationWriter::Visit 16ms 0.13% 63.25% 214ms 1.76% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.016% 63.26% 203ms 1.67% alternateaxes 0 0% 63.26% 202ms 1.66% TetrahedralMesh::RefreshJacobianCachedData 186ms 1.53% 64.79% 201ms 1.65% vertexmedian 0 0% 64.79% 199ms 1.63% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.09% 64.88% 198ms 1.63% std::vector::push_back (inline) 29ms 0.24% 65.12% 197ms 1.62% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0082% 65.13% 197ms 1.62% std::set::set (inline) 15ms 0.12% 65.25% 193ms 1.58% std::num_put::_M_insert_float 9ms 0.074% 65.32% 191ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.016% 65.34% 190ms 1.56% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 65.34% 190ms 1.56% MeshBasedCellPopulation::GetDampingConstant 13ms 0.11% 65.45% 181ms 1.49% std::_Rb_tree::_M_erase_aux (inline) 9ms 0.074% 65.52% 180ms 1.48% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.09% 65.61% 178ms 1.46% std::vector::_M_realloc_insert 14ms 0.11% 65.73% 177ms 1.45% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.033% 65.76% 174ms 1.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 18ms 0.15% 65.91% 174ms 1.43% std::_Rb_tree::_M_copy (inline) 169ms 1.39% 67.29% 170ms 1.40% std::vector::operator[] (inline) 22ms 0.18% 67.47% 166ms 1.36% AbstractTetrahedralElement::RefreshJacobian 8ms 0.066% 67.54% 165ms 1.35% Element::MarkAsDeleted 9ms 0.074% 67.61% 161ms 1.32% TetrahedralMesh::Clear 4ms 0.033% 67.65% 159ms 1.31% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.016% 67.66% 159ms 1.31% std::__cxx11::collate::do_transform 0 0% 67.66% 156ms 1.28% ___vsnprintf 1ms 0.0082% 67.67% 156ms 1.28% __vsnprintf_internal (inline) 13ms 0.11% 67.78% 155ms 1.27% __printf_buffer 44ms 0.36% 68.14% 148ms 1.22% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0082% 68.15% 145ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 68.15% 142ms 1.17% OffLatticeSimulation::ApplyBoundaries 3ms 0.025% 68.17% 132ms 1.08% CellProliferativeTypesWriter::VisitCell 7ms 0.057% 68.23% 132ms 1.08% __printf_fp_l_buffer 0 0% 68.23% 132ms 1.08% __printf_fp_spec (inline) 6ms 0.049% 68.28% 132ms 1.08% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 90ms 0.74% 69.02% 128ms 1.05% malloc_consolidate 128ms 1.05% 70.07% 128ms 1.05% std::_Rb_tree_insert_and_rebalance 47ms 0.39% 70.45% 126ms 1.03% AbstractElement::GetNodeLocation 125ms 1.03% 71.48% 125ms 1.03% std::vector::size (inline) 83ms 0.68% 72.16% 124ms 1.02% AbstractElement::GetNodeGlobalIndex 21ms 0.17% 72.33% 121ms 0.99% TetrahedralMesh::EdgesEnd (partial-inline) 51ms 0.42% 72.75% 118ms 0.97% __printf_fp_buffer_1 115ms 0.94% 73.70% 115ms 0.94% incircle 6ms 0.049% 73.75% 114ms 0.94% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 1ms 0.0082% 73.75% 114ms 0.94% boost::numeric::ublas::vector_assign (inline) 113ms 0.93% 74.68% 113ms 0.93% unlink_chunk 111ms 0.91% 75.59% 111ms 0.91% Node::GetIndex 64ms 0.53% 76.12% 110ms 0.9% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.016% 76.13% 109ms 0.89% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0082% 76.14% 108ms 0.89% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.066% 76.21% 103ms 0.85% Node::~Node 101ms 0.83% 77.04% 101ms 0.83% boost::shared_ptr::operator-> (inline) 68ms 0.56% 77.60% 101ms 0.83% std::_Rb_tree::equal_range (inline) 7ms 0.057% 77.65% 100ms 0.82% boost::numeric::ublas::c_vector::c_vector (inline) 89ms 0.73% 78.38% 99ms 0.81% vertexsort 1ms 0.0082% 78.39% 98ms 0.8% Cell::SetCellProliferativeType 0 0% 78.39% 96ms 0.79% AbstractCellBasedWriter::OpenOutputFileForAppend 51ms 0.42% 78.81% 95ms 0.78% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 31ms 0.25% 79.07% 95ms 0.78% boost::numeric::ublas::indexing_vector_assign 6ms 0.049% 79.12% 94ms 0.77% CellPropertyCollection::HasProperty 0 0% 79.12% 94ms 0.77% OutputFileHandler::OpenOutputFile 0 0% 79.12% 92ms 0.76% Cell::HasCellProperty (inline) 0 0% 79.12% 91ms 0.75% AbstractCellBasedSimulation::DoCellRemoval (inline) 44ms 0.36% 79.48% 90ms 0.74% boost::shared_ptr::shared_ptr (inline) 0 0% 79.48% 89ms 0.73% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 8ms 0.066% 79.54% 89ms 0.73% boost::detail::shared_count::~shared_count (inline) 0 0% 79.54% 89ms 0.73% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.54% 86ms 0.71% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 31ms 0.25% 79.80% 81ms 0.66% std::__ostream_insert 17ms 0.14% 79.94% 81ms 0.66% std::num_put::_M_insert_int 8ms 0.066% 80.00% 80ms 0.66% MeshBasedCellPopulation::SpringIterator::SpringIterator 77ms 0.63% 80.63% 77ms 0.63% std::_Rb_tree_rebalance_for_erase 54ms 0.44% 81.08% 76ms 0.62% TimeStepper::AdvanceOneTimeStep 69ms 0.57% 81.64% 76ms 0.62% boost::detail::sp_counted_base::release 75ms 0.62% 82.26% 75ms 0.62% std::_Rb_tree_increment 6ms 0.049% 82.31% 74ms 0.61% Cylindrical2dMesh::CreateMirrorNodes 3ms 0.025% 82.33% 74ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.033% 82.37% 73ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.016% 82.38% 72ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 72ms 0.59% 82.97% 72ms 0.59% counterclockwise 71ms 0.58% 83.56% 71ms 0.58% TetrahedralMesh::EdgeIterator::operator!= 0 0% 83.56% 70ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 30ms 0.25% 83.80% 69ms 0.57% AbstractTetrahedralMesh::GetElement 69ms 0.57% 84.37% 69ms 0.57% Node::rGetLocation 3ms 0.025% 84.39% 67ms 0.55% CellLocationIndexWriter::VisitCell 0 0% 84.39% 66ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 36ms 0.3% 84.69% 66ms 0.54% boost::numeric::ublas::c_matrix::operator() 24ms 0.2% 84.89% 66ms 0.54% std::basic_filebuf::xsputn 0 0% 84.89% 66ms 0.54% std::operator<< (inline) 62ms 0.51% 85.40% 62ms 0.51% boost::numeric::ublas::c_vector::operator() (partial-inline)