File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12909ms, 78.90% of 16362ms total Dropped 863 nodes (cum <= 81.81ms) flat flat% sum% cum cum% 0 0% 0% 16314ms 99.71% __libc_start_call_main 0 0% 0% 16314ms 99.71% __libc_start_main_impl 0 0% 0% 16314ms 99.71% _start 0 0% 0% 16293ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16293ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16293ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16293ms 99.58% main 0 0% 0% 16253ms 99.33% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16253ms 99.33% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16253ms 99.33% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16228ms 99.18% AbstractCellBasedSimulation::Solve 0 0% 0% 11706ms 71.54% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.024% 0.024% 6336ms 38.72% AbstractCellBasedSimulation::DoCellBirth 18ms 0.11% 0.13% 6214ms 37.98% Cell::ReadyToDivide 7ms 0.043% 0.18% 6112ms 37.35% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.012% 0.19% 5917ms 36.16% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 27ms 0.17% 0.35% 5902ms 36.07% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.037% 0.39% 5872ms 35.89% CellCycleModelOdeHandler::SolveOdeToTime 7ms 0.043% 0.43% 5687ms 34.76% CvodeAdaptor::Solve 0 0% 0.43% 5262ms 32.16% MeshBasedCellPopulation::Update 74ms 0.45% 0.89% 5181ms 31.66% CVode 51ms 0.31% 1.20% 4643ms 28.38% CVodeFree 4ms 0.024% 1.22% 4080ms 24.94% Cylindrical2dMesh::ReMesh 144ms 0.88% 2.10% 3737ms 22.84% cvRescale 0 0% 2.10% 3417ms 20.88% SUNNonlinSolSolve 53ms 0.32% 2.43% 3417ms 20.88% SUNNonlinSolSolve_Newton 78ms 0.48% 2.90% 3308ms 20.22% cvNlsInit 0 0% 2.90% 2497ms 15.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 2.90% 2245ms 13.72% MutableMesh::ReMesh 1ms 0.0061% 2.91% 2173ms 13.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.092% 3.00% 2125ms 12.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0061% 3.01% 2021ms 12.35% AbstractCellPopulation::WriteResultsToFiles 19ms 0.12% 3.12% 1983ms 12.12% cvLsSetup 766ms 4.68% 7.80% 1852ms 11.32% std::_Rb_tree::_M_lower_bound (inline) 168ms 1.03% 8.83% 1741ms 10.64% TetrahedralMesh::EdgeIterator::operator++ 11ms 0.067% 8.90% 1452ms 8.87% cvLsDQJtimes 62ms 0.38% 9.28% 1369ms 8.37% std::_Rb_tree::find (inline) 0 0% 9.28% 1141ms 6.97% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.037% 9.31% 1134ms 6.93% TetrahedralMesh::ImportFromMesher 6ms 0.037% 9.35% 1132ms 6.92% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 269ms 1.64% 10.99% 1099ms 6.72% __GI___libc_malloc 42ms 0.26% 11.25% 1090ms 6.66% operator new 10ms 0.061% 11.31% 1044ms 6.38% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.067% 11.38% 1029ms 6.29% std::set::insert (inline) 25ms 0.15% 11.53% 1018ms 6.22% std::_Rb_tree::_M_insert_unique 36ms 0.22% 11.75% 955ms 5.84% std::__new_allocator::allocate (inline) 0 0% 11.75% 947ms 5.79% std::allocator_traits::allocate (inline) 0 0% 11.75% 846ms 5.17% std::set::count (inline) 0 0% 11.75% 836ms 5.11% triangulate 1ms 0.0061% 11.76% 755ms 4.61% delaunay 5ms 0.031% 11.79% 753ms 4.60% divconqdelaunay 7ms 0.043% 11.83% 743ms 4.54% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 427ms 2.61% 14.44% 740ms 4.52% _int_malloc 53ms 0.32% 14.77% 701ms 4.28% std::map::operator[] (partial-inline) 685ms 4.19% 18.95% 685ms 4.19% std::_Rb_tree::_S_right (inline) 1ms 0.0061% 18.96% 681ms 4.16% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.055% 19.01% 671ms 4.10% CellPopulationElementWriter::Visit 19ms 0.12% 19.13% 671ms 4.10% std::less::operator() (inline) 44ms 0.27% 19.40% 669ms 4.09% cvLsSolve 652ms 3.98% 23.38% 652ms 3.98% std::operator< (inline) 35ms 0.21% 23.60% 646ms 3.95% std::_Rb_tree::_M_insert_ (inline) 192ms 1.17% 24.77% 634ms 3.87% __dynamic_cast 7ms 0.043% 24.81% 619ms 3.78% CellPropertyCollection::GetPropertiesType (inline) 0 0% 24.81% 605ms 3.70% std::_Rb_tree::_M_create_node (inline) 594ms 3.63% 28.44% 594ms 3.63% N_VBufUnpack_Serial 21ms 0.13% 28.57% 589ms 3.60% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.037% 28.61% 588ms 3.59% MeshBasedCellPopulation::AcceptCellWriter 34ms 0.21% 28.82% 580ms 3.54% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 28.82% 576ms 3.52% std::_Rb_tree::_M_get_node (inline) 39ms 0.24% 29.06% 574ms 3.51% N_VWrmsNorm 0 0% 29.06% 573ms 3.50% std::_Rb_tree::lower_bound (inline) 0 0% 29.06% 573ms 3.50% std::map::lower_bound (inline) 0 0% 29.06% 558ms 3.41% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.061% 29.12% 548ms 3.35% Element::Element 195ms 1.19% 30.31% 545ms 3.33% __GI___libc_free 5ms 0.031% 30.34% 542ms 3.31% MutableMesh::ReIndex 166ms 1.01% 31.35% 542ms 3.31% cvRestore 7ms 0.043% 31.40% 537ms 3.28% SUNLinSolSolve 102ms 0.62% 32.02% 535ms 3.27% N_VWrmsNorm_Serial 15ms 0.092% 32.11% 530ms 3.24% SUNLinSolSolve_Dense 59ms 0.36% 32.47% 525ms 3.21% std::ostream::_M_insert 0 0% 32.47% 525ms 3.21% std::ostream::operator<< (inline) 0 0% 32.47% 518ms 3.17% std::map::find (inline) 2ms 0.012% 32.48% 517ms 3.16% cvLsDQJac 124ms 0.76% 33.24% 515ms 3.15% N_VLinearSum_Serial 63ms 0.39% 33.63% 515ms 3.15% cvLsDenseDQJac 4ms 0.024% 33.65% 508ms 3.10% AbstractCellProperty::IsSubType (inline) 10ms 0.061% 33.71% 507ms 3.10% SUNLinSolSetup 8ms 0.049% 33.76% 501ms 3.06% Element::RegisterWithNodes (inline) 6ms 0.037% 33.80% 497ms 3.04% SUNLinSolSetup_Dense 14ms 0.086% 33.88% 494ms 3.02% Cylindrical2dMesh::ReconstructCylindricalMesh 7ms 0.043% 33.93% 487ms 2.98% Node::AddElement 472ms 2.88% 36.81% 472ms 2.88% SUNDlsMat_denseGETRF 13ms 0.079% 36.89% 471ms 2.88% Cylindrical2dMesh::CorrectNonPeriodicMesh 40ms 0.24% 37.13% 465ms 2.84% N_VLinearSum 10ms 0.061% 37.20% 459ms 2.81% CvodeRhsAdaptor 455ms 2.78% 39.98% 455ms 2.78% __strcmp_avx2 2ms 0.012% 39.99% 447ms 2.73% SUNMatScaleAddI 445ms 2.72% 42.71% 445ms 2.72% SUNMatScaleAddI_Dense 10ms 0.061% 42.77% 426ms 2.60% SUNMatCopy 422ms 2.58% 45.35% 422ms 2.58% SUNDlsMat_denseGETRS 5ms 0.031% 45.38% 417ms 2.55% CvodeAdaptor::SetupCvode 400ms 2.44% 47.82% 416ms 2.54% SUNMatCopy_Dense 2ms 0.012% 47.84% 407ms 2.49% std::set::erase (inline) 12ms 0.073% 47.91% 406ms 2.48% std::_Rb_tree::erase 159ms 0.97% 48.88% 405ms 2.48% WntCellCycleOdeSystem::EvaluateYDerivatives 10ms 0.061% 48.94% 401ms 2.45% AbstractCellProperty::IsType (inline) 9ms 0.055% 49.00% 399ms 2.44% Node::RemoveElement 381ms 2.33% 51.33% 381ms 2.33% N_VWSqrSumLocal_Serial 106ms 0.65% 51.97% 378ms 2.31% std::_Rb_tree::_M_erase 4ms 0.024% 52.00% 375ms 2.29% std::_Vector_base::_M_allocate (inline) 16ms 0.098% 52.10% 371ms 2.27% std::__new_allocator::deallocate (inline) 0 0% 52.10% 363ms 2.22% std::allocator_traits::deallocate (inline) 25ms 0.15% 52.25% 356ms 2.18% Element::ResetIndex 27ms 0.17% 52.41% 351ms 2.15% std::_Rb_tree::~_Rb_tree (inline) 14ms 0.086% 52.50% 349ms 2.13% divconqrecurse 136ms 0.83% 53.33% 347ms 2.12% std::_Rb_tree::_M_get_insert_unique_pos 288ms 1.76% 55.09% 346ms 2.11% _int_free 0 0% 55.09% 339ms 2.07% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.09% 334ms 2.04% Cell::GetCellProliferativeType 0 0% 55.09% 332ms 2.03% NodeLocationWriter::Visit 85ms 0.52% 55.61% 329ms 2.01% mergehulls 2ms 0.012% 55.62% 328ms 2.00% Cell::GetMutationState 7ms 0.043% 55.67% 317ms 1.94% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 55.67% 316ms 1.93% std::set::~set (inline) 139ms 0.85% 56.52% 303ms 1.85% __cxxabiv1::__si_class_type_info::__do_dyncast 85ms 0.52% 57.03% 300ms 1.83% AbstractCellProperty::IsSame 0 0% 57.03% 298ms 1.82% std::_Rb_tree::_M_put_node (inline) 2ms 0.012% 57.05% 296ms 1.81% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.1% 57.15% 296ms 1.81% std::num_put::_M_insert_float 35ms 0.21% 57.36% 294ms 1.80% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0061% 57.37% 289ms 1.77% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.024% 57.40% 289ms 1.77% LegacyCellProliferativeTypesWriter::VisitCell 12ms 0.073% 57.47% 287ms 1.75% std::vector::push_back (inline) 13ms 0.079% 57.55% 282ms 1.72% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.018% 57.57% 268ms 1.64% alternateaxes 24ms 0.15% 57.71% 263ms 1.61% std::vector::_M_realloc_insert 243ms 1.49% 59.20% 262ms 1.60% vertexmedian 17ms 0.1% 59.30% 256ms 1.56% AbstractTetrahedralElement::CalculateJacobian 0 0% 59.30% 255ms 1.56% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.024% 59.33% 253ms 1.55% std::set::set (inline) 16ms 0.098% 59.42% 245ms 1.50% std::_Rb_tree::_M_copy (inline) 6ms 0.037% 59.46% 242ms 1.48% AbstractCellPopulation::IsCellAttachedToLocationIndex 33ms 0.2% 59.66% 240ms 1.47% N_VScale 16ms 0.098% 59.76% 240ms 1.47% std::_Rb_tree::_M_erase_aux (inline) 35ms 0.21% 59.97% 238ms 1.45% N_VScale_Serial 3ms 0.018% 59.99% 237ms 1.45% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.012% 60.00% 229ms 1.40% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.031% 60.04% 225ms 1.38% std::__cxx11::collate::do_transform 88ms 0.54% 60.57% 224ms 1.37% std::_Rb_tree::_M_clone_node (inline) 32ms 0.2% 60.77% 215ms 1.31% std::type_info::operator== (inline) 14ms 0.086% 60.85% 214ms 1.31% Element::MarkAsDeleted 0 0% 60.85% 213ms 1.30% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.049% 60.90% 213ms 1.30% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 60.90% 213ms 1.30% MeshBasedCellPopulation::GetDampingConstant 23ms 0.14% 61.04% 213ms 1.30% TetrahedralMesh::Clear 3ms 0.018% 61.06% 212ms 1.30% ___vsnprintf 0 0% 61.06% 209ms 1.28% __vsnprintf_internal (inline) 33ms 0.2% 61.26% 204ms 1.25% __printf_buffer 204ms 1.25% 62.51% 204ms 1.25% std::_Rb_tree_insert_and_rebalance 14ms 0.086% 62.60% 202ms 1.23% AbstractTetrahedralElement::RefreshJacobian 150ms 0.92% 63.51% 199ms 1.22% AbstractElement::GetNodeGlobalIndex 5ms 0.031% 63.54% 194ms 1.19% CellProliferativeTypesWriter::VisitCell 148ms 0.9% 64.45% 193ms 1.18% malloc_consolidate 0 0% 64.45% 188ms 1.15% OffLatticeSimulation::ApplyBoundaries 1ms 0.0061% 64.45% 181ms 1.11% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 11ms 0.067% 64.52% 180ms 1.10% CVodeSetLinearSolver 19ms 0.12% 64.64% 174ms 1.06% cvEwtSet 68ms 0.42% 65.05% 171ms 1.05% AbstractElement::GetNodeLocation 111ms 0.68% 65.73% 170ms 1.04% std::_Rb_tree::equal_range (inline) 1ms 0.0061% 65.74% 165ms 1.01% CellPropertyCollection::HasProperty 0 0% 65.74% 162ms 0.99% Cell::HasCellProperty (inline) 162ms 0.99% 66.73% 162ms 0.99% Node::GetIndex 8ms 0.049% 66.78% 162ms 0.99% __printf_fp_l_buffer 0 0% 66.78% 162ms 0.99% __printf_fp_spec (inline) 9ms 0.055% 66.83% 162ms 0.99% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 5ms 0.031% 66.86% 159ms 0.97% AbstractTetrahedralElement::AbstractTetrahedralElement 153ms 0.94% 67.80% 153ms 0.94% incircle 149ms 0.91% 68.71% 149ms 0.91% unlink_chunk 74ms 0.45% 69.16% 148ms 0.9% __printf_fp_buffer_1 1ms 0.0061% 69.17% 144ms 0.88% Cell::SetCellProliferativeType 142ms 0.87% 70.03% 142ms 0.87% std::vector::size (inline) 5ms 0.031% 70.06% 140ms 0.86% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 4ms 0.024% 70.09% 129ms 0.79% boost::numeric::ublas::vector_assign (inline) 0 0% 70.09% 122ms 0.75% AbstractCellBasedWriter::OpenOutputFileForAppend 67ms 0.41% 70.50% 122ms 0.75% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 70.50% 121ms 0.74% OutputFileHandler::OpenOutputFile 24ms 0.15% 70.65% 121ms 0.74% std::num_put::_M_insert_int 112ms 0.68% 71.33% 119ms 0.73% vertexsort 5ms 0.031% 71.36% 117ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 11ms 0.067% 71.43% 117ms 0.72% boost::numeric::ublas::c_vector::c_vector (partial-inline) 32ms 0.2% 71.62% 114ms 0.7% N_VScaleAddMulti 17ms 0.1% 71.73% 114ms 0.7% boost::detail::shared_count::~shared_count (inline) 0 0% 71.73% 114ms 0.7% boost::shared_ptr::~shared_ptr (inline) 30ms 0.18% 71.91% 112ms 0.68% TetrahedralMesh::EdgesEnd 6ms 0.037% 71.95% 111ms 0.68% N_VCloneEmpty_Serial 18ms 0.11% 72.06% 111ms 0.68% Node::~Node 110ms 0.67% 72.73% 110ms 0.67% AbstractElement::IsDeleted 109ms 0.67% 73.40% 109ms 0.67% std::_Rb_tree_rebalance_for_erase 0 0% 73.40% 107ms 0.65% std::vector::resize (inline) 0 0% 73.40% 106ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.061% 73.46% 105ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 73.46% 104ms 0.64% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 54ms 0.33% 73.79% 104ms 0.64% SUNDenseMatrix 0 0% 73.79% 104ms 0.64% std::vector::_M_default_append 103ms 0.63% 74.42% 103ms 0.63% [libchaste_mesh.so] 102ms 0.62% 75.04% 102ms 0.62% std::_Rb_tree_increment 9ms 0.055% 75.09% 99ms 0.61% N_VClone 2ms 0.012% 75.11% 99ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 34ms 0.21% 75.31% 97ms 0.59% std::__ostream_insert 0 0% 75.31% 96ms 0.59% NodeMap::NodeMap 0 0% 75.31% 96ms 0.59% tcache_get (inline) 96ms 0.59% 75.90% 96ms 0.59% tcache_get_n (inline) 3ms 0.018% 75.92% 95ms 0.58% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 92ms 0.56% 76.48% 94ms 0.57% boost::detail::sp_counted_base::release 3ms 0.018% 76.50% 93ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 7ms 0.043% 76.54% 90ms 0.55% N_VClone_Serial 23ms 0.14% 76.68% 87ms 0.53% boost::numeric::ublas::indexing_vector_assign 87ms 0.53% 77.22% 87ms 0.53% counterclockwise 49ms 0.3% 77.51% 85ms 0.52% AbstractTetrahedralMesh::GetElement 85ms 0.52% 78.03% 85ms 0.52% Node::rGetLocation 85ms 0.52% 78.55% 85ms 0.52% TetrahedralMesh::EdgeIterator::operator!= 3ms 0.018% 78.57% 84ms 0.51% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 6ms 0.037% 78.61% 83ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 35ms 0.21% 78.82% 83ms 0.51% boost::shared_ptr::shared_ptr (inline) 2ms 0.012% 78.84% 83ms 0.51% std::operator<< (inline) 10ms 0.061% 78.90% 82ms 0.5% SUNRpowerR 0 0% 78.90% 82ms 0.5% std::vector::vector (inline)