File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 9989ms, 78.86% of 12667ms total Dropped 813 nodes (cum <= 63.34ms) flat flat% sum% cum cum% 0 0% 0% 12629ms 99.70% __libc_start_call_main 0 0% 0% 12629ms 99.70% __libc_start_main_impl 0 0% 0% 12629ms 99.70% _start 0 0% 0% 12612ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 12612ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 12612ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 12612ms 99.57% main 0 0% 0% 12575ms 99.27% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 12575ms 99.27% CxxTest::TestRunner::runTest (inline) 0 0% 0% 12575ms 99.27% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 12556ms 99.12% AbstractCellBasedSimulation::Solve 0 0% 0% 9088ms 71.75% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.032% 0.032% 4954ms 39.11% AbstractCellBasedSimulation::DoCellBirth 12ms 0.095% 0.13% 4851ms 38.30% Cell::ReadyToDivide 3ms 0.024% 0.15% 4764ms 37.61% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.15% 4595ms 36.28% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.095% 0.24% 4587ms 36.21% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0079% 0.25% 4571ms 36.09% CellCycleModelOdeHandler::SolveOdeToTime 6ms 0.047% 0.3% 4441ms 35.06% CvodeAdaptor::Solve 65ms 0.51% 0.81% 4049ms 31.96% CVode 1ms 0.0079% 0.82% 4048ms 31.96% MeshBasedCellPopulation::Update 32ms 0.25% 1.07% 3651ms 28.82% CVodeFree 3ms 0.024% 1.10% 3117ms 24.61% Cylindrical2dMesh::ReMesh 152ms 1.20% 2.30% 2863ms 22.60% cvRescale 7ms 0.055% 2.35% 2537ms 20.03% SUNNonlinSolSolve 33ms 0.26% 2.61% 2530ms 19.97% SUNNonlinSolSolve_Newton 55ms 0.43% 3.05% 2438ms 19.25% cvNlsInit 4ms 0.032% 3.08% 1908ms 15.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0079% 3.09% 1740ms 13.74% MutableMesh::ReMesh 0 0% 3.09% 1645ms 12.99% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.063% 3.15% 1602ms 12.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 3.15% 1554ms 12.27% AbstractCellPopulation::WriteResultsToFiles 14ms 0.11% 3.26% 1464ms 11.56% cvLsSetup 629ms 4.97% 8.23% 1373ms 10.84% std::_Rb_tree::_M_lower_bound (inline) 125ms 0.99% 9.21% 1287ms 10.16% TetrahedralMesh::EdgeIterator::operator++ 12ms 0.095% 9.31% 1058ms 8.35% cvLsDQJtimes 42ms 0.33% 9.64% 1045ms 8.25% std::_Rb_tree::find (inline) 1ms 0.0079% 9.65% 904ms 7.14% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.071% 9.72% 881ms 6.96% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 8ms 0.063% 9.78% 835ms 6.59% TetrahedralMesh::ImportFromMesher 5ms 0.039% 9.82% 800ms 6.32% MeshBasedCellPopulation::SpringIterator::operator++ 28ms 0.22% 10.04% 800ms 6.32% operator new 223ms 1.76% 11.80% 797ms 6.29% __GI___libc_malloc 10ms 0.079% 11.88% 751ms 5.93% std::set::insert (inline) 11ms 0.087% 11.97% 741ms 5.85% std::_Rb_tree::_M_insert_unique 31ms 0.24% 12.21% 709ms 5.60% std::__new_allocator::allocate (inline) 0 0% 12.21% 703ms 5.55% std::allocator_traits::allocate (inline) 0 0% 12.21% 670ms 5.29% triangulate 0 0% 12.21% 648ms 5.12% std::set::count (inline) 0 0% 12.21% 611ms 4.82% delaunay 2ms 0.016% 12.23% 611ms 4.82% divconqdelaunay 4ms 0.032% 12.26% 575ms 4.54% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 4ms 0.032% 12.29% 563ms 4.44% CellPopulationElementWriter::Visit 25ms 0.2% 12.49% 556ms 4.39% cvLsSolve 154ms 1.22% 13.70% 519ms 4.10% __dynamic_cast 514ms 4.06% 17.76% 514ms 4.06% N_VBufUnpack_Serial 1ms 0.0079% 17.77% 497ms 3.92% AbstractTwoBodyInteractionForce::AddForceContribution 48ms 0.38% 18.15% 497ms 3.92% std::map::operator[] (partial-inline) 1ms 0.0079% 18.16% 493ms 3.89% CellPropertyCollection::GetPropertiesType (inline) 13ms 0.1% 18.26% 484ms 3.82% std::less::operator() (inline) 268ms 2.12% 20.38% 482ms 3.81% _int_malloc 482ms 3.81% 24.18% 482ms 3.81% std::_Rb_tree::_S_right (inline) 471ms 3.72% 27.90% 471ms 3.72% std::operator< (inline) 82ms 0.65% 28.55% 468ms 3.69% N_VLinearSum_Serial 5ms 0.039% 28.59% 462ms 3.65% SUNLinSolSolve 136ms 1.07% 29.66% 460ms 3.63% cvRestore 15ms 0.12% 29.78% 457ms 3.61% SUNLinSolSolve_Dense 0 0% 29.78% 456ms 3.60% std::_Rb_tree::_M_create_node (inline) 3ms 0.024% 29.80% 455ms 3.59% MeshBasedCellPopulation::AcceptCellWriter 136ms 1.07% 30.88% 438ms 3.46% __GI___libc_free 0 0% 30.88% 437ms 3.45% std::_Rb_tree::_M_get_node (inline) 16ms 0.13% 31.00% 432ms 3.41% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.047% 31.05% 430ms 3.39% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 27ms 0.21% 31.26% 430ms 3.39% std::_Rb_tree::_M_insert_ (inline) 4ms 0.032% 31.29% 421ms 3.32% cvLsDQJac 9ms 0.071% 31.36% 418ms 3.30% Cylindrical2dMesh::ReconstructCylindricalMesh 37ms 0.29% 31.66% 417ms 3.29% cvLsDenseDQJac 0 0% 31.66% 417ms 3.29% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.032% 31.69% 414ms 3.27% Element::Element 42ms 0.33% 32.02% 408ms 3.22% N_VLinearSum 1ms 0.0079% 32.03% 407ms 3.21% AbstractCellProperty::IsSubType (inline) 24ms 0.19% 32.22% 400ms 3.16% N_VWrmsNorm 0 0% 32.22% 392ms 3.09% std::map::find (inline) 9ms 0.071% 32.29% 391ms 3.09% MutableMesh::ReIndex 391ms 3.09% 35.38% 391ms 3.09% SUNDlsMat_denseGETRS 0 0% 35.38% 391ms 3.09% std::_Rb_tree::lower_bound (inline) 0 0% 35.38% 391ms 3.09% std::map::lower_bound (inline) 4ms 0.032% 35.41% 386ms 3.05% SUNLinSolSetup 5ms 0.039% 35.45% 382ms 3.02% SUNLinSolSetup_Dense 96ms 0.76% 36.20% 376ms 2.97% N_VWrmsNorm_Serial 6ms 0.047% 36.25% 368ms 2.91% Element::RegisterWithNodes (inline) 364ms 2.87% 39.13% 364ms 2.87% __strcmp_evex 6ms 0.047% 39.17% 360ms 2.84% Node::AddElement 355ms 2.80% 41.98% 355ms 2.80% SUNDlsMat_denseGETRF 74ms 0.58% 42.56% 354ms 2.79% std::ostream::_M_insert 0 0% 42.56% 354ms 2.79% std::ostream::operator<< (inline) 3ms 0.024% 42.58% 350ms 2.76% SUNMatScaleAddI 347ms 2.74% 45.32% 347ms 2.74% SUNMatScaleAddI_Dense 6ms 0.047% 45.37% 341ms 2.69% CvodeRhsAdaptor 83ms 0.66% 46.03% 328ms 2.59% std::_Rb_tree::_M_erase 8ms 0.063% 46.09% 322ms 2.54% std::_Rb_tree::erase 0 0% 46.09% 321ms 2.53% std::set::erase (inline) 11ms 0.087% 46.18% 320ms 2.53% std::__new_allocator::deallocate (inline) 5ms 0.039% 46.21% 318ms 2.51% AbstractCellProperty::IsType (inline) 2ms 0.016% 46.23% 317ms 2.50% CvodeAdaptor::SetupCvode 15ms 0.12% 46.35% 317ms 2.50% divconqrecurse 0 0% 46.35% 316ms 2.49% std::allocator_traits::deallocate (inline) 7ms 0.055% 46.40% 313ms 2.47% Cylindrical2dMesh::CorrectNonPeriodicMesh 6ms 0.047% 46.45% 313ms 2.47% Node::RemoveElement 24ms 0.19% 46.64% 313ms 2.47% std::_Rb_tree::~_Rb_tree (inline) 250ms 1.97% 48.61% 302ms 2.38% _int_free 0 0% 48.61% 301ms 2.38% std::_Rb_tree::_M_drop_node (inline) 123ms 0.97% 49.59% 300ms 2.37% std::_Rb_tree::_M_get_insert_unique_pos 113ms 0.89% 50.48% 297ms 2.34% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.024% 50.50% 296ms 2.34% Cell::GetCellProliferativeType 86ms 0.68% 51.18% 295ms 2.33% mergehulls 0 0% 51.18% 291ms 2.30% std::set::~set (inline) 0 0% 51.18% 266ms 2.10% std::_Vector_base::_M_allocate (inline) 0 0% 51.18% 261ms 2.06% std::_Rb_tree::_M_put_node (inline) 132ms 1.04% 52.22% 255ms 2.01% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.15% 52.37% 253ms 2.00% Element::ResetIndex 242ms 1.91% 54.28% 242ms 1.91% N_VWSqrSumLocal_Serial 51ms 0.4% 54.69% 237ms 1.87% AbstractCellProperty::IsSame 0 0% 54.69% 234ms 1.85% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.024% 54.71% 234ms 1.85% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0079% 54.72% 233ms 1.84% Cell::GetMutationState 4ms 0.032% 54.75% 232ms 1.83% AbstractCellPopulation::GetLocationIndexUsingCell 38ms 0.3% 55.05% 228ms 1.80% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.047% 55.10% 226ms 1.78% SUNMatCopy 209ms 1.65% 56.75% 220ms 1.74% SUNMatCopy_Dense 7ms 0.055% 56.80% 218ms 1.72% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0079% 56.81% 216ms 1.71% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.095% 56.90% 209ms 1.65% std::vector::push_back (inline) 3ms 0.024% 56.93% 202ms 1.59% alternateaxes 0 0% 56.93% 199ms 1.57% NodeLocationWriter::Visit 6ms 0.047% 56.97% 199ms 1.57% std::_Rb_tree::_Rb_tree (partial-inline) 190ms 1.50% 58.47% 199ms 1.57% vertexmedian 15ms 0.12% 58.59% 198ms 1.56% std::_Rb_tree::_M_erase_aux (inline) 16ms 0.13% 58.72% 191ms 1.51% std::vector::_M_realloc_insert 13ms 0.1% 58.82% 189ms 1.49% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.11% 58.93% 188ms 1.48% AbstractTetrahedralElement::CalculateJacobian 34ms 0.27% 59.20% 186ms 1.47% std::type_info::operator== (inline) 3ms 0.024% 59.22% 180ms 1.42% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.016% 59.24% 180ms 1.42% std::set::set (inline) 15ms 0.12% 59.36% 175ms 1.38% std::_Rb_tree::_M_copy (inline) 8ms 0.063% 59.42% 173ms 1.37% Element::MarkAsDeleted 9ms 0.071% 59.49% 173ms 1.37% std::num_put::_M_insert_float 6ms 0.047% 59.54% 171ms 1.35% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 37ms 0.29% 59.83% 165ms 1.30% N_VScale_Serial 0 0% 59.83% 165ms 1.30% OffLatticeSimulation::ApplyBoundaries 19ms 0.15% 59.98% 165ms 1.30% cvEwtSet 22ms 0.17% 60.16% 164ms 1.29% N_VScale 17ms 0.13% 60.29% 163ms 1.29% TetrahedralMesh::Clear 1ms 0.0079% 60.30% 162ms 1.28% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 45ms 0.36% 60.65% 159ms 1.26% std::_Rb_tree::_M_clone_node (inline) 3ms 0.024% 60.68% 157ms 1.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.024% 60.70% 152ms 1.20% CellPropertyCollection::HasProperty 2ms 0.016% 60.72% 149ms 1.18% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 60.72% 149ms 1.18% MeshBasedCellPopulation::GetDampingConstant 4ms 0.032% 60.75% 148ms 1.17% std::__cxx11::collate::do_transform 0 0% 60.75% 147ms 1.16% Cell::HasCellProperty (inline) 0 0% 60.75% 147ms 1.16% CellProliferativeTypesWriter::VisitCell 1ms 0.0079% 60.76% 141ms 1.11% Cell::SetCellProliferativeType 0 0% 60.76% 140ms 1.11% ___vsnprintf 0 0% 60.76% 140ms 1.11% __vsnprintf_internal (inline) 19ms 0.15% 60.91% 138ms 1.09% __printf_buffer 11ms 0.087% 60.99% 134ms 1.06% AbstractTetrahedralElement::RefreshJacobian 92ms 0.73% 61.72% 134ms 1.06% malloc_consolidate 98ms 0.77% 62.49% 133ms 1.05% AbstractElement::GetNodeGlobalIndex 9ms 0.071% 62.56% 133ms 1.05% CVodeSetLinearSolver 6ms 0.047% 62.61% 127ms 1.00% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.047% 62.66% 124ms 0.98% AbstractTetrahedralElement::AbstractTetrahedralElement 82ms 0.65% 63.31% 124ms 0.98% std::_Rb_tree::equal_range (inline) 123ms 0.97% 64.28% 123ms 0.97% incircle 81ms 0.64% 64.92% 121ms 0.96% Cylindrical2dMesh::GetVectorFromAtoB 6ms 0.047% 64.96% 120ms 0.95% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 117ms 0.92% 65.89% 117ms 0.92% Node::GetIndex 46ms 0.36% 66.25% 114ms 0.9% AbstractElement::GetNodeLocation 24ms 0.19% 66.44% 113ms 0.89% N_VScaleAddMulti 29ms 0.23% 66.67% 111ms 0.88% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.024% 66.69% 111ms 0.88% __printf_fp_l_buffer 0 0% 66.69% 111ms 0.88% __printf_fp_spec (inline) 107ms 0.84% 67.54% 107ms 0.84% unlink_chunk 105ms 0.83% 68.37% 105ms 0.83% std::_Rb_tree_insert_and_rebalance 49ms 0.39% 68.75% 104ms 0.82% __printf_fp_buffer_1 5ms 0.039% 68.79% 103ms 0.81% MeshBasedCellPopulation::SpringsEnd (inline) 13ms 0.1% 68.90% 103ms 0.81% boost::detail::shared_count::~shared_count (inline) 0 0% 68.90% 103ms 0.81% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0079% 68.90% 101ms 0.8% boost::numeric::ublas::vector_assign (inline) 101ms 0.8% 69.70% 101ms 0.8% std::vector::size (inline) 5ms 0.039% 69.74% 93ms 0.73% Node::~Node 9ms 0.071% 69.81% 92ms 0.73% SUNRpowerR 0 0% 69.81% 91ms 0.72% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 69.81% 91ms 0.72% OutputFileHandler::OpenOutputFile 51ms 0.4% 70.21% 90ms 0.71% boost::shared_ptr::shared_ptr (inline) 6ms 0.047% 70.26% 87ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 80ms 0.63% 70.89% 87ms 0.69% vertexsort 6ms 0.047% 70.94% 86ms 0.68% N_VCloneEmpty_Serial 86ms 0.68% 71.62% 86ms 0.68% TetrahedralMesh::EdgeIterator::operator!= 0 0% 71.62% 86ms 0.68% tcache_get (inline) 86ms 0.68% 72.30% 86ms 0.68% tcache_get_n (inline) 23ms 0.18% 72.48% 85ms 0.67% std::__ostream_insert 84ms 0.66% 73.14% 84ms 0.66% [libchaste_cell_based.so] 1ms 0.0079% 73.15% 83ms 0.66% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 9ms 0.071% 73.22% 83ms 0.66% __pow 0 0% 73.22% 82ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0079% 73.23% 82ms 0.65% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 7ms 0.055% 73.28% 82ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 77ms 0.61% 73.89% 81ms 0.64% boost::detail::sp_counted_base::release 81ms 0.64% 74.53% 81ms 0.64% std::_Rb_tree_increment 3ms 0.024% 74.56% 80ms 0.63% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 79ms 0.62% 75.18% 79ms 0.62% counterclockwise 18ms 0.14% 75.32% 79ms 0.62% std::num_put::_M_insert_int 78ms 0.62% 75.94% 78ms 0.62% std::_Rb_tree_rebalance_for_erase 11ms 0.087% 76.02% 77ms 0.61% Cylindrical2dMesh::CreateMirrorNodes 19ms 0.15% 76.17% 77ms 0.61% boost::numeric::ublas::indexing_vector_assign 9ms 0.071% 76.25% 74ms 0.58% MeshBasedCellPopulation::SpringIterator::SpringIterator 58ms 0.46% 76.70% 74ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 7ms 0.055% 76.76% 74ms 0.58% __ieee754_pow_fma 1ms 0.0079% 76.77% 73ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 41ms 0.32% 77.09% 73ms 0.58% boost::numeric::ublas::c_matrix::operator() 0 0% 77.09% 73ms 0.58% std::vector::resize (inline) 33ms 0.26% 77.35% 72ms 0.57% AbstractTetrahedralMesh::GetElement 30ms 0.24% 77.59% 72ms 0.57% std::basic_filebuf::xsputn 70ms 0.55% 78.14% 70ms 0.55% [libchaste_mesh.so] 2ms 0.016% 78.16% 70ms 0.55% std::operator<< (inline) 0 0% 78.16% 70ms 0.55% std::vector::_M_default_append 5ms 0.039% 78.20% 69ms 0.54% N_VClone 66ms 0.52% 78.72% 66ms 0.52% AbstractElement::IsDeleted 1ms 0.0079% 78.72% 66ms 0.52% NodeMap::NodeMap 12ms 0.095% 78.82% 65ms 0.51% std::_Vector_base::_M_deallocate (inline) 5ms 0.039% 78.86% 64ms 0.51% N_VClone_Serial