File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5861ms, 85.21% of 6878ms total Dropped 541 nodes (cum <= 34.39ms) flat flat% sum% cum cum% 0 0% 0% 6844ms 99.51% __libc_start_call_main 0 0% 0% 6844ms 99.51% __libc_start_main_impl 0 0% 0% 6844ms 99.51% _start 0 0% 0% 6830ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6830ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6830ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6830ms 99.30% main 0 0% 0% 6799ms 98.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6799ms 98.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6799ms 98.85% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.015% 0.015% 6796ms 98.81% AbstractCellBasedSimulation::Solve 0 0% 0.015% 3236ms 47.05% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.044% 0.058% 2811ms 40.87% MeshBasedCellPopulation::Update 1ms 0.015% 0.073% 2191ms 31.86% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.073% 1415ms 20.57% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.073% 1367ms 19.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.073% 1331ms 19.35% MutableMesh::ReMesh 33ms 0.48% 0.55% 1252ms 18.20% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.015% 0.57% 1203ms 17.49% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.015% 0.58% 1150ms 16.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 118ms 1.72% 2.30% 1031ms 14.99% TetrahedralMesh::EdgeIterator::operator++ 430ms 6.25% 8.55% 846ms 12.30% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.073% 8.62% 838ms 12.18% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.16% 8.78% 806ms 11.72% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 192ms 2.79% 11.57% 798ms 11.60% __dynamic_cast 8ms 0.12% 11.69% 780ms 11.34% CellPopulationElementWriter::Visit 34ms 0.49% 12.18% 756ms 10.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 0 0% 12.18% 724ms 10.53% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.087% 12.27% 685ms 9.96% TetrahedralMesh::ImportFromMesher 15ms 0.22% 12.49% 679ms 9.87% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.12% 12.61% 657ms 9.55% MeshBasedCellPopulation::AcceptCellWriter 46ms 0.67% 13.27% 654ms 9.51% operator new 7ms 0.1% 13.38% 613ms 8.91% AbstractCellProperty::IsSubType (inline) 216ms 3.14% 16.52% 600ms 8.72% __GI___libc_malloc 7ms 0.1% 16.62% 596ms 8.67% std::set::insert (inline) 14ms 0.2% 16.82% 589ms 8.56% std::_Rb_tree::_M_insert_unique 17ms 0.25% 17.07% 586ms 8.52% std::__new_allocator::allocate (inline) 0 0% 17.07% 581ms 8.45% std::allocator_traits::allocate (inline) 18ms 0.26% 17.33% 526ms 7.65% std::_Rb_tree::find (inline) 76ms 1.10% 18.44% 518ms 7.53% std::_Rb_tree::~_Rb_tree (inline) 0 0% 18.44% 487ms 7.08% std::set::~set (inline) 1ms 0.015% 18.45% 485ms 7.05% triangulate 0 0% 18.45% 479ms 6.96% std::set::count (inline) 474ms 6.89% 25.34% 474ms 6.89% __strcmp_evex 0 0% 25.34% 472ms 6.86% std::_Rb_tree::_M_create_node (inline) 5ms 0.073% 25.41% 466ms 6.78% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.015% 25.43% 459ms 6.67% std::ostream::operator<< (inline) 60ms 0.87% 26.30% 457ms 6.64% std::ostream::_M_insert 0 0% 26.30% 456ms 6.63% std::_Rb_tree::_M_get_node (inline) 2ms 0.029% 26.33% 454ms 6.60% Cell::GetCellProliferativeType 0 0% 26.33% 449ms 6.53% std::_Rb_tree::_Alloc_node::operator() (inline) 31ms 0.45% 26.78% 448ms 6.51% std::map::operator[] (partial-inline) 51ms 0.74% 27.52% 439ms 6.38% std::_Rb_tree::_M_erase 0 0% 27.52% 432ms 6.28% delaunay 1ms 0.015% 27.54% 432ms 6.28% divconqdelaunay 0 0% 27.54% 410ms 5.96% AbstractCellBasedSimulation::DoCellBirth 174ms 2.53% 30.07% 402ms 5.84% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 30.07% 383ms 5.57% std::_Rb_tree::_M_drop_node (inline) 28ms 0.41% 30.47% 379ms 5.51% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.47% 367ms 5.34% std::_Rb_tree::lower_bound (inline) 0 0% 30.47% 367ms 5.34% std::map::lower_bound (inline) 8ms 0.12% 30.59% 363ms 5.28% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.029% 30.62% 332ms 4.83% std::set::set (inline) 32ms 0.47% 31.08% 328ms 4.77% std::_Rb_tree::_M_copy (inline) 2ms 0.029% 31.11% 320ms 4.65% boost::detail::shared_count::~shared_count (inline) 0 0% 31.11% 320ms 4.65% boost::shared_ptr::~shared_ptr (inline) 1ms 0.015% 31.13% 315ms 4.58% Cell::GetMutationState 4ms 0.058% 31.19% 312ms 4.54% Element::Element 308ms 4.48% 35.66% 309ms 4.49% boost::detail::sp_counted_base::release 223ms 3.24% 38.91% 300ms 4.36% _int_malloc 65ms 0.95% 39.85% 296ms 4.30% __GI___libc_free 4ms 0.058% 39.91% 291ms 4.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.015% 39.92% 291ms 4.23% NodeLocationWriter::Visit 111ms 1.61% 41.54% 286ms 4.16% std::_Rb_tree::_M_clone_node (inline) 6ms 0.087% 41.63% 264ms 3.84% divconqrecurse 11ms 0.16% 41.79% 263ms 3.82% std::__new_allocator::deallocate (inline) 0 0% 41.79% 260ms 3.78% std::allocator_traits::deallocate (inline) 259ms 3.77% 45.55% 259ms 3.77% std::_Rb_tree::_S_right (inline) 69ms 1.00% 46.55% 254ms 3.69% mergehulls 1ms 0.015% 46.57% 252ms 3.66% MeshBasedCellPopulation::GetDampingConstant 0 0% 46.57% 250ms 3.63% Cell::ReadyToDivide 6ms 0.087% 46.66% 248ms 3.61% AbstractCentreBasedCellPopulation::GetDampingConstant 29ms 0.42% 47.08% 248ms 3.61% std::num_put::_M_insert_float 4ms 0.058% 47.14% 232ms 3.37% Element::RegisterWithNodes (inline) 186ms 2.70% 49.84% 229ms 3.33% _int_free 0 0% 49.84% 228ms 3.31% std::_Rb_tree::_M_put_node (inline) 8ms 0.12% 49.96% 225ms 3.27% Node::AddElement 7ms 0.1% 50.06% 225ms 3.27% std::less::operator() (inline) 4ms 0.058% 50.12% 218ms 3.17% AbstractPhaseBasedCellCycleModel::ReadyToDivide 218ms 3.17% 53.29% 218ms 3.17% std::operator< (inline) 5ms 0.073% 53.36% 208ms 3.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 208ms 3.02% 56.38% 208ms 3.02% [libchaste_cell_based.so] 3ms 0.044% 56.43% 197ms 2.86% std::__cxx11::collate::do_transform 88ms 1.28% 57.71% 196ms 2.85% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.029% 57.73% 190ms 2.76% ___vsnprintf 1ms 0.015% 57.75% 188ms 2.73% __vsnprintf_internal (inline) 20ms 0.29% 58.04% 184ms 2.68% __printf_buffer 9ms 0.13% 58.17% 166ms 2.41% AbstractCellProperty::IsType (inline) 8ms 0.12% 58.29% 165ms 2.40% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 58.29% 163ms 2.37% Cell::HasCellProperty (inline) 4ms 0.058% 58.35% 163ms 2.37% CellPropertyCollection::HasProperty 0 0% 58.35% 158ms 2.30% TetrahedralMesh::Clear 0 0% 58.35% 157ms 2.28% CellProliferativeTypesWriter::VisitCell 0 0% 58.35% 155ms 2.25% std::_Rb_tree::_M_destroy_node (inline) 0 0% 58.35% 155ms 2.25% std::__new_allocator::destroy (inline) 0 0% 58.35% 155ms 2.25% std::allocator_traits::destroy (inline) 3ms 0.044% 58.39% 152ms 2.21% __printf_fp_l_buffer 0 0% 58.39% 152ms 2.21% __printf_fp_spec (inline) 1ms 0.015% 58.40% 149ms 2.17% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.12% 58.52% 147ms 2.14% AbstractTetrahedralElement::CalculateJacobian 65ms 0.95% 59.46% 145ms 2.11% __printf_fp_buffer_1 4ms 0.058% 59.52% 137ms 1.99% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 59.52% 132ms 1.92% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 59.52% 132ms 1.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 59.52% 129ms 1.88% OutputFileHandler::OpenOutputFile 16ms 0.23% 59.76% 127ms 1.85% TetrahedralMesh::EdgesEnd (partial-inline) 127ms 1.85% 61.60% 127ms 1.85% [libchaste_mesh.so] 1ms 0.015% 61.62% 126ms 1.83% std::_Vector_base::_M_allocate (inline) 0 0% 61.62% 120ms 1.74% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.15% 61.76% 119ms 1.73% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.029% 61.79% 116ms 1.69% std::vector::push_back (inline) 2ms 0.029% 61.82% 114ms 1.66% boost::numeric::ublas::vector_assign (inline) 9ms 0.13% 61.95% 113ms 1.64% AbstractCellProperty::IsSame 3ms 0.044% 61.99% 113ms 1.64% alternateaxes 112ms 1.63% 63.62% 112ms 1.63% incircle 26ms 0.38% 64.00% 110ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 102ms 1.48% 65.48% 110ms 1.60% vertexmedian 27ms 0.39% 65.88% 109ms 1.58% std::num_put::_M_insert_int 2ms 0.029% 65.91% 108ms 1.57% std::vector::_M_realloc_insert 2ms 0.029% 65.93% 106ms 1.54% boost::numeric::ublas::c_vector::c_vector (inline) 13ms 0.19% 66.12% 104ms 1.51% std::type_info::operator== (inline) 5ms 0.073% 66.20% 103ms 1.50% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 17ms 0.25% 66.44% 102ms 1.48% AbstractTetrahedralElement::RefreshJacobian 58ms 0.84% 67.29% 99ms 1.44% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 67.29% 98ms 1.42% Node::~Node 94ms 1.37% 68.65% 94ms 1.37% [libstdc++.so.6.0.33] 3ms 0.044% 68.70% 93ms 1.35% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 42ms 0.61% 69.31% 92ms 1.34% std::__ostream_insert 90ms 1.31% 70.62% 90ms 1.31% std::_Rb_tree_insert_and_rebalance 6ms 0.087% 70.70% 87ms 1.26% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 70.70% 82ms 1.19% std::basic_ofstream::basic_ofstream (inline) 2ms 0.029% 70.73% 81ms 1.18% std::basic_filebuf::open 3ms 0.044% 70.78% 80ms 1.16% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 70.78% 80ms 1.16% std::basic_ofstream::open (inline) 1ms 0.015% 70.79% 80ms 1.16% std::operator<< (inline) 23ms 0.33% 71.13% 79ms 1.15% boost::numeric::ublas::indexing_vector_assign 1ms 0.015% 71.14% 77ms 1.12% Cell::GetCellId 9ms 0.13% 71.27% 77ms 1.12% CellPropertyCollection::AddProperty 27ms 0.39% 71.66% 76ms 1.10% AbstractElement::GetNodeLocation 0 0% 71.66% 74ms 1.08% tcache_get (inline) 74ms 1.08% 72.74% 74ms 1.08% tcache_get_n (inline) 9ms 0.13% 72.87% 70ms 1.02% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 72.87% 64ms 0.93% AbstractCellBasedWriter::CloseFile 0 0% 72.87% 64ms 0.93% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 72.87% 64ms 0.93% std::basic_filebuf::close 0 0% 72.87% 64ms 0.93% std::basic_ofstream::close (inline) 52ms 0.76% 73.63% 63ms 0.92% malloc_consolidate 62ms 0.9% 74.53% 62ms 0.9% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 61ms 0.89% 75.41% 61ms 0.89% counterclockwise 0 0% 75.41% 59ms 0.86% OutputFileHandler::CommonConstructor 0 0% 75.41% 59ms 0.86% OutputFileHandler::OutputFileHandler 0 0% 75.41% 57ms 0.83% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 75.41% 55ms 0.8% OutputFileHandler::MakeFoldersAndReturnFullPath 3ms 0.044% 75.46% 54ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeA 54ms 0.79% 76.24% 54ms 0.79% __memcpy_avx512_unaligned_erms 38ms 0.55% 76.80% 53ms 0.77% CellPropertyCollection::GetProperty 21ms 0.31% 77.10% 52ms 0.76% AbstractElement::GetNodeGlobalIndex 52ms 0.76% 77.86% 52ms 0.76% std::vector::size (inline) 2ms 0.029% 77.89% 51ms 0.74% std::_Rb_tree_const_iterator::operator++ (inline) 15ms 0.22% 78.10% 50ms 0.73% Determinant (inline) 0 0% 78.10% 50ms 0.73% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.10% 50ms 0.73% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.058% 78.16% 50ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 50ms 0.73% 78.89% 50ms 0.73% std::_Rb_tree::_S_left (inline) 1ms 0.015% 78.90% 50ms 0.73% std::__basic_file::open 5ms 0.073% 78.98% 49ms 0.71% Node::ConstructNodeAttributes (inline) 0 0% 78.98% 49ms 0.71% _IO_new_fopen 0 0% 78.98% 49ms 0.71% __fopen_internal (inline) 24ms 0.35% 79.33% 49ms 0.71% hack_digit 1ms 0.015% 79.34% 48ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 79.34% 48ms 0.7% std::basic_filebuf::_M_terminate_output 0 0% 79.34% 48ms 0.7% std::basic_filebuf::overflow 33ms 0.48% 79.82% 48ms 0.7% std::basic_streambuf::xsputn 45ms 0.65% 80.47% 47ms 0.68% __GI___libc_write 0 0% 80.47% 47ms 0.68% std::__basic_file::xsputn 23ms 0.33% 80.81% 47ms 0.68% std::basic_filebuf::xsputn 46ms 0.67% 81.48% 47ms 0.68% vertexsort 1ms 0.015% 81.49% 46ms 0.67% Node::ClearAppliedForce 39ms 0.57% 82.06% 46ms 0.67% boost::numeric::ublas::c_matrix::operator() 0 0% 82.06% 45ms 0.65% _IO_new_file_fopen 0 0% 82.06% 44ms 0.64% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 82.06% 44ms 0.64% __GI__IO_file_open 28ms 0.41% 82.47% 44ms 0.64% boost::shared_ptr::shared_ptr (inline) 0 0% 82.47% 44ms 0.64% std::map::map (inline) 31ms 0.45% 82.92% 43ms 0.63% AbstractTetrahedralMesh::GetElement 1ms 0.015% 82.93% 42ms 0.61% AbstractCentreBasedCellPopulation::IsMarkedSpring 42ms 0.61% 83.54% 42ms 0.61% std::_Rb_tree_increment 0 0% 83.54% 41ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 83.54% 40ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.54% 40ms 0.58% std::map::find (inline) 40ms 0.58% 84.12% 40ms 0.58% tcache_put (inline) 0 0% 84.12% 39ms 0.57% BoundaryNodeWriter::Visit 31ms 0.45% 84.57% 39ms 0.57% std::num_put::do_put 0 0% 84.57% 39ms 0.57% std::vector::vector (inline) 36ms 0.52% 85.10% 38ms 0.55% __libc_open64 8ms 0.12% 85.21% 37ms 0.54% Inverse 0 0% 85.21% 36ms 0.52% std::_Vector_base::_Vector_base (inline) 0 0% 85.21% 35ms 0.51% std::_Vector_base::_M_create_storage (inline)