File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5733ms, 85.14% of 6734ms total Dropped 512 nodes (cum <= 33.67ms) flat flat% sum% cum cum% 0 0% 0% 6705ms 99.57% __libc_start_call_main 0 0% 0% 6705ms 99.57% __libc_start_main_impl 0 0% 0% 6705ms 99.57% _start 0 0% 0% 6690ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6690ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6690ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6690ms 99.35% main 0 0% 0% 6660ms 98.90% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6660ms 98.90% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6660ms 98.90% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6659ms 98.89% AbstractCellBasedSimulation::Solve 0 0% 0% 3146ms 46.72% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.059% 0.059% 2738ms 40.66% MeshBasedCellPopulation::Update 0 0% 0.059% 2152ms 31.96% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.059% 1411ms 20.95% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.059% 1357ms 20.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.03% 0.089% 1269ms 18.84% MutableMesh::ReMesh 26ms 0.39% 0.48% 1232ms 18.30% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.48% 1207ms 17.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.015% 0.49% 1161ms 17.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 109ms 1.62% 2.11% 990ms 14.70% TetrahedralMesh::EdgeIterator::operator++ 11ms 0.16% 2.27% 870ms 12.92% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.045% 2.32% 866ms 12.86% AbstractTwoBodyInteractionForce::AddForceContribution 33ms 0.49% 2.81% 785ms 11.66% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 363ms 5.39% 8.20% 771ms 11.45% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.015% 8.21% 765ms 11.36% CellPropertyCollection::GetPropertiesType (inline) 197ms 2.93% 11.14% 763ms 11.33% __dynamic_cast 18ms 0.27% 11.40% 712ms 10.57% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.1% 11.51% 711ms 10.56% CellPopulationElementWriter::Visit 9ms 0.13% 11.64% 704ms 10.45% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.074% 11.72% 639ms 9.49% TetrahedralMesh::ImportFromMesher 34ms 0.5% 12.22% 609ms 9.04% operator new 5ms 0.074% 12.30% 608ms 9.03% AbstractCellProperty::IsSubType (inline) 223ms 3.31% 15.61% 568ms 8.43% __GI___libc_malloc 6ms 0.089% 15.70% 555ms 8.24% std::set::insert (inline) 8ms 0.12% 15.82% 549ms 8.15% std::_Rb_tree::_M_insert_unique 23ms 0.34% 16.16% 540ms 8.02% std::__new_allocator::allocate (inline) 0 0% 16.16% 537ms 7.97% std::allocator_traits::allocate (inline) 1ms 0.015% 16.17% 488ms 7.25% Cell::GetCellProliferativeType 11ms 0.16% 16.34% 481ms 7.14% std::_Rb_tree::find (inline) 93ms 1.38% 17.72% 478ms 7.10% std::_Rb_tree::~_Rb_tree (inline) 0 0% 17.72% 477ms 7.08% triangulate 1ms 0.015% 17.73% 463ms 6.88% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 17.73% 455ms 6.76% std::set::~set (inline) 0 0% 17.73% 445ms 6.61% std::_Rb_tree::_M_create_node (inline) 0 0% 17.73% 445ms 6.61% std::set::count (inline) 1ms 0.015% 17.75% 441ms 6.55% std::ostream::operator<< (inline) 67ms 0.99% 18.74% 437ms 6.49% std::ostream::_M_insert 0 0% 18.74% 433ms 6.43% delaunay 2ms 0.03% 18.77% 433ms 6.43% divconqdelaunay 49ms 0.73% 19.50% 431ms 6.40% std::map::operator[] (partial-inline) 0 0% 19.50% 429ms 6.37% std::_Rb_tree::_M_get_node (inline) 0 0% 19.50% 419ms 6.22% std::_Rb_tree::_Alloc_node::operator() (inline) 410ms 6.09% 25.59% 410ms 6.09% __strcmp_evex 0 0% 25.59% 401ms 5.95% AbstractCellBasedSimulation::DoCellBirth 182ms 2.70% 28.29% 390ms 5.79% __cxxabiv1::__si_class_type_info::__do_dyncast 51ms 0.76% 29.05% 385ms 5.72% std::_Rb_tree::_M_erase 19ms 0.28% 29.33% 382ms 5.67% std::_Rb_tree::_Rb_tree (partial-inline) 42ms 0.62% 29.95% 365ms 5.42% std::_Rb_tree::_M_insert_ (inline) 4ms 0.059% 30.01% 355ms 5.27% std::set::set (inline) 24ms 0.36% 30.37% 335ms 4.97% std::_Rb_tree::_M_copy (inline) 0 0% 30.37% 334ms 4.96% std::_Rb_tree::_M_drop_node (inline) 0 0% 30.37% 333ms 4.95% std::_Rb_tree::lower_bound (inline) 0 0% 30.37% 333ms 4.95% std::map::lower_bound (inline) 3ms 0.045% 30.41% 318ms 4.72% Cell::GetMutationState 129ms 1.92% 32.33% 300ms 4.46% std::_Rb_tree::_M_clone_node (inline) 2ms 0.03% 32.36% 285ms 4.23% NodeLocationWriter::Visit 5ms 0.074% 32.43% 276ms 4.10% Element::Element 46ms 0.68% 33.12% 274ms 4.07% __GI___libc_free 6ms 0.089% 33.20% 269ms 3.99% boost::detail::shared_count::~shared_count (inline) 0 0% 33.20% 269ms 3.99% boost::shared_ptr::~shared_ptr (inline) 9ms 0.13% 33.34% 267ms 3.96% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.15% 33.49% 261ms 3.88% std::__new_allocator::deallocate (inline) 260ms 3.86% 37.35% 260ms 3.86% std::_Rb_tree::_S_right (inline) 0 0% 37.35% 258ms 3.83% std::allocator_traits::deallocate (inline) 182ms 2.70% 40.05% 256ms 3.80% _int_malloc 255ms 3.79% 43.84% 256ms 3.80% boost::detail::sp_counted_base::release 2ms 0.03% 43.87% 254ms 3.77% Cell::ReadyToDivide 21ms 0.31% 44.18% 252ms 3.74% std::num_put::_M_insert_float 4ms 0.059% 44.24% 249ms 3.70% divconqrecurse 7ms 0.1% 44.34% 245ms 3.64% std::less::operator() (inline) 238ms 3.53% 47.88% 238ms 3.53% std::operator< (inline) 76ms 1.13% 49.01% 237ms 3.52% mergehulls 1ms 0.015% 49.02% 236ms 3.50% MeshBasedCellPopulation::GetDampingConstant 1ms 0.015% 49.03% 235ms 3.49% AbstractCentreBasedCellPopulation::GetDampingConstant 190ms 2.82% 51.86% 222ms 3.30% _int_free 0 0% 51.86% 209ms 3.10% std::_Rb_tree::_M_put_node (inline) 205ms 3.04% 54.90% 205ms 3.04% [libchaste_cell_based.so] 2ms 0.03% 54.93% 204ms 3.03% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.03% 54.96% 201ms 2.98% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.13% 55.09% 201ms 2.98% std::__cxx11::collate::do_transform 3ms 0.045% 55.14% 200ms 2.97% Element::RegisterWithNodes (inline) 0 0% 55.14% 198ms 2.94% CellProliferativeTypesWriter::VisitCell 10ms 0.15% 55.29% 193ms 2.87% Node::AddElement 8ms 0.12% 55.41% 190ms 2.82% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.03% 55.44% 190ms 2.82% ___vsnprintf 0 0% 55.44% 188ms 2.79% __vsnprintf_internal (inline) 18ms 0.27% 55.70% 183ms 2.72% __printf_buffer 7ms 0.1% 55.81% 181ms 2.69% AbstractCellProperty::IsType (inline) 45ms 0.67% 56.47% 177ms 2.63% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 56.47% 173ms 2.57% Cell::HasCellProperty (inline) 3ms 0.045% 56.52% 173ms 2.57% CellPropertyCollection::HasProperty 27ms 0.4% 56.92% 154ms 2.29% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.059% 56.98% 147ms 2.18% __printf_fp_l_buffer 0 0% 56.98% 147ms 2.18% __printf_fp_spec (inline) 8ms 0.12% 57.10% 140ms 2.08% AbstractTetrahedralElement::CalculateJacobian 0 0% 57.10% 138ms 2.05% TetrahedralMesh::RefreshJacobianCachedData 65ms 0.97% 58.06% 135ms 2.00% __printf_fp_buffer_1 0 0% 58.06% 130ms 1.93% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.059% 58.12% 130ms 1.93% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 58.12% 129ms 1.92% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 58.12% 128ms 1.90% OutputFileHandler::OpenOutputFile 1ms 0.015% 58.14% 128ms 1.90% TetrahedralMesh::Clear 2ms 0.03% 58.17% 128ms 1.90% boost::numeric::ublas::vector_assign (inline) 0 0% 58.17% 125ms 1.86% std::_Rb_tree::_M_destroy_node (inline) 0 0% 58.17% 125ms 1.86% std::__new_allocator::destroy (inline) 0 0% 58.17% 125ms 1.86% std::allocator_traits::destroy (inline) 3ms 0.045% 58.21% 123ms 1.83% boost::numeric::ublas::c_vector::c_vector (inline) 23ms 0.34% 58.55% 122ms 1.81% MeshBasedCellPopulation::SpringIterator::SpringIterator 29ms 0.43% 58.98% 121ms 1.80% AbstractCellProperty::IsSame 3ms 0.045% 59.03% 115ms 1.71% alternateaxes 2ms 0.03% 59.06% 115ms 1.71% std::vector::push_back (inline) 93ms 1.38% 60.44% 112ms 1.66% vertexmedian 82ms 1.22% 61.66% 109ms 1.62% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.015% 61.67% 109ms 1.62% std::_Vector_base::_M_allocate (inline) 6ms 0.089% 61.76% 107ms 1.59% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 61.76% 107ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.13% 61.89% 106ms 1.57% std::vector::_M_realloc_insert 101ms 1.50% 63.39% 101ms 1.50% [libstdc++.so.6.0.33] 100ms 1.49% 64.88% 100ms 1.49% incircle 17ms 0.25% 65.13% 98ms 1.46% boost::numeric::ublas::indexing_vector_assign 18ms 0.27% 65.40% 97ms 1.44% AbstractTetrahedralElement::RefreshJacobian 97ms 1.44% 66.84% 97ms 1.44% [libchaste_mesh.so] 14ms 0.21% 67.05% 92ms 1.37% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 15ms 0.22% 67.27% 92ms 1.37% std::type_info::operator== (inline) 30ms 0.45% 67.72% 90ms 1.34% std::num_put::_M_insert_int 36ms 0.53% 68.25% 89ms 1.32% std::__ostream_insert 0 0% 68.25% 88ms 1.31% Cell::GetCellId 4ms 0.059% 68.31% 84ms 1.25% CellPropertyCollection::AddProperty 2ms 0.03% 68.34% 83ms 1.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.03% 68.37% 78ms 1.16% Node::~Node 77ms 1.14% 69.51% 77ms 1.14% std::_Rb_tree_insert_and_rebalance 0 0% 69.51% 77ms 1.14% tcache_get (inline) 77ms 1.14% 70.66% 77ms 1.14% tcache_get_n (inline) 1ms 0.015% 70.67% 76ms 1.13% AbstractTetrahedralElement::AbstractTetrahedralElement 30ms 0.45% 71.12% 73ms 1.08% AbstractElement::GetNodeLocation 4ms 0.059% 71.18% 71ms 1.05% std::_Rb_tree_const_iterator::operator++ (inline) 68ms 1.01% 72.19% 68ms 1.01% std::vector::size (inline) 67ms 0.99% 73.18% 67ms 0.99% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 73.18% 67ms 0.99% std::operator<< (inline) 3ms 0.045% 73.23% 65ms 0.97% AbstractCellPopulation::GetLocationIndexUsingCell 46ms 0.68% 73.91% 65ms 0.97% CellPropertyCollection::GetProperty 12ms 0.18% 74.09% 63ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeB 41ms 0.61% 74.70% 63ms 0.94% malloc_consolidate 0 0% 74.70% 63ms 0.94% std::basic_ofstream::basic_ofstream (inline) 0 0% 74.70% 62ms 0.92% std::basic_filebuf::open 0 0% 74.70% 61ms 0.91% std::basic_ofstream::open (inline) 0 0% 74.70% 59ms 0.88% OutputFileHandler::CommonConstructor 0 0% 74.70% 59ms 0.88% OutputFileHandler::OutputFileHandler 0 0% 74.70% 59ms 0.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.70% 59ms 0.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 58ms 0.86% 75.56% 58ms 0.86% counterclockwise 53ms 0.79% 76.34% 58ms 0.86% vertexsort 0 0% 76.34% 55ms 0.82% OutputFileHandler::MakeFoldersAndReturnFullPath 55ms 0.82% 77.16% 55ms 0.82% std::_Rb_tree_increment 1ms 0.015% 77.18% 55ms 0.82% std::basic_filebuf::close 0 0% 77.18% 54ms 0.8% AbstractCellBasedWriter::CloseFile 0 0% 77.18% 54ms 0.8% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 77.18% 54ms 0.8% std::basic_ofstream::close (inline) 1ms 0.015% 77.19% 53ms 0.79% AbstractCentreBasedCellPopulation::CreateCellPair 28ms 0.42% 77.61% 52ms 0.77% boost::shared_ptr::shared_ptr (inline) 51ms 0.76% 78.36% 51ms 0.76% Node::GetIndex 3ms 0.045% 78.41% 51ms 0.76% TetrahedralMesh::EdgeIterator::GetNodeA 19ms 0.28% 78.69% 50ms 0.74% AbstractElement::GetNodeGlobalIndex 50ms 0.74% 79.43% 50ms 0.74% std::_Rb_tree::_S_left (inline) 37ms 0.55% 79.98% 49ms 0.73% AbstractTetrahedralMesh::GetElement 4ms 0.059% 80.04% 49ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 27ms 0.4% 80.44% 47ms 0.7% hack_digit 0 0% 80.44% 47ms 0.7% std::vector::vector (inline) 0 0% 80.44% 46ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 80.44% 46ms 0.68% boost::numeric::ublas::norm_2 (inline) 7ms 0.1% 80.55% 46ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 1ms 0.015% 80.56% 46ms 0.68% std::_Vector_base::_M_deallocate (inline) 0 0% 80.56% 46ms 0.68% std::_Vector_base::_Vector_base (inline) 31ms 0.46% 81.02% 46ms 0.68% std::basic_streambuf::xsputn 2ms 0.03% 81.05% 45ms 0.67% std::_Vector_base::_M_create_storage (inline) 12ms 0.18% 81.23% 44ms 0.65% Determinant (inline) 3ms 0.045% 81.27% 44ms 0.65% Node::ConstructNodeAttributes (inline) 31ms 0.46% 81.73% 43ms 0.64% boost::numeric::ublas::c_matrix::operator() 0 0% 81.73% 42ms 0.62% Node::ClearAppliedForce 41ms 0.61% 82.34% 42ms 0.62% __GI___libc_write 0 0% 82.34% 42ms 0.62% std::__basic_file::xsputn 0 0% 82.34% 42ms 0.62% std::basic_filebuf::_M_convert_to_external 0 0% 82.34% 42ms 0.62% std::basic_filebuf::_M_terminate_output 0 0% 82.34% 42ms 0.62% std::basic_filebuf::overflow 0 0% 82.34% 42ms 0.62% std::map::map (inline) 41ms 0.61% 82.95% 41ms 0.61% __memcpy_avx512_unaligned_erms 0 0% 82.95% 40ms 0.59% AbstractCentreBasedCellPopulation::IsMarkedSpring 1ms 0.015% 82.97% 40ms 0.59% _IO_new_fopen 40ms 0.59% 83.56% 40ms 0.59% boost::numeric::ublas::same_impl_ex 0 0% 83.56% 40ms 0.59% std::__basic_file::open 21ms 0.31% 83.87% 40ms 0.59% std::basic_filebuf::xsputn 0 0% 83.87% 39ms 0.58% __fopen_internal (inline) 0 0% 83.87% 38ms 0.56% FilesystemPermissions::SetFilePermissions (inline) 38ms 0.56% 84.44% 38ms 0.56% __GI_fchmodat 0 0% 84.44% 38ms 0.56% std::filesystem::permissions 0 0% 84.44% 37ms 0.55% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 84.44% 37ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 37ms 0.55% 84.99% 37ms 0.55% boost::shared_ptr::operator-> (inline) 10ms 0.15% 85.14% 35ms 0.52% Inverse 0 0% 85.14% 35ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 85.14% 34ms 0.5% _IO_new_file_fopen