File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6744ms, 84.10% of 8019ms total Dropped 592 nodes (cum <= 40.09ms) flat flat% sum% cum cum% 0 0% 0% 7979ms 99.50% __libc_start_call_main 0 0% 0% 7979ms 99.50% __libc_start_main_impl 0 0% 0% 7979ms 99.50% _start 0 0% 0% 7959ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7959ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7959ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7959ms 99.25% main 0 0% 0% 7916ms 98.72% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7916ms 98.72% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7916ms 98.72% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7913ms 98.68% AbstractCellBasedSimulation::Solve 0 0% 0% 3463ms 43.18% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.062% 0.062% 2999ms 37.40% MeshBasedCellPopulation::Update 2ms 0.025% 0.087% 2902ms 36.19% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.1% 1540ms 19.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.11% 1486ms 18.53% MutableMesh::ReMesh 2ms 0.025% 0.14% 1457ms 18.17% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.14% 1406ms 17.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.062% 0.2% 1350ms 16.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 23ms 0.29% 0.49% 1256ms 15.66% MeshBasedCellPopulation::SpringIterator::operator++ 125ms 1.56% 2.05% 1024ms 12.77% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 2.07% 971ms 12.11% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.037% 2.11% 955ms 11.91% AbstractTwoBodyInteractionForce::AddForceContribution 421ms 5.25% 7.36% 942ms 11.75% std::_Rb_tree::_M_lower_bound (inline) 281ms 3.50% 10.86% 937ms 11.68% __dynamic_cast 5ms 0.062% 10.92% 926ms 11.55% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.075% 11.00% 899ms 11.21% CellPopulationElementWriter::Visit 46ms 0.57% 11.57% 845ms 10.54% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 6ms 0.075% 11.65% 805ms 10.04% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.34% 11.98% 771ms 9.61% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.062% 12.05% 741ms 9.24% AbstractCellProperty::IsSubType (inline) 5ms 0.062% 12.11% 717ms 8.94% TetrahedralMesh::ImportFromMesher 2ms 0.025% 12.13% 599ms 7.47% triangulate 41ms 0.51% 12.64% 579ms 7.22% operator new 55ms 0.69% 13.33% 579ms 7.22% std::map::operator[] (partial-inline) 88ms 1.10% 14.43% 554ms 6.91% std::ostream::_M_insert 0 0% 14.43% 554ms 6.91% std::ostream::operator<< (inline) 177ms 2.21% 16.64% 537ms 6.70% __GI___libc_malloc 30ms 0.37% 17.01% 529ms 6.60% std::__new_allocator::allocate (inline) 3ms 0.037% 17.05% 527ms 6.57% Cell::GetCellProliferativeType 0 0% 17.05% 527ms 6.57% std::allocator_traits::allocate (inline) 522ms 6.51% 23.56% 522ms 6.51% __strcmp_avx2 0 0% 23.56% 520ms 6.48% delaunay 7ms 0.087% 23.64% 518ms 6.46% divconqdelaunay 4ms 0.05% 23.69% 517ms 6.45% LegacyCellProliferativeTypesWriter::VisitCell 10ms 0.12% 23.82% 514ms 6.41% std::set::insert (inline) 23ms 0.29% 24.11% 512ms 6.38% std::_Rb_tree::find (inline) 5ms 0.062% 24.17% 504ms 6.29% std::_Rb_tree::_M_insert_unique 0 0% 24.17% 485ms 6.05% std::_Rb_tree::lower_bound (inline) 0 0% 24.17% 485ms 6.05% std::map::lower_bound (inline) 0 0% 24.17% 471ms 5.87% std::set::count (inline) 228ms 2.84% 27.01% 466ms 5.81% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.062% 27.07% 448ms 5.59% AbstractCellBasedSimulation::DoCellBirth 38ms 0.47% 27.55% 437ms 5.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.55% 432ms 5.39% std::_Rb_tree::_M_create_node (inline) 0 0% 27.55% 413ms 5.15% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.55% 410ms 5.11% std::set::~set (inline) 0 0% 27.55% 403ms 5.03% std::_Rb_tree::_M_get_node (inline) 78ms 0.97% 28.52% 396ms 4.94% std::_Rb_tree::_M_erase 1ms 0.012% 28.53% 379ms 4.73% Cell::GetMutationState 11ms 0.14% 28.67% 367ms 4.58% std::less::operator() (inline) 35ms 0.44% 29.11% 356ms 4.44% std::_Rb_tree::_Rb_tree (partial-inline) 356ms 4.44% 33.55% 356ms 4.44% std::operator< (inline) 4ms 0.05% 33.60% 325ms 4.05% std::set::set (inline) 0 0% 33.60% 323ms 4.03% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.60% 322ms 4.02% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.60% 318ms 3.97% NodeLocationWriter::Visit 0 0% 33.60% 318ms 3.97% OutputFileHandler::OpenOutputFile 90ms 1.12% 34.72% 316ms 3.94% __GI___libc_free 18ms 0.22% 34.94% 313ms 3.90% AbstractCellPopulation::IsCellAttachedToLocationIndex 21ms 0.26% 35.20% 310ms 3.87% std::_Rb_tree::_M_insert_ (inline) 1ms 0.012% 35.22% 307ms 3.83% MeshBasedCellPopulation::GetDampingConstant 3ms 0.037% 35.25% 306ms 3.82% AbstractCentreBasedCellPopulation::GetDampingConstant 306ms 3.82% 39.07% 306ms 3.82% std::_Rb_tree::_S_right (inline) 2ms 0.025% 39.09% 302ms 3.77% Cell::ReadyToDivide 14ms 0.17% 39.27% 300ms 3.74% std::__new_allocator::deallocate (inline) 0 0% 39.27% 297ms 3.70% std::allocator_traits::deallocate (inline) 7ms 0.087% 39.36% 295ms 3.68% Element::Element 26ms 0.32% 39.68% 294ms 3.67% std::_Rb_tree::_M_copy (inline) 0 0% 39.68% 293ms 3.65% std::_Rb_tree::_M_drop_node (inline) 17ms 0.21% 39.89% 288ms 3.59% std::num_put::_M_insert_float 184ms 2.29% 42.19% 281ms 3.50% _int_malloc 6ms 0.075% 42.26% 268ms 3.34% AbstractCellProperty::IsType (inline) 9ms 0.11% 42.37% 263ms 3.28% divconqrecurse 58ms 0.72% 43.10% 263ms 3.28% std::_Rb_tree::_M_clone_node (inline) 5ms 0.062% 43.16% 261ms 3.25% CellPropertyCollection::HasProperty 0 0% 43.16% 258ms 3.22% Cell::HasCellProperty (inline) 0 0% 43.16% 253ms 3.16% CellProliferativeTypesWriter::VisitCell 0 0% 43.16% 248ms 3.09% std::_Rb_tree::_M_put_node (inline) 10ms 0.12% 43.28% 248ms 3.09% std::__cxx11::collate::do_transform 76ms 0.95% 44.23% 245ms 3.06% mergehulls 193ms 2.41% 46.64% 226ms 2.82% _int_free 1ms 0.012% 46.65% 220ms 2.74% ___vsnprintf 0 0% 46.65% 219ms 2.73% __vsnprintf_internal (inline) 25ms 0.31% 46.96% 213ms 2.66% __printf_buffer 17ms 0.21% 47.18% 209ms 2.61% TetrahedralMesh::Clear 1ms 0.012% 47.19% 204ms 2.54% AbstractPhaseBasedCellCycleModel::ReadyToDivide 11ms 0.14% 47.33% 204ms 2.54% MeshBasedCellPopulation::SpringsEnd (inline) 46ms 0.57% 47.90% 200ms 2.49% AbstractCellProperty::IsSame 4ms 0.05% 47.95% 200ms 2.49% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 62ms 0.77% 48.72% 189ms 2.36% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 48.72% 173ms 2.16% Element::RegisterWithNodes (inline) 37ms 0.46% 49.18% 173ms 2.16% TetrahedralMesh::EdgesEnd (partial-inline) 9ms 0.11% 49.30% 173ms 2.16% __printf_fp_l_buffer 0 0% 49.30% 173ms 2.16% __printf_fp_spec (inline) 13ms 0.16% 49.46% 172ms 2.14% AbstractTetrahedralElement::CalculateJacobian 4ms 0.05% 49.51% 170ms 2.12% Node::AddElement 78ms 0.97% 50.48% 163ms 2.03% __printf_fp_buffer_1 0 0% 50.48% 157ms 1.96% OutputFileHandler::CommonConstructor 0 0% 50.48% 157ms 1.96% OutputFileHandler::OutputFileHandler 35ms 0.44% 50.92% 154ms 1.92% std::type_info::operator== (inline) 4ms 0.05% 50.97% 153ms 1.91% alternateaxes 0 0% 50.97% 153ms 1.91% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.97% 151ms 1.88% AbstractCellBasedWriter::CloseFile 0 0% 50.97% 151ms 1.88% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 50.99% 151ms 1.88% std::basic_filebuf::close 0 0% 50.99% 151ms 1.88% std::basic_ofstream::close (inline) 0 0% 50.99% 149ms 1.86% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 50.99% 149ms 1.86% TetrahedralMesh::RefreshJacobianCachedData 135ms 1.68% 52.67% 148ms 1.85% vertexmedian 1ms 0.012% 52.69% 147ms 1.83% std::basic_filebuf::open 1ms 0.012% 52.70% 147ms 1.83% std::basic_ofstream::open (inline) 7ms 0.087% 52.79% 139ms 1.73% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.79% 139ms 1.73% FilesystemPermissions::SetFilePermissions (inline) 139ms 1.73% 54.52% 139ms 1.73% __GI_fchmodat 3ms 0.037% 54.56% 139ms 1.73% boost::numeric::ublas::vector_assign (inline) 0 0% 54.56% 139ms 1.73% std::filesystem::permissions 53ms 0.66% 55.22% 138ms 1.72% std::__ostream_insert 30ms 0.37% 55.59% 136ms 1.70% AbstractTetrahedralElement::RefreshJacobian 1ms 0.012% 55.61% 134ms 1.67% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.062% 55.67% 131ms 1.63% Node::~Node 34ms 0.42% 56.09% 131ms 1.63% std::num_put::_M_insert_int 15ms 0.19% 56.28% 129ms 1.61% MeshBasedCellPopulation::SpringIterator::SpringIterator 97ms 1.21% 57.49% 128ms 1.60% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 57.51% 126ms 1.57% std::_Vector_base::_M_allocate (inline) 4ms 0.05% 57.56% 124ms 1.55% AbstractTetrahedralElement::AbstractTetrahedralElement 119ms 1.48% 59.05% 119ms 1.48% incircle 1ms 0.012% 59.06% 117ms 1.46% std::operator<< (inline) 7ms 0.087% 59.15% 115ms 1.43% std::vector::push_back (inline) 13ms 0.16% 59.31% 111ms 1.38% boost::detail::shared_count::~shared_count (inline) 0 0% 59.31% 111ms 1.38% boost::shared_ptr::~shared_ptr (inline) 3ms 0.037% 59.35% 111ms 1.38% std::__basic_file::open 0 0% 59.35% 110ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.11% 59.46% 109ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 59.46% 109ms 1.36% _IO_new_fopen 0 0% 59.46% 109ms 1.36% __fopen_internal (inline) 1ms 0.012% 59.47% 107ms 1.33% _IO_new_file_fopen 61ms 0.76% 60.23% 107ms 1.33% boost::shared_ptr::shared_ptr (inline) 1ms 0.012% 60.24% 107ms 1.33% std::basic_filebuf::_M_terminate_output 105ms 1.31% 61.55% 105ms 1.31% [libchaste_cell_based.so] 2ms 0.025% 61.58% 105ms 1.31% __GI__IO_file_open 1ms 0.012% 61.59% 105ms 1.31% std::basic_filebuf::_M_convert_to_external 0 0% 61.59% 105ms 1.31% std::basic_filebuf::overflow 34ms 0.42% 62.02% 104ms 1.30% boost::numeric::ublas::indexing_vector_assign 6ms 0.075% 62.09% 104ms 1.30% std::vector::_M_realloc_insert 0 0% 62.09% 103ms 1.28% std::__basic_file::xsputn 101ms 1.26% 63.35% 102ms 1.27% __GI___libc_write 98ms 1.22% 64.57% 98ms 1.22% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.025% 64.60% 92ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 64.60% 91ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 43ms 0.54% 65.13% 91ms 1.13% AbstractElement::GetNodeLocation 89ms 1.11% 66.24% 89ms 1.11% __libc_open64 88ms 1.10% 67.34% 89ms 1.11% boost::detail::sp_counted_base::release 89ms 1.11% 68.45% 89ms 1.11% std::_Rb_tree_insert_and_rebalance 0 0% 68.45% 85ms 1.06% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 68.46% 85ms 1.06% std::filesystem::create_directory 0 0% 68.46% 84ms 1.05% Cell::GetCellId 50ms 0.62% 69.09% 84ms 1.05% malloc_consolidate 70ms 0.87% 69.96% 82ms 1.02% vertexsort 6ms 0.075% 70.03% 81ms 1.01% std::_Rb_tree_const_iterator::operator++ (inline) 39ms 0.49% 70.52% 77ms 0.96% std::basic_filebuf::xsputn 76ms 0.95% 71.47% 76ms 0.95% __GI___fstatat64 76ms 0.95% 72.42% 76ms 0.95% std::_Rb_tree_increment 0 0% 72.42% 76ms 0.95% std::filesystem::status 2ms 0.025% 72.44% 75ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.1% 72.54% 72ms 0.9% CellPropertyCollection::AddProperty 4ms 0.05% 72.59% 72ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeB 71ms 0.89% 73.48% 71ms 0.89% __memcpy_avx_unaligned_erms 55ms 0.69% 74.16% 70ms 0.87% AbstractElement::GetNodeGlobalIndex 0 0% 74.16% 70ms 0.87% tcache_get (inline) 70ms 0.87% 75.03% 70ms 0.87% tcache_get_n (inline) 3ms 0.037% 75.07% 67ms 0.84% TetrahedralMesh::EdgeIterator::GetNodeA 41ms 0.51% 75.58% 66ms 0.82% std::basic_streambuf::xsputn 63ms 0.79% 76.37% 63ms 0.79% Node::GetIndex 51ms 0.64% 77.00% 60ms 0.75% std::num_put::do_put 0 0% 77.00% 59ms 0.74% std::vector::vector (inline) 35ms 0.44% 77.44% 57ms 0.71% boost::numeric::ublas::c_matrix::operator() (partial-inline) 57ms 0.71% 78.15% 57ms 0.71% boost::shared_ptr::operator-> (inline) 56ms 0.7% 78.85% 56ms 0.7% [libchaste_mesh.so] 55ms 0.69% 79.54% 55ms 0.69% std::vector::size (inline) 26ms 0.32% 79.86% 54ms 0.67% AbstractTetrahedralMesh::GetElement 0 0% 79.86% 54ms 0.67% std::_Vector_base::_Vector_base (inline) 4ms 0.05% 79.91% 52ms 0.65% Node::ConstructNodeAttributes (inline) 2ms 0.025% 79.94% 52ms 0.65% std::_Vector_base::_M_create_storage (inline) 1ms 0.012% 79.95% 50ms 0.62% Node::ClearAppliedForce 50ms 0.62% 80.57% 50ms 0.62% counterclockwise 1ms 0.012% 80.58% 48ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 80.58% 48ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 48ms 0.6% 81.18% 48ms 0.6% boost::numeric::ublas::same_impl_ex 47ms 0.59% 81.77% 47ms 0.59% __GI___mkdir 1ms 0.012% 81.78% 47ms 0.59% std::_Vector_base::_M_deallocate (inline) 45ms 0.56% 82.34% 46ms 0.57% boost::detail::shared_count::shared_count (inline) 45ms 0.56% 82.90% 45ms 0.56% Node::rGetLocation 0 0% 82.90% 45ms 0.56% _dl_init 0 0% 82.90% 45ms 0.56% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.90% 45ms 0.56% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 82.90% 45ms 0.56% call_init (inline) 31ms 0.39% 83.29% 45ms 0.56% hack_digit 0 0% 83.29% 45ms 0.56% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.29% 45ms 0.56% std::__new_allocator::destroy (inline) 0 0% 83.29% 45ms 0.56% std::allocator_traits::destroy (inline) 0 0% 83.29% 44ms 0.55% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.29% 44ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 19ms 0.24% 83.53% 43ms 0.54% AbstractCellCycleModel::GetAge 0 0% 83.53% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 5ms 0.062% 83.59% 41ms 0.51% NodeAttributes::NodeAttributes 41ms 0.51% 84.10% 41ms 0.51% unlink_chunk