File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5565ms, 85.69% of 6494ms total Dropped 512 nodes (cum <= 32.47ms) flat flat% sum% cum cum% 0 0% 0% 6465ms 99.55% __libc_start_call_main 0 0% 0% 6465ms 99.55% __libc_start_main_impl 0 0% 0% 6465ms 99.55% _start 0 0% 0% 6450ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6450ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6450ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6450ms 99.32% main 0 0% 0% 6418ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6418ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6418ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6415ms 98.78% AbstractCellBasedSimulation::Solve 0 0% 0% 3061ms 47.14% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.031% 0.031% 2648ms 40.78% MeshBasedCellPopulation::Update 0 0% 0.031% 2132ms 32.83% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.031% 1365ms 21.02% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.031% 1235ms 19.02% MutableMesh::ReMesh 1ms 0.015% 0.046% 1217ms 18.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 26ms 0.4% 0.45% 1194ms 18.39% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.046% 0.49% 1081ms 16.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.015% 0.51% 1034ms 15.92% AbstractNumericalMethod::ComputeForcesIncludingDamping 90ms 1.39% 1.89% 940ms 14.47% TetrahedralMesh::EdgeIterator::operator++ 13ms 0.2% 2.09% 829ms 12.77% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.031% 2.13% 762ms 11.73% AbstractTwoBodyInteractionForce::AddForceContribution 382ms 5.88% 8.01% 759ms 11.69% std::_Rb_tree::_M_lower_bound (inline) 170ms 2.62% 10.63% 724ms 11.15% __dynamic_cast 19ms 0.29% 10.92% 714ms 10.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.11% 11.03% 698ms 10.75% CellPopulationElementWriter::Visit 3ms 0.046% 11.07% 676ms 10.41% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.12% 11.19% 671ms 10.33% MeshBasedCellPopulation::AcceptCellWriter 12ms 0.18% 11.38% 648ms 9.98% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.092% 11.47% 611ms 9.41% TetrahedralMesh::ImportFromMesher 30ms 0.46% 11.93% 580ms 8.93% operator new 3ms 0.046% 11.98% 570ms 8.78% AbstractCellProperty::IsSubType (inline) 214ms 3.30% 15.28% 541ms 8.33% __GI___libc_malloc 6ms 0.092% 15.37% 496ms 7.64% std::set::insert (inline) 7ms 0.11% 15.48% 490ms 7.55% std::_Rb_tree::_M_insert_unique 14ms 0.22% 15.69% 487ms 7.50% std::__new_allocator::allocate (inline) 0 0% 15.69% 481ms 7.41% std::allocator_traits::allocate (inline) 10ms 0.15% 15.85% 479ms 7.38% std::_Rb_tree::find (inline) 1ms 0.015% 15.86% 474ms 7.30% triangulate 79ms 1.22% 17.08% 468ms 7.21% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.046% 17.12% 464ms 7.15% LegacyCellProliferativeTypesWriter::VisitCell 452ms 6.96% 24.08% 452ms 6.96% __strcmp_evex 0 0% 24.08% 445ms 6.85% std::set::count (inline) 0 0% 24.08% 444ms 6.84% std::set::~set (inline) 68ms 1.05% 25.13% 433ms 6.67% std::map::operator[] (partial-inline) 0 0% 25.13% 432ms 6.65% delaunay 2ms 0.031% 25.16% 432ms 6.65% divconqdelaunay 1ms 0.015% 25.18% 432ms 6.65% std::ostream::operator<< (inline) 60ms 0.92% 26.10% 428ms 6.59% std::ostream::_M_insert 1ms 0.015% 26.12% 427ms 6.58% Cell::GetCellProliferativeType 0 0% 26.12% 403ms 6.21% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.12% 402ms 6.19% std::_Rb_tree::_M_create_node (inline) 151ms 2.33% 28.44% 388ms 5.97% __cxxabiv1::__si_class_type_info::__do_dyncast 44ms 0.68% 29.12% 385ms 5.93% std::_Rb_tree::_M_erase 0 0% 29.12% 384ms 5.91% std::_Rb_tree::_M_get_node (inline) 0 0% 29.12% 361ms 5.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 29.12% 339ms 5.22% std::_Rb_tree::_M_drop_node (inline) 24ms 0.37% 29.49% 321ms 4.94% std::_Rb_tree::_M_insert_ (inline) 0 0% 29.49% 314ms 4.84% std::_Rb_tree::lower_bound (inline) 0 0% 29.49% 314ms 4.84% std::map::lower_bound (inline) 13ms 0.2% 29.69% 313ms 4.82% std::_Rb_tree::_Rb_tree (partial-inline) 58ms 0.89% 30.58% 299ms 4.60% __GI___libc_free 1ms 0.015% 30.60% 293ms 4.51% std::set::set (inline) 4ms 0.062% 30.66% 283ms 4.36% boost::detail::shared_count::~shared_count (inline) 0 0% 30.66% 283ms 4.36% boost::shared_ptr::~shared_ptr (inline) 3ms 0.046% 30.71% 274ms 4.22% NodeLocationWriter::Visit 32ms 0.49% 31.20% 273ms 4.20% std::_Rb_tree::_M_copy (inline) 268ms 4.13% 35.32% 269ms 4.14% boost::detail::sp_counted_base::release 5ms 0.077% 35.40% 265ms 4.08% Element::Element 0 0% 35.40% 263ms 4.05% Cell::GetMutationState 8ms 0.12% 35.53% 260ms 4.00% AbstractCellPopulation::IsCellAttachedToLocationIndex 11ms 0.17% 35.69% 258ms 3.97% std::__new_allocator::deallocate (inline) 0 0% 35.69% 254ms 3.91% std::allocator_traits::deallocate (inline) 173ms 2.66% 38.36% 249ms 3.83% _int_malloc 6ms 0.092% 38.45% 248ms 3.82% Cell::ReadyToDivide 13ms 0.2% 38.65% 246ms 3.79% std::less::operator() (inline) 189ms 2.91% 41.56% 235ms 3.62% _int_free 95ms 1.46% 43.02% 233ms 3.59% std::_Rb_tree::_M_clone_node (inline) 233ms 3.59% 46.61% 233ms 3.59% std::operator< (inline) 12ms 0.18% 46.80% 231ms 3.56% divconqrecurse 24ms 0.37% 47.17% 225ms 3.46% std::num_put::_M_insert_float 68ms 1.05% 48.21% 212ms 3.26% mergehulls 7ms 0.11% 48.32% 209ms 3.22% CellPropertyCollection::HasProperty 209ms 3.22% 51.54% 209ms 3.22% [libchaste_cell_based.so] 0 0% 51.54% 208ms 3.20% Cell::HasCellProperty (inline) 0 0% 51.54% 203ms 3.13% std::_Rb_tree::_M_put_node (inline) 6ms 0.092% 51.63% 200ms 3.08% AbstractCellProperty::IsType (inline) 3ms 0.046% 51.68% 199ms 3.06% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 51.68% 199ms 3.06% MeshBasedCellPopulation::GetDampingConstant 193ms 2.97% 54.65% 193ms 2.97% std::_Rb_tree::_S_right (inline) 2ms 0.031% 54.68% 180ms 2.77% Element::RegisterWithNodes (inline) 2ms 0.031% 54.71% 175ms 2.69% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.14% 54.85% 175ms 2.69% Node::AddElement 0 0% 54.85% 174ms 2.68% CellProliferativeTypesWriter::VisitCell 3ms 0.046% 54.90% 173ms 2.66% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.11% 55.00% 172ms 2.65% std::__cxx11::collate::do_transform 8ms 0.12% 55.13% 170ms 2.62% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.015% 55.14% 163ms 2.51% ___vsnprintf 20ms 0.31% 55.45% 162ms 2.49% __printf_buffer 0 0% 55.45% 162ms 2.49% __vsnprintf_internal (inline) 66ms 1.02% 56.47% 162ms 2.49% std::_Rb_tree::_M_get_insert_unique_pos (inline) 22ms 0.34% 56.81% 160ms 2.46% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 56.81% 154ms 2.37% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 56.81% 154ms 2.37% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 56.81% 150ms 2.31% OutputFileHandler::OpenOutputFile 7ms 0.11% 56.91% 141ms 2.17% AbstractTetrahedralElement::CalculateJacobian 22ms 0.34% 57.25% 138ms 2.13% AbstractCellProperty::IsSame 0 0% 57.25% 136ms 2.09% std::_Rb_tree::_M_destroy_node (inline) 0 0% 57.25% 136ms 2.09% std::__new_allocator::destroy (inline) 0 0% 57.25% 136ms 2.09% std::allocator_traits::destroy (inline) 1ms 0.015% 57.27% 133ms 2.05% TetrahedralMesh::Clear 0 0% 57.27% 130ms 2.00% TetrahedralMesh::RefreshJacobianCachedData 14ms 0.22% 57.48% 129ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 57.48% 127ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.046% 57.53% 123ms 1.89% __printf_fp_l_buffer 0 0% 57.53% 123ms 1.89% __printf_fp_spec (inline) 8ms 0.12% 57.65% 123ms 1.89% std::vector::push_back (inline) 4ms 0.062% 57.71% 122ms 1.88% alternateaxes 6ms 0.092% 57.81% 119ms 1.83% AbstractTetrahedralElement::CalculateInverseJacobian 119ms 1.83% 59.64% 119ms 1.83% [libchaste_mesh.so] 87ms 1.34% 60.98% 118ms 1.82% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 52ms 0.8% 61.78% 117ms 1.80% __printf_fp_buffer_1 2ms 0.031% 61.81% 117ms 1.80% boost::numeric::ublas::c_vector::c_vector (inline) 109ms 1.68% 63.49% 117ms 1.80% vertexmedian 13ms 0.2% 63.69% 116ms 1.79% std::type_info::operator== (inline) 1ms 0.015% 63.70% 115ms 1.77% boost::numeric::ublas::vector_assign (inline) 23ms 0.35% 64.06% 111ms 1.71% MeshBasedCellPopulation::SpringIterator::SpringIterator 4ms 0.062% 64.12% 111ms 1.71% std::vector::_M_realloc_insert 11ms 0.17% 64.29% 104ms 1.60% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 8ms 0.12% 64.41% 101ms 1.56% AbstractTetrahedralElement::RefreshJacobian 28ms 0.43% 64.84% 101ms 1.56% std::num_put::_M_insert_int 1ms 0.015% 64.86% 98ms 1.51% std::_Vector_base::_M_allocate (inline) 4ms 0.062% 64.92% 96ms 1.48% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 40ms 0.62% 65.54% 95ms 1.46% std::__ostream_insert 93ms 1.43% 66.97% 93ms 1.43% incircle 90ms 1.39% 68.36% 90ms 1.39% [libstdc++.so.6.0.33] 1ms 0.015% 68.37% 85ms 1.31% std::operator<< (inline) 32ms 0.49% 68.86% 83ms 1.28% AbstractElement::GetNodeLocation 11ms 0.17% 69.03% 83ms 1.28% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 69.03% 82ms 1.26% std::basic_ofstream::basic_ofstream (inline) 1ms 0.015% 69.05% 81ms 1.25% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.031% 69.08% 78ms 1.20% Cell::GetCellId 2ms 0.031% 69.11% 77ms 1.19% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 69.11% 77ms 1.19% std::basic_filebuf::open 0 0% 69.11% 77ms 1.19% std::basic_ofstream::open (inline) 73ms 1.12% 70.23% 73ms 1.12% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 73ms 1.12% 71.36% 73ms 1.12% std::_Rb_tree_insert_and_rebalance 65ms 1.00% 72.36% 73ms 1.12% vertexsort 21ms 0.32% 72.68% 71ms 1.09% boost::numeric::ublas::indexing_vector_assign 0 0% 72.68% 68ms 1.05% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.68% 68ms 1.05% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.68% 66ms 1.02% OutputFileHandler::CommonConstructor 0 0% 72.68% 66ms 1.02% OutputFileHandler::OutputFileHandler 11ms 0.17% 72.85% 66ms 1.02% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 72.85% 66ms 1.02% tcache_get (inline) 66ms 1.02% 73.87% 66ms 1.02% tcache_get_n (inline) 0 0% 73.87% 64ms 0.99% Node::~Node 0 0% 73.87% 63ms 0.97% OutputFileHandler::MakeFoldersAndReturnFullPath 42ms 0.65% 74.51% 61ms 0.94% malloc_consolidate 60ms 0.92% 75.44% 60ms 0.92% std::vector::size (inline) 0 0% 75.44% 58ms 0.89% AbstractCellPopulation::CloseRoundRobinWritersFiles 6ms 0.092% 75.53% 57ms 0.88% CellPropertyCollection::AddProperty 0 0% 75.53% 56ms 0.86% AbstractCellBasedWriter::CloseFile 0 0% 75.53% 56ms 0.86% std::basic_filebuf::close 0 0% 75.53% 56ms 0.86% std::basic_ofstream::close (inline) 1ms 0.015% 75.55% 54ms 0.83% Node::ClearAppliedForce 3ms 0.046% 75.59% 54ms 0.83% std::_Rb_tree_const_iterator::operator++ (inline) 36ms 0.55% 76.15% 54ms 0.83% std::basic_streambuf::xsputn 0 0% 76.15% 53ms 0.82% Node::ConstructNodeAttributes (inline) 0 0% 76.15% 52ms 0.8% CellPropertyCollection::~CellPropertyCollection (inline) 29ms 0.45% 76.59% 51ms 0.79% boost::shared_ptr::shared_ptr (inline) 0 0% 76.59% 51ms 0.79% std::_Rb_tree::_M_emplace_hint_unique 43ms 0.66% 77.26% 51ms 0.79% std::num_put::do_put 0 0% 77.26% 49ms 0.75% std::_Vector_base::_M_deallocate (inline) 48ms 0.74% 78.00% 48ms 0.74% counterclockwise 48ms 0.74% 78.73% 48ms 0.74% std::_Rb_tree::_S_left (inline) 0 0% 78.73% 47ms 0.72% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 78.73% 46ms 0.71% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 46ms 0.71% 79.44% 46ms 0.71% std::_Rb_tree_increment 0 0% 79.44% 45ms 0.69% boost::numeric::ublas::norm_2 (inline) 10ms 0.15% 79.60% 45ms 0.69% boost::numeric::ublas::vector_norm_2::apply (inline) 27ms 0.42% 80.01% 45ms 0.69% std::basic_filebuf::xsputn 10ms 0.15% 80.17% 44ms 0.68% Determinant (inline) 2ms 0.031% 80.20% 44ms 0.68% std::basic_filebuf::overflow 32ms 0.49% 80.69% 42ms 0.65% AbstractTetrahedralMesh::GetElement 1ms 0.015% 80.71% 42ms 0.65% std::basic_filebuf::_M_convert_to_external 0 0% 80.71% 42ms 0.65% std::basic_filebuf::_M_terminate_output 22ms 0.34% 81.04% 41ms 0.63% AbstractElement::GetNodeGlobalIndex 0 0% 81.04% 41ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 41ms 0.63% 81.68% 41ms 0.63% __GI___libc_write 0 0% 81.68% 41ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 81.68% 41ms 0.63% std::__basic_file::xsputn 41ms 0.63% 82.31% 41ms 0.63% tcache_put (inline) 1ms 0.015% 82.32% 39ms 0.6% NodeAttributes::NodeAttributes 39ms 0.6% 82.92% 39ms 0.6% __memcpy_avx512_unaligned_erms 30ms 0.46% 83.38% 39ms 0.6% boost::numeric::ublas::c_matrix::operator() 1ms 0.015% 83.40% 39ms 0.6% std::__basic_file::open 1ms 0.015% 83.42% 38ms 0.59% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.42% 38ms 0.59% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 83.42% 37ms 0.57% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.015% 83.43% 37ms 0.57% _IO_new_fopen 37ms 0.57% 84.00% 37ms 0.57% __GI_fchmodat 37ms 0.57% 84.57% 37ms 0.57% boost::numeric::ublas::c_vector::operator() (partial-inline) 15ms 0.23% 84.80% 37ms 0.57% hack_digit 0 0% 84.80% 37ms 0.57% std::filesystem::permissions 25ms 0.38% 85.19% 36ms 0.55% CellPropertyCollection::GetProperty 0 0% 85.19% 36ms 0.55% _IO_new_file_fopen 0 0% 85.19% 36ms 0.55% __fopen_internal (inline) 0 0% 85.19% 35ms 0.54% BoundaryNodeWriter::Visit 0 0% 85.19% 35ms 0.54% __GI__IO_file_open 33ms 0.51% 85.69% 33ms 0.51% Node::GetIndex