File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6660ms, 83.63% of 7964ms total Dropped 577 nodes (cum <= 39.82ms) flat flat% sum% cum cum% 0 0% 0% 7923ms 99.49% __libc_start_call_main 0 0% 0% 7923ms 99.49% __libc_start_main_impl 0 0% 0% 7923ms 99.49% _start 0 0% 0% 7906ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7906ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7906ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7906ms 99.27% main 0 0% 0% 7864ms 98.74% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7864ms 98.74% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7864ms 98.74% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7861ms 98.71% AbstractCellBasedSimulation::Solve 0 0% 0% 3387ms 42.53% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2952ms 37.07% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.025% 2891ms 36.30% MeshBasedCellPopulation::Update 2ms 0.025% 0.05% 1513ms 19.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.05% 1454ms 18.26% MutableMesh::ReMesh 1ms 0.013% 0.063% 1376ms 17.28% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.063% 1373ms 17.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.038% 0.1% 1319ms 16.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.34% 1204ms 15.12% MeshBasedCellPopulation::SpringIterator::operator++ 117ms 1.47% 1.81% 977ms 12.27% TetrahedralMesh::EdgeIterator::operator++ 439ms 5.51% 7.32% 974ms 12.23% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 7.35% 960ms 12.05% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 11ms 0.14% 7.48% 943ms 11.84% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.025% 7.51% 917ms 11.51% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.18% 7.68% 898ms 11.28% CellPopulationElementWriter::Visit 242ms 3.04% 10.72% 872ms 10.95% __dynamic_cast 45ms 0.57% 11.29% 821ms 10.31% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 3ms 0.038% 11.33% 802ms 10.07% MeshBasedCellPopulation::AcceptCellWriter 28ms 0.35% 11.68% 774ms 9.72% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 11.82% 751ms 9.43% TetrahedralMesh::ImportFromMesher 4ms 0.05% 11.87% 705ms 8.85% AbstractCellProperty::IsSubType (inline) 64ms 0.8% 12.67% 614ms 7.71% std::map::operator[] (partial-inline) 0 0% 12.67% 599ms 7.52% std::ostream::operator<< (inline) 83ms 1.04% 13.71% 598ms 7.51% std::ostream::_M_insert 56ms 0.7% 14.41% 578ms 7.26% operator new 9ms 0.11% 14.53% 562ms 7.06% Cell::GetCellProliferativeType 1ms 0.013% 14.54% 553ms 6.94% triangulate 28ms 0.35% 14.89% 530ms 6.65% std::_Rb_tree::find (inline) 3ms 0.038% 14.93% 524ms 6.58% LegacyCellProliferativeTypesWriter::VisitCell 181ms 2.27% 17.20% 524ms 6.58% __GI___libc_malloc 35ms 0.44% 17.64% 520ms 6.53% std::__new_allocator::allocate (inline) 0 0% 17.64% 515ms 6.47% std::allocator_traits::allocate (inline) 4ms 0.05% 17.69% 512ms 6.43% std::set::insert (inline) 10ms 0.13% 17.82% 508ms 6.38% std::_Rb_tree::_M_insert_unique 0 0% 17.82% 506ms 6.35% std::_Rb_tree::lower_bound (inline) 0 0% 17.82% 506ms 6.35% std::map::lower_bound (inline) 502ms 6.30% 24.12% 502ms 6.30% __strcmp_avx2 3ms 0.038% 24.16% 483ms 6.06% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.16% 483ms 6.06% std::set::count (inline) 0 0% 24.16% 481ms 6.04% delaunay 1ms 0.013% 24.17% 480ms 6.03% divconqdelaunay 229ms 2.88% 27.05% 449ms 5.64% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.05% 433ms 5.44% std::_Rb_tree::_M_create_node (inline) 27ms 0.34% 27.39% 429ms 5.39% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.39% 413ms 5.19% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.39% 408ms 5.12% std::set::~set (inline) 0 0% 27.39% 400ms 5.02% std::_Rb_tree::_M_get_node (inline) 77ms 0.97% 28.35% 398ms 5.00% std::_Rb_tree::_M_erase 0 0% 28.35% 390ms 4.90% NodeLocationWriter::Visit 2ms 0.025% 28.38% 387ms 4.86% Cell::GetMutationState 27ms 0.34% 28.72% 367ms 4.61% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.14% 28.85% 359ms 4.51% std::less::operator() (inline) 348ms 4.37% 33.22% 348ms 4.37% std::operator< (inline) 9ms 0.11% 33.34% 345ms 4.33% Cell::ReadyToDivide 31ms 0.39% 33.73% 339ms 4.26% std::num_put::_M_insert_float 0 0% 33.73% 338ms 4.24% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.73% 337ms 4.23% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.73% 332ms 4.17% OutputFileHandler::OpenOutputFile 331ms 4.16% 37.88% 331ms 4.16% std::_Rb_tree::_S_right (inline) 0 0% 37.88% 329ms 4.13% std::set::set (inline) 23ms 0.29% 38.17% 322ms 4.04% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 38.18% 318ms 3.99% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 38.21% 317ms 3.98% AbstractCentreBasedCellPopulation::GetDampingConstant 115ms 1.44% 39.65% 315ms 3.96% __GI___libc_free 34ms 0.43% 40.08% 309ms 3.88% std::_Rb_tree::_M_copy (inline) 10ms 0.13% 40.21% 301ms 3.78% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 40.21% 296ms 3.72% std::_Rb_tree::_M_drop_node (inline) 1ms 0.013% 40.22% 293ms 3.68% Element::Element 12ms 0.15% 40.37% 286ms 3.59% std::__new_allocator::deallocate (inline) 0 0% 40.37% 282ms 3.54% std::allocator_traits::deallocate (inline) 71ms 0.89% 41.26% 272ms 3.42% std::_Rb_tree::_M_clone_node (inline) 174ms 2.18% 43.45% 264ms 3.31% _int_malloc 8ms 0.1% 43.55% 264ms 3.31% divconqrecurse 8ms 0.1% 43.65% 259ms 3.25% std::__cxx11::collate::do_transform 9ms 0.11% 43.76% 255ms 3.20% CellPropertyCollection::HasProperty 4ms 0.05% 43.81% 253ms 3.18% AbstractCellProperty::IsType (inline) 0 0% 43.81% 253ms 3.18% Cell::HasCellProperty (inline) 5ms 0.063% 43.87% 247ms 3.10% CellProliferativeTypesWriter::VisitCell 84ms 1.05% 44.93% 247ms 3.10% mergehulls 5ms 0.063% 44.99% 243ms 3.05% ___vsnprintf 35ms 0.44% 45.43% 238ms 2.99% __printf_buffer 0 0% 45.43% 238ms 2.99% __vsnprintf_internal (inline) 0 0% 45.43% 233ms 2.93% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 45.45% 224ms 2.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 8ms 0.1% 45.55% 221ms 2.77% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.19% 45.74% 221ms 2.77% TetrahedralMesh::Clear 169ms 2.12% 47.87% 200ms 2.51% _int_free 4ms 0.05% 47.92% 197ms 2.47% Element::RegisterWithNodes (inline) 50ms 0.63% 48.54% 193ms 2.42% AbstractCellProperty::IsSame 4ms 0.05% 48.59% 191ms 2.40% Node::AddElement 2ms 0.025% 48.62% 188ms 2.36% __printf_fp_spec (inline) 5ms 0.063% 48.68% 186ms 2.34% __printf_fp_l_buffer 60ms 0.75% 49.43% 177ms 2.22% std::_Rb_tree::_M_get_insert_unique_pos (inline) 8ms 0.1% 49.54% 174ms 2.18% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 49.54% 168ms 2.11% std::basic_ofstream::basic_ofstream (inline) 74ms 0.93% 50.46% 164ms 2.06% __printf_fp_buffer_1 2ms 0.025% 50.49% 157ms 1.97% std::basic_ofstream::open (inline) 32ms 0.4% 50.89% 155ms 1.95% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.89% 154ms 1.93% std::basic_filebuf::open 1ms 0.013% 50.90% 150ms 1.88% std::basic_ofstream::close (inline) 0 0% 50.90% 149ms 1.87% AbstractCellBasedWriter::CloseFile 0 0% 50.90% 149ms 1.87% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.90% 149ms 1.87% OutputFileHandler::CommonConstructor 0 0% 50.90% 149ms 1.87% OutputFileHandler::OutputFileHandler 0 0% 50.90% 148ms 1.86% std::basic_filebuf::close 15ms 0.19% 51.09% 143ms 1.80% AbstractTetrahedralElement::CalculateJacobian 11ms 0.14% 51.23% 143ms 1.80% Node::~Node 24ms 0.3% 51.53% 143ms 1.80% std::type_info::operator== (inline) 0 0% 51.53% 139ms 1.75% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 51.56% 136ms 1.71% boost::numeric::ublas::vector_assign (inline) 0 0% 51.56% 134ms 1.68% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 51.57% 134ms 1.68% std::filesystem::permissions 133ms 1.67% 53.24% 133ms 1.67% __GI_fchmodat 1ms 0.013% 53.25% 131ms 1.64% TetrahedralMesh::RefreshJacobianCachedData 14ms 0.18% 53.43% 131ms 1.64% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.063% 53.49% 129ms 1.62% alternateaxes 2ms 0.025% 53.52% 128ms 1.61% boost::numeric::ublas::c_vector::c_vector (inline) 125ms 1.57% 55.09% 125ms 1.57% std::_Rb_tree_increment 63ms 0.79% 55.88% 125ms 1.57% std::__ostream_insert 114ms 1.43% 57.31% 124ms 1.56% vertexmedian 10ms 0.13% 57.43% 121ms 1.52% boost::detail::shared_count::~shared_count (inline) 0 0% 57.43% 121ms 1.52% boost::shared_ptr::~shared_ptr (inline) 0 0% 57.43% 120ms 1.51% _IO_new_fopen 0 0% 57.43% 120ms 1.51% __fopen_internal (inline) 0 0% 57.43% 120ms 1.51% std::__basic_file::open 29ms 0.36% 57.80% 120ms 1.51% std::num_put::_M_insert_int 2ms 0.025% 57.82% 117ms 1.47% std::_Vector_base::_M_allocate (inline) 7ms 0.088% 57.91% 117ms 1.47% std::vector::push_back (inline) 1ms 0.013% 57.92% 116ms 1.46% _IO_new_file_fopen 12ms 0.15% 58.07% 114ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.05% 58.12% 114ms 1.43% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 58.12% 114ms 1.43% __GI__IO_file_open 0 0% 58.12% 112ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 107ms 1.34% 59.47% 108ms 1.36% boost::detail::sp_counted_base::release 44ms 0.55% 60.02% 108ms 1.36% boost::shared_ptr::shared_ptr (inline) 4ms 0.05% 60.07% 107ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 18ms 0.23% 60.30% 105ms 1.32% MeshBasedCellPopulation::SpringIterator::SpringIterator 105ms 1.32% 61.61% 105ms 1.32% incircle 2ms 0.025% 61.64% 105ms 1.32% std::operator<< (inline) 9ms 0.11% 61.75% 104ms 1.31% AbstractTetrahedralElement::RefreshJacobian 2ms 0.025% 61.78% 104ms 1.31% std::basic_filebuf::_M_terminate_output 71ms 0.89% 62.67% 102ms 1.28% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 62.68% 102ms 1.28% std::basic_filebuf::overflow 4ms 0.05% 62.73% 102ms 1.28% std::vector::_M_realloc_insert 37ms 0.46% 63.20% 101ms 1.27% boost::numeric::ublas::indexing_vector_assign 101ms 1.27% 64.47% 101ms 1.27% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 64.48% 101ms 1.27% std::basic_filebuf::_M_convert_to_external 100ms 1.26% 65.73% 100ms 1.26% [libchaste_cell_based.so] 98ms 1.23% 66.96% 100ms 1.26% __GI___libc_write 100ms 1.26% 68.22% 100ms 1.26% __libc_open64 0 0% 68.22% 100ms 1.26% std::__basic_file::xsputn 4ms 0.05% 68.27% 91ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 33ms 0.41% 68.68% 86ms 1.08% AbstractElement::GetNodeLocation 0 0% 68.68% 85ms 1.07% Cell::GetCellId 3ms 0.038% 68.72% 84ms 1.05% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 10ms 0.13% 68.85% 79ms 0.99% CellPropertyCollection::AddProperty 72ms 0.9% 69.75% 79ms 0.99% vertexsort 1ms 0.013% 69.76% 75ms 0.94% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.94% 70.71% 75ms 0.94% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 56ms 0.7% 71.41% 75ms 0.94% malloc_consolidate 42ms 0.53% 71.94% 75ms 0.94% std::basic_filebuf::xsputn 0 0% 71.94% 72ms 0.9% tcache_get (inline) 72ms 0.9% 72.84% 72ms 0.9% tcache_get_n (inline) 1ms 0.013% 72.85% 71ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 72.87% 71ms 0.89% std::filesystem::status 70ms 0.88% 73.74% 70ms 0.88% __GI___fstatat64 0 0% 73.74% 69ms 0.87% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 73.74% 69ms 0.87% std::filesystem::create_directory 54ms 0.68% 74.42% 66ms 0.83% std::basic_streambuf::xsputn 64ms 0.8% 75.23% 64ms 0.8% boost::detail::shared_count::shared_count (inline) 56ms 0.7% 75.93% 64ms 0.8% std::num_put::do_put 0 0% 75.93% 63ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 75.93% 63ms 0.79% std::__new_allocator::destroy (inline) 0 0% 75.93% 63ms 0.79% std::allocator_traits::destroy (inline) 62ms 0.78% 76.71% 62ms 0.78% [libchaste_mesh.so] 0 0% 76.71% 60ms 0.75% AbstractCentreBasedCellPopulation::CreateCellPair 26ms 0.33% 77.03% 59ms 0.74% AbstractTetrahedralMesh::GetElement 59ms 0.74% 77.77% 59ms 0.74% Node::GetIndex 4ms 0.05% 77.83% 59ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 58ms 0.73% 78.55% 58ms 0.73% boost::shared_ptr::operator-> (inline) 58ms 0.73% 79.28% 58ms 0.73% std::vector::size (inline) 56ms 0.7% 79.98% 56ms 0.7% counterclockwise 5ms 0.063% 80.05% 52ms 0.65% Node::ConstructNodeAttributes (inline) 0 0% 80.05% 51ms 0.64% std::vector::vector (inline) 23ms 0.29% 80.34% 50ms 0.63% AbstractCellCycleModel::GetAge 34ms 0.43% 80.76% 50ms 0.63% boost::numeric::ublas::c_matrix::operator() 42ms 0.53% 81.29% 49ms 0.62% AbstractElement::GetNodeGlobalIndex 3ms 0.038% 81.33% 49ms 0.62% std::_Vector_base::_M_deallocate (inline) 48ms 0.6% 81.93% 48ms 0.6% boost::numeric::ublas::c_vector::operator() (inline) 0 0% 81.93% 47ms 0.59% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 81.93% 47ms 0.59% Node::ClearAppliedForce 28ms 0.35% 82.28% 47ms 0.59% hack_digit 0 0% 82.28% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 45ms 0.57% 82.85% 45ms 0.57% Node::IsDeleted 20ms 0.25% 83.10% 44ms 0.55% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 83.11% 44ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.11% 42ms 0.53% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.11% 42ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.11% 41ms 0.51% _dl_init 0 0% 83.11% 41ms 0.51% _dl_start_user 0 0% 83.11% 41ms 0.51% call_init (inline) 0 0% 83.11% 41ms 0.51% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 83.12% 41ms 0.51% std::__new_allocator::construct (inline) 0 0% 83.12% 41ms 0.51% std::allocator_traits::construct (inline) 0 0% 83.12% 41ms 0.51% std::map::map (inline) 40ms 0.5% 83.63% 40ms 0.5% AbstractElement::IsDeleted