File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6720ms, 85.19% of 7888ms total Dropped 610 nodes (cum <= 39.44ms) flat flat% sum% cum cum% 0 0% 0% 7849ms 99.51% __libc_start_call_main 0 0% 0% 7849ms 99.51% __libc_start_main_impl 0 0% 0% 7849ms 99.51% _start 0 0% 0% 7834ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7834ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7834ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7834ms 99.32% main 0 0% 0% 7793ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7793ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7793ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7790ms 98.76% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3426ms 43.43% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.051% 2938ms 37.25% MeshBasedCellPopulation::Update 3ms 0.038% 0.089% 2844ms 36.05% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.1% 1511ms 19.16% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.051% 0.15% 1473ms 18.67% MutableMesh::ReMesh 2ms 0.025% 0.18% 1393ms 17.66% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.19% 1373ms 17.41% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.063% 0.25% 1319ms 16.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 21ms 0.27% 0.52% 1217ms 15.43% MeshBasedCellPopulation::SpringIterator::operator++ 116ms 1.47% 1.99% 993ms 12.59% TetrahedralMesh::EdgeIterator::operator++ 447ms 5.67% 7.66% 970ms 12.30% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.15% 7.81% 925ms 11.73% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.025% 7.83% 919ms 11.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.051% 7.89% 892ms 11.31% AbstractTwoBodyInteractionForce::AddForceContribution 267ms 3.38% 11.27% 875ms 11.09% __dynamic_cast 7ms 0.089% 11.36% 843ms 10.69% CellPopulationElementWriter::Visit 49ms 0.62% 11.98% 792ms 10.04% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.013% 11.99% 744ms 9.43% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.38% 12.37% 739ms 9.37% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.051% 12.42% 716ms 9.08% AbstractCellProperty::IsSubType (inline) 12ms 0.15% 12.58% 710ms 9.00% TetrahedralMesh::ImportFromMesher 1ms 0.013% 12.59% 617ms 7.82% std::ostream::operator<< (inline) 75ms 0.95% 13.54% 615ms 7.80% std::ostream::_M_insert 39ms 0.49% 14.03% 584ms 7.40% operator new 42ms 0.53% 14.57% 575ms 7.29% std::map::operator[] (partial-inline) 1ms 0.013% 14.58% 572ms 7.25% triangulate 199ms 2.52% 17.10% 543ms 6.88% __GI___libc_malloc 38ms 0.48% 17.58% 534ms 6.77% std::__new_allocator::allocate (inline) 12ms 0.15% 17.74% 531ms 6.73% std::_Rb_tree::find (inline) 0 0% 17.74% 531ms 6.73% std::allocator_traits::allocate (inline) 4ms 0.051% 17.79% 525ms 6.66% Cell::GetCellProliferativeType 1ms 0.013% 17.80% 496ms 6.29% delaunay 5ms 0.063% 17.86% 496ms 6.29% std::set::insert (inline) 0 0% 17.86% 494ms 6.26% divconqdelaunay 12ms 0.15% 18.01% 491ms 6.22% std::_Rb_tree::_M_insert_unique 0 0% 18.01% 485ms 6.15% std::_Rb_tree::lower_bound (inline) 0 0% 18.01% 485ms 6.15% std::map::lower_bound (inline) 0 0% 18.01% 485ms 6.15% std::set::count (inline) 475ms 6.02% 24.04% 475ms 6.02% __strcmp_avx2 3ms 0.038% 24.07% 473ms 6.00% AbstractCellBasedSimulation::DoCellBirth 7ms 0.089% 24.16% 461ms 5.84% LegacyCellProliferativeTypesWriter::VisitCell 206ms 2.61% 26.77% 442ms 5.60% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.77% 440ms 5.58% std::_Rb_tree::_M_create_node (inline) 0 0% 26.77% 412ms 5.22% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.77% 399ms 5.06% std::_Rb_tree::_M_get_node (inline) 0 0% 26.77% 383ms 4.86% NodeLocationWriter::Visit 14ms 0.18% 26.95% 373ms 4.73% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.025% 26.98% 371ms 4.70% Cell::GetMutationState 21ms 0.27% 27.24% 370ms 4.69% std::_Rb_tree::~_Rb_tree (inline) 12ms 0.15% 27.40% 358ms 4.54% std::less::operator() (inline) 2ms 0.025% 27.42% 348ms 4.41% std::set::set (inline) 346ms 4.39% 31.81% 346ms 4.39% std::operator< (inline) 82ms 1.04% 32.85% 344ms 4.36% std::_Rb_tree::_M_erase 1ms 0.013% 32.86% 343ms 4.35% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 32.90% 342ms 4.34% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 32.90% 340ms 4.31% std::set::~set (inline) 32ms 0.41% 33.30% 334ms 4.23% std::num_put::_M_insert_float 35ms 0.44% 33.75% 327ms 4.15% std::_Rb_tree::_M_copy (inline) 9ms 0.11% 33.86% 326ms 4.13% Cell::ReadyToDivide 314ms 3.98% 37.84% 314ms 3.98% std::_Rb_tree::_S_right (inline) 1ms 0.013% 37.85% 300ms 3.80% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.85% 298ms 3.78% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.85% 296ms 3.75% OutputFileHandler::OpenOutputFile 14ms 0.18% 38.03% 296ms 3.75% std::_Rb_tree::_M_insert_ (inline) 98ms 1.24% 39.27% 292ms 3.70% __GI___libc_free 72ms 0.91% 40.19% 289ms 3.66% std::_Rb_tree::_M_clone_node (inline) 9ms 0.11% 40.30% 282ms 3.58% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 40.33% 277ms 3.51% Element::Element 175ms 2.22% 42.55% 274ms 3.47% _int_malloc 12ms 0.15% 42.70% 271ms 3.44% divconqrecurse 2ms 0.025% 42.72% 259ms 3.28% CellProliferativeTypesWriter::VisitCell 8ms 0.1% 42.82% 255ms 3.23% std::__new_allocator::deallocate (inline) 59ms 0.75% 43.57% 250ms 3.17% mergehulls 0 0% 43.57% 249ms 3.16% std::allocator_traits::deallocate (inline) 14ms 0.18% 43.75% 248ms 3.14% CellPropertyCollection::HasProperty 0 0% 43.75% 246ms 3.12% Cell::HasCellProperty (inline) 0 0% 43.75% 246ms 3.12% std::_Rb_tree::_M_drop_node (inline) 4ms 0.051% 43.80% 241ms 3.06% std::__cxx11::collate::do_transform 3ms 0.038% 43.84% 235ms 2.98% AbstractCellProperty::IsType (inline) 4ms 0.051% 43.89% 226ms 2.87% ___vsnprintf 0 0% 43.89% 222ms 2.81% __vsnprintf_internal (inline) 28ms 0.35% 44.24% 213ms 2.70% __printf_buffer 9ms 0.11% 44.36% 209ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 44.36% 206ms 2.61% std::_Rb_tree::_M_put_node (inline) 14ms 0.18% 44.54% 199ms 2.52% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.2% 44.74% 197ms 2.50% TetrahedralMesh::Clear 170ms 2.16% 46.89% 193ms 2.45% _int_free 60ms 0.76% 47.65% 183ms 2.32% std::_Rb_tree::_M_get_insert_unique_pos (inline) 52ms 0.66% 48.31% 178ms 2.26% AbstractCellProperty::IsSame 16ms 0.2% 48.52% 178ms 2.26% AbstractTetrahedralElement::CalculateJacobian 8ms 0.1% 48.62% 172ms 2.18% Element::RegisterWithNodes (inline) 7ms 0.089% 48.71% 170ms 2.16% __printf_fp_l_buffer 0 0% 48.71% 170ms 2.16% __printf_fp_spec (inline) 2ms 0.025% 48.73% 165ms 2.09% OutputFileHandler::OutputFileHandler 4ms 0.051% 48.78% 163ms 2.07% Node::AddElement 0 0% 48.78% 163ms 2.07% OutputFileHandler::CommonConstructor 10ms 0.13% 48.91% 162ms 2.05% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 48.92% 161ms 2.04% TetrahedralMesh::RefreshJacobianCachedData 0 0% 48.92% 157ms 1.99% OutputFileHandler::MakeFoldersAndReturnFullPath 74ms 0.94% 49.86% 150ms 1.90% __printf_fp_buffer_1 4ms 0.051% 49.91% 147ms 1.86% AbstractTetrahedralElement::CalculateInverseJacobian 36ms 0.46% 50.37% 146ms 1.85% std::num_put::_M_insert_int 0 0% 50.37% 145ms 1.84% std::basic_ofstream::basic_ofstream (inline) 36ms 0.46% 50.82% 142ms 1.80% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.82% 139ms 1.76% std::basic_filebuf::open 0 0% 50.82% 139ms 1.76% std::basic_ofstream::open (inline) 0 0% 50.82% 137ms 1.74% AbstractCellBasedWriter::CloseFile 0 0% 50.82% 137ms 1.74% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.82% 137ms 1.74% std::basic_filebuf::close 0 0% 50.82% 137ms 1.74% std::basic_ofstream::close (inline) 1ms 0.013% 50.84% 133ms 1.69% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 50.85% 131ms 1.66% alternateaxes 122ms 1.55% 52.40% 129ms 1.64% vertexmedian 128ms 1.62% 54.02% 128ms 1.62% std::_Rb_tree_increment 59ms 0.75% 54.77% 127ms 1.61% std::__ostream_insert 8ms 0.1% 54.87% 126ms 1.60% std::_Rb_tree_const_iterator::operator++ (inline) 31ms 0.39% 55.26% 126ms 1.60% std::type_info::operator== (inline) 5ms 0.063% 55.32% 123ms 1.56% std::vector::push_back (inline) 0 0% 55.32% 121ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 121ms 1.53% 56.86% 121ms 1.53% __GI_fchmodat 0 0% 56.86% 121ms 1.53% std::filesystem::permissions 18ms 0.23% 57.09% 120ms 1.52% AbstractTetrahedralElement::RefreshJacobian 20ms 0.25% 57.34% 118ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 57.34% 118ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 12ms 0.15% 57.49% 116ms 1.47% std::vector::_M_realloc_insert 6ms 0.076% 57.57% 115ms 1.46% Node::~Node 1ms 0.013% 57.58% 114ms 1.45% std::operator<< (inline) 7ms 0.089% 57.67% 113ms 1.43% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.076% 57.75% 113ms 1.43% boost::numeric::ublas::vector_assign (inline) 113ms 1.43% 59.18% 113ms 1.43% incircle 12ms 0.15% 59.33% 109ms 1.38% MeshBasedCellPopulation::SpringIterator::SpringIterator 4ms 0.051% 59.38% 108ms 1.37% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.13% 59.51% 105ms 1.33% boost::detail::shared_count::~shared_count (inline) 0 0% 59.51% 105ms 1.33% boost::shared_ptr::~shared_ptr (inline) 0 0% 59.51% 105ms 1.33% std::__basic_file::open 0 0% 59.51% 104ms 1.32% _IO_new_fopen 0 0% 59.51% 104ms 1.32% __fopen_internal (inline) 2ms 0.025% 59.53% 101ms 1.28% _IO_new_file_fopen 0 0% 59.53% 98ms 1.24% std::basic_filebuf::_M_terminate_output 3ms 0.038% 59.57% 98ms 1.24% std::basic_filebuf::overflow 1ms 0.013% 59.58% 97ms 1.23% __GI__IO_file_open 97ms 1.23% 60.81% 97ms 1.23% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 60.83% 95ms 1.20% std::basic_filebuf::_M_convert_to_external 94ms 1.19% 62.02% 94ms 1.19% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 94ms 1.19% 63.21% 94ms 1.19% [libchaste_cell_based.so] 94ms 1.19% 64.40% 94ms 1.19% __GI___libc_write 54ms 0.68% 65.09% 94ms 1.19% boost::shared_ptr::shared_ptr (inline) 0 0% 65.09% 94ms 1.19% std::__basic_file::xsputn 1ms 0.013% 65.10% 94ms 1.19% std::filesystem::status 93ms 1.18% 66.28% 93ms 1.18% __GI___fstatat64 31ms 0.39% 66.67% 92ms 1.17% AbstractElement::GetNodeLocation 60ms 0.76% 67.43% 92ms 1.17% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 90ms 1.14% 68.57% 90ms 1.14% boost::detail::sp_counted_base::release 1ms 0.013% 68.59% 87ms 1.10% Cell::GetCellId 52ms 0.66% 69.24% 83ms 1.05% std::basic_filebuf::xsputn 4ms 0.051% 69.30% 82ms 1.04% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 69.30% 82ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 82ms 1.04% 70.33% 82ms 1.04% __libc_open64 19ms 0.24% 70.58% 82ms 1.04% boost::numeric::ublas::indexing_vector_assign 49ms 0.62% 71.20% 79ms 1.00% malloc_consolidate 78ms 0.99% 72.19% 78ms 0.99% counterclockwise 0 0% 72.19% 77ms 0.98% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 72.21% 77ms 0.98% std::filesystem::create_directory 68ms 0.86% 73.07% 76ms 0.96% vertexsort 71ms 0.9% 73.97% 71ms 0.9% Node::GetIndex 4ms 0.051% 74.02% 71ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeB 57ms 0.72% 74.75% 70ms 0.89% std::num_put::do_put 0 0% 74.75% 68ms 0.86% AbstractCellPopulation::GetLocationIndexUsingCell 66ms 0.84% 75.58% 66ms 0.84% __memcpy_avx_unaligned_erms 42ms 0.53% 76.12% 65ms 0.82% boost::numeric::ublas::c_matrix::operator() (partial-inline) 64ms 0.81% 76.93% 64ms 0.81% boost::shared_ptr::operator-> (inline) 6ms 0.076% 77.00% 63ms 0.8% CellPropertyCollection::AddProperty 45ms 0.57% 77.57% 63ms 0.8% std::basic_streambuf::xsputn 4ms 0.051% 77.62% 62ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.62% 59ms 0.75% tcache_get (inline) 59ms 0.75% 78.37% 59ms 0.75% tcache_get_n (inline) 1ms 0.013% 78.38% 58ms 0.74% AbstractCentreBasedCellPopulation::CreateCellPair 18ms 0.23% 78.61% 56ms 0.71% Determinant (inline) 56ms 0.71% 79.32% 56ms 0.71% Node::IsDeleted 0 0% 79.32% 54ms 0.68% std::vector::vector (inline) 53ms 0.67% 79.99% 53ms 0.67% std::vector::size (inline) 0 0% 79.99% 52ms 0.66% std::_Vector_base::_Vector_base (inline) 51ms 0.65% 80.64% 51ms 0.65% [libchaste_mesh.so] 0 0% 80.64% 50ms 0.63% std::_Vector_base::_M_create_storage (inline) 26ms 0.33% 80.97% 49ms 0.62% AbstractTetrahedralMesh::GetElement 49ms 0.62% 81.59% 49ms 0.62% Node::rGetLocation 40ms 0.51% 82.10% 48ms 0.61% AbstractElement::GetNodeGlobalIndex 48ms 0.61% 82.71% 48ms 0.61% [libstdc++.so.6.0.33] 0 0% 82.71% 48ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.025% 82.73% 47ms 0.6% BoundaryNodeWriter::Visit 1ms 0.013% 82.75% 47ms 0.6% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 0 0% 82.75% 44ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 3ms 0.038% 82.78% 44ms 0.56% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 82.80% 43ms 0.55% std::__new_allocator::construct (inline) 0 0% 82.80% 43ms 0.55% std::allocator_traits::construct (inline) 9ms 0.11% 82.91% 42ms 0.53% Inverse 27ms 0.34% 83.25% 42ms 0.53% hack_digit 0 0% 83.25% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.25% 41ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.25% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 41ms 0.52% 83.77% 41ms 0.52% std::ostream::sentry::sentry 0 0% 83.77% 40ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 39ms 0.49% 84.27% 40ms 0.51% boost::detail::shared_count::shared_count (inline) 40ms 0.51% 84.77% 40ms 0.51% boost::numeric::ublas::c_vector::operator() (inline) 0 0% 84.77% 40ms 0.51% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.77% 40ms 0.51% std::__new_allocator::destroy (inline) 0 0% 84.77% 40ms 0.51% std::allocator_traits::destroy (inline) 33ms 0.42% 85.19% 40ms 0.51% writeedges