File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6619ms, 84.05% of 7875ms total Dropped 609 nodes (cum <= 39.38ms) flat flat% sum% cum cum% 0 0% 0% 7837ms 99.52% __libc_start_call_main 0 0% 0% 7837ms 99.52% __libc_start_main_impl 0 0% 0% 7837ms 99.52% _start 0 0% 0% 7820ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7820ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7820ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7820ms 99.30% main 0 0% 0% 7782ms 98.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7782ms 98.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7782ms 98.82% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7778ms 98.77% AbstractCellBasedSimulation::Solve 0 0% 0% 3389ms 43.03% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2900ms 36.83% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2854ms 36.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.038% 1521ms 19.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.063% 1423ms 18.07% MutableMesh::ReMesh 0 0% 0.063% 1402ms 17.80% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.089% 1391ms 17.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.11% 1333ms 16.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 9ms 0.11% 0.23% 1223ms 15.53% MeshBasedCellPopulation::SpringIterator::operator++ 111ms 1.41% 1.64% 1023ms 12.99% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.66% 961ms 12.20% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 430ms 5.46% 7.12% 955ms 12.13% std::_Rb_tree::_M_lower_bound (inline) 14ms 0.18% 7.30% 945ms 12.00% CellPropertyCollection::GetPropertiesType (inline) 311ms 3.95% 11.25% 915ms 11.62% __dynamic_cast 1ms 0.013% 11.26% 901ms 11.44% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.11% 11.38% 845ms 10.73% CellPopulationElementWriter::Visit 3ms 0.038% 11.42% 815ms 10.35% MeshBasedCellPopulation::AcceptCellWriter 56ms 0.71% 12.13% 805ms 10.22% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 2ms 0.025% 12.15% 750ms 9.52% AbstractCellProperty::IsSubType (inline) 13ms 0.17% 12.32% 713ms 9.05% TetrahedralMesh::ImportFromMesher 28ms 0.36% 12.67% 701ms 8.90% AbstractCellPopulation::GetCellUsingLocationIndex 93ms 1.18% 13.85% 600ms 7.62% std::ostream::_M_insert 0 0% 13.85% 600ms 7.62% std::ostream::operator<< (inline) 37ms 0.47% 14.32% 576ms 7.31% operator new 45ms 0.57% 14.90% 562ms 7.14% std::map::operator[] (partial-inline) 1ms 0.013% 14.91% 551ms 7.00% triangulate 7ms 0.089% 15.00% 541ms 6.87% Cell::GetCellProliferativeType 31ms 0.39% 15.39% 540ms 6.86% std::_Rb_tree::find (inline) 186ms 2.36% 17.75% 532ms 6.76% __GI___libc_malloc 6ms 0.076% 17.83% 516ms 6.55% std::set::insert (inline) 30ms 0.38% 18.21% 513ms 6.51% std::__new_allocator::allocate (inline) 10ms 0.13% 18.34% 510ms 6.48% std::_Rb_tree::_M_insert_unique 0 0% 18.34% 509ms 6.46% std::allocator_traits::allocate (inline) 0 0% 18.34% 492ms 6.25% std::set::count (inline) 9ms 0.11% 18.45% 488ms 6.20% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 18.45% 486ms 6.17% delaunay 2ms 0.025% 18.48% 485ms 6.16% divconqdelaunay 479ms 6.08% 24.56% 479ms 6.08% __strcmp_avx2 2ms 0.025% 24.58% 469ms 5.96% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.58% 469ms 5.96% std::_Rb_tree::lower_bound (inline) 0 0% 24.58% 469ms 5.96% std::map::lower_bound (inline) 209ms 2.65% 27.24% 417ms 5.30% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.025% 27.26% 412ms 5.23% Cell::GetMutationState 0 0% 27.26% 410ms 5.21% std::_Rb_tree::_M_create_node (inline) 0 0% 27.26% 388ms 4.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.26% 385ms 4.89% std::_Rb_tree::_M_get_node (inline) 4ms 0.051% 27.31% 371ms 4.71% NodeLocationWriter::Visit 29ms 0.37% 27.68% 357ms 4.53% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.13% 27.81% 350ms 4.44% std::less::operator() (inline) 22ms 0.28% 28.09% 344ms 4.37% std::_Rb_tree::_M_insert_ (inline) 30ms 0.38% 28.47% 344ms 4.37% std::_Rb_tree::_Rb_tree (partial-inline) 340ms 4.32% 32.79% 340ms 4.32% std::operator< (inline) 0 0% 32.79% 340ms 4.32% std::set::~set (inline) 1ms 0.013% 32.80% 339ms 4.30% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 32.81% 338ms 4.29% AbstractCentreBasedCellPopulation::GetDampingConstant 74ms 0.94% 33.75% 327ms 4.15% std::_Rb_tree::_M_erase 26ms 0.33% 34.08% 324ms 4.11% std::num_put::_M_insert_float 4ms 0.051% 34.13% 317ms 4.03% std::set::set (inline) 5ms 0.063% 34.20% 313ms 3.97% Cell::ReadyToDivide 305ms 3.87% 38.07% 305ms 3.87% std::_Rb_tree::_S_right (inline) 0 0% 38.07% 296ms 3.76% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.07% 295ms 3.75% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.07% 292ms 3.71% OutputFileHandler::OpenOutputFile 4ms 0.051% 38.12% 291ms 3.70% Element::Element 35ms 0.44% 38.57% 291ms 3.70% std::_Rb_tree::_M_copy (inline) 200ms 2.54% 41.10% 290ms 3.68% _int_malloc 10ms 0.13% 41.23% 287ms 3.64% divconqrecurse 1ms 0.013% 41.24% 280ms 3.56% CellProliferativeTypesWriter::VisitCell 12ms 0.15% 41.40% 278ms 3.53% AbstractCellPopulation::IsCellAttachedToLocationIndex 92ms 1.17% 42.57% 272ms 3.45% __GI___libc_free 75ms 0.95% 43.52% 267ms 3.39% mergehulls 7ms 0.089% 43.61% 258ms 3.28% std::__cxx11::collate::do_transform 78ms 0.99% 44.60% 252ms 3.20% std::_Rb_tree::_M_clone_node (inline) 2ms 0.025% 44.62% 239ms 3.03% ___vsnprintf 6ms 0.076% 44.70% 238ms 3.02% AbstractCellProperty::IsType (inline) 6ms 0.076% 44.77% 238ms 3.02% std::__new_allocator::deallocate (inline) 0 0% 44.77% 237ms 3.01% __vsnprintf_internal (inline) 29ms 0.37% 45.14% 234ms 2.97% __printf_buffer 0 0% 45.14% 232ms 2.95% std::_Rb_tree::_M_drop_node (inline) 0 0% 45.14% 232ms 2.95% std::allocator_traits::deallocate (inline) 6ms 0.076% 45.22% 219ms 2.78% CellPropertyCollection::HasProperty 0 0% 45.22% 218ms 2.77% Cell::HasCellProperty (inline) 2ms 0.025% 45.24% 207ms 2.63% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.076% 45.32% 201ms 2.55% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.013% 45.33% 199ms 2.53% Element::RegisterWithNodes (inline) 5ms 0.063% 45.40% 196ms 2.49% Node::AddElement 54ms 0.69% 46.08% 186ms 2.36% AbstractCellProperty::IsSame 16ms 0.2% 46.29% 186ms 2.36% TetrahedralMesh::Clear 14ms 0.18% 46.46% 184ms 2.34% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 46.46% 184ms 2.34% std::_Rb_tree::_M_put_node (inline) 7ms 0.089% 46.55% 180ms 2.29% __printf_fp_l_buffer 0 0% 46.55% 180ms 2.29% __printf_fp_spec (inline) 148ms 1.88% 48.43% 179ms 2.27% _int_free 1ms 0.013% 48.44% 168ms 2.13% OutputFileHandler::OutputFileHandler 0 0% 48.44% 167ms 2.12% OutputFileHandler::CommonConstructor 86ms 1.09% 49.54% 167ms 2.12% __printf_fp_buffer_1 0 0% 49.54% 159ms 2.02% OutputFileHandler::MakeFoldersAndReturnFullPath 50ms 0.63% 50.17% 157ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 50.17% 157ms 1.99% std::basic_ofstream::basic_ofstream (inline) 77ms 0.98% 51.15% 156ms 1.98% std::__ostream_insert 0 0% 51.15% 153ms 1.94% std::basic_filebuf::open 0 0% 51.15% 153ms 1.94% std::basic_ofstream::open (inline) 34ms 0.43% 51.58% 151ms 1.92% TetrahedralMesh::EdgesEnd (partial-inline) 13ms 0.17% 51.75% 144ms 1.83% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.75% 141ms 1.79% TetrahedralMesh::RefreshJacobianCachedData 37ms 0.47% 52.22% 132ms 1.68% std::type_info::operator== (inline) 8ms 0.1% 52.32% 131ms 1.66% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 52.33% 131ms 1.66% alternateaxes 18ms 0.23% 52.56% 130ms 1.65% AbstractCellPopulation::Iterator::IsRealCell (inline) 40ms 0.51% 53.07% 130ms 1.65% std::num_put::_M_insert_int 7ms 0.089% 53.16% 128ms 1.63% std::vector::push_back (inline) 112ms 1.42% 54.58% 128ms 1.63% vertexmedian 0 0% 54.58% 126ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.025% 54.60% 126ms 1.60% std::_Vector_base::_M_allocate (inline) 121ms 1.54% 56.14% 121ms 1.54% incircle 1ms 0.013% 56.15% 121ms 1.54% std::operator<< (inline) 1ms 0.013% 56.17% 119ms 1.51% _IO_new_fopen 4ms 0.051% 56.22% 119ms 1.51% boost::numeric::ublas::vector_assign (inline) 0 0% 56.22% 119ms 1.51% std::__basic_file::open 1ms 0.013% 56.23% 118ms 1.50% __fopen_internal (inline) 1ms 0.013% 56.24% 116ms 1.47% AbstractCellPopulation::CloseRoundRobinWritersFiles 5ms 0.063% 56.30% 116ms 1.47% std::vector::_M_realloc_insert 0 0% 56.30% 115ms 1.46% AbstractCellBasedWriter::CloseFile 1ms 0.013% 56.32% 115ms 1.46% _IO_new_file_fopen 3ms 0.038% 56.36% 115ms 1.46% std::basic_filebuf::close 0 0% 56.36% 115ms 1.46% std::basic_ofstream::close (inline) 114ms 1.45% 57.80% 114ms 1.45% std::_Rb_tree_insert_and_rebalance 0 0% 57.80% 113ms 1.43% FilesystemPermissions::SetFilePermissions (inline) 113ms 1.43% 59.24% 113ms 1.43% __GI_fchmodat 0 0% 59.24% 113ms 1.43% std::filesystem::permissions 18ms 0.23% 59.47% 112ms 1.42% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 59.47% 112ms 1.42% __GI__IO_file_open 16ms 0.2% 59.67% 110ms 1.40% AbstractTetrahedralElement::RefreshJacobian 3ms 0.038% 59.71% 110ms 1.40% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.13% 59.83% 108ms 1.37% Node::~Node 12ms 0.15% 59.99% 108ms 1.37% std::_Rb_tree_const_iterator::operator++ (inline) 11ms 0.14% 60.13% 106ms 1.35% boost::detail::shared_count::~shared_count (inline) 0 0% 60.13% 106ms 1.35% boost::shared_ptr::~shared_ptr (inline) 4ms 0.051% 60.18% 105ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 42ms 0.53% 60.71% 104ms 1.32% boost::shared_ptr::shared_ptr (inline) 101ms 1.28% 61.99% 101ms 1.28% std::_Rb_tree_increment 57ms 0.72% 62.72% 100ms 1.27% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 62.74% 95ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 62.77% 95ms 1.21% AbstractTetrahedralElement::AbstractTetrahedralElement 95ms 1.21% 63.97% 95ms 1.21% __libc_open64 90ms 1.14% 65.12% 93ms 1.18% boost::detail::sp_counted_base::release 85ms 1.08% 66.20% 85ms 1.08% [libchaste_cell_based.so] 3ms 0.038% 66.23% 85ms 1.08% std::basic_filebuf::overflow 5ms 0.063% 66.30% 84ms 1.07% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 66.30% 83ms 1.05% std::basic_filebuf::_M_terminate_output 0 0% 66.30% 82ms 1.04% std::__basic_file::xsputn 0 0% 66.30% 82ms 1.04% std::basic_filebuf::_M_convert_to_external 81ms 1.03% 67.33% 81ms 1.03% Node::GetIndex 79ms 1.00% 68.33% 81ms 1.03% __GI___libc_write 65ms 0.83% 69.16% 81ms 1.03% std::basic_streambuf::xsputn 16ms 0.2% 69.36% 79ms 1.00% boost::numeric::ublas::indexing_vector_assign 30ms 0.38% 69.74% 78ms 0.99% AbstractElement::GetNodeLocation 0 0% 69.74% 74ms 0.94% Cell::GetCellId 64ms 0.81% 70.55% 73ms 0.93% AbstractElement::GetNodeGlobalIndex 72ms 0.91% 71.47% 72ms 0.91% __GI___fstatat64 61ms 0.77% 72.24% 72ms 0.91% malloc_consolidate 2ms 0.025% 72.27% 71ms 0.9% std::filesystem::status 0 0% 72.27% 70ms 0.89% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 70ms 0.89% 73.16% 70ms 0.89% counterclockwise 0 0% 73.16% 70ms 0.89% std::filesystem::create_directory 70ms 0.89% 74.04% 70ms 0.89% std::vector::size (inline) 43ms 0.55% 74.59% 69ms 0.88% std::basic_filebuf::xsputn 67ms 0.85% 75.44% 67ms 0.85% [libchaste_mesh.so] 66ms 0.84% 76.28% 66ms 0.84% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 61ms 0.77% 77.05% 62ms 0.79% boost::detail::shared_count::shared_count (inline) 10ms 0.13% 77.18% 60ms 0.76% CellPropertyCollection::AddProperty 59ms 0.75% 77.93% 59ms 0.75% __memcpy_avx_unaligned_erms 25ms 0.32% 78.25% 58ms 0.74% AbstractTetrahedralMesh::GetElement 5ms 0.063% 78.31% 58ms 0.74% Node::ConstructNodeAttributes (inline) 45ms 0.57% 78.88% 57ms 0.72% std::num_put::do_put 2ms 0.025% 78.91% 56ms 0.71% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.051% 78.96% 55ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeB 52ms 0.66% 79.62% 55ms 0.7% vertexsort 0 0% 79.62% 53ms 0.67% Node::ClearAppliedForce 1ms 0.013% 79.63% 52ms 0.66% BoundaryNodeWriter::Visit 0 0% 79.63% 52ms 0.66% tcache_get (inline) 52ms 0.66% 80.29% 52ms 0.66% tcache_get_n (inline) 4ms 0.051% 80.34% 51ms 0.65% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 80.36% 50ms 0.63% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 3ms 0.038% 80.39% 49ms 0.62% TetrahedralMesh::EdgeIterator::GetNodeA 49ms 0.62% 81.02% 49ms 0.62% [libstdc++.so.6.0.33] 48ms 0.61% 81.63% 48ms 0.61% Node::IsDeleted 0 0% 81.63% 48ms 0.61% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.013% 81.64% 48ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.64% 48ms 0.61% std::__new_allocator::destroy (inline) 0 0% 81.64% 48ms 0.61% std::allocator_traits::destroy (inline) 24ms 0.3% 81.94% 47ms 0.6% AbstractCellCycleModel::GetAge 23ms 0.29% 82.23% 47ms 0.6% boost::numeric::ublas::c_matrix::operator() (partial-inline) 47ms 0.6% 82.83% 47ms 0.6% boost::shared_ptr::operator-> (inline) 28ms 0.36% 83.19% 46ms 0.58% hack_digit 13ms 0.17% 83.35% 45ms 0.57% AbstractTetrahedralMesh::GetNumAllElements 0 0% 83.35% 44ms 0.56% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 44ms 0.56% 83.91% 44ms 0.56% __GI___mkdir 0 0% 83.91% 42ms 0.53% CellPropertyCollection::~CellPropertyCollection (inline) 11ms 0.14% 84.05% 42ms 0.53% Inverse 0 0% 84.05% 42ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.05% 41ms 0.52% std::map::find (inline)