File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6693ms, 84.82% of 7891ms total Dropped 595 nodes (cum <= 39.45ms) flat flat% sum% cum cum% 0 0% 0% 7854ms 99.53% __libc_start_call_main 0 0% 0% 7854ms 99.53% __libc_start_main_impl 0 0% 0% 7854ms 99.53% _start 0 0% 0% 7838ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7838ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7838ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7838ms 99.33% main 0 0% 0% 7801ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7801ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7801ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7796ms 98.80% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.025% 3290ms 41.69% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.025% 2934ms 37.18% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.051% 2839ms 35.98% MeshBasedCellPopulation::Update 0 0% 0.051% 1555ms 19.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.051% 1422ms 18.02% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.063% 1405ms 17.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.063% 1366ms 17.31% MutableMesh::ReMesh 7ms 0.089% 0.15% 1342ms 17.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.19% 0.34% 1228ms 15.56% MeshBasedCellPopulation::SpringIterator::operator++ 112ms 1.42% 1.76% 1012ms 12.82% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.79% 994ms 12.60% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 9ms 0.11% 1.90% 971ms 12.31% CellPropertyCollection::GetPropertiesType (inline) 429ms 5.44% 7.34% 935ms 11.85% std::_Rb_tree::_M_lower_bound (inline) 278ms 3.52% 10.86% 913ms 11.57% __dynamic_cast 1ms 0.013% 10.87% 907ms 11.49% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.13% 11.00% 870ms 11.03% CellPopulationElementWriter::Visit 3ms 0.038% 11.04% 837ms 10.61% MeshBasedCellPopulation::AcceptCellWriter 65ms 0.82% 11.86% 799ms 10.13% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.063% 11.92% 750ms 9.50% AbstractCellProperty::IsSubType (inline) 5ms 0.063% 11.99% 733ms 9.29% TetrahedralMesh::ImportFromMesher 32ms 0.41% 12.39% 728ms 9.23% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 12.41% 622ms 7.88% std::ostream::operator<< (inline) 90ms 1.14% 13.55% 619ms 7.84% std::ostream::_M_insert 27ms 0.34% 13.89% 570ms 7.22% operator new 43ms 0.54% 14.43% 564ms 7.15% std::map::operator[] (partial-inline) 5ms 0.063% 14.50% 562ms 7.12% Cell::GetCellProliferativeType 43ms 0.54% 15.04% 541ms 6.86% std::__new_allocator::allocate (inline) 192ms 2.43% 17.48% 540ms 6.84% __GI___libc_malloc 0 0% 17.48% 537ms 6.81% std::allocator_traits::allocate (inline) 4ms 0.051% 17.53% 528ms 6.69% std::set::insert (inline) 5ms 0.063% 17.59% 527ms 6.68% LegacyCellProliferativeTypesWriter::VisitCell 14ms 0.18% 17.77% 523ms 6.63% std::_Rb_tree::_M_insert_unique 512ms 6.49% 24.26% 512ms 6.49% __strcmp_avx2 15ms 0.19% 24.45% 501ms 6.35% std::_Rb_tree::find (inline) 3ms 0.038% 24.48% 486ms 6.16% triangulate 0 0% 24.48% 477ms 6.04% std::_Rb_tree::lower_bound (inline) 0 0% 24.48% 477ms 6.04% std::map::lower_bound (inline) 0 0% 24.48% 462ms 5.85% std::set::count (inline) 0 0% 24.48% 451ms 5.72% std::_Rb_tree::_M_create_node (inline) 0 0% 24.48% 437ms 5.54% AbstractCellBasedSimulation::DoCellBirth 212ms 2.69% 27.17% 436ms 5.53% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.17% 430ms 5.45% delaunay 2ms 0.025% 27.20% 428ms 5.42% divconqdelaunay 3ms 0.038% 27.23% 422ms 5.35% Cell::GetMutationState 0 0% 27.23% 421ms 5.34% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.23% 410ms 5.20% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 27.25% 399ms 5.06% NodeLocationWriter::Visit 28ms 0.35% 27.60% 383ms 4.85% std::_Rb_tree::_Rb_tree (partial-inline) 23ms 0.29% 27.89% 368ms 4.66% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.038% 27.93% 352ms 4.46% std::set::set (inline) 31ms 0.39% 28.32% 345ms 4.37% std::num_put::_M_insert_float 55ms 0.7% 29.02% 341ms 4.32% std::_Rb_tree::_M_erase 11ms 0.14% 29.16% 339ms 4.30% std::less::operator() (inline) 0 0% 29.16% 338ms 4.28% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 29.20% 337ms 4.27% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 29.20% 337ms 4.27% std::set::~set (inline) 23ms 0.29% 29.49% 334ms 4.23% std::_Rb_tree::_M_insert_ (inline) 328ms 4.16% 33.65% 328ms 4.16% std::operator< (inline) 40ms 0.51% 34.15% 324ms 4.11% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 34.18% 322ms 4.08% Cell::ReadyToDivide 110ms 1.39% 35.57% 319ms 4.04% __GI___libc_free 6ms 0.076% 35.65% 315ms 3.99% Element::Element 1ms 0.013% 35.66% 297ms 3.76% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 35.66% 295ms 3.74% AbstractCellBasedWriter::OpenOutputFileForAppend 294ms 3.73% 39.39% 294ms 3.73% std::_Rb_tree::_S_right (inline) 0 0% 39.39% 290ms 3.68% OutputFileHandler::OpenOutputFile 8ms 0.1% 39.49% 283ms 3.59% AbstractCellPopulation::IsCellAttachedToLocationIndex 185ms 2.34% 41.83% 283ms 3.59% _int_malloc 1ms 0.013% 41.85% 281ms 3.56% CellProliferativeTypesWriter::VisitCell 75ms 0.95% 42.80% 280ms 3.55% std::_Rb_tree::_M_clone_node (inline) 10ms 0.13% 42.92% 276ms 3.50% AbstractCellProperty::IsType (inline) 6ms 0.076% 43.00% 275ms 3.48% CellPropertyCollection::HasProperty 0 0% 43.00% 274ms 3.47% Cell::HasCellProperty (inline) 7ms 0.089% 43.09% 274ms 3.47% std::__new_allocator::deallocate (inline) 0 0% 43.09% 271ms 3.43% std::allocator_traits::deallocate (inline) 0 0% 43.09% 265ms 3.36% std::_Rb_tree::_M_drop_node (inline) 1ms 0.013% 43.10% 263ms 3.33% std::__cxx11::collate::do_transform 10ms 0.13% 43.23% 257ms 3.26% divconqrecurse 1ms 0.013% 43.24% 251ms 3.18% ___vsnprintf 0 0% 43.24% 250ms 3.17% __vsnprintf_internal (inline) 38ms 0.48% 43.72% 244ms 3.09% __printf_buffer 63ms 0.8% 44.52% 237ms 3.00% mergehulls 0 0% 44.52% 218ms 2.76% std::_Rb_tree::_M_put_node (inline) 27ms 0.34% 44.86% 217ms 2.75% TetrahedralMesh::Clear 4ms 0.051% 44.91% 211ms 2.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 182ms 2.31% 47.22% 209ms 2.65% _int_free 10ms 0.13% 47.35% 205ms 2.60% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 68ms 0.86% 48.21% 202ms 2.56% AbstractCellProperty::IsSame 1ms 0.013% 48.22% 195ms 2.47% __printf_fp_spec (inline) 6ms 0.076% 48.30% 194ms 2.46% __printf_fp_l_buffer 4ms 0.051% 48.35% 190ms 2.41% Element::RegisterWithNodes (inline) 10ms 0.13% 48.47% 186ms 2.36% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 48.49% 183ms 2.32% Node::AddElement 74ms 0.94% 49.42% 175ms 2.22% std::_Rb_tree::_M_get_insert_unique_pos (inline) 92ms 1.17% 50.59% 174ms 2.21% __printf_fp_buffer_1 12ms 0.15% 50.74% 155ms 1.96% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.74% 149ms 1.89% OutputFileHandler::OutputFileHandler 29ms 0.37% 51.11% 149ms 1.89% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.11% 148ms 1.88% OutputFileHandler::CommonConstructor 0 0% 51.11% 143ms 1.81% std::basic_ofstream::basic_ofstream (inline) 59ms 0.75% 51.86% 141ms 1.79% std::__ostream_insert 1ms 0.013% 51.87% 140ms 1.77% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.87% 139ms 1.76% std::basic_filebuf::close 0 0% 51.87% 138ms 1.75% AbstractCellBasedWriter::CloseFile 0 0% 51.87% 138ms 1.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 9ms 0.11% 51.98% 138ms 1.75% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 51.98% 138ms 1.75% std::basic_ofstream::close (inline) 1ms 0.013% 52.00% 137ms 1.74% std::basic_ofstream::open (inline) 2ms 0.025% 52.02% 136ms 1.72% boost::numeric::ublas::vector_assign (inline) 136ms 1.72% 53.74% 136ms 1.72% std::_Rb_tree_increment 1ms 0.013% 53.76% 136ms 1.72% std::basic_filebuf::open 30ms 0.38% 54.14% 134ms 1.70% std::type_info::operator== (inline) 2ms 0.025% 54.16% 129ms 1.63% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 54.18% 128ms 1.62% std::_Vector_base::_M_allocate (inline) 0 0% 54.18% 126ms 1.60% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.038% 54.21% 125ms 1.58% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 54.21% 122ms 1.55% std::operator<< (inline) 27ms 0.34% 54.56% 121ms 1.53% std::num_put::_M_insert_int 0 0% 54.56% 119ms 1.51% FilesystemPermissions::SetFilePermissions (inline) 10ms 0.13% 54.68% 119ms 1.51% Node::~Node 1ms 0.013% 54.70% 119ms 1.51% std::filesystem::permissions 15ms 0.19% 54.89% 117ms 1.48% MeshBasedCellPopulation::SpringIterator::SpringIterator 116ms 1.47% 56.36% 116ms 1.47% __GI_fchmodat 12ms 0.15% 56.51% 112ms 1.42% AbstractTetrahedralElement::RefreshJacobian 112ms 1.42% 57.93% 112ms 1.42% incircle 4ms 0.051% 57.98% 110ms 1.39% AbstractTetrahedralElement::CalculateInverseJacobian 109ms 1.38% 59.36% 109ms 1.38% [libchaste_cell_based.so] 69ms 0.87% 60.23% 108ms 1.37% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 7ms 0.089% 60.32% 108ms 1.37% boost::detail::shared_count::~shared_count (inline) 54ms 0.68% 61.01% 108ms 1.37% boost::shared_ptr::shared_ptr (inline) 0 0% 61.01% 108ms 1.37% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 61.02% 106ms 1.34% std::__basic_file::open 1ms 0.013% 61.03% 106ms 1.34% std::basic_filebuf::_M_convert_to_external 0 0% 61.03% 106ms 1.34% std::basic_filebuf::_M_terminate_output 0 0% 61.03% 106ms 1.34% std::basic_filebuf::overflow 0 0% 61.03% 105ms 1.33% _IO_new_fopen 1ms 0.013% 61.04% 105ms 1.33% __fopen_internal (inline) 1ms 0.013% 61.06% 105ms 1.33% std::__basic_file::xsputn 103ms 1.31% 62.36% 104ms 1.32% __GI___libc_write 4ms 0.051% 62.41% 104ms 1.32% std::vector::push_back (inline) 1ms 0.013% 62.43% 103ms 1.31% alternateaxes 18ms 0.23% 62.65% 102ms 1.29% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 62.65% 102ms 1.29% _IO_new_file_fopen 97ms 1.23% 63.88% 102ms 1.29% vertexmedian 1ms 0.013% 63.90% 99ms 1.25% __GI__IO_file_open 98ms 1.24% 65.14% 98ms 1.24% std::_Rb_tree_insert_and_rebalance 0 0% 65.14% 97ms 1.23% AbstractCellPopulation::Iterator::operator++ (inline) 96ms 1.22% 66.35% 97ms 1.23% boost::detail::sp_counted_base::release 5ms 0.063% 66.42% 94ms 1.19% std::vector::_M_realloc_insert 35ms 0.44% 66.86% 91ms 1.15% boost::numeric::ublas::indexing_vector_assign 87ms 1.10% 67.96% 87ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 62ms 0.79% 68.75% 86ms 1.09% malloc_consolidate 35ms 0.44% 69.19% 84ms 1.06% AbstractElement::GetNodeLocation 83ms 1.05% 70.24% 84ms 1.06% __libc_open64 47ms 0.6% 70.84% 80ms 1.01% std::basic_filebuf::xsputn 2ms 0.025% 70.87% 79ms 1.00% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 77ms 0.98% 71.84% 77ms 0.98% Node::GetIndex 2ms 0.025% 71.87% 74ms 0.94% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.076% 71.94% 74ms 0.94% CellPropertyCollection::AddProperty 3ms 0.038% 71.98% 74ms 0.94% std::filesystem::status 0 0% 71.98% 73ms 0.93% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 52ms 0.66% 72.64% 73ms 0.93% std::basic_streambuf::xsputn 5ms 0.063% 72.70% 73ms 0.93% std::filesystem::create_directory 2ms 0.025% 72.73% 72ms 0.91% Cell::GetCellId 72ms 0.91% 73.64% 72ms 0.91% __GI___fstatat64 59ms 0.75% 74.39% 71ms 0.9% AbstractElement::GetNodeGlobalIndex 0 0% 74.39% 67ms 0.85% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.025% 74.41% 65ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeB 54ms 0.68% 75.10% 64ms 0.81% vertexsort 0 0% 75.10% 63ms 0.8% std::vector::vector (inline) 60ms 0.76% 75.86% 60ms 0.76% counterclockwise 46ms 0.58% 76.44% 60ms 0.76% std::num_put::do_put 0 0% 76.44% 60ms 0.76% tcache_get (inline) 60ms 0.76% 77.20% 60ms 0.76% tcache_get_n (inline) 2ms 0.025% 77.23% 59ms 0.75% Node::ConstructNodeAttributes (inline) 59ms 0.75% 77.97% 59ms 0.75% [libchaste_mesh.so] 26ms 0.33% 78.30% 58ms 0.74% AbstractTetrahedralMesh::GetElement 1ms 0.013% 78.32% 58ms 0.74% Node::ClearAppliedForce 58ms 0.74% 79.05% 58ms 0.74% std::vector::size (inline) 37ms 0.47% 79.52% 57ms 0.72% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.52% 57ms 0.72% std::_Vector_base::_Vector_base (inline) 2ms 0.025% 79.55% 56ms 0.71% TetrahedralMesh::EdgeIterator::GetNodeA 54ms 0.68% 80.23% 54ms 0.68% __memcpy_avx_unaligned_erms 52ms 0.66% 80.89% 54ms 0.68% boost::detail::shared_count::shared_count (inline) 0 0% 80.89% 54ms 0.68% std::_Vector_base::_M_create_storage (inline) 1ms 0.013% 80.90% 52ms 0.66% std::_Vector_base::_M_deallocate (inline) 19ms 0.24% 81.14% 51ms 0.65% Determinant (inline) 0 0% 81.14% 48ms 0.61% BoundaryNodeWriter::Visit 0 0% 81.14% 47ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.14% 47ms 0.6% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.14% 47ms 0.6% std::__new_allocator::destroy (inline) 0 0% 81.14% 47ms 0.6% std::allocator_traits::destroy (inline) 0 0% 81.14% 46ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.025% 81.17% 46ms 0.58% std::__new_allocator::construct (inline) 0 0% 81.17% 46ms 0.58% std::allocator_traits::construct (inline) 0 0% 81.17% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 45ms 0.57% 81.74% 45ms 0.57% [libstdc++.so.6.0.33] 45ms 0.57% 82.31% 45ms 0.57% std::ostream::sentry::sentry 2ms 0.025% 82.33% 44ms 0.56% NodeAttributes::NodeAttributes 1ms 0.013% 82.35% 44ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 16ms 0.2% 82.55% 42ms 0.53% AbstractTetrahedralMesh::GetNumAllElements 10ms 0.13% 82.68% 42ms 0.53% Inverse 23ms 0.29% 82.97% 41ms 0.52% AbstractCellCycleModel::GetAge 41ms 0.52% 83.49% 41ms 0.52% Node::rGetLocation 25ms 0.32% 83.80% 41ms 0.52% hack_digit 0 0% 83.80% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 40ms 0.51% 84.31% 40ms 0.51% boost::numeric::ublas::c_vector::operator() (inline) 40ms 0.51% 84.82% 40ms 0.51% boost::shared_ptr::operator-> (inline)