File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6772ms, 84.38% of 8026ms total Dropped 597 nodes (cum <= 40.13ms) flat flat% sum% cum cum% 0 0% 0% 7986ms 99.50% __libc_start_call_main 0 0% 0% 7986ms 99.50% __libc_start_main_impl 0 0% 0% 7986ms 99.50% _start 0 0% 0% 7968ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7968ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7968ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7968ms 99.28% main 0 0% 0% 7924ms 98.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7924ms 98.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7924ms 98.73% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 7921ms 98.69% AbstractCellBasedSimulation::Solve 0 0% 0.012% 3433ms 42.77% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.037% 2962ms 36.91% MeshBasedCellPopulation::Update 0 0% 0.037% 2934ms 36.56% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.05% 1544ms 19.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.075% 1463ms 18.23% MutableMesh::ReMesh 2ms 0.025% 0.1% 1450ms 18.07% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.1% 1397ms 17.41% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.062% 0.16% 1349ms 16.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 22ms 0.27% 0.44% 1268ms 15.80% MeshBasedCellPopulation::SpringIterator::operator++ 102ms 1.27% 1.71% 1022ms 12.73% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.037% 1.74% 1019ms 12.70% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 436ms 5.43% 7.18% 984ms 12.26% std::_Rb_tree::_M_lower_bound (inline) 274ms 3.41% 10.59% 955ms 11.90% __dynamic_cast 12ms 0.15% 10.74% 939ms 11.70% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.037% 10.78% 930ms 11.59% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.14% 10.91% 886ms 11.04% CellPopulationElementWriter::Visit 3ms 0.037% 10.95% 850ms 10.59% MeshBasedCellPopulation::AcceptCellWriter 53ms 0.66% 11.61% 833ms 10.38% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 45ms 0.56% 12.17% 797ms 9.93% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.012% 12.19% 746ms 9.29% AbstractCellProperty::IsSubType (inline) 16ms 0.2% 12.38% 715ms 8.91% TetrahedralMesh::ImportFromMesher 0 0% 12.38% 588ms 7.33% triangulate 57ms 0.71% 13.09% 585ms 7.29% std::map::operator[] (partial-inline) 7ms 0.087% 13.18% 569ms 7.09% Cell::GetCellProliferativeType 0 0% 13.18% 563ms 7.01% std::ostream::operator<< (inline) 30ms 0.37% 13.56% 562ms 7.00% operator new 87ms 1.08% 14.64% 559ms 6.96% std::ostream::_M_insert 28ms 0.35% 14.99% 553ms 6.89% std::_Rb_tree::find (inline) 544ms 6.78% 21.77% 544ms 6.78% __strcmp_avx2 7ms 0.087% 21.85% 540ms 6.73% std::set::insert (inline) 6ms 0.075% 21.93% 535ms 6.67% std::_Rb_tree::_M_insert_unique 3ms 0.037% 21.97% 532ms 6.63% LegacyCellProliferativeTypesWriter::VisitCell 188ms 2.34% 24.31% 522ms 6.50% __GI___libc_malloc 0 0% 24.31% 519ms 6.47% delaunay 3ms 0.037% 24.35% 517ms 6.44% divconqdelaunay 29ms 0.36% 24.71% 514ms 6.40% std::__new_allocator::allocate (inline) 0 0% 24.71% 512ms 6.38% std::allocator_traits::allocate (inline) 0 0% 24.71% 493ms 6.14% std::set::count (inline) 240ms 2.99% 27.70% 488ms 6.08% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.70% 482ms 6.01% std::_Rb_tree::lower_bound (inline) 0 0% 27.70% 482ms 6.01% std::map::lower_bound (inline) 0 0% 27.70% 465ms 5.79% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.70% 437ms 5.44% std::_Rb_tree::_M_create_node (inline) 0 0% 27.70% 418ms 5.21% std::_Rb_tree::_Alloc_node::operator() (inline) 35ms 0.44% 28.13% 415ms 5.17% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.13% 401ms 5.00% std::_Rb_tree::_M_get_node (inline) 0 0% 28.13% 385ms 4.80% std::set::~set (inline) 2ms 0.025% 28.16% 381ms 4.75% Cell::GetMutationState 89ms 1.11% 29.27% 380ms 4.73% std::_Rb_tree::_M_erase 11ms 0.14% 29.40% 379ms 4.72% std::less::operator() (inline) 368ms 4.59% 33.99% 369ms 4.60% std::operator< (inline) 17ms 0.21% 34.20% 357ms 4.45% std::_Rb_tree::_Rb_tree (partial-inline) 24ms 0.3% 34.50% 344ms 4.29% std::_Rb_tree::_M_insert_ (inline) 0 0% 34.50% 334ms 4.16% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.50% 334ms 4.16% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.012% 34.51% 332ms 4.14% NodeLocationWriter::Visit 0 0% 34.51% 330ms 4.11% OutputFileHandler::OpenOutputFile 2ms 0.025% 34.54% 330ms 4.11% std::set::set (inline) 2ms 0.025% 34.56% 326ms 4.06% MeshBasedCellPopulation::GetDampingConstant 5ms 0.062% 34.62% 324ms 4.04% AbstractCentreBasedCellPopulation::GetDampingConstant 313ms 3.90% 38.52% 313ms 3.90% std::_Rb_tree::_S_right (inline) 11ms 0.14% 38.66% 309ms 3.85% Cell::ReadyToDivide 104ms 1.30% 39.96% 308ms 3.84% __GI___libc_free 22ms 0.27% 40.23% 307ms 3.83% std::num_put::_M_insert_float 35ms 0.44% 40.67% 305ms 3.80% std::_Rb_tree::_M_copy (inline) 1ms 0.012% 40.68% 289ms 3.60% Element::Element 9ms 0.11% 40.79% 285ms 3.55% divconqrecurse 10ms 0.12% 40.92% 283ms 3.53% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.05% 40.97% 278ms 3.46% CellProliferativeTypesWriter::VisitCell 0 0% 40.97% 276ms 3.44% std::_Rb_tree::_M_drop_node (inline) 13ms 0.16% 41.13% 275ms 3.43% std::__new_allocator::deallocate (inline) 0 0% 41.13% 273ms 3.40% std::allocator_traits::deallocate (inline) 86ms 1.07% 42.20% 268ms 3.34% mergehulls 0 0% 42.20% 263ms 3.28% Cell::HasCellProperty (inline) 2ms 0.025% 42.23% 262ms 3.26% CellPropertyCollection::HasProperty 70ms 0.87% 43.10% 261ms 3.25% std::_Rb_tree::_M_clone_node (inline) 1ms 0.012% 43.11% 258ms 3.21% AbstractCellProperty::IsType (inline) 157ms 1.96% 45.07% 246ms 3.07% _int_malloc 6ms 0.075% 45.14% 245ms 3.05% std::__cxx11::collate::do_transform 2ms 0.025% 45.17% 231ms 2.88% ___vsnprintf 36ms 0.45% 45.61% 229ms 2.85% __printf_buffer 0 0% 45.61% 229ms 2.85% __vsnprintf_internal (inline) 0 0% 45.61% 227ms 2.83% std::_Rb_tree::_M_put_node (inline) 12ms 0.15% 45.76% 214ms 2.67% TetrahedralMesh::Clear 4ms 0.05% 45.81% 213ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.075% 45.89% 209ms 2.60% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.075% 45.96% 205ms 2.55% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 176ms 2.19% 48.16% 204ms 2.54% _int_free 38ms 0.47% 48.63% 198ms 2.47% AbstractCellProperty::IsSame 2ms 0.025% 48.65% 195ms 2.43% Element::RegisterWithNodes (inline) 6ms 0.075% 48.73% 189ms 2.35% Node::AddElement 66ms 0.82% 49.55% 185ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 38ms 0.47% 50.02% 183ms 2.28% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.05% 50.07% 183ms 2.28% __printf_fp_l_buffer 0 0% 50.07% 183ms 2.28% __printf_fp_spec (inline) 0 0% 50.07% 179ms 2.23% std::basic_ofstream::basic_ofstream (inline) 90ms 1.12% 51.20% 174ms 2.17% __printf_fp_buffer_1 2ms 0.025% 51.22% 173ms 2.16% std::basic_filebuf::open 0 0% 51.22% 173ms 2.16% std::basic_ofstream::open (inline) 39ms 0.49% 51.71% 160ms 1.99% std::type_info::operator== (inline) 15ms 0.19% 51.89% 152ms 1.89% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.89% 147ms 1.83% TetrahedralMesh::RefreshJacobianCachedData 23ms 0.29% 52.18% 146ms 1.82% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.087% 52.27% 137ms 1.71% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.087% 52.35% 137ms 1.71% Node::~Node 0 0% 52.35% 137ms 1.71% _IO_new_fopen 1ms 0.012% 52.37% 137ms 1.71% __fopen_internal (inline) 0 0% 52.37% 137ms 1.71% std::__basic_file::open 0 0% 52.37% 136ms 1.69% AbstractCellBasedWriter::CloseFile 0 0% 52.37% 136ms 1.69% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.37% 136ms 1.69% alternateaxes 0 0% 52.37% 136ms 1.69% std::basic_filebuf::close 0 0% 52.37% 136ms 1.69% std::basic_ofstream::close (inline) 122ms 1.52% 53.89% 135ms 1.68% vertexmedian 1ms 0.012% 53.90% 133ms 1.66% OutputFileHandler::OutputFileHandler 44ms 0.55% 54.45% 133ms 1.66% std::__ostream_insert 0 0% 54.45% 132ms 1.64% OutputFileHandler::CommonConstructor 1ms 0.012% 54.46% 132ms 1.64% _IO_new_file_fopen 0 0% 54.46% 131ms 1.63% __GI__IO_file_open 2ms 0.025% 54.49% 129ms 1.61% boost::numeric::ublas::vector_assign (inline) 80ms 1% 55.48% 128ms 1.59% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 55.48% 127ms 1.58% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 55.48% 122ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 13ms 0.16% 55.64% 120ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 116ms 1.45% 57.09% 118ms 1.47% __libc_open64 1ms 0.012% 57.10% 118ms 1.47% boost::numeric::ublas::c_vector::c_vector (inline) 59ms 0.74% 57.84% 116ms 1.45% boost::shared_ptr::shared_ptr (inline) 15ms 0.19% 58.02% 115ms 1.43% AbstractTetrahedralElement::RefreshJacobian 0 0% 58.02% 114ms 1.42% FilesystemPermissions::SetFilePermissions (inline) 0 0% 58.02% 114ms 1.42% std::filesystem::permissions 113ms 1.41% 59.43% 113ms 1.41% __GI_fchmodat 12ms 0.15% 59.58% 111ms 1.38% boost::detail::shared_count::~shared_count (inline) 0 0% 59.58% 111ms 1.38% boost::shared_ptr::~shared_ptr (inline) 0 0% 59.58% 111ms 1.38% std::_Vector_base::_M_allocate (inline) 5ms 0.062% 59.64% 110ms 1.37% std::basic_filebuf::overflow 3ms 0.037% 59.68% 110ms 1.37% std::operator<< (inline) 109ms 1.36% 61.04% 109ms 1.36% incircle 4ms 0.05% 61.09% 107ms 1.33% std::vector::push_back (inline) 3ms 0.037% 61.13% 106ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 61.13% 106ms 1.32% std::basic_filebuf::_M_terminate_output 35ms 0.44% 61.56% 106ms 1.32% std::num_put::_M_insert_int 6ms 0.075% 61.64% 105ms 1.31% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.012% 61.65% 105ms 1.31% std::basic_filebuf::_M_convert_to_external 104ms 1.30% 62.95% 104ms 1.30% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 104ms 1.30% 64.24% 104ms 1.30% std::_Rb_tree_increment 0 0% 64.24% 104ms 1.30% std::__basic_file::xsputn 3ms 0.037% 64.28% 103ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 101ms 1.26% 65.54% 103ms 1.28% __GI___libc_write 100ms 1.25% 66.78% 100ms 1.25% [libchaste_cell_based.so] 0 0% 66.78% 98ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 7ms 0.087% 66.87% 96ms 1.20% std::vector::_M_realloc_insert 95ms 1.18% 68.05% 95ms 1.18% std::_Rb_tree_insert_and_rebalance 88ms 1.10% 69.15% 91ms 1.13% boost::detail::sp_counted_base::release 2ms 0.025% 69.18% 90ms 1.12% AbstractCellPopulation::GetLocationIndexUsingCell 32ms 0.4% 69.57% 86ms 1.07% boost::numeric::ublas::indexing_vector_assign 80ms 1% 70.57% 85ms 1.06% vertexsort 32ms 0.4% 70.97% 84ms 1.05% AbstractElement::GetNodeLocation 2ms 0.025% 70.99% 84ms 1.05% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 70.99% 83ms 1.03% tcache_get (inline) 83ms 1.03% 72.03% 83ms 1.03% tcache_get_n (inline) 43ms 0.54% 72.56% 73ms 0.91% malloc_consolidate 73ms 0.91% 73.47% 73ms 0.91% std::vector::size (inline) 44ms 0.55% 74.02% 71ms 0.88% std::basic_filebuf::xsputn 1ms 0.012% 74.03% 69ms 0.86% Cell::GetCellId 0 0% 74.03% 69ms 0.86% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 74.03% 69ms 0.86% std::filesystem::create_directory 68ms 0.85% 74.88% 68ms 0.85% counterclockwise 7ms 0.087% 74.97% 67ms 0.83% CellPropertyCollection::AddProperty 3ms 0.037% 75.01% 63ms 0.78% std::filesystem::status 51ms 0.64% 75.64% 63ms 0.78% std::num_put::do_put 39ms 0.49% 76.13% 62ms 0.77% std::basic_streambuf::xsputn 61ms 0.76% 76.89% 61ms 0.76% __GI___fstatat64 46ms 0.57% 77.46% 60ms 0.75% AbstractElement::GetNodeGlobalIndex 60ms 0.75% 78.21% 60ms 0.75% [libchaste_mesh.so] 1ms 0.012% 78.22% 58ms 0.72% Node::ConstructNodeAttributes (inline) 0 0% 78.22% 57ms 0.71% Node::ClearAppliedForce 57ms 0.71% 78.93% 57ms 0.71% Node::GetIndex 4ms 0.05% 78.98% 57ms 0.71% TetrahedralMesh::EdgeIterator::GetNodeA 56ms 0.7% 79.68% 57ms 0.71% boost::detail::shared_count::shared_count (inline) 0 0% 79.68% 57ms 0.71% std::vector::vector (inline) 56ms 0.7% 80.38% 56ms 0.7% __memcpy_avx_unaligned_erms 27ms 0.34% 80.71% 54ms 0.67% hack_digit 0 0% 80.71% 53ms 0.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 80.71% 53ms 0.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 53ms 0.66% 81.37% 53ms 0.66% boost::shared_ptr::operator-> (inline) 1ms 0.012% 81.39% 52ms 0.65% BoundaryNodeWriter::Visit 52ms 0.65% 82.03% 52ms 0.65% [libstdc++.so.6.0.33] 0 0% 82.03% 52ms 0.65% std::_Vector_base::_Vector_base (inline) 0 0% 82.03% 51ms 0.64% std::_Vector_base::_M_create_storage (inline) 28ms 0.35% 82.38% 50ms 0.62% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 82.38% 50ms 0.62% std::__new_allocator::destroy (inline) 0 0% 82.38% 50ms 0.62% std::allocator_traits::destroy (inline) 0 0% 82.38% 50ms 0.62% std::map::find (inline) 0 0% 82.38% 49ms 0.61% std::_Rb_tree::_M_destroy_node (inline) 13ms 0.16% 82.54% 48ms 0.6% AbstractTetrahedralMesh::GetNumAllElements 48ms 0.6% 83.14% 48ms 0.6% Node::rGetLocation 4ms 0.05% 83.19% 48ms 0.6% std::_Vector_base::_M_deallocate (inline) 24ms 0.3% 83.49% 47ms 0.59% AbstractTetrahedralMesh::GetElement 2ms 0.025% 83.52% 47ms 0.59% NodeAttributes::NodeAttributes 0 0% 83.52% 46ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.52% 45ms 0.56% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 83.52% 44ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 36ms 0.45% 83.96% 44ms 0.55% writeedges 18ms 0.22% 84.19% 43ms 0.54% AbstractCellCycleModel::GetAge 0 0% 84.19% 42ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 84.19% 42ms 0.52% _dl_init 0 0% 84.19% 42ms 0.52% call_init (inline) 2ms 0.025% 84.21% 42ms 0.52% std::__new_allocator::construct (inline) 0 0% 84.21% 42ms 0.52% std::allocator_traits::construct (inline) 0 0% 84.21% 41ms 0.51% CxxTest::RealWorldDescription::setUp 13ms 0.16% 84.38% 41ms 0.51% Determinant (inline) 0 0% 84.38% 41ms 0.51% PetscInitialize 0 0% 84.38% 41ms 0.51% PetscSetup::setUpWorld 0 0% 84.38% 41ms 0.51% PetscSetupUtils::CommonSetup 0 0% 84.38% 41ms 0.51% PetscSetupUtils::InitialisePetsc