File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5198ms, 84.21% of 6173ms total Dropped 548 nodes (cum <= 30.86ms) flat flat% sum% cum cum% 0 0% 0% 6141ms 99.48% __libc_start_call_main 0 0% 0% 6141ms 99.48% __libc_start_main_impl 0 0% 0% 6141ms 99.48% _start 0 0% 0% 6124ms 99.21% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6124ms 99.21% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6124ms 99.21% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6124ms 99.21% main 0 0% 0% 6085ms 98.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6085ms 98.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6085ms 98.57% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 6083ms 98.54% AbstractCellBasedSimulation::Solve 1ms 0.016% 0.016% 2665ms 43.17% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.016% 0.032% 2271ms 36.79% MeshBasedCellPopulation::Update 0 0% 0.032% 2261ms 36.63% AbstractCellPopulation::WriteResultsToFiles 1ms 0.016% 0.049% 1159ms 18.78% MutableMesh::ReMesh 1ms 0.016% 0.065% 1150ms 18.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.065% 1067ms 17.28% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.032% 0.097% 1026ms 16.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.081% 0.18% 978ms 15.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 8ms 0.13% 0.31% 916ms 14.84% MeshBasedCellPopulation::SpringIterator::operator++ 371ms 6.01% 6.32% 790ms 12.80% std::_Rb_tree::_M_lower_bound (inline) 81ms 1.31% 7.63% 744ms 12.05% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.032% 7.66% 736ms 11.92% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 194ms 3.14% 10.81% 717ms 11.62% __dynamic_cast 9ms 0.15% 10.95% 716ms 11.60% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.065% 11.02% 707ms 11.45% CellPopulationElementWriter::Visit 3ms 0.049% 11.06% 674ms 10.92% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.097% 11.16% 624ms 10.11% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.44% 11.60% 603ms 9.77% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.26% 11.86% 590ms 9.56% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.13% 11.99% 582ms 9.43% TetrahedralMesh::ImportFromMesher 2ms 0.032% 12.02% 579ms 9.38% AbstractCellProperty::IsSubType (inline) 44ms 0.71% 12.73% 532ms 8.62% std::map::operator[] (partial-inline) 25ms 0.4% 13.14% 455ms 7.37% operator new 3ms 0.049% 13.19% 453ms 7.34% Cell::GetCellProliferativeType 1ms 0.016% 13.20% 446ms 7.23% std::ostream::operator<< (inline) 0 0% 13.20% 445ms 7.21% std::_Rb_tree::lower_bound (inline) 0 0% 13.20% 445ms 7.21% std::map::lower_bound (inline) 81ms 1.31% 14.51% 444ms 7.19% std::ostream::_M_insert 433ms 7.01% 21.53% 433ms 7.01% __strcmp_evex 0 0% 21.53% 428ms 6.93% triangulate 155ms 2.51% 24.04% 420ms 6.80% __GI___libc_malloc 4ms 0.065% 24.10% 396ms 6.42% std::set::insert (inline) 22ms 0.36% 24.46% 393ms 6.37% std::__new_allocator::allocate (inline) 0 0% 24.46% 392ms 6.35% delaunay 3ms 0.049% 24.51% 392ms 6.35% std::_Rb_tree::_M_insert_unique 1ms 0.016% 24.53% 391ms 6.33% divconqdelaunay 0 0% 24.53% 390ms 6.32% std::allocator_traits::allocate (inline) 0 0% 24.53% 385ms 6.24% LegacyCellProliferativeTypesWriter::VisitCell 15ms 0.24% 24.77% 382ms 6.19% std::_Rb_tree::find (inline) 7ms 0.11% 24.88% 374ms 6.06% AbstractCellBasedSimulation::DoCellBirth 165ms 2.67% 27.56% 366ms 5.93% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.5% 28.06% 353ms 5.72% std::_Rb_tree::~_Rb_tree (inline) 0 0% 28.06% 350ms 5.67% std::set::count (inline) 0 0% 28.06% 332ms 5.38% std::set::~set (inline) 57ms 0.92% 28.98% 320ms 5.18% std::_Rb_tree::_M_erase 0 0% 28.98% 319ms 5.17% std::_Rb_tree::_M_create_node (inline) 0 0% 28.98% 301ms 4.88% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.98% 294ms 4.76% std::_Rb_tree::_M_get_node (inline) 0 0% 28.98% 277ms 4.49% NodeLocationWriter::Visit 13ms 0.21% 29.19% 270ms 4.37% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.016% 29.21% 269ms 4.36% Cell::GetMutationState 7ms 0.11% 29.32% 267ms 4.33% std::less::operator() (inline) 262ms 4.24% 33.57% 262ms 4.24% std::_Rb_tree::_S_right (inline) 260ms 4.21% 37.78% 260ms 4.21% std::operator< (inline) 73ms 1.18% 38.96% 258ms 4.18% __GI___libc_free 3ms 0.049% 39.01% 256ms 4.15% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 39.01% 256ms 4.15% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 39.01% 255ms 4.13% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 39.01% 254ms 4.11% OutputFileHandler::OpenOutputFile 0 0% 39.01% 243ms 3.94% std::_Rb_tree::_M_drop_node (inline) 3ms 0.049% 39.06% 242ms 3.92% Cell::ReadyToDivide 16ms 0.26% 39.32% 240ms 3.89% std::num_put::_M_insert_float 3ms 0.049% 39.36% 240ms 3.89% std::set::set (inline) 1ms 0.016% 39.38% 238ms 3.86% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 39.38% 238ms 3.86% MeshBasedCellPopulation::GetDampingConstant 9ms 0.15% 39.53% 238ms 3.86% std::__new_allocator::deallocate (inline) 0 0% 39.53% 236ms 3.82% std::allocator_traits::deallocate (inline) 18ms 0.29% 39.82% 227ms 3.68% std::_Rb_tree::_M_copy (inline) 18ms 0.29% 40.11% 226ms 3.66% std::_Rb_tree::_M_insert_ (inline) 6ms 0.097% 40.21% 223ms 3.61% divconqrecurse 137ms 2.22% 42.43% 214ms 3.47% _int_malloc 50ms 0.81% 43.24% 211ms 3.42% mergehulls 3ms 0.049% 43.29% 209ms 3.39% Element::Element 0 0% 43.29% 208ms 3.37% CellProliferativeTypesWriter::VisitCell 46ms 0.75% 44.03% 205ms 3.32% std::_Rb_tree::_M_clone_node (inline) 5ms 0.081% 44.11% 202ms 3.27% std::__cxx11::collate::do_transform 0 0% 44.11% 201ms 3.26% std::_Rb_tree::_M_put_node (inline) 0 0% 44.11% 196ms 3.18% AbstractCellProperty::IsType (inline) 2ms 0.032% 44.14% 193ms 3.13% ___vsnprintf 0 0% 44.14% 191ms 3.09% __vsnprintf_internal (inline) 21ms 0.34% 44.48% 190ms 3.08% __printf_buffer 152ms 2.46% 46.95% 185ms 3.00% _int_free 2ms 0.032% 46.98% 174ms 2.82% CellPropertyCollection::HasProperty 0 0% 46.98% 173ms 2.80% Cell::HasCellProperty (inline) 5ms 0.081% 47.06% 172ms 2.79% AbstractPhaseBasedCellCycleModel::ReadyToDivide 7ms 0.11% 47.17% 172ms 2.79% TetrahedralMesh::Clear 4ms 0.065% 47.24% 166ms 2.69% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.081% 47.32% 164ms 2.66% MeshBasedCellPopulation::SpringsEnd (inline) 58ms 0.94% 48.26% 163ms 2.64% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.016% 48.27% 159ms 2.58% __printf_fp_spec (inline) 5ms 0.081% 48.36% 158ms 2.56% __printf_fp_l_buffer 74ms 1.20% 49.55% 151ms 2.45% __printf_fp_buffer_1 2ms 0.032% 49.59% 149ms 2.41% Element::RegisterWithNodes (inline) 9ms 0.15% 49.73% 146ms 2.37% Node::AddElement 0 0% 49.73% 135ms 2.19% std::basic_ofstream::basic_ofstream (inline) 26ms 0.42% 50.15% 132ms 2.14% AbstractCellProperty::IsSame 0 0% 50.15% 131ms 2.12% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.15% 130ms 2.11% std::basic_filebuf::open 0 0% 50.15% 130ms 2.11% std::basic_ofstream::open (inline) 4ms 0.065% 50.22% 124ms 2.01% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.19% 50.41% 117ms 1.90% MeshBasedCellPopulation::SpringIterator::SpringIterator 8ms 0.13% 50.54% 116ms 1.88% AbstractTetrahedralElement::CalculateJacobian 1ms 0.016% 50.56% 112ms 1.81% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.56% 111ms 1.80% AbstractCellBasedWriter::CloseFile 28ms 0.45% 51.01% 111ms 1.80% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.016% 51.03% 111ms 1.80% std::basic_filebuf::close 0 0% 51.03% 111ms 1.80% std::basic_ofstream::close (inline) 4ms 0.065% 51.09% 107ms 1.73% Node::~Node 2ms 0.032% 51.13% 106ms 1.72% std::__basic_file::open 16ms 0.26% 51.39% 106ms 1.72% std::type_info::operator== (inline) 0 0% 51.39% 105ms 1.70% _IO_new_fopen 0 0% 51.39% 105ms 1.70% __fopen_internal (inline) 0 0% 51.39% 103ms 1.67% _IO_new_file_fopen 1ms 0.016% 51.40% 103ms 1.67% __GI__IO_file_open 0 0% 51.40% 102ms 1.65% OutputFileHandler::CommonConstructor 0 0% 51.40% 102ms 1.65% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.40% 102ms 1.65% OutputFileHandler::OutputFileHandler 7ms 0.11% 51.51% 101ms 1.64% AbstractCellPopulation::Iterator::IsRealCell (inline) 32ms 0.52% 52.03% 100ms 1.62% std::__ostream_insert 99ms 1.60% 53.64% 99ms 1.60% incircle 0 0% 53.64% 98ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.032% 53.67% 98ms 1.59% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.081% 53.75% 98ms 1.59% std::vector::push_back (inline) 1ms 0.016% 53.77% 97ms 1.57% std::_Vector_base::_M_allocate (inline) 1ms 0.016% 53.78% 96ms 1.56% boost::numeric::ublas::vector_assign (inline) 2ms 0.032% 53.82% 95ms 1.54% alternateaxes 0 0% 53.82% 94ms 1.52% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.016% 53.83% 94ms 1.52% std::filesystem::permissions 93ms 1.51% 55.34% 93ms 1.51% __GI_fchmodat 87ms 1.41% 56.75% 93ms 1.51% vertexmedian 64ms 1.04% 57.78% 92ms 1.49% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 89ms 1.44% 59.23% 89ms 1.44% __libc_open64 13ms 0.21% 59.44% 89ms 1.44% std::vector::_M_realloc_insert 9ms 0.15% 59.58% 86ms 1.39% boost::detail::shared_count::~shared_count (inline) 0 0% 59.58% 86ms 1.39% boost::shared_ptr::~shared_ptr (inline) 0 0% 59.58% 85ms 1.38% std::operator<< (inline) 11ms 0.18% 59.76% 84ms 1.36% AbstractTetrahedralElement::RefreshJacobian 1ms 0.016% 59.78% 83ms 1.34% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.081% 59.86% 81ms 1.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 80ms 1.30% 61.15% 80ms 1.30% std::_Rb_tree_increment 80ms 1.30% 62.45% 80ms 1.30% std::_Rb_tree_insert_and_rebalance 39ms 0.63% 63.08% 77ms 1.25% boost::shared_ptr::shared_ptr (inline) 18ms 0.29% 63.37% 77ms 1.25% std::num_put::_M_insert_int 2ms 0.032% 63.41% 76ms 1.23% std::basic_filebuf::_M_convert_to_external 0 0% 63.41% 76ms 1.23% std::basic_filebuf::_M_terminate_output 0 0% 63.41% 76ms 1.23% std::basic_filebuf::overflow 75ms 1.21% 64.62% 75ms 1.21% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 75ms 1.21% 65.84% 75ms 1.21% __GI___libc_write 0 0% 65.84% 74ms 1.20% std::__basic_file::xsputn 23ms 0.37% 66.21% 70ms 1.13% boost::numeric::ublas::indexing_vector_assign 68ms 1.10% 67.31% 69ms 1.12% boost::detail::sp_counted_base::release 3ms 0.049% 67.36% 69ms 1.12% std::_Rb_tree_const_iterator::operator++ (inline) 64ms 1.04% 68.39% 69ms 1.12% vertexsort 34ms 0.55% 68.95% 65ms 1.05% AbstractElement::GetNodeLocation 2ms 0.032% 68.98% 65ms 1.05% AbstractTetrahedralElement::AbstractTetrahedralElement 65ms 1.05% 70.03% 65ms 1.05% [libchaste_cell_based.so] 2ms 0.032% 70.06% 63ms 1.02% AbstractCellPopulation::GetLocationIndexUsingCell 35ms 0.57% 70.63% 63ms 1.02% std::basic_filebuf::xsputn 0 0% 70.63% 62ms 1.00% Cell::GetCellId 62ms 1.00% 71.63% 62ms 1.00% counterclockwise 48ms 0.78% 72.41% 61ms 0.99% AbstractElement::GetNodeGlobalIndex 38ms 0.62% 73.03% 61ms 0.99% malloc_consolidate 8ms 0.13% 73.16% 55ms 0.89% CellPropertyCollection::AddProperty 55ms 0.89% 74.05% 55ms 0.89% __GI___fstatat64 1ms 0.016% 74.06% 54ms 0.87% std::filesystem::status 0 0% 74.06% 53ms 0.86% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 74.06% 53ms 0.86% std::filesystem::create_directory 9ms 0.15% 74.21% 51ms 0.83% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 74.21% 48ms 0.78% std::vector::vector (inline) 0 0% 74.21% 47ms 0.76% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 33ms 0.53% 74.74% 46ms 0.75% hack_digit 1ms 0.016% 74.76% 46ms 0.75% tcache_get (inline) 29ms 0.47% 75.23% 45ms 0.73% boost::numeric::ublas::c_matrix::operator() 45ms 0.73% 75.96% 45ms 0.73% tcache_get_n (inline) 44ms 0.71% 76.67% 44ms 0.71% Node::GetIndex 44ms 0.71% 77.39% 44ms 0.71% std::vector::size (inline) 1ms 0.016% 77.40% 43ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 14ms 0.23% 77.63% 42ms 0.68% Determinant (inline) 6ms 0.097% 77.73% 42ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.73% 42ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.73% 42ms 0.68% std::_Vector_base::_Vector_base (inline) 0 0% 77.73% 42ms 0.68% std::__new_allocator::destroy (inline) 0 0% 77.73% 42ms 0.68% std::allocator_traits::destroy (inline) 0 0% 77.73% 41ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 8ms 0.13% 77.86% 41ms 0.66% Inverse 41ms 0.66% 78.52% 41ms 0.66% [libstdc++.so.6.0.33] 32ms 0.52% 79.04% 41ms 0.66% std::num_put::do_put 0 0% 79.04% 40ms 0.65% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 79.04% 40ms 0.65% BoundaryNodeWriter::Visit 1ms 0.016% 79.05% 40ms 0.65% Node::ConstructNodeAttributes (inline) 40ms 0.65% 79.70% 40ms 0.65% boost::shared_ptr::operator-> (inline) 27ms 0.44% 80.14% 40ms 0.65% std::basic_streambuf::xsputn 17ms 0.28% 80.41% 39ms 0.63% AbstractTetrahedralMesh::GetElement 0 0% 80.41% 39ms 0.63% Node::ClearAppliedForce 0 0% 80.41% 39ms 0.63% std::_Vector_base::_M_create_storage (inline) 0 0% 80.41% 38ms 0.62% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 38ms 0.62% 81.03% 38ms 0.62% __memcpy_avx512_unaligned_erms 36ms 0.58% 81.61% 38ms 0.62% boost::detail::shared_count::shared_count (inline) 38ms 0.62% 82.23% 38ms 0.62% boost::numeric::ublas::same_impl_ex 19ms 0.31% 82.54% 37ms 0.6% AbstractCellCycleModel::GetAge 3ms 0.049% 82.59% 37ms 0.6% std::_Vector_base::_M_deallocate (inline) 0 0% 82.59% 35ms 0.57% CxxTest::RealWorldDescription::setUp 0 0% 82.59% 35ms 0.57% PetscInitialize 0 0% 82.59% 35ms 0.57% PetscSetup::setUpWorld 0 0% 82.59% 35ms 0.57% PetscSetupUtils::CommonSetup 0 0% 82.59% 35ms 0.57% PetscSetupUtils::InitialisePetsc 35ms 0.57% 83.15% 35ms 0.57% [libchaste_mesh.so] 0 0% 83.15% 34ms 0.55% PMPI_Init_thread 0 0% 83.15% 34ms 0.55% _dl_init 0 0% 83.15% 34ms 0.55% call_init (inline) 0 0% 83.15% 34ms 0.55% ompi_mpi_init 0 0% 83.15% 34ms 0.55% std::map::map (inline) 2ms 0.032% 83.18% 32ms 0.52% NodeAttributes::NodeAttributes 0 0% 83.18% 32ms 0.52% _IO_new_fclose 0 0% 83.18% 32ms 0.52% _dl_start_user 0 0% 83.18% 32ms 0.52% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.18% 32ms 0.52% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 83.18% 32ms 0.52% std::__basic_file::close 32ms 0.52% 83.70% 32ms 0.52% std::ostream::sentry::sentry 31ms 0.5% 84.21% 31ms 0.5% Node::IsDeleted