File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6756ms, 84.96% of 7952ms total Dropped 568 nodes (cum <= 39.76ms) flat flat% sum% cum cum% 0 0% 0% 7914ms 99.52% __libc_start_call_main 0 0% 0% 7914ms 99.52% __libc_start_main_impl 0 0% 0% 7914ms 99.52% _start 0 0% 0% 7895ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7895ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7895ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7895ms 99.28% main 0 0% 0% 7848ms 98.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7848ms 98.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7848ms 98.69% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7846ms 98.67% AbstractCellBasedSimulation::Solve 0 0% 0% 3449ms 43.37% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 3003ms 37.76% MeshBasedCellPopulation::Update 0 0% 0% 2914ms 36.64% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.025% 1520ms 19.11% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.025% 1475ms 18.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.025% 1422ms 17.88% MutableMesh::ReMesh 0 0% 0.025% 1321ms 16.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 26ms 0.33% 0.35% 1309ms 16.46% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.11% 0.47% 1273ms 16.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 111ms 1.40% 1.86% 1056ms 13.28% TetrahedralMesh::EdgeIterator::operator++ 455ms 5.72% 7.58% 995ms 12.51% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 7.61% 938ms 11.80% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 261ms 3.28% 10.89% 926ms 11.64% __dynamic_cast 11ms 0.14% 11.03% 899ms 11.31% CellPopulationElementWriter::Visit 3ms 0.038% 11.07% 885ms 11.13% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.14% 11.20% 884ms 11.12% CellPropertyCollection::GetPropertiesType (inline) 54ms 0.68% 11.88% 792ms 9.96% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.1% 11.98% 784ms 9.86% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.38% 12.36% 735ms 9.24% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 12.36% 733ms 9.22% AbstractCellProperty::IsSubType (inline) 8ms 0.1% 12.46% 696ms 8.75% TetrahedralMesh::ImportFromMesher 0 0% 12.46% 631ms 7.94% std::ostream::operator<< (inline) 95ms 1.19% 13.66% 630ms 7.92% std::ostream::_M_insert 47ms 0.59% 14.25% 592ms 7.44% std::map::operator[] (partial-inline) 3ms 0.038% 14.29% 569ms 7.16% triangulate 27ms 0.34% 14.63% 550ms 6.92% operator new 26ms 0.33% 14.95% 546ms 6.87% std::_Rb_tree::find (inline) 13ms 0.16% 15.12% 533ms 6.70% std::set::insert (inline) 525ms 6.60% 21.72% 525ms 6.60% __strcmp_avx2 9ms 0.11% 21.83% 520ms 6.54% std::_Rb_tree::_M_insert_unique 25ms 0.31% 22.15% 517ms 6.50% std::__new_allocator::allocate (inline) 0 0% 22.15% 513ms 6.45% std::allocator_traits::allocate (inline) 7ms 0.088% 22.23% 512ms 6.44% LegacyCellProliferativeTypesWriter::VisitCell 158ms 1.99% 24.22% 512ms 6.44% __GI___libc_malloc 1ms 0.013% 24.23% 512ms 6.44% delaunay 6ms 0.075% 24.31% 511ms 6.43% divconqdelaunay 0 0% 24.31% 510ms 6.41% std::_Rb_tree::lower_bound (inline) 0 0% 24.31% 510ms 6.41% std::map::lower_bound (inline) 0 0% 24.31% 503ms 6.33% std::set::count (inline) 6ms 0.075% 24.38% 490ms 6.16% Cell::GetCellProliferativeType 226ms 2.84% 27.23% 464ms 5.84% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.23% 435ms 5.47% std::_Rb_tree::_M_create_node (inline) 5ms 0.063% 27.29% 431ms 5.42% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.29% 416ms 5.23% std::_Rb_tree::_Alloc_node::operator() (inline) 43ms 0.54% 27.83% 411ms 5.17% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.83% 392ms 4.93% std::_Rb_tree::_M_get_node (inline) 15ms 0.19% 28.02% 387ms 4.87% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.02% 382ms 4.80% NodeLocationWriter::Visit 0 0% 28.02% 375ms 4.72% Cell::GetMutationState 0 0% 28.02% 369ms 4.64% std::set::~set (inline) 82ms 1.03% 29.05% 361ms 4.54% std::_Rb_tree::_M_erase 6ms 0.075% 29.12% 360ms 4.53% std::less::operator() (inline) 354ms 4.45% 33.58% 354ms 4.45% std::operator< (inline) 28ms 0.35% 33.93% 352ms 4.43% std::num_put::_M_insert_float 3ms 0.038% 33.97% 352ms 4.43% std::set::set (inline) 333ms 4.19% 38.15% 333ms 4.19% std::_Rb_tree::_S_right (inline) 11ms 0.14% 38.29% 325ms 4.09% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 38.30% 320ms 4.02% MeshBasedCellPopulation::GetDampingConstant 29ms 0.36% 38.67% 320ms 4.02% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 38.68% 317ms 3.99% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 38.68% 312ms 3.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.68% 311ms 3.91% AbstractCellBasedWriter::OpenOutputFileForAppend 25ms 0.31% 39.00% 311ms 3.91% std::_Rb_tree::_M_insert_ (inline) 0 0% 39.00% 308ms 3.87% OutputFileHandler::OpenOutputFile 4ms 0.05% 39.05% 299ms 3.76% Element::Element 6ms 0.075% 39.12% 298ms 3.75% divconqrecurse 80ms 1.01% 40.13% 292ms 3.67% __GI___libc_free 83ms 1.04% 41.17% 285ms 3.58% std::_Rb_tree::_M_clone_node (inline) 8ms 0.1% 41.27% 283ms 3.56% std::__cxx11::collate::do_transform 79ms 0.99% 42.27% 277ms 3.48% mergehulls 7ms 0.088% 42.35% 275ms 3.46% Cell::ReadyToDivide 184ms 2.31% 44.67% 273ms 3.43% _int_malloc 0 0% 44.67% 265ms 3.33% ___vsnprintf 0 0% 44.67% 265ms 3.33% __vsnprintf_internal (inline) 8ms 0.1% 44.77% 264ms 3.32% std::__new_allocator::deallocate (inline) 0 0% 44.77% 262ms 3.29% std::allocator_traits::deallocate (inline) 28ms 0.35% 45.12% 260ms 3.27% __printf_buffer 0 0% 45.12% 256ms 3.22% std::_Rb_tree::_M_drop_node (inline) 4ms 0.05% 45.17% 229ms 2.88% CellPropertyCollection::HasProperty 0 0% 45.17% 226ms 2.84% Cell::HasCellProperty (inline) 2ms 0.025% 45.20% 224ms 2.82% CellProliferativeTypesWriter::VisitCell 2ms 0.025% 45.22% 222ms 2.79% AbstractCellProperty::IsType (inline) 8ms 0.1% 45.32% 219ms 2.75% __printf_fp_l_buffer 0 0% 45.32% 219ms 2.75% __printf_fp_spec (inline) 0 0% 45.32% 213ms 2.68% std::_Rb_tree::_M_put_node (inline) 180ms 2.26% 47.59% 211ms 2.65% _int_free 11ms 0.14% 47.72% 210ms 2.64% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.025% 47.75% 202ms 2.54% Element::RegisterWithNodes (inline) 78ms 0.98% 48.73% 200ms 2.52% std::_Rb_tree::_M_get_insert_unique_pos (inline) 9ms 0.11% 48.84% 196ms 2.46% Node::AddElement 100ms 1.26% 50.10% 194ms 2.44% __printf_fp_buffer_1 17ms 0.21% 50.31% 190ms 2.39% TetrahedralMesh::Clear 6ms 0.075% 50.39% 183ms 2.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 39ms 0.49% 50.88% 178ms 2.24% AbstractCellProperty::IsSame 6ms 0.075% 50.96% 174ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 33ms 0.41% 51.37% 164ms 2.06% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.37% 156ms 1.96% OutputFileHandler::OutputFileHandler 0 0% 51.37% 156ms 1.96% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.37% 155ms 1.95% OutputFileHandler::CommonConstructor 0 0% 51.37% 152ms 1.91% OutputFileHandler::MakeFoldersAndReturnFullPath 14ms 0.18% 51.55% 150ms 1.89% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 51.56% 150ms 1.89% std::basic_filebuf::open 0 0% 51.56% 150ms 1.89% std::basic_ofstream::open (inline) 61ms 0.77% 52.33% 146ms 1.84% std::__ostream_insert 94ms 1.18% 53.51% 143ms 1.80% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 21ms 0.26% 53.77% 142ms 1.79% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 53.77% 140ms 1.76% TetrahedralMesh::RefreshJacobianCachedData 32ms 0.4% 54.18% 139ms 1.75% std::type_info::operator== (inline) 0 0% 54.18% 135ms 1.70% AbstractCellBasedWriter::CloseFile 0 0% 54.18% 135ms 1.70% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 54.18% 135ms 1.70% std::basic_filebuf::close 0 0% 54.18% 135ms 1.70% std::basic_ofstream::close (inline) 4ms 0.05% 54.23% 132ms 1.66% alternateaxes 5ms 0.063% 54.29% 129ms 1.62% AbstractTetrahedralElement::CalculateInverseJacobian 35ms 0.44% 54.73% 127ms 1.60% std::num_put::_M_insert_int 118ms 1.48% 56.21% 127ms 1.60% vertexmedian 0 0% 56.21% 126ms 1.58% FilesystemPermissions::SetFilePermissions (inline) 126ms 1.58% 57.80% 126ms 1.58% incircle 1ms 0.013% 57.81% 126ms 1.58% std::filesystem::permissions 125ms 1.57% 59.38% 125ms 1.57% __GI_fchmodat 2ms 0.025% 59.41% 121ms 1.52% boost::numeric::ublas::vector_assign (inline) 0 0% 59.41% 121ms 1.52% std::_Vector_base::_M_allocate (inline) 2ms 0.025% 59.43% 120ms 1.51% std::operator<< (inline) 0 0% 59.43% 118ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.025% 59.46% 117ms 1.47% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 59.49% 116ms 1.46% Node::~Node 15ms 0.19% 59.68% 115ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 59.70% 114ms 1.43% std::__basic_file::open 0 0% 59.70% 113ms 1.42% _IO_new_file_fopen 0 0% 59.70% 113ms 1.42% _IO_new_fopen 0 0% 59.70% 113ms 1.42% __fopen_internal (inline) 0 0% 59.70% 112ms 1.41% __GI__IO_file_open 6ms 0.075% 59.77% 109ms 1.37% std::vector::push_back (inline) 53ms 0.67% 60.44% 108ms 1.36% boost::shared_ptr::shared_ptr (inline) 12ms 0.15% 60.59% 103ms 1.30% boost::detail::shared_count::~shared_count (inline) 0 0% 60.59% 103ms 1.30% boost::shared_ptr::~shared_ptr (inline) 5ms 0.063% 60.65% 100ms 1.26% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.063% 60.71% 99ms 1.24% std::vector::_M_realloc_insert 98ms 1.23% 61.95% 98ms 1.23% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 6ms 0.075% 62.02% 97ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 13ms 0.16% 62.19% 97ms 1.22% AbstractTetrahedralElement::RefreshJacobian 96ms 1.21% 63.39% 96ms 1.21% __libc_open64 21ms 0.26% 63.66% 96ms 1.21% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 63.68% 95ms 1.19% std::basic_filebuf::overflow 1ms 0.013% 63.69% 93ms 1.17% std::basic_filebuf::_M_convert_to_external 0 0% 63.69% 93ms 1.17% std::basic_filebuf::_M_terminate_output 90ms 1.13% 64.83% 92ms 1.16% __GI___libc_write 0 0% 64.83% 92ms 1.16% std::__basic_file::xsputn 91ms 1.14% 65.97% 91ms 1.14% [libchaste_cell_based.so] 2ms 0.025% 66.00% 85ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 66.00% 84ms 1.06% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 66.01% 84ms 1.06% std::filesystem::create_directory 79ms 0.99% 67.00% 81ms 1.02% boost::detail::sp_counted_base::release 47ms 0.59% 67.59% 81ms 1.02% std::basic_filebuf::xsputn 80ms 1.01% 68.60% 80ms 1.01% std::_Rb_tree_increment 2ms 0.025% 68.62% 79ms 0.99% std::filesystem::status 77ms 0.97% 69.59% 77ms 0.97% __GI___fstatat64 1ms 0.013% 69.61% 76ms 0.96% Cell::GetCellId 4ms 0.05% 69.66% 76ms 0.96% std::_Rb_tree_const_iterator::operator++ (inline) 64ms 0.8% 70.46% 75ms 0.94% AbstractElement::GetNodeGlobalIndex 33ms 0.41% 70.88% 75ms 0.94% AbstractElement::GetNodeLocation 59ms 0.74% 71.62% 75ms 0.94% malloc_consolidate 0 0% 71.62% 74ms 0.93% tcache_get (inline) 74ms 0.93% 72.55% 74ms 0.93% tcache_get_n (inline) 1ms 0.013% 72.56% 73ms 0.92% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.038% 72.60% 73ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeA 73ms 0.92% 73.52% 73ms 0.92% __memcpy_avx_unaligned_erms 73ms 0.92% 74.43% 73ms 0.92% std::_Rb_tree_insert_and_rebalance 3ms 0.038% 74.47% 72ms 0.91% TetrahedralMesh::EdgeIterator::GetNodeB 51ms 0.64% 75.11% 72ms 0.91% std::basic_streambuf::xsputn 71ms 0.89% 76.01% 71ms 0.89% counterclockwise 70ms 0.88% 76.89% 70ms 0.88% Node::GetIndex 67ms 0.84% 77.73% 70ms 0.88% vertexsort 45ms 0.57% 78.29% 66ms 0.83% std::num_put::do_put 3ms 0.038% 78.33% 60ms 0.75% CellPropertyCollection::AddProperty 22ms 0.28% 78.61% 57ms 0.72% AbstractTetrahedralMesh::GetElement 57ms 0.72% 79.33% 57ms 0.72% std::vector::size (inline) 0 0% 79.33% 56ms 0.7% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 54ms 0.68% 80.01% 55ms 0.69% boost::detail::shared_count::shared_count (inline) 33ms 0.41% 80.42% 54ms 0.68% hack_digit 0 0% 80.42% 53ms 0.67% std::vector::vector (inline) 19ms 0.24% 80.66% 52ms 0.65% Determinant (inline) 0 0% 80.66% 51ms 0.64% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.66% 50ms 0.63% BoundaryNodeWriter::Visit 3ms 0.038% 80.70% 50ms 0.63% std::_Vector_base::_M_deallocate (inline) 0 0% 80.70% 49ms 0.62% std::_Vector_base::_Vector_base (inline) 0 0% 80.70% 48ms 0.6% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 4ms 0.05% 80.75% 48ms 0.6% std::_Rb_tree_header::_Rb_tree_header (inline) 47ms 0.59% 81.34% 47ms 0.59% boost::numeric::ublas::same_impl_ex 47ms 0.59% 81.93% 47ms 0.59% boost::shared_ptr::operator-> (inline) 0 0% 81.93% 47ms 0.59% std::_Vector_base::_M_create_storage (inline) 0 0% 81.93% 46ms 0.58% AbstractCentreBasedCellPopulation::CreateCellPair 46ms 0.58% 82.51% 46ms 0.58% [libstdc++.so.6.0.33] 35ms 0.44% 82.95% 46ms 0.58% boost::numeric::ublas::c_matrix::operator() 0 0% 82.95% 46ms 0.58% std::__new_allocator::construct (inline) 0 0% 82.95% 46ms 0.58% std::allocator_traits::construct (inline) 26ms 0.33% 83.27% 45ms 0.57% AbstractCellCycleModel::GetAge 44ms 0.55% 83.83% 44ms 0.55% __GI___mkdir 44ms 0.55% 84.38% 44ms 0.55% std::_Rb_tree_header::_M_reset (inline) 0 0% 84.38% 43ms 0.54% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 84.38% 43ms 0.54% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 84.38% 43ms 0.54% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.38% 43ms 0.54% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.38% 43ms 0.54% std::__new_allocator::destroy (inline) 0 0% 84.38% 43ms 0.54% std::allocator_traits::destroy (inline) 42ms 0.53% 84.91% 42ms 0.53% [libchaste_mesh.so] 0 0% 84.91% 42ms 0.53% _dl_init 0 0% 84.91% 42ms 0.53% call_init (inline) 0 0% 84.91% 42ms 0.53% std::map::~map (inline) 0 0% 84.91% 41ms 0.52% CxxTest::RealWorldDescription::setUp 0 0% 84.91% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 84.91% 41ms 0.52% PetscInitialize 0 0% 84.91% 41ms 0.52% PetscSetup::setUpWorld 0 0% 84.91% 41ms 0.52% PetscSetupUtils::CommonSetup 0 0% 84.91% 41ms 0.52% PetscSetupUtils::InitialisePetsc 0 0% 84.91% 40ms 0.5% PMPI_Init_thread 0 0% 84.91% 40ms 0.5% ompi_mpi_init 4ms 0.05% 84.96% 40ms 0.5% std::__copy_move::__copy_m (inline) 0 0% 84.96% 40ms 0.5% std::__copy_move_a (inline) 0 0% 84.96% 40ms 0.5% std::__copy_move_a1 (inline) 0 0% 84.96% 40ms 0.5% std::__copy_move_a2 (inline) 0 0% 84.96% 40ms 0.5% std::copy (inline)