File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 3787ms, 86.19% of 4394ms total Dropped 451 nodes (cum <= 21.97ms) flat flat% sum% cum cum% 0 0% 0% 4371ms 99.48% __libc_start_call_main 0 0% 0% 4371ms 99.48% __libc_start_main_impl 0 0% 0% 4371ms 99.48% _start 0 0% 0% 4359ms 99.20% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4359ms 99.20% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4359ms 99.20% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4359ms 99.20% main 0 0% 0% 4326ms 98.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4326ms 98.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4326ms 98.45% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 4325ms 98.43% AbstractCellBasedSimulation::Solve 0 0% 0% 2002ms 45.56% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.023% 0.023% 1755ms 39.94% MeshBasedCellPopulation::Update 3ms 0.068% 0.091% 1507ms 34.30% AbstractCellPopulation::WriteResultsToFiles 5ms 0.11% 0.2% 970ms 22.08% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.2% 0.41% 866ms 19.71% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.023% 0.43% 812ms 18.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.43% 764ms 17.39% MutableMesh::ReMesh 81ms 1.84% 2.28% 727ms 16.55% TetrahedralMesh::EdgeIterator::operator++ 0 0% 2.28% 724ms 16.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 2.28% 696ms 15.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 280ms 6.37% 8.65% 531ms 12.08% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.2% 8.85% 523ms 11.90% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.068% 8.92% 498ms 11.33% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.091% 9.01% 497ms 11.31% CellPopulationElementWriter::Visit 15ms 0.34% 9.35% 458ms 10.42% AbstractCellPopulation::GetCellUsingLocationIndex 27ms 0.61% 9.97% 442ms 10.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.11% 10.08% 409ms 9.31% TetrahedralMesh::ImportFromMesher 5ms 0.11% 10.20% 406ms 9.24% CellPropertyCollection::GetPropertiesType (inline) 98ms 2.23% 12.43% 405ms 9.22% __dynamic_cast 7ms 0.16% 12.59% 398ms 9.06% MeshBasedCellPopulation::AcceptCellWriter 19ms 0.43% 13.02% 374ms 8.51% std::_Rb_tree::find (inline) 62ms 1.41% 14.43% 369ms 8.40% std::_Rb_tree::~_Rb_tree (inline) 22ms 0.5% 14.93% 367ms 8.35% operator new 5ms 0.11% 15.04% 367ms 8.35% std::set::insert (inline) 9ms 0.2% 15.25% 362ms 8.24% std::_Rb_tree::_M_insert_unique 0 0% 15.25% 356ms 8.10% std::set::count (inline) 0 0% 15.25% 354ms 8.06% std::set::~set (inline) 132ms 3.00% 18.25% 334ms 7.60% __GI___libc_malloc 0 0% 18.25% 321ms 7.31% AbstractCellProperty::IsSubType (inline) 10ms 0.23% 18.48% 319ms 7.26% std::__new_allocator::allocate (inline) 0 0% 18.48% 315ms 7.17% std::allocator_traits::allocate (inline) 2ms 0.046% 18.53% 306ms 6.96% std::ostream::operator<< (inline) 20ms 0.46% 18.98% 305ms 6.94% std::_Rb_tree::_M_erase 34ms 0.77% 19.75% 303ms 6.90% std::ostream::_M_insert 2ms 0.046% 19.80% 286ms 6.51% Cell::GetCellProliferativeType 0 0% 19.80% 281ms 6.40% std::_Rb_tree::_M_drop_node (inline) 0 0% 19.80% 281ms 6.40% triangulate 1ms 0.023% 19.82% 255ms 5.80% LegacyCellProliferativeTypesWriter::VisitCell 11ms 0.25% 20.07% 254ms 5.78% boost::detail::shared_count::~shared_count (inline) 0 0% 20.07% 254ms 5.78% boost::shared_ptr::~shared_ptr (inline) 0 0% 20.07% 254ms 5.78% delaunay 0 0% 20.07% 254ms 5.78% divconqdelaunay 0 0% 20.07% 243ms 5.53% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.07% 243ms 5.53% std::_Rb_tree::_M_create_node (inline) 15ms 0.34% 20.41% 241ms 5.48% std::_Rb_tree::_Rb_tree (partial-inline) 24ms 0.55% 20.96% 241ms 5.48% std::map::operator[] (partial-inline) 239ms 5.44% 26.40% 239ms 5.44% __strcmp_evex 10ms 0.23% 26.63% 239ms 5.44% std::less::operator() (inline) 237ms 5.39% 32.02% 238ms 5.42% boost::detail::sp_counted_base::release 0 0% 32.02% 234ms 5.33% std::_Rb_tree::_M_get_node (inline) 0 0% 32.02% 229ms 5.21% std::_Rb_tree::_Alloc_node::operator() (inline) 229ms 5.21% 37.23% 229ms 5.21% std::operator< (inline) 1ms 0.023% 37.26% 226ms 5.14% std::set::set (inline) 27ms 0.61% 37.87% 218ms 4.96% std::_Rb_tree::_M_insert_ (inline) 24ms 0.55% 38.42% 214ms 4.87% std::_Rb_tree::_M_copy (inline) 46ms 1.05% 39.46% 209ms 4.76% __GI___libc_free 97ms 2.21% 41.67% 205ms 4.67% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.046% 41.72% 196ms 4.46% NodeLocationWriter::Visit 105ms 2.39% 44.11% 190ms 4.32% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.11% 187ms 4.26% std::_Rb_tree::lower_bound (inline) 0 0% 44.11% 187ms 4.26% std::map::lower_bound (inline) 4ms 0.091% 44.20% 176ms 4.01% Element::Element 1ms 0.023% 44.22% 176ms 4.01% std::__new_allocator::deallocate (inline) 0 0% 44.22% 175ms 3.98% std::allocator_traits::deallocate (inline) 1ms 0.023% 44.24% 172ms 3.91% Cell::GetMutationState 12ms 0.27% 44.52% 171ms 3.89% std::num_put::_M_insert_float 2ms 0.046% 44.56% 167ms 3.80% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.068% 44.63% 163ms 3.71% Cell::ReadyToDivide 151ms 3.44% 48.07% 163ms 3.71% _int_free 2ms 0.046% 48.11% 152ms 3.46% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 48.11% 152ms 3.46% MeshBasedCellPopulation::GetDampingConstant 0 0% 48.11% 152ms 3.46% std::_Rb_tree::_M_put_node (inline) 96ms 2.18% 50.30% 151ms 3.44% _int_malloc 4ms 0.091% 50.39% 142ms 3.23% std::__cxx11::collate::do_transform 49ms 1.12% 51.50% 135ms 3.07% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.068% 51.57% 133ms 3.03% ___vsnprintf 6ms 0.14% 51.71% 131ms 2.98% divconqrecurse 0 0% 51.71% 130ms 2.96% __vsnprintf_internal (inline) 0 0% 51.71% 129ms 2.94% std::_Rb_tree::_M_destroy_node (inline) 0 0% 51.71% 129ms 2.94% std::__new_allocator::destroy (inline) 0 0% 51.71% 129ms 2.94% std::allocator_traits::destroy (inline) 18ms 0.41% 52.12% 127ms 2.89% __printf_buffer 3ms 0.068% 52.18% 125ms 2.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.091% 52.28% 121ms 2.75% Element::RegisterWithNodes (inline) 0 0% 52.28% 119ms 2.71% CellProliferativeTypesWriter::VisitCell 1ms 0.023% 52.30% 117ms 2.66% Node::AddElement 7ms 0.16% 52.46% 116ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 25ms 0.57% 53.03% 115ms 2.62% mergehulls 4ms 0.091% 53.12% 114ms 2.59% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.046% 53.16% 103ms 2.34% CellPropertyCollection::HasProperty 0 0% 53.16% 101ms 2.30% Cell::HasCellProperty (inline) 1ms 0.023% 53.19% 99ms 2.25% TetrahedralMesh::Clear 1ms 0.023% 53.21% 96ms 2.18% AbstractCellProperty::IsType (inline) 1ms 0.023% 53.23% 95ms 2.16% __printf_fp_l_buffer 0 0% 53.23% 95ms 2.16% __printf_fp_spec (inline) 0 0% 53.23% 93ms 2.12% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 53.23% 93ms 2.12% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 44ms 1.00% 54.23% 93ms 2.12% __printf_fp_buffer_1 92ms 2.09% 56.33% 92ms 2.09% std::_Rb_tree::_S_right (inline) 0 0% 56.33% 91ms 2.07% std::basic_ofstream::basic_ofstream (inline) 0 0% 56.33% 90ms 2.05% OutputFileHandler::OpenOutputFile 0 0% 56.33% 89ms 2.03% std::basic_filebuf::open 0 0% 56.33% 89ms 2.03% std::basic_ofstream::open (inline) 0 0% 56.33% 84ms 1.91% AbstractCellBasedWriter::CloseFile 0 0% 56.33% 84ms 1.91% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.023% 56.35% 84ms 1.91% std::basic_ofstream::close (inline) 0 0% 56.35% 83ms 1.89% std::basic_filebuf::close 0 0% 56.35% 81ms 1.84% std::_Vector_base::_M_allocate (inline) 4ms 0.091% 56.44% 78ms 1.78% alternateaxes 0 0% 56.44% 77ms 1.75% OutputFileHandler::CommonConstructor 0 0% 56.44% 77ms 1.75% OutputFileHandler::OutputFileHandler 9ms 0.2% 56.65% 75ms 1.71% AbstractTetrahedralElement::CalculateJacobian 0 0% 56.65% 75ms 1.71% OutputFileHandler::MakeFoldersAndReturnFullPath 17ms 0.39% 57.03% 75ms 1.71% std::num_put::_M_insert_int 67ms 1.52% 58.56% 74ms 1.68% vertexmedian 2ms 0.046% 58.60% 73ms 1.66% std::vector::push_back (inline) 21ms 0.48% 59.08% 72ms 1.64% AbstractCellProperty::IsSame 10ms 0.23% 59.31% 72ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.023% 59.33% 72ms 1.64% std::__basic_file::open 12ms 0.27% 59.60% 71ms 1.62% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 59.60% 71ms 1.62% _IO_new_fopen 0 0% 59.60% 71ms 1.62% __fopen_internal (inline) 55ms 1.25% 60.86% 70ms 1.59% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.11% 60.97% 69ms 1.57% std::vector::_M_realloc_insert 1ms 0.023% 60.99% 68ms 1.55% _IO_new_file_fopen 4ms 0.091% 61.08% 68ms 1.55% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 61.08% 67ms 1.52% __GI__IO_file_open 4ms 0.091% 61.17% 66ms 1.50% boost::numeric::ublas::vector_assign (inline) 2ms 0.046% 61.22% 63ms 1.43% std::basic_filebuf::overflow 62ms 1.41% 62.63% 62ms 1.41% __libc_open64 0 0% 62.63% 62ms 1.41% std::basic_filebuf::_M_terminate_output 0 0% 62.63% 61ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 61ms 1.39% 64.02% 61ms 1.39% __GI___libc_write 0 0% 64.02% 61ms 1.39% std::__basic_file::xsputn 0 0% 64.02% 61ms 1.39% std::basic_filebuf::_M_convert_to_external 60ms 1.37% 65.38% 60ms 1.37% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 65.38% 59ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 65.38% 59ms 1.34% Node::~Node 0 0% 65.38% 57ms 1.30% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.046% 65.43% 56ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 54ms 1.23% 66.66% 54ms 1.23% std::_Rb_tree_insert_and_rebalance 53ms 1.21% 67.87% 53ms 1.21% [libchaste_cell_based.so] 12ms 0.27% 68.14% 53ms 1.21% std::__ostream_insert 4ms 0.091% 68.23% 52ms 1.18% CellPropertyCollection::AddProperty 2ms 0.046% 68.27% 51ms 1.16% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.068% 68.34% 51ms 1.16% std::type_info::operator== (inline) 50ms 1.14% 69.48% 50ms 1.14% incircle 0 0% 69.48% 49ms 1.12% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.8% 70.28% 49ms 1.12% malloc_consolidate 2ms 0.046% 70.32% 49ms 1.12% std::filesystem::create_directory 9ms 0.2% 70.53% 48ms 1.09% AbstractTetrahedralElement::RefreshJacobian 35ms 0.8% 71.32% 47ms 1.07% AbstractElement::GetNodeGlobalIndex 46ms 1.05% 72.37% 46ms 1.05% __GI___fstatat64 0 0% 72.37% 46ms 1.05% std::filesystem::status 46ms 1.05% 73.42% 46ms 1.05% std::vector::size (inline) 45ms 1.02% 74.44% 45ms 1.02% [libstdc++.so.6.0.33] 3ms 0.068% 74.51% 45ms 1.02% std::operator<< (inline) 18ms 0.41% 74.92% 44ms 1.00% boost::numeric::ublas::indexing_vector_assign 4ms 0.091% 75.01% 43ms 0.98% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 75.01% 43ms 0.98% tcache_get (inline) 43ms 0.98% 75.99% 43ms 0.98% tcache_get_n (inline) 29ms 0.66% 76.65% 42ms 0.96% std::basic_filebuf::xsputn 41ms 0.93% 77.58% 41ms 0.93% counterclockwise 3ms 0.068% 77.65% 40ms 0.91% Node::ConstructNodeAttributes (inline) 40ms 0.91% 78.56% 40ms 0.91% __memcpy_avx512_unaligned_erms 0 0% 78.56% 40ms 0.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.56% 40ms 0.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 78.56% 40ms 0.91% std::vector::vector (inline) 36ms 0.82% 79.38% 40ms 0.91% vertexsort 0 0% 79.38% 38ms 0.86% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.023% 79.40% 38ms 0.86% Node::ClearAppliedForce 0 0% 79.40% 36ms 0.82% Cell::GetCellId 3ms 0.068% 79.47% 36ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 79.47% 36ms 0.82% std::_Vector_base::_Vector_base (inline) 0 0% 79.47% 35ms 0.8% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 79.47% 34ms 0.77% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 23ms 0.52% 80.00% 34ms 0.77% boost::numeric::ublas::c_matrix::operator() (partial-inline) 19ms 0.43% 80.43% 34ms 0.77% std::basic_streambuf::xsputn 12ms 0.27% 80.70% 33ms 0.75% AbstractTetrahedralMesh::GetElement 3ms 0.068% 80.77% 33ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeA 33ms 0.75% 81.52% 33ms 0.75% [libchaste_mesh.so] 1ms 0.023% 81.54% 33ms 0.75% std::_Vector_base::_M_create_storage (inline) 0 0% 81.54% 32ms 0.73% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 81.54% 31ms 0.71% CxxTest::RealWorldDescription::setUp 0 0% 81.54% 31ms 0.71% PetscInitialize 0 0% 81.54% 31ms 0.71% PetscSetup::setUpWorld 0 0% 81.54% 31ms 0.71% PetscSetupUtils::CommonSetup 0 0% 81.54% 31ms 0.71% PetscSetupUtils::InitialisePetsc 31ms 0.71% 82.25% 31ms 0.71% std::_Rb_tree_increment 24ms 0.55% 82.79% 31ms 0.71% std::num_put::do_put 17ms 0.39% 83.18% 30ms 0.68% AbstractElement::GetNodeLocation 0 0% 83.18% 30ms 0.68% PMPI_Init_thread 0 0% 83.18% 30ms 0.68% boost::numeric::ublas::norm_2 (inline) 4ms 0.091% 83.27% 30ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 25ms 0.57% 83.84% 30ms 0.68% boost::shared_ptr::shared_ptr (inline) 0 0% 83.84% 30ms 0.68% ompi_mpi_init 3ms 0.068% 83.91% 30ms 0.68% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.068% 83.98% 29ms 0.66% std::_Rb_tree_const_iterator::operator++ (inline) 25ms 0.57% 84.55% 27ms 0.61% CellPropertyCollection::GetProperty 15ms 0.34% 84.89% 27ms 0.61% hack_digit 3ms 0.068% 84.96% 26ms 0.59% 6ms 0.14% 85.09% 26ms 0.59% Determinant (inline) 0 0% 85.09% 26ms 0.59% _dl_init 1ms 0.023% 85.12% 26ms 0.59% call_init (inline) 25ms 0.57% 85.69% 25ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 85.69% 24ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.69% 24ms 0.55% BoundaryNodeWriter::Visit 0 0% 85.69% 22ms 0.5% _dl_start_user 22ms 0.5% 86.19% 22ms 0.5% boost::numeric::ublas::c_vector::operator() 0 0% 86.19% 22ms 0.5% std::_Vector_base::_M_deallocate (inline)