File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 4427ms, 84.63% of 5231ms total Dropped 456 nodes (cum <= 26.16ms) flat flat% sum% cum cum% 0 0% 0% 5203ms 99.46% __libc_start_call_main 0 0% 0% 5203ms 99.46% __libc_start_main_impl 0 0% 0% 5203ms 99.46% _start 0 0% 0% 5190ms 99.22% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5190ms 99.22% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5190ms 99.22% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5190ms 99.22% main 0 0% 0% 5153ms 98.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5153ms 98.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5153ms 98.51% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 5152ms 98.49% AbstractCellBasedSimulation::Solve 0 0% 0% 2414ms 46.15% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2149ms 41.08% MeshBasedCellPopulation::Update 3ms 0.057% 0.057% 1760ms 33.65% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.057% 1081ms 20.67% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.057% 1022ms 19.54% MutableMesh::ReMesh 0 0% 0.057% 976ms 18.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.34% 0.4% 945ms 18.07% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.4% 854ms 16.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.038% 0.44% 822ms 15.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 90ms 1.72% 2.16% 770ms 14.72% TetrahedralMesh::EdgeIterator::operator++ 15ms 0.29% 2.45% 641ms 12.25% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 286ms 5.47% 7.91% 624ms 11.93% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.11% 8.03% 623ms 11.91% CellPopulationElementWriter::Visit 2ms 0.038% 8.07% 591ms 11.30% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.17% 8.24% 551ms 10.53% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.15% 8.39% 539ms 10.30% TetrahedralMesh::ImportFromMesher 14ms 0.27% 8.66% 534ms 10.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.057% 8.72% 523ms 10.00% MeshBasedCellPopulation::AcceptCellWriter 131ms 2.50% 11.22% 523ms 10.00% __dynamic_cast 8ms 0.15% 11.37% 515ms 9.85% CellPropertyCollection::GetPropertiesType (inline) 33ms 0.63% 12.01% 477ms 9.12% operator new 141ms 2.70% 14.70% 437ms 8.35% __GI___libc_malloc 2ms 0.038% 14.74% 423ms 8.09% std::set::insert (inline) 3ms 0.057% 14.80% 422ms 8.07% AbstractCellProperty::IsSubType (inline) 4ms 0.076% 14.87% 421ms 8.05% std::_Rb_tree::_M_insert_unique 9ms 0.17% 15.04% 416ms 7.95% std::__new_allocator::allocate (inline) 0 0% 15.04% 413ms 7.90% std::allocator_traits::allocate (inline) 56ms 1.07% 16.12% 398ms 7.61% std::_Rb_tree::~_Rb_tree (inline) 0 0% 16.12% 396ms 7.57% std::ostream::operator<< (inline) 55ms 1.05% 17.17% 391ms 7.47% std::ostream::_M_insert 1ms 0.019% 17.19% 375ms 7.17% triangulate 0 0% 17.19% 373ms 7.13% std::set::~set (inline) 41ms 0.78% 17.97% 371ms 7.09% std::map::operator[] (partial-inline) 11ms 0.21% 18.18% 362ms 6.92% std::_Rb_tree::find (inline) 3ms 0.057% 18.24% 342ms 6.54% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 18.24% 341ms 6.52% delaunay 0 0% 18.24% 341ms 6.52% divconqdelaunay 45ms 0.86% 19.10% 341ms 6.52% std::_Rb_tree::_M_erase 0 0% 19.10% 338ms 6.46% std::set::count (inline) 0 0% 19.10% 333ms 6.37% std::_Rb_tree::_M_create_node (inline) 0 0% 19.10% 321ms 6.14% std::_Rb_tree::_M_get_node (inline) 0 0% 19.10% 319ms 6.10% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.038% 19.14% 301ms 5.75% Cell::GetCellProliferativeType 0 0% 19.14% 292ms 5.58% std::_Rb_tree::lower_bound (inline) 0 0% 19.14% 292ms 5.58% std::map::lower_bound (inline) 0 0% 19.14% 289ms 5.52% std::_Rb_tree::_M_drop_node (inline) 21ms 0.4% 19.54% 281ms 5.37% std::_Rb_tree::_M_insert_ (inline) 275ms 5.26% 24.79% 275ms 5.26% __strcmp_evex 132ms 2.52% 27.32% 273ms 5.22% __cxxabiv1::__si_class_type_info::__do_dyncast 15ms 0.29% 27.60% 269ms 5.14% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.057% 27.66% 262ms 5.01% boost::detail::shared_count::~shared_count (inline) 0 0% 27.66% 262ms 5.01% boost::shared_ptr::~shared_ptr (inline) 0 0% 27.66% 259ms 4.95% AbstractCellBasedSimulation::DoCellBirth 252ms 4.82% 32.48% 253ms 4.84% boost::detail::sp_counted_base::release 1ms 0.019% 32.50% 252ms 4.82% Cell::GetMutationState 3ms 0.057% 32.56% 245ms 4.68% Element::Element 1ms 0.019% 32.58% 245ms 4.68% NodeLocationWriter::Visit 1ms 0.019% 32.59% 245ms 4.68% std::set::set (inline) 18ms 0.34% 32.94% 238ms 4.55% std::_Rb_tree::_M_copy (inline) 55ms 1.05% 33.99% 217ms 4.15% __GI___libc_free 217ms 4.15% 38.14% 217ms 4.15% std::_Rb_tree::_S_right (inline) 150ms 2.87% 41.01% 214ms 4.09% _int_malloc 2ms 0.038% 41.04% 212ms 4.05% AbstractCellPopulation::IsCellAttachedToLocationIndex 72ms 1.38% 42.42% 212ms 4.05% std::_Rb_tree::_M_clone_node (inline) 20ms 0.38% 42.80% 210ms 4.01% std::num_put::_M_insert_float 7ms 0.13% 42.94% 196ms 3.75% divconqrecurse 66ms 1.26% 44.20% 186ms 3.56% mergehulls 2ms 0.038% 44.24% 186ms 3.56% std::__new_allocator::deallocate (inline) 0 0% 44.24% 184ms 3.52% std::allocator_traits::deallocate (inline) 1ms 0.019% 44.26% 183ms 3.50% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 44.26% 183ms 3.50% MeshBasedCellPopulation::GetDampingConstant 7ms 0.13% 44.39% 174ms 3.33% std::less::operator() (inline) 3ms 0.057% 44.45% 173ms 3.31% Element::RegisterWithNodes (inline) 5ms 0.096% 44.54% 170ms 3.25% std::__cxx11::collate::do_transform 9ms 0.17% 44.71% 169ms 3.23% Node::AddElement 167ms 3.19% 47.91% 167ms 3.19% std::operator< (inline) 1ms 0.019% 47.93% 160ms 3.06% ___vsnprintf 141ms 2.70% 50.62% 160ms 3.06% _int_free 0 0% 50.62% 159ms 3.04% __vsnprintf_internal (inline) 0 0% 50.62% 157ms 3.00% std::_Rb_tree::_M_put_node (inline) 20ms 0.38% 51.00% 154ms 2.94% __printf_buffer 1ms 0.019% 51.02% 153ms 2.92% Cell::ReadyToDivide 153ms 2.92% 53.95% 153ms 2.92% [libchaste_cell_based.so] 0 0% 53.95% 147ms 2.81% CellProliferativeTypesWriter::VisitCell 56ms 1.07% 55.02% 136ms 2.60% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 55.02% 132ms 2.52% std::_Rb_tree::_M_destroy_node (inline) 0 0% 55.02% 132ms 2.52% std::__new_allocator::destroy (inline) 0 0% 55.02% 132ms 2.52% std::allocator_traits::destroy (inline) 2ms 0.038% 55.06% 130ms 2.49% AbstractCellProperty::IsType (inline) 5ms 0.096% 55.15% 127ms 2.43% CellPropertyCollection::HasProperty 0 0% 55.15% 125ms 2.39% Cell::HasCellProperty (inline) 8ms 0.15% 55.30% 123ms 2.35% MeshBasedCellPopulation::SpringsEnd (inline) 9ms 0.17% 55.48% 121ms 2.31% __printf_fp_l_buffer 0 0% 55.48% 121ms 2.31% __printf_fp_spec (inline) 0 0% 55.48% 118ms 2.26% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 55.48% 118ms 2.26% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 55.48% 117ms 2.24% OutputFileHandler::OpenOutputFile 1ms 0.019% 55.50% 117ms 2.24% TetrahedralMesh::Clear 1ms 0.019% 55.52% 112ms 2.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.057% 55.57% 108ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 57ms 1.09% 56.66% 108ms 2.06% __printf_fp_buffer_1 3ms 0.057% 56.72% 100ms 1.91% AbstractTetrahedralElement::CalculateJacobian 96ms 1.84% 58.55% 96ms 1.84% [libchaste_mesh.so] 0 0% 58.55% 95ms 1.82% TetrahedralMesh::RefreshJacobianCachedData 30ms 0.57% 59.13% 94ms 1.80% std::num_put::_M_insert_int 16ms 0.31% 59.43% 93ms 1.78% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 59.43% 92ms 1.76% std::_Vector_base::_M_allocate (inline) 7ms 0.13% 59.57% 89ms 1.70% AbstractTetrahedralElement::CalculateInverseJacobian 88ms 1.68% 61.25% 88ms 1.68% std::_Rb_tree_insert_and_rebalance 24ms 0.46% 61.71% 85ms 1.62% AbstractCellProperty::IsSame 2ms 0.038% 61.75% 83ms 1.59% alternateaxes 17ms 0.32% 62.07% 82ms 1.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 30ms 0.57% 62.65% 82ms 1.57% std::__ostream_insert 3ms 0.057% 62.70% 82ms 1.57% std::vector::push_back (inline) 4ms 0.076% 62.78% 81ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 62.78% 81ms 1.55% AbstractCellPopulation::Iterator::operator++ (inline) 70ms 1.34% 64.12% 80ms 1.53% vertexmedian 3ms 0.057% 64.18% 79ms 1.51% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.057% 64.23% 79ms 1.51% boost::numeric::ublas::vector_assign (inline) 78ms 1.49% 65.72% 78ms 1.49% incircle 9ms 0.17% 65.90% 75ms 1.43% std::vector::_M_realloc_insert 2ms 0.038% 65.93% 74ms 1.41% AbstractTetrahedralElement::AbstractTetrahedralElement 71ms 1.36% 67.29% 71ms 1.36% [libstdc++.so.6.0.33] 0 0% 67.29% 71ms 1.36% tcache_get (inline) 71ms 1.36% 68.65% 71ms 1.36% tcache_get_n (inline) 5ms 0.096% 68.74% 70ms 1.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 7ms 0.13% 68.88% 70ms 1.34% AbstractTetrahedralElement::RefreshJacobian 0 0% 68.88% 65ms 1.24% Node::~Node 53ms 1.01% 69.89% 65ms 1.24% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.019% 69.91% 65ms 1.24% std::operator<< (inline) 0 0% 69.91% 61ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.096% 70.01% 61ms 1.17% std::type_info::operator== (inline) 61ms 1.17% 71.17% 61ms 1.17% std::vector::size (inline) 0 0% 71.17% 60ms 1.15% std::basic_ofstream::basic_ofstream (inline) 38ms 0.73% 71.90% 58ms 1.11% malloc_consolidate 0 0% 71.90% 58ms 1.11% std::basic_filebuf::open 0 0% 71.90% 58ms 1.11% std::basic_ofstream::open (inline) 51ms 0.97% 72.87% 57ms 1.09% vertexsort 1ms 0.019% 72.89% 52ms 0.99% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.29% 73.18% 52ms 0.99% AbstractElement::GetNodeLocation 9ms 0.17% 73.35% 50ms 0.96% TetrahedralMesh::EdgeIterator::GetNodeB 8ms 0.15% 73.50% 50ms 0.96% boost::numeric::ublas::indexing_vector_assign 48ms 0.92% 74.42% 48ms 0.92% __memcpy_avx512_unaligned_erms 26ms 0.5% 74.92% 48ms 0.92% std::basic_streambuf::xsputn 46ms 0.88% 75.80% 46ms 0.88% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 6ms 0.11% 75.91% 46ms 0.88% std::_Rb_tree_const_iterator::operator++ (inline) 23ms 0.44% 76.35% 44ms 0.84% std::basic_filebuf::xsputn 3ms 0.057% 76.41% 43ms 0.82% CellPropertyCollection::AddProperty 0 0% 76.41% 43ms 0.82% FilesystemPermissions::SetFilePermissions (inline) 43ms 0.82% 77.23% 43ms 0.82% Node::GetIndex 0 0% 77.23% 43ms 0.82% OutputFileHandler::CommonConstructor 0 0% 77.23% 43ms 0.82% OutputFileHandler::OutputFileHandler 43ms 0.82% 78.05% 43ms 0.82% __GI_fchmodat 0 0% 78.05% 43ms 0.82% std::filesystem::permissions 0 0% 78.05% 42ms 0.8% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.05% 42ms 0.8% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 41ms 0.78% 78.84% 41ms 0.78% std::_Rb_tree::_S_left (inline) 15ms 0.29% 79.12% 40ms 0.76% Determinant (inline) 0 0% 79.12% 40ms 0.76% OutputFileHandler::MakeFoldersAndReturnFullPath 40ms 0.76% 79.89% 40ms 0.76% std::_Rb_tree_increment 32ms 0.61% 80.50% 40ms 0.76% std::num_put::do_put 0 0% 80.50% 40ms 0.76% std::vector::vector (inline) 0 0% 80.50% 39ms 0.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 6ms 0.11% 80.62% 39ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 80.62% 38ms 0.73% AbstractCellBasedWriter::CloseFile 1ms 0.019% 80.63% 38ms 0.73% Cell::GetCellId 3ms 0.057% 80.69% 38ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.69% 38ms 0.73% std::basic_filebuf::close 0 0% 80.69% 38ms 0.73% std::basic_ofstream::close (inline) 15ms 0.29% 80.98% 37ms 0.71% AbstractElement::GetNodeGlobalIndex 32ms 0.61% 81.59% 37ms 0.71% CellPropertyCollection::GetProperty 0 0% 81.59% 37ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 20ms 0.38% 81.97% 37ms 0.71% boost::shared_ptr::shared_ptr (inline) 36ms 0.69% 82.66% 36ms 0.69% counterclockwise 0 0% 82.66% 36ms 0.69% std::__basic_file::open 0 0% 82.66% 35ms 0.67% Node::ClearAppliedForce 0 0% 82.66% 35ms 0.67% Node::ConstructNodeAttributes (inline) 0 0% 82.66% 35ms 0.67% _IO_new_fopen 0 0% 82.66% 35ms 0.67% __fopen_internal (inline) 20ms 0.38% 83.04% 34ms 0.65% AbstractTetrahedralMesh::GetElement 0 0% 83.04% 34ms 0.65% BoundaryNodeWriter::Visit 0 0% 83.04% 34ms 0.65% CxxTest::RealWorldDescription::setUp 1ms 0.019% 83.06% 34ms 0.65% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 83.06% 34ms 0.65% PMPI_Init_thread 0 0% 83.06% 34ms 0.65% PetscInitialize 0 0% 83.06% 34ms 0.65% PetscSetup::setUpWorld 0 0% 83.06% 34ms 0.65% PetscSetupUtils::CommonSetup 0 0% 83.06% 34ms 0.65% PetscSetupUtils::InitialisePetsc 0 0% 83.06% 34ms 0.65% ompi_mpi_init 0 0% 83.06% 33ms 0.63% _IO_new_file_fopen 1ms 0.019% 83.08% 33ms 0.63% __GI__IO_file_open 0 0% 83.08% 33ms 0.63% std::_Vector_base::_M_create_storage (inline) 0 0% 83.08% 33ms 0.63% std::_Vector_base::_Vector_base (inline) 0 0% 83.08% 32ms 0.61% CellPropertyCollection::~CellPropertyCollection (inline) 21ms 0.4% 83.48% 32ms 0.61% hack_digit 0 0% 83.48% 31ms 0.59% _dl_init 0 0% 83.48% 31ms 0.59% call_init (inline) 0 0% 83.48% 31ms 0.59% std::map::map (inline) 0 0% 83.48% 30ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 30ms 0.57% 84.06% 30ms 0.57% __GI___libc_write 0 0% 84.06% 30ms 0.57% std::__basic_file::xsputn 0 0% 84.06% 30ms 0.57% std::basic_filebuf::_M_convert_to_external 0 0% 84.06% 30ms 0.57% std::basic_filebuf::_M_terminate_output 0 0% 84.06% 30ms 0.57% std::basic_filebuf::overflow 3ms 0.057% 84.11% 29ms 0.55% Inverse 0 0% 84.11% 28ms 0.54% 0 0% 84.11% 28ms 0.54% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 84.11% 28ms 0.54% _dl_start_user 20ms 0.38% 84.50% 28ms 0.54% boost::numeric::ublas::c_matrix::operator() 0 0% 84.50% 27ms 0.52% boost::numeric::ublas::norm_2 (inline) 7ms 0.13% 84.63% 27ms 0.52% boost::numeric::ublas::vector_norm_2::apply (inline)