File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6617ms, 83.78% of 7898ms total Dropped 583 nodes (cum <= 39.49ms) flat flat% sum% cum cum% 0 0% 0% 7863ms 99.56% __libc_start_call_main 0 0% 0% 7863ms 99.56% __libc_start_main_impl 0 0% 0% 7863ms 99.56% _start 0 0% 0% 7848ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7848ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7848ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7848ms 99.37% main 0 0% 0% 7813ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7813ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7813ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7811ms 98.90% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3370ms 42.67% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2933ms 37.14% MeshBasedCellPopulation::Update 0 0% 0.013% 2912ms 36.87% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 1517ms 19.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1445ms 18.30% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.051% 1426ms 18.06% MutableMesh::ReMesh 0 0% 0.051% 1364ms 17.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.063% 1327ms 16.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.24% 1265ms 16.02% MeshBasedCellPopulation::SpringIterator::operator++ 119ms 1.51% 1.75% 1042ms 13.19% TetrahedralMesh::EdgeIterator::operator++ 419ms 5.31% 7.05% 1014ms 12.84% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.10% 943ms 11.94% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.051% 7.15% 918ms 11.62% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.1% 7.26% 912ms 11.55% CellPopulationElementWriter::Visit 15ms 0.19% 7.44% 901ms 11.41% CellPropertyCollection::GetPropertiesType (inline) 271ms 3.43% 10.88% 870ms 11.02% __dynamic_cast 33ms 0.42% 11.29% 805ms 10.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.013% 11.31% 791ms 10.02% MeshBasedCellPopulation::AcceptCellWriter 35ms 0.44% 11.75% 744ms 9.42% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.13% 11.88% 711ms 9.00% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.91% 695ms 8.80% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.93% 617ms 7.81% std::ostream::operator<< (inline) 106ms 1.34% 13.27% 616ms 7.80% std::ostream::_M_insert 37ms 0.47% 13.74% 611ms 7.74% std::map::operator[] (partial-inline) 3ms 0.038% 13.78% 554ms 7.01% triangulate 21ms 0.27% 14.04% 544ms 6.89% std::_Rb_tree::find (inline) 7ms 0.089% 14.13% 544ms 6.89% std::set::insert (inline) 49ms 0.62% 14.75% 542ms 6.86% operator new 14ms 0.18% 14.93% 537ms 6.80% std::_Rb_tree::_M_insert_unique 0 0% 14.93% 523ms 6.62% std::_Rb_tree::lower_bound (inline) 0 0% 14.93% 523ms 6.62% std::map::lower_bound (inline) 4ms 0.051% 14.98% 518ms 6.56% Cell::GetCellProliferativeType 39ms 0.49% 15.47% 496ms 6.28% std::__new_allocator::allocate (inline) 0 0% 15.47% 493ms 6.24% delaunay 0 0% 15.47% 493ms 6.24% std::set::count (inline) 0 0% 15.47% 492ms 6.23% divconqdelaunay 160ms 2.03% 17.50% 490ms 6.20% __GI___libc_malloc 0 0% 17.50% 489ms 6.19% std::allocator_traits::allocate (inline) 4ms 0.051% 17.55% 471ms 5.96% LegacyCellProliferativeTypesWriter::VisitCell 470ms 5.95% 23.50% 470ms 5.95% __strcmp_avx2 0 0% 23.50% 430ms 5.44% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 23.51% 421ms 5.33% AbstractCellBasedSimulation::DoCellBirth 200ms 2.53% 26.04% 416ms 5.27% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.04% 409ms 5.18% std::_Rb_tree::_Alloc_node::operator() (inline) 39ms 0.49% 26.54% 391ms 4.95% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.089% 26.63% 381ms 4.82% Cell::GetMutationState 0 0% 26.63% 381ms 4.82% std::_Rb_tree::_M_get_node (inline) 6ms 0.076% 26.70% 381ms 4.82% std::less::operator() (inline) 375ms 4.75% 31.45% 375ms 4.75% std::operator< (inline) 373ms 4.72% 36.17% 373ms 4.72% std::_Rb_tree::_S_right (inline) 19ms 0.24% 36.41% 366ms 4.63% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 36.41% 362ms 4.58% std::set::~set (inline) 2ms 0.025% 36.44% 360ms 4.56% NodeLocationWriter::Visit 86ms 1.09% 37.53% 350ms 4.43% std::_Rb_tree::_M_erase 25ms 0.32% 37.85% 340ms 4.30% std::_Rb_tree::_M_insert_ (inline) 2ms 0.025% 37.87% 326ms 4.13% std::set::set (inline) 1ms 0.013% 37.88% 324ms 4.10% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 37.91% 323ms 4.09% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 37.91% 319ms 4.04% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 6ms 0.076% 37.98% 317ms 4.01% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 38.00% 315ms 3.99% AbstractCellBasedWriter::OpenOutputFileForAppend 19ms 0.24% 38.24% 314ms 3.98% std::num_put::_M_insert_float 0 0% 38.24% 309ms 3.91% OutputFileHandler::OpenOutputFile 39ms 0.49% 38.73% 306ms 3.87% std::_Rb_tree::_M_copy (inline) 8ms 0.1% 38.83% 298ms 3.77% Element::Element 0 0% 38.83% 284ms 3.60% CellProliferativeTypesWriter::VisitCell 97ms 1.23% 40.06% 284ms 3.60% __GI___libc_free 3ms 0.038% 40.10% 276ms 3.49% Cell::ReadyToDivide 5ms 0.063% 40.16% 273ms 3.46% divconqrecurse 74ms 0.94% 41.10% 266ms 3.37% std::_Rb_tree::_M_clone_node (inline) 6ms 0.076% 41.17% 259ms 3.28% std::__cxx11::collate::do_transform 70ms 0.89% 42.06% 258ms 3.27% mergehulls 163ms 2.06% 44.13% 253ms 3.20% _int_malloc 1ms 0.013% 44.14% 250ms 3.17% ___vsnprintf 0 0% 44.14% 249ms 3.15% __vsnprintf_internal (inline) 0 0% 44.14% 241ms 3.05% std::_Rb_tree::_M_drop_node (inline) 26ms 0.33% 44.47% 240ms 3.04% __printf_buffer 9ms 0.11% 44.58% 230ms 2.91% CellPropertyCollection::HasProperty 7ms 0.089% 44.67% 229ms 2.90% std::__new_allocator::deallocate (inline) 0 0% 44.67% 228ms 2.89% std::allocator_traits::deallocate (inline) 0 0% 44.67% 226ms 2.86% Cell::HasCellProperty (inline) 2ms 0.025% 44.69% 213ms 2.70% AbstractCellProperty::IsType (inline) 1ms 0.013% 44.71% 195ms 2.47% __printf_fp_spec (inline) 21ms 0.27% 44.97% 194ms 2.46% TetrahedralMesh::Clear 7ms 0.089% 45.06% 194ms 2.46% __printf_fp_l_buffer 0 0% 45.06% 191ms 2.42% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 45.10% 190ms 2.41% Element::RegisterWithNodes (inline) 152ms 1.92% 47.02% 187ms 2.37% _int_free 10ms 0.13% 47.15% 184ms 2.33% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.076% 47.23% 184ms 2.33% Node::AddElement 57ms 0.72% 47.95% 183ms 2.32% std::_Rb_tree::_M_get_insert_unique_pos (inline) 4ms 0.051% 48.00% 182ms 2.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 93ms 1.18% 49.18% 180ms 2.28% __printf_fp_buffer_1 14ms 0.18% 49.35% 174ms 2.20% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.14% 49.49% 167ms 2.11% AbstractTetrahedralElement::CalculateJacobian 50ms 0.63% 50.13% 158ms 2.00% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.13% 154ms 1.95% std::basic_ofstream::basic_ofstream (inline) 40ms 0.51% 50.63% 152ms 1.92% AbstractCellProperty::IsSame 2ms 0.025% 50.66% 151ms 1.91% boost::numeric::ublas::vector_assign (inline) 0 0% 50.66% 151ms 1.91% std::basic_ofstream::open (inline) 1ms 0.013% 50.67% 150ms 1.90% std::basic_filebuf::open 1ms 0.013% 50.68% 141ms 1.79% TetrahedralMesh::RefreshJacobianCachedData 69ms 0.87% 51.56% 140ms 1.77% std::__ostream_insert 0 0% 51.56% 139ms 1.76% OutputFileHandler::CommonConstructor 0 0% 51.56% 139ms 1.76% OutputFileHandler::OutputFileHandler 4ms 0.051% 51.61% 139ms 1.76% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 51.63% 136ms 1.72% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 51.66% 135ms 1.71% AbstractCellBasedWriter::CloseFile 0 0% 51.66% 135ms 1.71% AbstractCellPopulation::CloseRoundRobinWritersFiles 39ms 0.49% 52.15% 135ms 1.71% std::num_put::_M_insert_int 1ms 0.013% 52.17% 133ms 1.68% std::basic_ofstream::close (inline) 0 0% 52.17% 132ms 1.67% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 52.18% 132ms 1.67% std::basic_filebuf::close 1ms 0.013% 52.19% 132ms 1.67% std::filesystem::permissions 130ms 1.65% 53.84% 130ms 1.65% __GI_fchmodat 2ms 0.025% 53.86% 130ms 1.65% alternateaxes 19ms 0.24% 54.10% 129ms 1.63% AbstractTetrahedralElement::RefreshJacobian 6ms 0.076% 54.18% 128ms 1.62% AbstractTetrahedralElement::CalculateInverseJacobian 110ms 1.39% 55.57% 128ms 1.62% vertexmedian 21ms 0.27% 55.84% 122ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 55.84% 122ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 55.85% 119ms 1.51% std::__basic_file::open 1ms 0.013% 55.86% 118ms 1.49% _IO_new_fopen 0 0% 55.86% 117ms 1.48% __fopen_internal (inline) 1ms 0.013% 55.87% 116ms 1.47% _IO_new_file_fopen 116ms 1.47% 57.34% 116ms 1.47% incircle 12ms 0.15% 57.50% 116ms 1.47% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.089% 57.58% 116ms 1.47% std::operator<< (inline) 1ms 0.013% 57.60% 115ms 1.46% AbstractTetrahedralElement::AbstractTetrahedralElement 115ms 1.46% 59.05% 115ms 1.46% std::_Rb_tree_increment 0 0% 59.05% 114ms 1.44% __GI__IO_file_open 18ms 0.23% 59.28% 113ms 1.43% MeshBasedCellPopulation::SpringIterator::SpringIterator 22ms 0.28% 59.56% 112ms 1.42% std::type_info::operator== (inline) 111ms 1.41% 60.96% 111ms 1.41% std::_Rb_tree_insert_and_rebalance 27ms 0.34% 61.31% 110ms 1.39% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 61.33% 110ms 1.39% std::_Vector_base::_M_allocate (inline) 6ms 0.076% 61.41% 107ms 1.35% Node::~Node 41ms 0.52% 61.93% 107ms 1.35% boost::shared_ptr::shared_ptr (inline) 9ms 0.11% 62.04% 106ms 1.34% boost::detail::shared_count::~shared_count (inline) 0 0% 62.04% 106ms 1.34% boost::shared_ptr::~shared_ptr (inline) 104ms 1.32% 63.36% 105ms 1.33% __libc_open64 5ms 0.063% 63.42% 104ms 1.32% std::vector::push_back (inline) 12ms 0.15% 63.57% 97ms 1.23% std::vector::_M_realloc_insert 0 0% 63.57% 96ms 1.22% std::basic_filebuf::_M_terminate_output 1ms 0.013% 63.59% 96ms 1.22% std::basic_filebuf::overflow 2ms 0.025% 63.61% 95ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 43ms 0.54% 64.16% 95ms 1.20% AbstractElement::GetNodeLocation 95ms 1.20% 65.36% 95ms 1.20% __GI___libc_write 0 0% 65.36% 95ms 1.20% std::__basic_file::xsputn 0 0% 65.36% 95ms 1.20% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 65.38% 93ms 1.18% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 93ms 1.18% 66.56% 93ms 1.18% boost::detail::sp_counted_base::release 55ms 0.7% 67.26% 90ms 1.14% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 85ms 1.08% 68.33% 85ms 1.08% [libchaste_cell_based.so] 82ms 1.04% 69.37% 82ms 1.04% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.025% 69.40% 79ms 1.00% AbstractCellPopulation::GetLocationIndexUsingCell 72ms 0.91% 70.31% 79ms 1.00% vertexsort 5ms 0.063% 70.37% 76ms 0.96% CellPropertyCollection::AddProperty 1ms 0.013% 70.38% 74ms 0.94% Cell::GetCellId 55ms 0.7% 71.08% 73ms 0.92% malloc_consolidate 50ms 0.63% 71.71% 73ms 0.92% std::basic_streambuf::xsputn 0 0% 71.71% 72ms 0.91% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 71.71% 72ms 0.91% std::filesystem::create_directory 59ms 0.75% 72.46% 72ms 0.91% std::num_put::do_put 71ms 0.9% 73.36% 71ms 0.9% counterclockwise 71ms 0.9% 74.26% 71ms 0.9% std::vector::size (inline) 70ms 0.89% 75.15% 70ms 0.89% Node::GetIndex 0 0% 75.15% 70ms 0.89% tcache_get (inline) 70ms 0.89% 76.03% 70ms 0.89% tcache_get_n (inline) 67ms 0.85% 76.88% 67ms 0.85% __GI___fstatat64 63ms 0.8% 77.68% 66ms 0.84% boost::detail::shared_count::shared_count (inline) 39ms 0.49% 78.17% 66ms 0.84% std::basic_filebuf::xsputn 0 0% 78.17% 66ms 0.84% std::filesystem::status 7ms 0.089% 78.26% 65ms 0.82% Node::ConstructNodeAttributes (inline) 0 0% 78.26% 65ms 0.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.26% 65ms 0.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.038% 78.30% 62ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeB 61ms 0.77% 79.07% 61ms 0.77% [libchaste_mesh.so] 59ms 0.75% 79.82% 59ms 0.75% __memcpy_avx_unaligned_erms 0 0% 79.82% 58ms 0.73% Node::ClearAppliedForce 58ms 0.73% 80.55% 58ms 0.73% boost::numeric::ublas::c_vector::operator() (partial-inline) 2ms 0.025% 80.58% 55ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeA 45ms 0.57% 81.15% 54ms 0.68% AbstractElement::GetNodeGlobalIndex 0 0% 81.15% 54ms 0.68% BoundaryNodeWriter::Visit 53ms 0.67% 81.82% 53ms 0.67% boost::shared_ptr::operator-> (inline) 2ms 0.025% 81.84% 51ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.025% 81.87% 51ms 0.65% std::__new_allocator::construct (inline) 0 0% 81.87% 51ms 0.65% std::allocator_traits::construct (inline) 16ms 0.2% 82.07% 50ms 0.63% AbstractTetrahedralMesh::GetElement 6ms 0.076% 82.15% 50ms 0.63% NodeAttributes::NodeAttributes 0 0% 82.15% 50ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.15% 50ms 0.63% std::__new_allocator::destroy (inline) 0 0% 82.15% 50ms 0.63% std::allocator_traits::destroy (inline) 0 0% 82.15% 49ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 82.15% 48ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 82.15% 48ms 0.61% std::vector::vector (inline) 0 0% 82.15% 46ms 0.58% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 82.15% 46ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 28ms 0.35% 82.50% 46ms 0.58% boost::numeric::ublas::c_matrix::operator() 0 0% 82.50% 46ms 0.58% std::map::find (inline) 44ms 0.56% 83.06% 44ms 0.56% Node::rGetLocation 0 0% 83.06% 44ms 0.56% std::map::map (inline) 0 0% 83.06% 43ms 0.54% boost::numeric::ublas::norm_2 (inline) 11ms 0.14% 83.20% 43ms 0.54% boost::numeric::ublas::vector_norm_2::apply (inline) 26ms 0.33% 83.53% 43ms 0.54% hack_digit 13ms 0.16% 83.69% 42ms 0.53% AbstractTetrahedralMesh::GetNumAllElements 0 0% 83.69% 42ms 0.53% std::_Vector_base::_Vector_base (inline) 0 0% 83.69% 41ms 0.52% std::_Vector_base::_M_create_storage (inline) 0 0% 83.69% 40ms 0.51% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 7ms 0.089% 83.78% 40ms 0.51% std::_Rb_tree_header::_Rb_tree_header (inline)