File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5574ms, 85.58% of 6513ms total Dropped 507 nodes (cum <= 32.56ms) flat flat% sum% cum cum% 0 0% 0% 6486ms 99.59% __libc_start_call_main 0 0% 0% 6486ms 99.59% __libc_start_main_impl 0 0% 0% 6486ms 99.59% _start 0 0% 0% 6472ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 6472ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 6472ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 6472ms 99.37% main 0 0% 0% 6436ms 98.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 6436ms 98.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 6436ms 98.82% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.015% 0.015% 6434ms 98.79% AbstractCellBasedSimulation::Solve 0 0% 0.015% 3045ms 46.75% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.031% 0.046% 2688ms 41.27% MeshBasedCellPopulation::Update 0 0% 0.046% 2161ms 33.18% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.046% 1370ms 21.03% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.046% 1275ms 19.58% MutableMesh::ReMesh 0 0% 0.046% 1224ms 18.79% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.31% 0.35% 1198ms 18.39% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.35% 1085ms 16.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.031% 0.38% 1049ms 16.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 99ms 1.52% 1.90% 981ms 15.06% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.015% 1.92% 800ms 12.28% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.2% 2.12% 770ms 11.82% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 398ms 6.11% 8.23% 764ms 11.73% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.28% 8.51% 734ms 11.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 164ms 2.52% 11.02% 713ms 10.95% __dynamic_cast 3ms 0.046% 11.07% 699ms 10.73% CellPopulationElementWriter::Visit 22ms 0.34% 11.41% 680ms 10.44% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.15% 11.56% 679ms 10.43% TetrahedralMesh::ImportFromMesher 4ms 0.061% 11.62% 664ms 10.19% CellPropertyCollection::GetPropertiesType (inline) 29ms 0.45% 12.07% 639ms 9.81% operator new 195ms 2.99% 15.06% 608ms 9.34% __GI___libc_malloc 14ms 0.21% 15.28% 607ms 9.32% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.061% 15.34% 571ms 8.77% AbstractCellProperty::IsSubType (inline) 20ms 0.31% 15.65% 568ms 8.72% std::__new_allocator::allocate (inline) 0 0% 15.65% 562ms 8.63% std::allocator_traits::allocate (inline) 8ms 0.12% 15.77% 554ms 8.51% std::set::insert (inline) 15ms 0.23% 16.00% 546ms 8.38% std::_Rb_tree::_M_insert_unique 15ms 0.23% 16.23% 494ms 7.58% std::_Rb_tree::find (inline) 2ms 0.031% 16.26% 487ms 7.48% std::ostream::operator<< (inline) 64ms 0.98% 17.24% 483ms 7.42% std::ostream::_M_insert 0 0% 17.24% 463ms 7.11% std::set::count (inline) 64ms 0.98% 18.23% 457ms 7.02% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.015% 18.24% 455ms 6.99% triangulate 0 0% 18.24% 435ms 6.68% std::_Rb_tree::_M_create_node (inline) 0 0% 18.24% 434ms 6.66% std::set::~set (inline) 1ms 0.015% 18.26% 423ms 6.49% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 18.26% 422ms 6.48% std::_Rb_tree::_M_get_node (inline) 421ms 6.46% 24.72% 421ms 6.46% __strcmp_evex 0 0% 24.72% 411ms 6.31% std::_Rb_tree::_Alloc_node::operator() (inline) 49ms 0.75% 25.47% 411ms 6.31% std::map::operator[] (partial-inline) 1ms 0.015% 25.49% 406ms 6.23% Cell::GetCellProliferativeType 0 0% 25.49% 394ms 6.05% delaunay 1ms 0.015% 25.50% 392ms 6.02% divconqdelaunay 43ms 0.66% 26.16% 390ms 5.99% std::_Rb_tree::_M_erase 154ms 2.36% 28.53% 366ms 5.62% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.2% 28.73% 362ms 5.56% std::_Rb_tree::_Rb_tree (partial-inline) 32ms 0.49% 29.22% 356ms 5.47% std::_Rb_tree::_M_insert_ (inline) 2ms 0.031% 29.25% 351ms 5.39% AbstractCellBasedSimulation::DoCellBirth 0 0% 29.25% 343ms 5.27% std::_Rb_tree::_M_drop_node (inline) 1ms 0.015% 29.26% 335ms 5.14% std::set::set (inline) 1ms 0.015% 29.28% 332ms 5.10% NodeLocationWriter::Visit 224ms 3.44% 32.72% 325ms 4.99% _int_malloc 30ms 0.46% 33.18% 320ms 4.91% std::_Rb_tree::_M_copy (inline) 0 0% 33.18% 313ms 4.81% std::_Rb_tree::lower_bound (inline) 0 0% 33.18% 313ms 4.81% std::map::lower_bound (inline) 2ms 0.031% 33.21% 310ms 4.76% Element::Element 6ms 0.092% 33.30% 308ms 4.73% boost::detail::shared_count::~shared_count (inline) 0 0% 33.30% 308ms 4.73% boost::shared_ptr::~shared_ptr (inline) 294ms 4.51% 37.82% 295ms 4.53% boost::detail::sp_counted_base::release 53ms 0.81% 38.63% 287ms 4.41% __GI___libc_free 115ms 1.77% 40.40% 284ms 4.36% std::_Rb_tree::_M_clone_node (inline) 23ms 0.35% 40.75% 284ms 4.36% std::num_put::_M_insert_float 1ms 0.015% 40.76% 266ms 4.08% Cell::GetMutationState 5ms 0.077% 40.84% 247ms 3.79% std::__new_allocator::deallocate (inline) 3ms 0.046% 40.89% 246ms 3.78% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 40.89% 241ms 3.70% std::allocator_traits::deallocate (inline) 6ms 0.092% 40.98% 229ms 3.52% std::less::operator() (inline) 6ms 0.092% 41.07% 227ms 3.49% Element::RegisterWithNodes (inline) 198ms 3.04% 44.11% 226ms 3.47% _int_free 10ms 0.15% 44.27% 226ms 3.47% std::__cxx11::collate::do_transform 5ms 0.077% 44.34% 225ms 3.45% Cell::ReadyToDivide 223ms 3.42% 47.77% 223ms 3.42% std::operator< (inline) 10ms 0.15% 47.92% 218ms 3.35% Node::AddElement 7ms 0.11% 48.03% 214ms 3.29% divconqrecurse 214ms 3.29% 51.31% 214ms 3.29% std::_Rb_tree::_S_right (inline) 1ms 0.015% 51.33% 210ms 3.22% ___vsnprintf 2ms 0.031% 51.36% 209ms 3.21% __vsnprintf_internal (inline) 0 0% 51.36% 205ms 3.15% std::_Rb_tree::_M_put_node (inline) 25ms 0.38% 51.74% 202ms 3.10% __printf_buffer 59ms 0.91% 52.65% 202ms 3.10% mergehulls 2ms 0.031% 52.68% 199ms 3.06% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 52.68% 199ms 3.06% MeshBasedCellPopulation::GetDampingConstant 185ms 2.84% 55.52% 185ms 2.84% [libchaste_cell_based.so] 59ms 0.91% 56.43% 175ms 2.69% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.015% 56.44% 167ms 2.56% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.046% 56.49% 166ms 2.55% CellPropertyCollection::HasProperty 0 0% 56.49% 165ms 2.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 6ms 0.092% 56.58% 164ms 2.52% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 56.58% 163ms 2.50% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 56.58% 163ms 2.50% Cell::HasCellProperty (inline) 0 0% 56.58% 160ms 2.46% OutputFileHandler::OpenOutputFile 4ms 0.061% 56.64% 157ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.015% 56.66% 156ms 2.40% __printf_fp_spec (inline) 4ms 0.061% 56.72% 155ms 2.38% AbstractCellProperty::IsType (inline) 2ms 0.031% 56.75% 155ms 2.38% __printf_fp_l_buffer 9ms 0.14% 56.89% 148ms 2.27% AbstractTetrahedralElement::CalculateJacobian 1ms 0.015% 56.90% 148ms 2.27% CellProliferativeTypesWriter::VisitCell 75ms 1.15% 58.05% 146ms 2.24% __printf_fp_buffer_1 2ms 0.031% 58.08% 142ms 2.18% TetrahedralMesh::Clear 0 0% 58.08% 140ms 2.15% std::_Vector_base::_M_allocate (inline) 0 0% 58.08% 138ms 2.12% std::_Rb_tree::_M_destroy_node (inline) 0 0% 58.08% 138ms 2.12% std::__new_allocator::destroy (inline) 0 0% 58.08% 138ms 2.12% std::allocator_traits::destroy (inline) 19ms 0.29% 58.38% 136ms 2.09% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.015% 58.39% 132ms 2.03% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.046% 58.44% 123ms 1.89% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.031% 58.47% 121ms 1.86% std::vector::push_back (inline) 2ms 0.031% 58.50% 118ms 1.81% alternateaxes 98ms 1.50% 60.00% 115ms 1.77% vertexmedian 19ms 0.29% 60.29% 112ms 1.72% AbstractTetrahedralElement::RefreshJacobian 5ms 0.077% 60.37% 112ms 1.72% std::vector::_M_realloc_insert 107ms 1.64% 62.01% 107ms 1.64% [libchaste_mesh.so] 12ms 0.18% 62.20% 105ms 1.61% AbstractCellProperty::IsSame 23ms 0.35% 62.55% 102ms 1.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 22ms 0.34% 62.89% 102ms 1.57% std::num_put::_M_insert_int 72ms 1.11% 64.00% 97ms 1.49% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 96ms 1.47% 65.47% 96ms 1.47% [libstdc++.so.6.0.33] 9ms 0.14% 65.61% 93ms 1.43% std::type_info::operator== (inline) 1ms 0.015% 65.62% 92ms 1.41% boost::numeric::ublas::vector_assign (inline) 36ms 0.55% 66.18% 92ms 1.41% std::__ostream_insert 5ms 0.077% 66.25% 91ms 1.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.25% 91ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.046% 66.30% 91ms 1.40% boost::numeric::ublas::c_vector::c_vector (inline) 86ms 1.32% 67.62% 86ms 1.32% std::_Rb_tree_insert_and_rebalance 0 0% 67.62% 85ms 1.31% std::basic_ofstream::basic_ofstream (inline) 1ms 0.015% 67.63% 84ms 1.29% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.031% 67.66% 83ms 1.27% std::operator<< (inline) 6ms 0.092% 67.76% 82ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 67.76% 82ms 1.26% std::basic_filebuf::open 0 0% 67.76% 82ms 1.26% std::basic_ofstream::open (inline) 70ms 1.07% 68.83% 81ms 1.24% malloc_consolidate 27ms 0.41% 69.25% 80ms 1.23% AbstractElement::GetNodeLocation 80ms 1.23% 70.47% 80ms 1.23% incircle 2ms 0.031% 70.51% 75ms 1.15% Cell::GetCellId 5ms 0.077% 70.58% 74ms 1.14% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 70.58% 73ms 1.12% tcache_get (inline) 73ms 1.12% 71.70% 73ms 1.12% tcache_get_n (inline) 1ms 0.015% 71.72% 72ms 1.11% Node::~Node 0 0% 71.72% 71ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 38ms 0.58% 72.30% 69ms 1.06% std::basic_streambuf::xsputn 68ms 1.04% 73.35% 68ms 1.04% std::vector::size (inline) 67ms 1.03% 74.37% 67ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.046% 74.42% 65ms 1% AbstractCellPopulation::GetLocationIndexUsingCell 61ms 0.94% 75.36% 61ms 0.94% __memcpy_avx512_unaligned_erms 17ms 0.26% 75.62% 61ms 0.94% boost::numeric::ublas::indexing_vector_assign 1ms 0.015% 75.63% 61ms 0.94% std::basic_filebuf::close 0 0% 75.63% 60ms 0.92% AbstractCellBasedWriter::CloseFile 0 0% 75.63% 60ms 0.92% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 75.63% 60ms 0.92% std::basic_ofstream::close (inline) 1ms 0.015% 75.65% 59ms 0.91% OutputFileHandler::CommonConstructor 0 0% 75.65% 59ms 0.91% OutputFileHandler::OutputFileHandler 58ms 0.89% 76.54% 58ms 0.89% counterclockwise 0 0% 76.54% 56ms 0.86% OutputFileHandler::MakeFoldersAndReturnFullPath 55ms 0.84% 77.38% 55ms 0.84% std::_Rb_tree::_S_left (inline) 47ms 0.72% 78.11% 55ms 0.84% vertexsort 0 0% 78.11% 54ms 0.83% FilesystemPermissions::SetFilePermissions (inline) 54ms 0.83% 78.93% 54ms 0.83% __GI_fchmodat 2ms 0.031% 78.97% 54ms 0.83% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 78.97% 54ms 0.83% std::filesystem::permissions 0 0% 78.97% 54ms 0.83% std::vector::vector (inline) 0 0% 78.97% 52ms 0.8% std::_Vector_base::_M_create_storage (inline) 0 0% 78.97% 52ms 0.8% std::_Vector_base::_Vector_base (inline) 5ms 0.077% 79.04% 51ms 0.78% CellPropertyCollection::AddProperty 9ms 0.14% 79.18% 51ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 79.18% 50ms 0.77% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.031% 79.21% 49ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.015% 79.23% 48ms 0.74% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 79.23% 48ms 0.74% _IO_new_fopen 0 0% 79.23% 48ms 0.74% __fopen_internal (inline) 0 0% 79.23% 48ms 0.74% std::__basic_file::open 0 0% 79.23% 47ms 0.72% _IO_new_file_fopen 0 0% 79.23% 47ms 0.72% __GI__IO_file_open 30ms 0.46% 79.69% 47ms 0.72% boost::shared_ptr::shared_ptr (inline) 25ms 0.38% 80.07% 47ms 0.72% hack_digit 45ms 0.69% 80.76% 45ms 0.69% std::_Rb_tree_increment 24ms 0.37% 81.13% 45ms 0.69% std::basic_filebuf::xsputn 0 0% 81.13% 44ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 14ms 0.21% 81.35% 44ms 0.68% Determinant (inline) 42ms 0.64% 81.99% 44ms 0.68% __GI___libc_write 43ms 0.66% 82.65% 43ms 0.66% Node::rGetLocation 0 0% 82.65% 43ms 0.66% std::__basic_file::xsputn 0 0% 82.65% 43ms 0.66% std::basic_filebuf::_M_convert_to_external 0 0% 82.65% 43ms 0.66% std::basic_filebuf::_M_terminate_output 0 0% 82.65% 43ms 0.66% std::basic_filebuf::overflow 1ms 0.015% 82.67% 42ms 0.64% BoundaryNodeWriter::Visit 0 0% 82.67% 41ms 0.63% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 41ms 0.63% 83.29% 41ms 0.63% __libc_open64 18ms 0.28% 83.57% 39ms 0.6% AbstractElement::GetNodeGlobalIndex 0 0% 83.57% 39ms 0.6% Node::ClearAppliedForce 0 0% 83.57% 39ms 0.6% Node::ConstructNodeAttributes (inline) 1ms 0.015% 83.59% 38ms 0.58% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 83.59% 38ms 0.58% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.59% 38ms 0.58% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 83.59% 38ms 0.58% std::map::map (inline) 25ms 0.38% 83.97% 36ms 0.55% std::num_put::do_put 20ms 0.31% 84.28% 35ms 0.54% AbstractTetrahedralMesh::GetElement 26ms 0.4% 84.68% 34ms 0.52% CellPropertyCollection::GetProperty 34ms 0.52% 85.20% 34ms 0.52% Node::GetIndex 1ms 0.015% 85.21% 34ms 0.52% std::_Vector_base::_M_deallocate (inline) 0 0% 85.21% 34ms 0.52% std::basic_filebuf::_M_allocate_internal_buffer 24ms 0.37% 85.58% 33ms 0.51% boost::numeric::ublas::c_matrix::operator()