File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6460ms, 86.10% of 7503ms total Dropped 580 nodes (cum <= 37.52ms) flat flat% sum% cum cum% 0 0% 0% 7469ms 99.55% __libc_start_call_main 0 0% 0% 7469ms 99.55% __libc_start_main_impl 0 0% 0% 7469ms 99.55% _start 0 0% 0% 7453ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7453ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7453ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7453ms 99.33% main 0 0% 0% 7414ms 98.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7414ms 98.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7414ms 98.81% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7411ms 98.77% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3499ms 46.63% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 3081ms 41.06% MeshBasedCellPopulation::Update 1ms 0.013% 0.027% 2441ms 32.53% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.04% 1582ms 21.08% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.027% 0.067% 1466ms 19.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.067% 1437ms 19.15% MutableMesh::ReMesh 37ms 0.49% 0.56% 1376ms 18.34% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.013% 0.57% 1280ms 17.06% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.57% 1245ms 16.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 132ms 1.76% 2.33% 1131ms 15.07% TetrahedralMesh::EdgeIterator::operator++ 9ms 0.12% 2.45% 946ms 12.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 439ms 5.85% 8.30% 923ms 12.30% std::_Rb_tree::_M_lower_bound (inline) 7ms 0.093% 8.40% 903ms 12.04% AbstractTwoBodyInteractionForce::AddForceContribution 205ms 2.73% 11.13% 864ms 11.52% __dynamic_cast 12ms 0.16% 11.29% 824ms 10.98% CellPopulationElementWriter::Visit 44ms 0.59% 11.88% 821ms 10.94% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.04% 11.92% 799ms 10.65% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.12% 12.04% 773ms 10.30% MeshBasedCellPopulation::AcceptCellWriter 19ms 0.25% 12.29% 737ms 9.82% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.067% 12.36% 730ms 9.73% TetrahedralMesh::ImportFromMesher 30ms 0.4% 12.75% 672ms 8.96% operator new 5ms 0.067% 12.82% 670ms 8.93% AbstractCellProperty::IsSubType (inline) 243ms 3.24% 16.06% 639ms 8.52% __GI___libc_malloc 10ms 0.13% 16.19% 609ms 8.12% std::set::insert (inline) 16ms 0.21% 16.41% 599ms 7.98% std::_Rb_tree::_M_insert_unique 21ms 0.28% 16.69% 596ms 7.94% std::__new_allocator::allocate (inline) 0 0% 16.69% 590ms 7.86% std::allocator_traits::allocate (inline) 14ms 0.19% 16.87% 564ms 7.52% std::_Rb_tree::find (inline) 89ms 1.19% 18.06% 564ms 7.52% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.027% 18.09% 536ms 7.14% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.013% 18.10% 536ms 7.14% triangulate 0 0% 18.10% 529ms 7.05% std::set::count (inline) 0 0% 18.10% 518ms 6.90% std::ostream::operator<< (inline) 0 0% 18.10% 517ms 6.89% std::set::~set (inline) 50ms 0.67% 18.77% 516ms 6.88% std::map::operator[] (partial-inline) 78ms 1.04% 19.81% 516ms 6.88% std::ostream::_M_insert 0 0% 19.81% 515ms 6.86% Cell::GetCellProliferativeType 512ms 6.82% 26.63% 512ms 6.82% __strcmp_evex 0 0% 26.63% 486ms 6.48% std::_Rb_tree::_M_create_node (inline) 54ms 0.72% 27.35% 474ms 6.32% std::_Rb_tree::_M_erase 0 0% 27.35% 467ms 6.22% std::_Rb_tree::_M_get_node (inline) 0 0% 27.35% 465ms 6.20% delaunay 1ms 0.013% 27.36% 463ms 6.17% divconqdelaunay 204ms 2.72% 30.08% 452ms 6.02% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 30.08% 451ms 6.01% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 30.08% 417ms 5.56% std::_Rb_tree::_M_drop_node (inline) 1ms 0.013% 30.09% 410ms 5.46% AbstractCellBasedSimulation::DoCellBirth 0 0% 30.09% 402ms 5.36% std::_Rb_tree::lower_bound (inline) 0 0% 30.09% 402ms 5.36% std::map::lower_bound (inline) 30ms 0.4% 30.49% 395ms 5.26% std::_Rb_tree::_M_insert_ (inline) 14ms 0.19% 30.68% 390ms 5.20% std::_Rb_tree::_Rb_tree (partial-inline) 84ms 1.12% 31.80% 366ms 4.88% __GI___libc_free 2ms 0.027% 31.83% 365ms 4.86% std::set::set (inline) 5ms 0.067% 31.89% 351ms 4.68% Cell::GetMutationState 36ms 0.48% 32.37% 342ms 4.56% std::_Rb_tree::_M_copy (inline) 12ms 0.16% 32.53% 336ms 4.48% Element::Element 7ms 0.093% 32.63% 326ms 4.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 12ms 0.16% 32.79% 325ms 4.33% std::__new_allocator::deallocate (inline) 2ms 0.027% 32.81% 321ms 4.28% NodeLocationWriter::Visit 0 0% 32.81% 320ms 4.26% std::allocator_traits::deallocate (inline) 6ms 0.08% 32.89% 319ms 4.25% boost::detail::shared_count::~shared_count (inline) 0 0% 32.89% 319ms 4.25% boost::shared_ptr::~shared_ptr (inline) 303ms 4.04% 36.93% 304ms 4.05% boost::detail::sp_counted_base::release 217ms 2.89% 39.82% 297ms 3.96% _int_malloc 122ms 1.63% 41.45% 297ms 3.96% std::_Rb_tree::_M_clone_node (inline) 14ms 0.19% 41.64% 277ms 3.69% std::less::operator() (inline) 235ms 3.13% 44.77% 276ms 3.68% _int_free 20ms 0.27% 45.04% 275ms 3.67% std::num_put::_M_insert_float 2ms 0.027% 45.06% 271ms 3.61% MeshBasedCellPopulation::GetDampingConstant 271ms 3.61% 48.67% 271ms 3.61% std::_Rb_tree::_S_right (inline) 0 0% 48.67% 270ms 3.60% std::_Rb_tree::_M_put_node (inline) 2ms 0.027% 48.70% 268ms 3.57% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.12% 48.82% 265ms 3.53% divconqrecurse 263ms 3.51% 52.33% 263ms 3.51% std::operator< (inline) 4ms 0.053% 52.38% 256ms 3.41% Cell::ReadyToDivide 81ms 1.08% 53.46% 246ms 3.28% mergehulls 3ms 0.04% 53.50% 234ms 3.12% Element::RegisterWithNodes (inline) 6ms 0.08% 53.58% 228ms 3.04% std::__cxx11::collate::do_transform 9ms 0.12% 53.70% 227ms 3.03% Node::AddElement 213ms 2.84% 56.54% 213ms 2.84% [libchaste_cell_based.so] 0 0% 56.54% 212ms 2.83% ___vsnprintf 1ms 0.013% 56.55% 212ms 2.83% __vsnprintf_internal (inline) 2ms 0.027% 56.58% 207ms 2.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 20ms 0.27% 56.84% 204ms 2.72% __printf_buffer 5ms 0.067% 56.91% 203ms 2.71% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.013% 56.92% 203ms 2.71% CellProliferativeTypesWriter::VisitCell 4ms 0.053% 56.98% 193ms 2.57% AbstractCellProperty::IsType (inline) 75ms 1% 57.98% 188ms 2.51% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 57.98% 185ms 2.47% Cell::HasCellProperty (inline) 3ms 0.04% 58.02% 185ms 2.47% CellPropertyCollection::HasProperty 19ms 0.25% 58.27% 178ms 2.37% AbstractTetrahedralElement::CalculateJacobian 11ms 0.15% 58.42% 172ms 2.29% __printf_fp_l_buffer 0 0% 58.42% 172ms 2.29% __printf_fp_spec (inline) 8ms 0.11% 58.52% 169ms 2.25% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 58.54% 160ms 2.13% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 58.54% 159ms 2.12% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 58.54% 157ms 2.09% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 58.55% 156ms 2.08% TetrahedralMesh::Clear 0 0% 58.55% 153ms 2.04% OutputFileHandler::OpenOutputFile 78ms 1.04% 59.59% 151ms 2.01% __printf_fp_buffer_1 16ms 0.21% 59.80% 148ms 1.97% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 59.80% 147ms 1.96% std::_Rb_tree::_M_destroy_node (inline) 0 0% 59.80% 147ms 1.96% std::__new_allocator::destroy (inline) 0 0% 59.80% 147ms 1.96% std::allocator_traits::destroy (inline) 3ms 0.04% 59.84% 146ms 1.95% AbstractTetrahedralElement::CalculateInverseJacobian 142ms 1.89% 61.74% 142ms 1.89% [libchaste_mesh.so] 17ms 0.23% 61.96% 132ms 1.76% AbstractCellProperty::IsSame 2ms 0.027% 61.99% 125ms 1.67% std::vector::push_back (inline) 84ms 1.12% 63.11% 124ms 1.65% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 63.12% 124ms 1.65% std::_Vector_base::_M_allocate (inline) 44ms 0.59% 63.71% 124ms 1.65% std::num_put::_M_insert_int 14ms 0.19% 63.89% 122ms 1.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 63.89% 120ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.067% 63.96% 119ms 1.59% std::vector::_M_realloc_insert 28ms 0.37% 64.33% 115ms 1.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 13ms 0.17% 64.51% 115ms 1.53% std::type_info::operator== (inline) 2ms 0.027% 64.53% 114ms 1.52% alternateaxes 114ms 1.52% 66.05% 114ms 1.52% incircle 1ms 0.013% 66.07% 112ms 1.49% boost::numeric::ublas::vector_assign (inline) 106ms 1.41% 67.48% 112ms 1.49% vertexmedian 12ms 0.16% 67.64% 108ms 1.44% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.027% 67.67% 107ms 1.43% boost::numeric::ublas::c_vector::c_vector (inline) 12ms 0.16% 67.83% 104ms 1.39% AbstractTetrahedralElement::RefreshJacobian 100ms 1.33% 69.16% 100ms 1.33% std::_Rb_tree_insert_and_rebalance 43ms 0.57% 69.73% 100ms 1.33% std::__ostream_insert 1ms 0.013% 69.75% 94ms 1.25% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.08% 69.83% 91ms 1.21% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.027% 69.85% 89ms 1.19% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.2% 70.05% 88ms 1.17% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 70.05% 86ms 1.15% Node::~Node 1ms 0.013% 70.07% 86ms 1.15% std::operator<< (inline) 0 0% 70.07% 83ms 1.11% tcache_get (inline) 83ms 1.11% 71.17% 83ms 1.11% tcache_get_n (inline) 82ms 1.09% 72.26% 82ms 1.09% [libstdc++.so.6.0.33] 32ms 0.43% 72.69% 81ms 1.08% AbstractElement::GetNodeLocation 21ms 0.28% 72.97% 79ms 1.05% boost::numeric::ublas::indexing_vector_assign 0 0% 72.97% 79ms 1.05% std::basic_ofstream::basic_ofstream (inline) 2ms 0.027% 73.00% 77ms 1.03% std::basic_filebuf::open 0 0% 73.00% 77ms 1.03% std::basic_ofstream::open (inline) 65ms 0.87% 73.86% 76ms 1.01% vertexsort 0 0% 73.86% 72ms 0.96% CellPropertyCollection::~CellPropertyCollection (inline) 9ms 0.12% 73.98% 71ms 0.95% CellPropertyCollection::AddProperty 8ms 0.11% 74.09% 70ms 0.93% TetrahedralMesh::EdgeIterator::GetNodeA 67ms 0.89% 74.98% 67ms 0.89% std::vector::size (inline) 0 0% 74.98% 66ms 0.88% AbstractCellPopulation::CloseRoundRobinWritersFiles 66ms 0.88% 75.86% 66ms 0.88% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 66ms 0.88% 76.74% 66ms 0.88% std::_Rb_tree::_S_left (inline) 0 0% 76.74% 65ms 0.87% AbstractCellBasedWriter::CloseFile 0 0% 76.74% 65ms 0.87% std::basic_filebuf::close 0 0% 76.74% 65ms 0.87% std::basic_ofstream::close (inline) 1ms 0.013% 76.76% 64ms 0.85% Cell::GetCellId 0 0% 76.76% 64ms 0.85% OutputFileHandler::CommonConstructor 0 0% 76.76% 64ms 0.85% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 76.76% 64ms 0.85% OutputFileHandler::OutputFileHandler 4ms 0.053% 76.81% 64ms 0.85% std::_Rb_tree::_M_emplace_hint_unique 28ms 0.37% 77.18% 63ms 0.84% Determinant (inline) 51ms 0.68% 77.86% 62ms 0.83% malloc_consolidate 4ms 0.053% 77.92% 62ms 0.83% std::_Rb_tree_const_iterator::operator++ (inline) 24ms 0.32% 78.24% 60ms 0.8% AbstractElement::GetNodeGlobalIndex 3ms 0.04% 78.28% 60ms 0.8% Node::ConstructNodeAttributes (inline) 0 0% 78.28% 59ms 0.79% Node::ClearAppliedForce 54ms 0.72% 79.00% 54ms 0.72% __memcpy_avx512_unaligned_erms 33ms 0.44% 79.43% 54ms 0.72% std::basic_streambuf::xsputn 52ms 0.69% 80.13% 52ms 0.69% std::_Rb_tree_increment 51ms 0.68% 80.81% 51ms 0.68% counterclockwise 30ms 0.4% 81.21% 51ms 0.68% hack_digit 50ms 0.67% 81.87% 50ms 0.67% __GI___libc_write 0 0% 81.87% 50ms 0.67% std::vector::vector (inline) 0 0% 81.87% 49ms 0.65% FilesystemPermissions::SetFilePermissions (inline) 4ms 0.053% 81.93% 49ms 0.65% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 81.93% 49ms 0.65% _IO_new_fopen 49ms 0.65% 82.58% 49ms 0.65% __GI_fchmodat 0 0% 82.58% 49ms 0.65% __fopen_internal (inline) 0 0% 82.58% 49ms 0.65% std::__basic_file::open 1ms 0.013% 82.59% 49ms 0.65% std::basic_filebuf::overflow 0 0% 82.59% 49ms 0.65% std::filesystem::permissions 36ms 0.48% 83.07% 48ms 0.64% CellPropertyCollection::GetProperty 22ms 0.29% 83.37% 48ms 0.64% boost::shared_ptr::shared_ptr (inline) 0 0% 83.37% 48ms 0.64% std::__basic_file::xsputn 0 0% 83.37% 48ms 0.64% std::basic_filebuf::_M_convert_to_external 0 0% 83.37% 48ms 0.64% std::basic_filebuf::_M_terminate_output 26ms 0.35% 83.71% 48ms 0.64% std::basic_filebuf::xsputn 40ms 0.53% 84.25% 48ms 0.64% std::num_put::do_put 0 0% 84.25% 47ms 0.63% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 84.25% 47ms 0.63% _IO_new_file_fopen 1ms 0.013% 84.26% 47ms 0.63% std::_Vector_base::_M_deallocate (inline) 0 0% 84.26% 47ms 0.63% std::map::~map (inline) 0 0% 84.26% 46ms 0.61% __GI__IO_file_open 0 0% 84.26% 45ms 0.6% std::_Vector_base::_Vector_base (inline) 30ms 0.4% 84.66% 43ms 0.57% AbstractTetrahedralMesh::GetElement 41ms 0.55% 85.21% 42ms 0.56% __libc_open64 0 0% 85.21% 41ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.21% 41ms 0.55% std::_Vector_base::_M_create_storage (inline) 40ms 0.53% 85.74% 40ms 0.53% tcache_put (inline) 27ms 0.36% 86.10% 40ms 0.53% writeedges 0 0% 86.10% 39ms 0.52% _dl_init 0 0% 86.10% 39ms 0.52% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 86.10% 39ms 0.52% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 86.10% 39ms 0.52% call_init (inline) 0 0% 86.10% 38ms 0.51% BoundaryNodeWriter::Visit