File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6721ms, 84.15% of 7987ms total Dropped 595 nodes (cum <= 39.94ms) flat flat% sum% cum cum% 0 0% 0% 7952ms 99.56% __libc_start_call_main 0 0% 0% 7952ms 99.56% __libc_start_main_impl 0 0% 0% 7952ms 99.56% _start 0 0% 0% 7938ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7938ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7938ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7938ms 99.39% main 0 0% 0% 7901ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7901ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7901ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7899ms 98.90% AbstractCellBasedSimulation::Solve 0 0% 0% 3391ms 42.46% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2948ms 36.91% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.013% 2906ms 36.38% MeshBasedCellPopulation::Update 0 0% 0.013% 1553ms 19.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 1499ms 18.77% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.025% 1407ms 17.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.13% 1351ms 16.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.14% 1347ms 16.86% MutableMesh::ReMesh 16ms 0.2% 0.34% 1288ms 16.13% MeshBasedCellPopulation::SpringIterator::operator++ 122ms 1.53% 1.87% 1059ms 13.26% TetrahedralMesh::EdgeIterator::operator++ 439ms 5.50% 7.36% 997ms 12.48% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.37% 990ms 12.40% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 13ms 0.16% 7.54% 986ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 285ms 3.57% 11.11% 959ms 12.01% __dynamic_cast 4ms 0.05% 11.16% 903ms 11.31% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.11% 11.27% 897ms 11.23% CellPopulationElementWriter::Visit 4ms 0.05% 11.32% 830ms 10.39% MeshBasedCellPopulation::AcceptCellWriter 23ms 0.29% 11.61% 780ms 9.77% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.063% 11.67% 755ms 9.45% AbstractCellProperty::IsSubType (inline) 30ms 0.38% 12.04% 718ms 8.99% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 12.08% 706ms 8.84% TetrahedralMesh::ImportFromMesher 3ms 0.038% 12.12% 621ms 7.78% std::ostream::operator<< (inline) 77ms 0.96% 13.08% 618ms 7.74% std::ostream::_M_insert 56ms 0.7% 13.78% 599ms 7.50% std::map::operator[] (partial-inline) 27ms 0.34% 14.12% 565ms 7.07% std::_Rb_tree::find (inline) 3ms 0.038% 14.16% 545ms 6.82% Cell::GetCellProliferativeType 543ms 6.80% 20.96% 543ms 6.80% __strcmp_avx2 5ms 0.063% 21.02% 539ms 6.75% std::set::insert (inline) 15ms 0.19% 21.21% 534ms 6.69% std::_Rb_tree::_M_insert_unique 7ms 0.088% 21.30% 530ms 6.64% LegacyCellProliferativeTypesWriter::VisitCell 36ms 0.45% 21.75% 530ms 6.64% operator new 0 0% 21.75% 520ms 6.51% std::set::count (inline) 159ms 1.99% 23.74% 490ms 6.13% __GI___libc_malloc 0 0% 23.74% 490ms 6.13% std::_Rb_tree::lower_bound (inline) 0 0% 23.74% 490ms 6.13% std::map::lower_bound (inline) 21ms 0.26% 24.00% 485ms 6.07% std::__new_allocator::allocate (inline) 213ms 2.67% 26.67% 482ms 6.03% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.67% 479ms 6.00% triangulate 0 0% 26.67% 478ms 5.98% std::allocator_traits::allocate (inline) 4ms 0.05% 26.72% 469ms 5.87% AbstractCellBasedSimulation::DoCellBirth 4ms 0.05% 26.77% 458ms 5.73% Cell::GetMutationState 0 0% 26.77% 427ms 5.35% delaunay 0 0% 26.77% 425ms 5.32% divconqdelaunay 0 0% 26.77% 412ms 5.16% std::_Rb_tree::_M_create_node (inline) 37ms 0.46% 27.23% 408ms 5.11% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.23% 391ms 4.90% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.23% 391ms 4.90% std::set::~set (inline) 11ms 0.14% 27.37% 386ms 4.83% std::less::operator() (inline) 375ms 4.70% 32.06% 375ms 4.70% std::operator< (inline) 0 0% 32.06% 367ms 4.59% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 32.08% 366ms 4.58% NodeLocationWriter::Visit 1ms 0.013% 32.09% 365ms 4.57% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 32.11% 364ms 4.56% AbstractCentreBasedCellPopulation::GetDampingConstant 83ms 1.04% 33.15% 363ms 4.54% std::_Rb_tree::_M_erase 17ms 0.21% 33.37% 344ms 4.31% std::_Rb_tree::_M_insert_ (inline) 18ms 0.23% 33.59% 334ms 4.18% std::_Rb_tree::_Rb_tree (partial-inline) 330ms 4.13% 37.72% 330ms 4.13% std::_Rb_tree::_S_right (inline) 2ms 0.025% 37.75% 326ms 4.08% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.75% 324ms 4.06% AbstractCellBasedWriter::OpenOutputFileForAppend 23ms 0.29% 38.04% 318ms 3.98% std::num_put::_M_insert_float 0 0% 38.04% 317ms 3.97% OutputFileHandler::OpenOutputFile 119ms 1.49% 39.53% 317ms 3.97% __GI___libc_free 3ms 0.038% 39.56% 314ms 3.93% Cell::ReadyToDivide 2ms 0.025% 39.59% 310ms 3.88% Element::Element 10ms 0.13% 39.71% 298ms 3.73% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.05% 39.76% 296ms 3.71% std::set::set (inline) 26ms 0.33% 40.09% 276ms 3.46% std::_Rb_tree::_M_copy (inline) 9ms 0.11% 40.20% 274ms 3.43% std::__new_allocator::deallocate (inline) 2ms 0.025% 40.23% 266ms 3.33% CellProliferativeTypesWriter::VisitCell 0 0% 40.23% 266ms 3.33% std::allocator_traits::deallocate (inline) 179ms 2.24% 42.47% 262ms 3.28% _int_malloc 0 0% 42.47% 260ms 3.26% std::_Rb_tree::_M_drop_node (inline) 4ms 0.05% 42.52% 252ms 3.16% std::__cxx11::collate::do_transform 10ms 0.13% 42.64% 250ms 3.13% CellPropertyCollection::HasProperty 7ms 0.088% 42.73% 248ms 3.11% divconqrecurse 0 0% 42.73% 246ms 3.08% Cell::HasCellProperty (inline) 3ms 0.038% 42.77% 245ms 3.07% AbstractCellProperty::IsType (inline) 76ms 0.95% 43.72% 244ms 3.05% std::_Rb_tree::_M_clone_node (inline) 4ms 0.05% 43.77% 234ms 2.93% ___vsnprintf 68ms 0.85% 44.62% 233ms 2.92% mergehulls 0 0% 44.62% 230ms 2.88% __vsnprintf_internal (inline) 32ms 0.4% 45.02% 223ms 2.79% __printf_buffer 0 0% 45.02% 211ms 2.64% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 45.05% 207ms 2.59% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.11% 45.16% 206ms 2.58% Element::RegisterWithNodes (inline) 7ms 0.088% 45.25% 203ms 2.54% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.13% 45.37% 200ms 2.50% MeshBasedCellPopulation::SpringsEnd (inline) 166ms 2.08% 47.45% 198ms 2.48% _int_free 3ms 0.038% 47.49% 196ms 2.45% Node::AddElement 14ms 0.18% 47.66% 193ms 2.42% TetrahedralMesh::Clear 48ms 0.6% 48.27% 185ms 2.32% AbstractCellProperty::IsSame 52ms 0.65% 48.92% 175ms 2.19% TetrahedralMesh::EdgesEnd (partial-inline) 44ms 0.55% 49.47% 175ms 2.19% std::_Rb_tree::_M_get_insert_unique_pos (inline) 9ms 0.11% 49.58% 170ms 2.13% __printf_fp_l_buffer 0 0% 49.58% 170ms 2.13% __printf_fp_spec (inline) 0 0% 49.58% 167ms 2.09% std::basic_ofstream::basic_ofstream (inline) 18ms 0.23% 49.81% 162ms 2.03% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 49.82% 162ms 2.03% std::basic_filebuf::open 0 0% 49.82% 162ms 2.03% std::basic_ofstream::open (inline) 4ms 0.05% 49.87% 159ms 1.99% boost::numeric::ublas::vector_assign (inline) 34ms 0.43% 50.29% 159ms 1.99% std::num_put::_M_insert_int 4ms 0.05% 50.34% 158ms 1.98% boost::numeric::ublas::c_vector::c_vector (inline) 80ms 1.00% 51.35% 154ms 1.93% __printf_fp_buffer_1 0 0% 51.35% 139ms 1.74% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.35% 139ms 1.74% OutputFileHandler::CommonConstructor 0 0% 51.35% 139ms 1.74% OutputFileHandler::OutputFileHandler 0 0% 51.35% 139ms 1.74% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.35% 139ms 1.74% std::basic_filebuf::close 0 0% 51.35% 138ms 1.73% AbstractCellBasedWriter::CloseFile 60ms 0.75% 52.10% 138ms 1.73% std::__ostream_insert 0 0% 52.10% 138ms 1.73% std::basic_ofstream::close (inline) 36ms 0.45% 52.55% 137ms 1.72% std::type_info::operator== (inline) 2ms 0.025% 52.57% 136ms 1.70% std::__basic_file::open 0 0% 52.57% 134ms 1.68% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 52.59% 134ms 1.68% _IO_new_fopen 1ms 0.013% 52.60% 133ms 1.67% __fopen_internal (inline) 20ms 0.25% 52.85% 131ms 1.64% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.075% 52.92% 131ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.025% 52.95% 131ms 1.64% _IO_new_file_fopen 1ms 0.013% 52.96% 129ms 1.62% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 52.96% 128ms 1.60% __GI__IO_file_open 21ms 0.26% 53.22% 127ms 1.59% std::_Rb_tree_const_iterator::operator++ (inline) 16ms 0.2% 53.42% 124ms 1.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.038% 53.46% 119ms 1.49% alternateaxes 118ms 1.48% 54.94% 118ms 1.48% std::_Rb_tree_insert_and_rebalance 44ms 0.55% 55.49% 117ms 1.46% boost::numeric::ublas::indexing_vector_assign 0 0% 55.49% 116ms 1.45% FilesystemPermissions::SetFilePermissions (inline) 7ms 0.088% 55.58% 116ms 1.45% Node::~Node 14ms 0.18% 55.75% 115ms 1.44% AbstractTetrahedralElement::RefreshJacobian 115ms 1.44% 57.19% 115ms 1.44% std::_Rb_tree_increment 1ms 0.013% 57.21% 115ms 1.44% std::filesystem::permissions 0 0% 57.21% 115ms 1.44% std::operator<< (inline) 103ms 1.29% 58.50% 115ms 1.44% vertexmedian 114ms 1.43% 59.92% 114ms 1.43% __libc_open64 3ms 0.038% 59.96% 113ms 1.41% AbstractTetrahedralElement::AbstractTetrahedralElement 113ms 1.41% 61.37% 113ms 1.41% __GI_fchmodat 2ms 0.025% 61.40% 113ms 1.41% std::_Vector_base::_M_allocate (inline) 43ms 0.54% 61.94% 112ms 1.40% boost::shared_ptr::shared_ptr (inline) 111ms 1.39% 63.33% 111ms 1.39% incircle 70ms 0.88% 64.20% 110ms 1.38% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.038% 64.24% 109ms 1.36% std::vector::push_back (inline) 9ms 0.11% 64.35% 107ms 1.34% boost::detail::shared_count::~shared_count (inline) 0 0% 64.35% 107ms 1.34% boost::shared_ptr::~shared_ptr (inline) 7ms 0.088% 64.44% 100ms 1.25% std::vector::_M_realloc_insert 1ms 0.013% 64.45% 97ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.025% 64.48% 97ms 1.21% std::basic_filebuf::overflow 1ms 0.013% 64.49% 96ms 1.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 95ms 1.19% 65.68% 96ms 1.20% boost::detail::sp_counted_base::release 0 0% 65.68% 96ms 1.20% std::basic_filebuf::_M_terminate_output 1ms 0.013% 65.69% 95ms 1.19% std::__basic_file::xsputn 0 0% 65.69% 95ms 1.19% std::basic_filebuf::_M_convert_to_external 94ms 1.18% 66.87% 94ms 1.18% __GI___libc_write 41ms 0.51% 67.38% 91ms 1.14% AbstractElement::GetNodeLocation 90ms 1.13% 68.51% 90ms 1.13% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.025% 68.54% 84ms 1.05% AbstractCellPopulation::GetLocationIndexUsingCell 82ms 1.03% 69.56% 82ms 1.03% [libchaste_cell_based.so] 52ms 0.65% 70.21% 82ms 1.03% std::basic_filebuf::xsputn 66ms 0.83% 71.04% 79ms 0.99% std::basic_streambuf::xsputn 61ms 0.76% 71.80% 75ms 0.94% std::num_put::do_put 3ms 0.038% 71.84% 74ms 0.93% CellPropertyCollection::AddProperty 4ms 0.05% 71.89% 72ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeA 46ms 0.58% 72.47% 72ms 0.9% malloc_consolidate 71ms 0.89% 73.36% 71ms 0.89% Node::GetIndex 0 0% 73.36% 70ms 0.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.36% 70ms 0.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 64ms 0.8% 74.16% 69ms 0.86% boost::detail::shared_count::shared_count (inline) 0 0% 74.16% 67ms 0.84% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 74.16% 67ms 0.84% std::filesystem::create_directory 54ms 0.68% 74.83% 65ms 0.81% AbstractElement::GetNodeGlobalIndex 4ms 0.05% 74.88% 65ms 0.81% std::filesystem::status 0 0% 74.88% 63ms 0.79% tcache_get (inline) 63ms 0.79% 75.67% 63ms 0.79% tcache_get_n (inline) 6ms 0.075% 75.75% 62ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 62ms 0.78% 76.52% 62ms 0.78% __GI___fstatat64 0 0% 76.52% 60ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 76.52% 59ms 0.74% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 5ms 0.063% 76.59% 57ms 0.71% std::_Vector_base::_M_deallocate (inline) 55ms 0.69% 77.28% 55ms 0.69% boost::shared_ptr::operator-> (inline) 55ms 0.69% 77.96% 55ms 0.69% counterclockwise 55ms 0.69% 78.65% 55ms 0.69% std::vector::size (inline) 0 0% 78.65% 54ms 0.68% boost::numeric::ublas::norm_2 (inline) 20ms 0.25% 78.90% 54ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.025% 78.93% 53ms 0.66% Cell::GetCellId 2ms 0.025% 78.95% 53ms 0.66% Node::ConstructNodeAttributes (inline) 2ms 0.025% 78.98% 53ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.98% 51ms 0.64% Node::ClearAppliedForce 28ms 0.35% 79.33% 51ms 0.64% boost::numeric::ublas::c_matrix::operator() 0 0% 79.33% 51ms 0.64% std::vector::vector (inline) 21ms 0.26% 79.59% 50ms 0.63% AbstractTetrahedralMesh::GetElement 50ms 0.63% 80.22% 50ms 0.63% __memcpy_avx_unaligned_erms 0 0% 80.22% 50ms 0.63% std::__new_allocator::construct (inline) 0 0% 80.22% 50ms 0.63% std::allocator_traits::construct (inline) 45ms 0.56% 80.78% 50ms 0.63% vertexsort 0 0% 80.78% 49ms 0.61% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.78% 49ms 0.61% std::__new_allocator::destroy (inline) 0 0% 80.78% 49ms 0.61% std::allocator_traits::destroy (inline) 49ms 0.61% 81.39% 49ms 0.61% std::ostream::sentry::sentry 48ms 0.6% 82.00% 48ms 0.6% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.00% 47ms 0.59% std::_Vector_base::_M_create_storage (inline) 0 0% 82.00% 47ms 0.59% std::_Vector_base::_Vector_base (inline) 46ms 0.58% 82.57% 46ms 0.58% Node::IsDeleted 2ms 0.025% 82.60% 46ms 0.58% NodeAttributes::NodeAttributes 0 0% 82.60% 45ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 82.60% 45ms 0.56% std::_Rb_tree::_M_construct_node (inline) 21ms 0.26% 82.86% 43ms 0.54% AbstractTetrahedralMesh::GetNumAllElements 0 0% 82.86% 43ms 0.54% std::map::map (inline) 1ms 0.013% 82.87% 42ms 0.53% BoundaryNodeWriter::Visit 42ms 0.53% 83.40% 42ms 0.53% [libchaste_mesh.so] 20ms 0.25% 83.65% 41ms 0.51% AbstractCellCycleModel::GetAge 40ms 0.5% 84.15% 40ms 0.5% [libstdc++.so.6.0.33] 0 0% 84.15% 40ms 0.5% std::map::find (inline)