File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6740ms, 84.62% of 7965ms total Dropped 564 nodes (cum <= 39.83ms) flat flat% sum% cum cum% 0 0% 0% 7927ms 99.52% __libc_start_call_main 0 0% 0% 7927ms 99.52% __libc_start_main_impl 0 0% 0% 7927ms 99.52% _start 0 0% 0% 7909ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7909ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7909ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7909ms 99.30% main 0 0% 0% 7867ms 98.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7867ms 98.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7867ms 98.77% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7864ms 98.73% AbstractCellBasedSimulation::Solve 0 0% 0% 3423ms 42.98% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2937ms 36.87% MeshBasedCellPopulation::Update 0 0% 0.013% 2849ms 35.77% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 1587ms 19.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.05% 1446ms 18.15% MutableMesh::ReMesh 3ms 0.038% 0.088% 1429ms 17.94% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.088% 1424ms 17.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.11% 0.2% 1369ms 17.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 26ms 0.33% 0.53% 1225ms 15.38% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.013% 0.54% 979ms 12.29% AbstractTwoBodyInteractionForce::AddForceContribution 94ms 1.18% 1.72% 969ms 12.17% TetrahedralMesh::EdgeIterator::operator++ 460ms 5.78% 7.50% 966ms 12.13% std::_Rb_tree::_M_lower_bound (inline) 298ms 3.74% 11.24% 939ms 11.79% __dynamic_cast 3ms 0.038% 11.27% 901ms 11.31% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 8ms 0.1% 11.37% 886ms 11.12% CellPopulationElementWriter::Visit 7ms 0.088% 11.46% 882ms 11.07% CellPropertyCollection::GetPropertiesType (inline) 46ms 0.58% 12.04% 872ms 10.95% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 28ms 0.35% 12.39% 793ms 9.96% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.075% 12.47% 730ms 9.17% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.038% 12.50% 719ms 9.03% AbstractCellProperty::IsSubType (inline) 4ms 0.05% 12.55% 706ms 8.86% TetrahedralMesh::ImportFromMesher 44ms 0.55% 13.11% 603ms 7.57% std::map::operator[] (partial-inline) 35ms 0.44% 13.55% 586ms 7.36% operator new 0 0% 13.55% 574ms 7.21% std::ostream::operator<< (inline) 101ms 1.27% 14.81% 572ms 7.18% std::ostream::_M_insert 4ms 0.05% 14.87% 570ms 7.16% triangulate 184ms 2.31% 17.18% 539ms 6.77% __GI___libc_malloc 26ms 0.33% 17.50% 534ms 6.70% std::__new_allocator::allocate (inline) 7ms 0.088% 17.59% 529ms 6.64% std::set::insert (inline) 0 0% 17.59% 528ms 6.63% std::allocator_traits::allocate (inline) 6ms 0.075% 17.66% 522ms 6.55% std::_Rb_tree::_M_insert_unique 1ms 0.013% 17.68% 514ms 6.45% Cell::GetCellProliferativeType 510ms 6.40% 24.08% 510ms 6.40% __strcmp_avx2 0 0% 24.08% 508ms 6.38% std::_Rb_tree::lower_bound (inline) 0 0% 24.08% 508ms 6.38% std::map::lower_bound (inline) 19ms 0.24% 24.32% 504ms 6.33% std::_Rb_tree::find (inline) 0 0% 24.32% 489ms 6.14% delaunay 4ms 0.05% 24.37% 487ms 6.11% divconqdelaunay 3ms 0.038% 24.41% 473ms 5.94% AbstractCellBasedSimulation::DoCellBirth 0 0% 24.41% 459ms 5.76% std::set::count (inline) 39ms 0.49% 24.90% 458ms 5.75% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.063% 24.96% 448ms 5.62% LegacyCellProliferativeTypesWriter::VisitCell 206ms 2.59% 27.55% 446ms 5.60% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.55% 435ms 5.46% std::_Rb_tree::_M_create_node (inline) 0 0% 27.55% 423ms 5.31% std::set::~set (inline) 0 0% 27.55% 416ms 5.22% std::_Rb_tree::_Alloc_node::operator() (inline) 81ms 1.02% 28.56% 412ms 5.17% std::_Rb_tree::_M_erase 0 0% 28.56% 405ms 5.08% std::_Rb_tree::_M_get_node (inline) 30ms 0.38% 28.94% 379ms 4.76% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 28.95% 373ms 4.68% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.95% 372ms 4.67% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 28.96% 362ms 4.54% OutputFileHandler::OpenOutputFile 2ms 0.025% 28.99% 357ms 4.48% Cell::GetMutationState 5ms 0.063% 29.05% 344ms 4.32% std::set::set (inline) 0 0% 29.05% 338ms 4.24% NodeLocationWriter::Visit 8ms 0.1% 29.15% 329ms 4.13% std::less::operator() (inline) 107ms 1.34% 30.50% 326ms 4.09% __GI___libc_free 19ms 0.24% 30.73% 324ms 4.07% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 30.75% 322ms 4.04% Cell::ReadyToDivide 321ms 4.03% 34.78% 321ms 4.03% std::_Rb_tree::_S_right (inline) 321ms 4.03% 38.81% 321ms 4.03% std::operator< (inline) 7ms 0.088% 38.90% 312ms 3.92% Element::Element 42ms 0.53% 39.42% 310ms 3.89% std::_Rb_tree::_M_copy (inline) 0 0% 39.42% 309ms 3.88% std::_Rb_tree::_M_drop_node (inline) 0 0% 39.42% 305ms 3.83% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 39.45% 304ms 3.82% AbstractCentreBasedCellPopulation::GetDampingConstant 13ms 0.16% 39.61% 301ms 3.78% std::__new_allocator::deallocate (inline) 0 0% 39.61% 299ms 3.75% std::allocator_traits::deallocate (inline) 9ms 0.11% 39.72% 292ms 3.67% AbstractCellPopulation::IsCellAttachedToLocationIndex 30ms 0.38% 40.10% 292ms 3.67% std::num_put::_M_insert_float 175ms 2.20% 42.30% 274ms 3.44% _int_malloc 62ms 0.78% 43.08% 261ms 3.28% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.08% 260ms 3.26% std::_Rb_tree::_M_put_node (inline) 9ms 0.11% 43.19% 259ms 3.25% divconqrecurse 2ms 0.025% 43.21% 246ms 3.09% CellProliferativeTypesWriter::VisitCell 74ms 0.93% 44.14% 238ms 2.99% mergehulls 6ms 0.075% 44.22% 229ms 2.88% CellPropertyCollection::HasProperty 3ms 0.038% 44.26% 229ms 2.88% std::__cxx11::collate::do_transform 0 0% 44.26% 228ms 2.86% Cell::HasCellProperty (inline) 2ms 0.025% 44.28% 224ms 2.81% AbstractCellProperty::IsType (inline) 3ms 0.038% 44.32% 219ms 2.75% ___vsnprintf 10ms 0.13% 44.44% 218ms 2.74% Element::RegisterWithNodes (inline) 188ms 2.36% 46.80% 218ms 2.74% _int_free 0 0% 46.80% 216ms 2.71% __vsnprintf_internal (inline) 16ms 0.2% 47.01% 210ms 2.64% __printf_buffer 3ms 0.038% 47.04% 209ms 2.62% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.05% 47.09% 204ms 2.56% MeshBasedCellPopulation::SpringsEnd (inline) 10ms 0.13% 47.22% 202ms 2.54% Node::AddElement 5ms 0.063% 47.28% 199ms 2.50% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.14% 47.42% 194ms 2.44% TetrahedralMesh::Clear 70ms 0.88% 48.30% 192ms 2.41% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 48.30% 182ms 2.28% std::basic_ofstream::basic_ofstream (inline) 42ms 0.53% 48.83% 179ms 2.25% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 48.84% 177ms 2.22% __printf_fp_spec (inline) 1ms 0.013% 48.85% 177ms 2.22% std::basic_filebuf::open 0 0% 48.85% 177ms 2.22% std::basic_ofstream::open (inline) 8ms 0.1% 48.95% 176ms 2.21% __printf_fp_l_buffer 43ms 0.54% 49.49% 166ms 2.08% AbstractCellProperty::IsSame 69ms 0.87% 50.36% 157ms 1.97% __printf_fp_buffer_1 0 0% 50.36% 152ms 1.91% FilesystemPermissions::SetFilePermissions (inline) 7ms 0.088% 50.45% 151ms 1.90% AbstractTetrahedralElement::CalculateJacobian 19ms 0.24% 50.68% 151ms 1.90% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 50.70% 151ms 1.90% std::filesystem::permissions 150ms 1.88% 52.58% 150ms 1.88% __GI_fchmodat 0 0% 52.58% 148ms 1.86% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 52.61% 148ms 1.86% std::basic_filebuf::close 0 0% 52.61% 147ms 1.85% AbstractCellBasedWriter::CloseFile 4ms 0.05% 52.66% 147ms 1.85% std::__basic_file::open 0 0% 52.66% 147ms 1.85% std::basic_ofstream::close (inline) 66ms 0.83% 53.48% 144ms 1.81% std::__ostream_insert 0 0% 53.48% 143ms 1.80% _IO_new_fopen 0 0% 53.48% 143ms 1.80% __fopen_internal (inline) 0 0% 53.48% 142ms 1.78% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 53.50% 141ms 1.77% _IO_new_file_fopen 4ms 0.05% 53.55% 141ms 1.77% alternateaxes 83ms 1.04% 54.59% 139ms 1.75% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 128ms 1.61% 56.20% 137ms 1.72% vertexmedian 1ms 0.013% 56.21% 136ms 1.71% __GI__IO_file_open 16ms 0.2% 56.41% 135ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (partial-inline) 7ms 0.088% 56.50% 131ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 56.50% 126ms 1.58% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 56.51% 125ms 1.57% std::operator<< (inline) 5ms 0.063% 56.57% 123ms 1.54% boost::numeric::ublas::vector_assign (inline) 0 0% 56.57% 123ms 1.54% std::_Vector_base::_M_allocate (inline) 28ms 0.35% 56.92% 123ms 1.54% std::type_info::operator== (inline) 6ms 0.075% 57.00% 122ms 1.53% Node::~Node 1ms 0.013% 57.01% 121ms 1.52% OutputFileHandler::CommonConstructor 0 0% 57.01% 121ms 1.52% OutputFileHandler::OutputFileHandler 16ms 0.2% 57.21% 119ms 1.49% AbstractTetrahedralElement::RefreshJacobian 0 0% 57.21% 118ms 1.48% OutputFileHandler::MakeFoldersAndReturnFullPath 115ms 1.44% 58.66% 117ms 1.47% __libc_open64 5ms 0.063% 58.72% 117ms 1.47% boost::numeric::ublas::c_vector::c_vector (inline) 30ms 0.38% 59.10% 116ms 1.46% std::num_put::_M_insert_int 15ms 0.19% 59.28% 109ms 1.37% boost::detail::shared_count::~shared_count (inline) 0 0% 59.28% 109ms 1.37% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 59.30% 107ms 1.34% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 59.31% 107ms 1.34% std::basic_filebuf::_M_terminate_output 0 0% 59.31% 107ms 1.34% std::basic_filebuf::overflow 2ms 0.025% 59.33% 106ms 1.33% std::__basic_file::xsputn 5ms 0.063% 59.40% 103ms 1.29% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 4ms 0.05% 59.45% 103ms 1.29% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 102ms 1.28% 60.73% 102ms 1.28% __GI___libc_write 3ms 0.038% 60.77% 99ms 1.24% std::vector::push_back (inline) 8ms 0.1% 60.87% 97ms 1.22% std::_Rb_tree_const_iterator::operator++ (inline) 95ms 1.19% 62.06% 95ms 1.19% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 62.07% 94ms 1.18% AbstractTetrahedralElement::AbstractTetrahedralElement 94ms 1.18% 63.25% 94ms 1.18% [libchaste_cell_based.so] 13ms 0.16% 63.41% 94ms 1.18% std::vector::_M_realloc_insert 44ms 0.55% 63.97% 93ms 1.17% boost::shared_ptr::shared_ptr (inline) 91ms 1.14% 65.11% 91ms 1.14% std::_Rb_tree_increment 90ms 1.13% 66.24% 90ms 1.13% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 88ms 1.10% 67.34% 88ms 1.10% incircle 5ms 0.063% 67.41% 86ms 1.08% TetrahedralMesh::EdgeIterator::GetNodeB 82ms 1.03% 68.44% 85ms 1.07% boost::detail::sp_counted_base::release 2ms 0.025% 68.46% 84ms 1.05% AbstractCellPopulation::GetLocationIndexUsingCell 38ms 0.48% 68.94% 84ms 1.05% AbstractElement::GetNodeLocation 49ms 0.62% 69.55% 84ms 1.05% malloc_consolidate 25ms 0.31% 69.87% 82ms 1.03% boost::numeric::ublas::indexing_vector_assign 82ms 1.03% 70.90% 82ms 1.03% std::vector::size (inline) 81ms 1.02% 71.91% 81ms 1.02% counterclockwise 0 0% 71.91% 77ms 0.97% Cell::GetCellId 71ms 0.89% 72.81% 75ms 0.94% vertexsort 73ms 0.92% 73.72% 73ms 0.92% __memcpy_avx_unaligned_erms 49ms 0.62% 74.34% 71ms 0.89% AbstractElement::GetNodeGlobalIndex 0 0% 74.34% 71ms 0.89% tcache_get (inline) 71ms 0.89% 75.23% 71ms 0.89% tcache_get_n (inline) 69ms 0.87% 76.10% 70ms 0.88% __GI___fstatat64 37ms 0.46% 76.56% 70ms 0.88% std::basic_filebuf::xsputn 1ms 0.013% 76.57% 70ms 0.88% std::filesystem::status 0 0% 76.57% 69ms 0.87% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 76.59% 69ms 0.87% std::filesystem::create_directory 0 0% 76.59% 68ms 0.85% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.59% 68ms 0.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 40ms 0.5% 77.09% 64ms 0.8% std::basic_streambuf::xsputn 6ms 0.075% 77.16% 63ms 0.79% CellPropertyCollection::AddProperty 0 0% 77.16% 63ms 0.79% std::vector::vector (inline) 61ms 0.77% 77.93% 61ms 0.77% Node::GetIndex 26ms 0.33% 78.25% 60ms 0.75% AbstractTetrahedralMesh::GetElement 0 0% 78.25% 60ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.063% 78.32% 59ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 78.32% 59ms 0.74% std::_Vector_base::_Vector_base (inline) 53ms 0.67% 78.98% 58ms 0.73% std::num_put::do_put 0 0% 78.98% 57ms 0.72% std::_Vector_base::_M_create_storage (inline) 29ms 0.36% 79.35% 56ms 0.7% hack_digit 55ms 0.69% 80.04% 55ms 0.69% [libchaste_mesh.so] 33ms 0.41% 80.45% 55ms 0.69% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 80.45% 54ms 0.68% boost::numeric::ublas::norm_2 (inline) 18ms 0.23% 80.68% 54ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.68% 53ms 0.67% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 6ms 0.075% 80.75% 52ms 0.65% Node::ConstructNodeAttributes (inline) 3ms 0.038% 80.79% 51ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 50ms 0.63% 81.42% 50ms 0.63% [libstdc++.so.6.0.33] 49ms 0.62% 82.03% 49ms 0.62% boost::detail::shared_count::shared_count (inline) 0 0% 82.03% 49ms 0.62% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.03% 49ms 0.62% std::__new_allocator::destroy (inline) 0 0% 82.03% 49ms 0.62% std::allocator_traits::destroy (inline) 0 0% 82.03% 48ms 0.6% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 48ms 0.6% 82.64% 48ms 0.6% unlink_chunk 27ms 0.34% 82.98% 47ms 0.59% AbstractCellCycleModel::GetAge 1ms 0.013% 82.99% 47ms 0.59% Node::ClearAppliedForce 45ms 0.56% 83.55% 45ms 0.56% boost::shared_ptr::operator-> (inline) 3ms 0.038% 83.59% 45ms 0.56% std::__copy_move::__copy_m (inline) 0 0% 83.59% 45ms 0.56% std::__copy_move_a (inline) 0 0% 83.59% 45ms 0.56% std::__copy_move_a1 (inline) 0 0% 83.59% 45ms 0.56% std::__copy_move_a2 (inline) 0 0% 83.59% 45ms 0.56% std::copy (inline) 0 0% 83.59% 44ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 36ms 0.45% 84.04% 44ms 0.55% writeedges 1ms 0.013% 84.06% 43ms 0.54% BoundaryNodeWriter::Visit 5ms 0.063% 84.12% 42ms 0.53% std::_Vector_base::_M_deallocate (inline) 0 0% 84.12% 41ms 0.51% _dl_init 0 0% 84.12% 41ms 0.51% call_init (inline) 0 0% 84.12% 40ms 0.5% std::map::find (inline) 0 0% 84.12% 40ms 0.5% std::map::map (inline) 40ms 0.5% 84.62% 40ms 0.5% std::ostream::sentry::sentry