File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6767ms, 84.65% of 7994ms total Dropped 572 nodes (cum <= 39.97ms) flat flat% sum% cum cum% 0 0% 0% 7955ms 99.51% __libc_start_call_main 0 0% 0% 7955ms 99.51% __libc_start_main_impl 0 0% 0% 7955ms 99.51% _start 0 0% 0% 7935ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7935ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7935ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7935ms 99.26% main 0 0% 0% 7897ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7897ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7897ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7895ms 98.76% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3452ms 43.18% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.025% 3006ms 37.60% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2874ms 35.95% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.05% 1558ms 19.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.063% 1475ms 18.45% MutableMesh::ReMesh 3ms 0.038% 0.1% 1466ms 18.34% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.11% 1401ms 17.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.063% 0.18% 1341ms 16.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.16% 0.34% 1238ms 15.49% MeshBasedCellPopulation::SpringIterator::operator++ 106ms 1.33% 1.66% 1000ms 12.51% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.66% 988ms 12.36% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 402ms 5.03% 6.69% 937ms 11.72% std::_Rb_tree::_M_lower_bound (inline) 0 0% 6.69% 936ms 11.71% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.075% 6.77% 925ms 11.57% CellPropertyCollection::GetPropertiesType (inline) 247ms 3.09% 9.86% 918ms 11.48% __dynamic_cast 4ms 0.05% 9.91% 878ms 10.98% CellPopulationElementWriter::Visit 59ms 0.74% 10.65% 831ms 10.40% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.063% 10.71% 828ms 10.36% MeshBasedCellPopulation::AcceptCellWriter 20ms 0.25% 10.96% 786ms 9.83% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 10.97% 728ms 9.11% AbstractCellProperty::IsSubType (inline) 10ms 0.13% 11.10% 723ms 9.04% TetrahedralMesh::ImportFromMesher 38ms 0.48% 11.57% 609ms 7.62% operator new 3ms 0.038% 11.61% 591ms 7.39% triangulate 188ms 2.35% 13.96% 568ms 7.11% __GI___libc_malloc 40ms 0.5% 14.46% 566ms 7.08% std::map::operator[] (partial-inline) 1ms 0.013% 14.47% 553ms 6.92% LegacyCellProliferativeTypesWriter::VisitCell 30ms 0.38% 14.85% 553ms 6.92% std::__new_allocator::allocate (inline) 0 0% 14.85% 548ms 6.86% std::allocator_traits::allocate (inline) 5ms 0.063% 14.91% 547ms 6.84% std::ostream::operator<< (inline) 89ms 1.11% 16.02% 539ms 6.74% std::ostream::_M_insert 529ms 6.62% 22.64% 529ms 6.62% __strcmp_avx2 33ms 0.41% 23.05% 528ms 6.60% std::_Rb_tree::find (inline) 0 0% 23.05% 520ms 6.50% delaunay 1ms 0.013% 23.07% 517ms 6.47% Cell::GetCellProliferativeType 3ms 0.038% 23.10% 517ms 6.47% divconqdelaunay 7ms 0.088% 23.19% 511ms 6.39% std::set::insert (inline) 14ms 0.18% 23.37% 504ms 6.30% std::_Rb_tree::_M_insert_unique 244ms 3.05% 26.42% 475ms 5.94% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.42% 466ms 5.83% std::_Rb_tree::lower_bound (inline) 0 0% 26.42% 466ms 5.83% std::map::lower_bound (inline) 0 0% 26.42% 464ms 5.80% std::set::count (inline) 0 0% 26.42% 439ms 5.49% std::_Rb_tree::_M_create_node (inline) 55ms 0.69% 27.11% 435ms 5.44% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.05% 27.16% 431ms 5.39% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.16% 410ms 5.13% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.16% 409ms 5.12% std::_Rb_tree::_M_get_node (inline) 0 0% 27.16% 408ms 5.10% std::set::~set (inline) 26ms 0.33% 27.48% 391ms 4.89% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.075% 27.56% 389ms 4.87% Cell::GetMutationState 82ms 1.03% 28.58% 373ms 4.67% std::_Rb_tree::_M_erase 7ms 0.088% 28.67% 369ms 4.62% std::less::operator() (inline) 9ms 0.11% 28.78% 368ms 4.60% std::set::set (inline) 362ms 4.53% 33.31% 362ms 4.53% std::operator< (inline) 42ms 0.53% 33.84% 331ms 4.14% std::_Rb_tree::_M_copy (inline) 0 0% 33.84% 329ms 4.12% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.84% 329ms 4.12% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 33.85% 328ms 4.10% OutputFileHandler::OpenOutputFile 1ms 0.013% 33.86% 327ms 4.09% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 33.89% 326ms 4.08% AbstractCentreBasedCellPopulation::GetDampingConstant 317ms 3.97% 37.85% 317ms 3.97% std::_Rb_tree::_S_right (inline) 1ms 0.013% 37.87% 310ms 3.88% NodeLocationWriter::Visit 21ms 0.26% 38.13% 305ms 3.82% std::_Rb_tree::_M_insert_ (inline) 4ms 0.05% 38.18% 302ms 3.78% Cell::ReadyToDivide 191ms 2.39% 40.57% 292ms 3.65% _int_malloc 6ms 0.075% 40.64% 291ms 3.64% Element::Element 83ms 1.04% 41.68% 284ms 3.55% __GI___libc_free 4ms 0.05% 41.73% 284ms 3.55% divconqrecurse 3ms 0.038% 41.77% 283ms 3.54% AbstractCellPopulation::IsCellAttachedToLocationIndex 76ms 0.95% 42.72% 280ms 3.50% std::_Rb_tree::_M_clone_node (inline) 1ms 0.013% 42.73% 278ms 3.48% AbstractCellProperty::IsType (inline) 21ms 0.26% 42.99% 269ms 3.37% std::num_put::_M_insert_float 88ms 1.10% 44.10% 267ms 3.34% mergehulls 0 0% 44.10% 260ms 3.25% Cell::HasCellProperty (inline) 2ms 0.025% 44.12% 260ms 3.25% CellPropertyCollection::HasProperty 0 0% 44.12% 256ms 3.20% std::_Rb_tree::_M_drop_node (inline) 11ms 0.14% 44.26% 243ms 3.04% std::__new_allocator::deallocate (inline) 0 0% 44.26% 241ms 3.01% std::allocator_traits::deallocate (inline) 4ms 0.05% 44.31% 236ms 2.95% CellProliferativeTypesWriter::VisitCell 8ms 0.1% 44.41% 219ms 2.74% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.075% 44.48% 217ms 2.71% std::__cxx11::collate::do_transform 12ms 0.15% 44.63% 211ms 2.64% TetrahedralMesh::Clear 51ms 0.64% 45.27% 207ms 2.59% AbstractCellProperty::IsSame 51ms 0.64% 45.91% 206ms 2.58% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 45.91% 205ms 2.56% ___vsnprintf 0 0% 45.91% 205ms 2.56% __vsnprintf_internal (inline) 0 0% 45.91% 205ms 2.56% std::_Rb_tree::_M_put_node (inline) 21ms 0.26% 46.17% 202ms 2.53% __printf_buffer 171ms 2.14% 48.31% 198ms 2.48% _int_free 6ms 0.075% 48.39% 197ms 2.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.075% 48.46% 190ms 2.38% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 54ms 0.68% 49.14% 185ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.063% 49.20% 173ms 2.16% Element::RegisterWithNodes (inline) 0 0% 49.20% 173ms 2.16% std::basic_ofstream::basic_ofstream (inline) 5ms 0.063% 49.26% 169ms 2.11% __printf_fp_l_buffer 0 0% 49.26% 169ms 2.11% __printf_fp_spec (inline) 5ms 0.063% 49.32% 166ms 2.08% Node::AddElement 2ms 0.025% 49.35% 165ms 2.06% std::basic_filebuf::open 0 0% 49.35% 165ms 2.06% std::basic_ofstream::open (inline) 83ms 1.04% 50.39% 159ms 1.99% __printf_fp_buffer_1 0 0% 50.39% 158ms 1.98% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.39% 157ms 1.96% AbstractCellBasedWriter::CloseFile 1ms 0.013% 50.40% 157ms 1.96% std::basic_filebuf::close 0 0% 50.40% 157ms 1.96% std::basic_ofstream::close (inline) 31ms 0.39% 50.79% 156ms 1.95% std::type_info::operator== (inline) 11ms 0.14% 50.93% 152ms 1.90% AbstractTetrahedralElement::CalculateJacobian 101ms 1.26% 52.19% 141ms 1.76% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 52.19% 141ms 1.76% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 52.20% 141ms 1.76% alternateaxes 0 0% 52.20% 140ms 1.75% OutputFileHandler::CommonConstructor 0 0% 52.20% 140ms 1.75% OutputFileHandler::OutputFileHandler 130ms 1.63% 53.83% 140ms 1.75% vertexmedian 0 0% 53.83% 139ms 1.74% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 53.84% 135ms 1.69% OutputFileHandler::MakeFoldersAndReturnFullPath 6ms 0.075% 53.92% 134ms 1.68% Node::~Node 21ms 0.26% 54.18% 132ms 1.65% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 54.19% 130ms 1.63% _IO_new_fopen 0 0% 54.19% 130ms 1.63% std::__basic_file::open 5ms 0.063% 54.25% 129ms 1.61% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.25% 129ms 1.61% __fopen_internal (inline) 0 0% 54.25% 125ms 1.56% FilesystemPermissions::SetFilePermissions (inline) 0 0% 54.25% 125ms 1.56% std::filesystem::permissions 1ms 0.013% 54.27% 124ms 1.55% _IO_new_file_fopen 124ms 1.55% 55.82% 124ms 1.55% __GI_fchmodat 0 0% 55.82% 123ms 1.54% __GI__IO_file_open 4ms 0.05% 55.87% 121ms 1.51% AbstractTetrahedralElement::AbstractTetrahedralElement 45ms 0.56% 56.43% 121ms 1.51% std::__ostream_insert 15ms 0.19% 56.62% 119ms 1.49% boost::detail::shared_count::~shared_count (inline) 0 0% 56.62% 119ms 1.49% boost::shared_ptr::~shared_ptr (inline) 119ms 1.49% 58.11% 119ms 1.49% incircle 28ms 0.35% 58.46% 119ms 1.49% std::num_put::_M_insert_int 2ms 0.025% 58.48% 113ms 1.41% std::basic_filebuf::_M_convert_to_external 0 0% 58.48% 113ms 1.41% std::basic_filebuf::_M_terminate_output 0 0% 58.48% 113ms 1.41% std::basic_filebuf::overflow 48ms 0.6% 59.08% 112ms 1.40% boost::shared_ptr::shared_ptr (inline) 0 0% 59.08% 111ms 1.39% std::__basic_file::xsputn 108ms 1.35% 60.43% 109ms 1.36% __GI___libc_write 6ms 0.075% 60.51% 108ms 1.35% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.05% 60.56% 108ms 1.35% boost::numeric::ublas::vector_assign (inline) 6ms 0.075% 60.63% 108ms 1.35% std::_Rb_tree_const_iterator::operator++ (inline) 22ms 0.28% 60.91% 107ms 1.34% AbstractTetrahedralElement::RefreshJacobian 5ms 0.063% 60.97% 107ms 1.34% std::vector::push_back (inline) 10ms 0.13% 61.10% 106ms 1.33% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 61.10% 106ms 1.33% AbstractCellPopulation::Iterator::operator++ (inline) 105ms 1.31% 62.41% 105ms 1.31% std::_Rb_tree_increment 101ms 1.26% 63.67% 102ms 1.28% __libc_open64 100ms 1.25% 64.92% 100ms 1.25% [libchaste_cell_based.so] 5ms 0.063% 64.99% 98ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 12ms 0.15% 65.14% 98ms 1.23% std::vector::_M_realloc_insert 95ms 1.19% 66.32% 95ms 1.19% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 66.32% 94ms 1.18% std::operator<< (inline) 2ms 0.025% 66.35% 93ms 1.16% Cell::GetCellId 91ms 1.14% 67.49% 93ms 1.16% boost::detail::sp_counted_base::release 53ms 0.66% 68.15% 93ms 1.16% std::basic_filebuf::xsputn 90ms 1.13% 69.28% 90ms 1.13% std::_Rb_tree_insert_and_rebalance 5ms 0.063% 69.34% 88ms 1.10% TetrahedralMesh::EdgeIterator::GetNodeB 2ms 0.025% 69.36% 87ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 69.39% 86ms 1.08% std::filesystem::status 85ms 1.06% 70.45% 85ms 1.06% __GI___fstatat64 51ms 0.64% 71.09% 84ms 1.05% malloc_consolidate 0 0% 71.09% 84ms 1.05% tcache_get (inline) 84ms 1.05% 72.14% 84ms 1.05% tcache_get_n (inline) 77ms 0.96% 73.10% 84ms 1.05% vertexsort 0 0% 73.10% 82ms 1.03% AbstractCellPopulation::GetLocationIndexUsingCell 78ms 0.98% 74.08% 78ms 0.98% std::vector::size (inline) 54ms 0.68% 74.76% 74ms 0.93% AbstractElement::GetNodeGlobalIndex 32ms 0.4% 75.16% 73ms 0.91% AbstractElement::GetNodeLocation 24ms 0.3% 75.46% 73ms 0.91% boost::numeric::ublas::indexing_vector_assign 0 0% 75.46% 71ms 0.89% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 75.47% 71ms 0.89% std::filesystem::create_directory 3ms 0.038% 75.51% 68ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 75.51% 67ms 0.84% std::vector::vector (inline) 7ms 0.088% 75.59% 66ms 0.83% CellPropertyCollection::AddProperty 63ms 0.79% 76.38% 64ms 0.8% boost::detail::shared_count::shared_count (inline) 62ms 0.78% 77.16% 62ms 0.78% counterclockwise 2ms 0.025% 77.18% 62ms 0.78% std::_Vector_base::_M_create_storage (inline) 0 0% 77.18% 62ms 0.78% std::_Vector_base::_Vector_base (inline) 61ms 0.76% 77.95% 61ms 0.76% Node::GetIndex 60ms 0.75% 78.70% 60ms 0.75% __memcpy_avx_unaligned_erms 30ms 0.38% 79.07% 60ms 0.75% boost::numeric::ublas::c_matrix::operator() (partial-inline) 2ms 0.025% 79.10% 60ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.013% 79.11% 58ms 0.73% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 79.11% 56ms 0.7% std::map::find (inline) 0 0% 79.11% 54ms 0.68% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 53ms 0.66% 79.77% 53ms 0.66% [libchaste_mesh.so] 53ms 0.66% 80.44% 53ms 0.66% boost::shared_ptr::operator-> (inline) 0 0% 80.44% 51ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.44% 51ms 0.64% std::__new_allocator::destroy (inline) 0 0% 80.44% 51ms 0.64% std::allocator_traits::destroy (inline) 19ms 0.24% 80.67% 49ms 0.61% AbstractTetrahedralMesh::GetElement 27ms 0.34% 81.01% 49ms 0.61% hack_digit 49ms 0.61% 81.62% 49ms 0.61% std::ostream::sentry::sentry 48ms 0.6% 82.22% 48ms 0.6% Node::IsDeleted 0 0% 82.22% 48ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.025% 82.25% 47ms 0.59% Node::ConstructNodeAttributes (inline) 18ms 0.23% 82.47% 46ms 0.58% Determinant (inline) 12ms 0.15% 82.62% 46ms 0.58% Inverse 1ms 0.013% 82.64% 46ms 0.58% Node::ClearAppliedForce 35ms 0.44% 83.07% 46ms 0.58% std::num_put::do_put 0 0% 83.07% 45ms 0.56% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 45ms 0.56% 83.64% 45ms 0.56% [libstdc++.so.6.0.33] 0 0% 83.64% 44ms 0.55% CellPropertyCollection::~CellPropertyCollection (inline) 24ms 0.3% 83.94% 44ms 0.55% std::basic_streambuf::xsputn 43ms 0.54% 84.48% 43ms 0.54% unlink_chunk 12ms 0.15% 84.63% 42ms 0.53% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 84.64% 41ms 0.51% BoundaryNodeWriter::Visit 1ms 0.013% 84.65% 40ms 0.5% std::__basic_file::close