File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6441ms, 82.05% of 7850ms total Dropped 577 nodes (cum <= 39.25ms) flat flat% sum% cum cum% 0 0% 0% 7815ms 99.55% __libc_start_call_main 0 0% 0% 7815ms 99.55% __libc_start_main_impl 0 0% 0% 7815ms 99.55% _start 0 0% 0% 7800ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7800ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7800ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7800ms 99.36% main 0 0% 0% 7763ms 98.89% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7763ms 98.89% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7763ms 98.89% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7762ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0% 3389ms 43.17% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2912ms 37.10% MeshBasedCellPopulation::Update 1ms 0.013% 0.025% 2774ms 35.34% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.038% 1591ms 20.27% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1455ms 18.54% MutableMesh::ReMesh 1ms 0.013% 0.051% 1432ms 18.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.064% 1394ms 17.76% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.051% 0.11% 1372ms 17.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 21ms 0.27% 0.38% 1214ms 15.46% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.089% 0.47% 972ms 12.38% AbstractTwoBodyInteractionForce::AddForceContribution 129ms 1.64% 2.11% 969ms 12.34% TetrahedralMesh::EdgeIterator::operator++ 452ms 5.76% 7.87% 962ms 12.25% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.17% 8.04% 896ms 11.41% CellPopulationElementWriter::Visit 0 0% 8.04% 882ms 11.24% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 9ms 0.11% 8.15% 860ms 10.96% CellPropertyCollection::GetPropertiesType (inline) 226ms 2.88% 11.03% 860ms 10.96% __dynamic_cast 32ms 0.41% 11.44% 829ms 10.56% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.15% 11.59% 737ms 9.39% TetrahedralMesh::ImportFromMesher 4ms 0.051% 11.64% 729ms 9.29% MeshBasedCellPopulation::AcceptCellWriter 33ms 0.42% 12.06% 722ms 9.20% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 12.10% 648ms 8.25% AbstractCellProperty::IsSubType (inline) 56ms 0.71% 12.82% 600ms 7.64% std::map::operator[] (partial-inline) 33ms 0.42% 13.24% 580ms 7.39% operator new 0 0% 13.24% 559ms 7.12% triangulate 1ms 0.013% 13.25% 549ms 6.99% std::ostream::operator<< (inline) 75ms 0.96% 14.20% 548ms 6.98% std::ostream::_M_insert 178ms 2.27% 16.47% 540ms 6.88% __GI___libc_malloc 21ms 0.27% 16.74% 518ms 6.60% std::_Rb_tree::find (inline) 515ms 6.56% 23.30% 515ms 6.56% __strcmp_avx2 32ms 0.41% 23.71% 514ms 6.55% std::__new_allocator::allocate (inline) 0 0% 23.71% 508ms 6.47% std::allocator_traits::allocate (inline) 7ms 0.089% 23.80% 494ms 6.29% std::set::insert (inline) 0 0% 23.80% 489ms 6.23% std::_Rb_tree::lower_bound (inline) 0 0% 23.80% 489ms 6.23% std::map::lower_bound (inline) 17ms 0.22% 24.01% 488ms 6.22% std::_Rb_tree::_M_insert_unique 1ms 0.013% 24.03% 481ms 6.13% delaunay 3ms 0.038% 24.06% 479ms 6.10% Cell::GetCellProliferativeType 1ms 0.013% 24.08% 478ms 6.09% divconqdelaunay 0 0% 24.08% 475ms 6.05% std::set::count (inline) 202ms 2.57% 26.65% 463ms 5.90% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.089% 26.74% 461ms 5.87% AbstractCellBasedSimulation::DoCellBirth 3ms 0.038% 26.78% 455ms 5.80% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.78% 433ms 5.52% std::_Rb_tree::_M_create_node (inline) 0 0% 26.78% 404ms 5.15% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.36% 27.13% 395ms 5.03% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.13% 392ms 4.99% std::_Rb_tree::_M_get_node (inline) 28ms 0.36% 27.49% 378ms 4.82% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.19% 27.68% 368ms 4.69% std::less::operator() (inline) 3ms 0.038% 27.72% 360ms 4.59% Cell::GetMutationState 0 0% 27.72% 360ms 4.59% std::set::~set (inline) 353ms 4.50% 32.22% 353ms 4.50% std::operator< (inline) 5ms 0.064% 32.28% 352ms 4.48% std::set::set (inline) 72ms 0.92% 33.20% 344ms 4.38% std::_Rb_tree::_M_erase 1ms 0.013% 33.21% 338ms 4.31% NodeLocationWriter::Visit 49ms 0.62% 33.83% 330ms 4.20% std::_Rb_tree::_M_copy (inline) 11ms 0.14% 33.97% 318ms 4.05% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 34.00% 316ms 4.03% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 34.04% 313ms 3.99% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.025% 34.06% 312ms 3.97% Cell::ReadyToDivide 27ms 0.34% 34.41% 307ms 3.91% std::num_put::_M_insert_float 0 0% 34.41% 296ms 3.77% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 34.41% 295ms 3.76% AbstractCellBasedWriter::OpenOutputFileForAppend 19ms 0.24% 34.65% 293ms 3.73% std::_Rb_tree::_M_insert_ (inline) 0 0% 34.65% 290ms 3.69% OutputFileHandler::OpenOutputFile 287ms 3.66% 38.31% 287ms 3.66% std::_Rb_tree::_S_right (inline) 197ms 2.51% 40.82% 283ms 3.61% _int_malloc 73ms 0.93% 41.75% 278ms 3.54% std::_Rb_tree::_M_clone_node (inline) 1ms 0.013% 41.76% 274ms 3.49% Element::Element 102ms 1.30% 43.06% 274ms 3.49% __GI___libc_free 12ms 0.15% 43.21% 255ms 3.25% divconqrecurse 5ms 0.064% 43.27% 251ms 3.20% CellPropertyCollection::HasProperty 5ms 0.064% 43.34% 249ms 3.17% AbstractCellProperty::IsType (inline) 0 0% 43.34% 247ms 3.15% Cell::HasCellProperty (inline) 0 0% 43.34% 239ms 3.04% std::_Rb_tree::_M_drop_node (inline) 6ms 0.076% 43.41% 238ms 3.03% std::__new_allocator::deallocate (inline) 1ms 0.013% 43.43% 235ms 2.99% CellProliferativeTypesWriter::VisitCell 64ms 0.82% 44.24% 234ms 2.98% mergehulls 0 0% 44.24% 234ms 2.98% std::allocator_traits::deallocate (inline) 5ms 0.064% 44.31% 227ms 2.89% std::__cxx11::collate::do_transform 19ms 0.24% 44.55% 226ms 2.88% TetrahedralMesh::Clear 0 0% 44.55% 218ms 2.78% ___vsnprintf 1ms 0.013% 44.56% 218ms 2.78% __vsnprintf_internal (inline) 25ms 0.32% 44.88% 214ms 2.73% __printf_buffer 6ms 0.076% 44.96% 202ms 2.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.038% 44.99% 198ms 2.52% MeshBasedCellPopulation::SpringsEnd (inline) 14ms 0.18% 45.17% 195ms 2.48% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 49ms 0.62% 45.80% 190ms 2.42% AbstractCellProperty::IsSame 2ms 0.025% 45.82% 184ms 2.34% Element::RegisterWithNodes (inline) 0 0% 45.82% 184ms 2.34% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 45.86% 179ms 2.28% Node::AddElement 10ms 0.13% 45.99% 179ms 2.28% __printf_fp_l_buffer 0 0% 45.99% 179ms 2.28% __printf_fp_spec (inline) 56ms 0.71% 46.70% 178ms 2.27% std::_Rb_tree::_M_get_insert_unique_pos (inline) 150ms 1.91% 48.61% 172ms 2.19% _int_free 48ms 0.61% 49.22% 166ms 2.11% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.15% 49.38% 161ms 2.05% AbstractTetrahedralElement::CalculateJacobian 88ms 1.12% 50.50% 159ms 2.03% __printf_fp_buffer_1 2ms 0.025% 50.52% 152ms 1.94% boost::numeric::ublas::vector_assign (inline) 0 0% 50.52% 149ms 1.90% OutputFileHandler::CommonConstructor 0 0% 50.52% 149ms 1.90% OutputFileHandler::OutputFileHandler 7ms 0.089% 50.61% 148ms 1.89% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 50.62% 146ms 1.86% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.14% 50.76% 144ms 1.83% Node::~Node 0 0% 50.76% 143ms 1.82% std::basic_ofstream::basic_ofstream (inline) 41ms 0.52% 51.29% 141ms 1.80% std::type_info::operator== (inline) 0 0% 51.29% 139ms 1.77% std::basic_filebuf::open 0 0% 51.29% 139ms 1.77% std::basic_ofstream::open (inline) 0 0% 51.29% 137ms 1.75% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.064% 51.35% 134ms 1.71% AbstractTetrahedralElement::CalculateInverseJacobian 42ms 0.54% 51.89% 133ms 1.69% std::num_put::_M_insert_int 18ms 0.23% 52.11% 132ms 1.68% MeshBasedCellPopulation::SpringIterator::SpringIterator 12ms 0.15% 52.27% 132ms 1.68% std::_Rb_tree_const_iterator::operator++ (inline) 57ms 0.73% 52.99% 132ms 1.68% std::__ostream_insert 0 0% 52.99% 131ms 1.67% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.99% 130ms 1.66% AbstractCellBasedWriter::CloseFile 1ms 0.013% 53.01% 130ms 1.66% alternateaxes 0 0% 53.01% 130ms 1.66% std::basic_filebuf::close 0 0% 53.01% 130ms 1.66% std::basic_ofstream::close (inline) 119ms 1.52% 54.52% 129ms 1.64% vertexmedian 127ms 1.62% 56.14% 127ms 1.62% std::_Rb_tree_increment 22ms 0.28% 56.42% 126ms 1.61% AbstractTetrahedralElement::RefreshJacobian 122ms 1.55% 57.97% 122ms 1.55% incircle 5ms 0.064% 58.04% 122ms 1.55% std::vector::push_back (inline) 39ms 0.5% 58.54% 121ms 1.54% boost::numeric::ublas::indexing_vector_assign 56ms 0.71% 59.25% 120ms 1.53% boost::shared_ptr::shared_ptr (inline) 0 0% 59.25% 118ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.25% 59.50% 117ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 59.52% 117ms 1.49% std::_Vector_base::_M_allocate (inline) 9ms 0.11% 59.63% 115ms 1.46% std::vector::_M_realloc_insert 0 0% 59.63% 114ms 1.45% FilesystemPermissions::SetFilePermissions (inline) 114ms 1.45% 61.08% 114ms 1.45% __GI_fchmodat 0 0% 61.08% 114ms 1.45% std::filesystem::permissions 72ms 0.92% 62.00% 111ms 1.41% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 62.00% 110ms 1.40% std::__basic_file::open 0 0% 62.00% 109ms 1.39% _IO_new_fopen 0 0% 62.00% 109ms 1.39% __fopen_internal (inline) 10ms 0.13% 62.13% 109ms 1.39% boost::detail::shared_count::~shared_count (inline) 0 0% 62.13% 109ms 1.39% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 62.14% 105ms 1.34% _IO_new_file_fopen 2ms 0.025% 62.17% 104ms 1.32% std::basic_filebuf::overflow 3ms 0.038% 62.20% 103ms 1.31% __GI__IO_file_open 1ms 0.013% 62.22% 102ms 1.30% std::basic_filebuf::_M_convert_to_external 0 0% 62.22% 102ms 1.30% std::basic_filebuf::_M_terminate_output 3ms 0.038% 62.25% 102ms 1.30% std::operator<< (inline) 101ms 1.29% 63.54% 101ms 1.29% __GI___libc_write 0 0% 63.54% 101ms 1.29% std::__basic_file::xsputn 96ms 1.22% 64.76% 97ms 1.24% boost::detail::sp_counted_base::release 92ms 1.17% 65.94% 92ms 1.17% [libchaste_cell_based.so] 55ms 0.7% 66.64% 91ms 1.16% AbstractElement::GetNodeLocation 7ms 0.089% 66.73% 91ms 1.16% AbstractTetrahedralElement::AbstractTetrahedralElement 87ms 1.11% 67.83% 87ms 1.11% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 86ms 1.10% 68.93% 86ms 1.10% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 68.96% 85ms 1.08% Cell::GetCellId 83ms 1.06% 70.01% 83ms 1.06% __libc_open64 1ms 0.013% 70.03% 80ms 1.02% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.025% 70.05% 80ms 1.02% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 53ms 0.68% 70.73% 80ms 1.02% std::basic_streambuf::xsputn 72ms 0.92% 71.64% 80ms 1.02% vertexsort 44ms 0.56% 72.20% 73ms 0.93% std::basic_filebuf::xsputn 0 0% 72.20% 70ms 0.89% tcache_get (inline) 70ms 0.89% 73.10% 70ms 0.89% tcache_get_n (inline) 3ms 0.038% 73.13% 68ms 0.87% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.11% 73.25% 68ms 0.87% CellPropertyCollection::AddProperty 68ms 0.87% 74.11% 68ms 0.87% __GI___fstatat64 0 0% 74.11% 68ms 0.87% std::filesystem::status 0 0% 74.11% 67ms 0.85% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 67ms 0.85% 74.97% 67ms 0.85% Node::GetIndex 5ms 0.064% 75.03% 67ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 75.04% 67ms 0.85% std::filesystem::create_directory 63ms 0.8% 75.85% 64ms 0.82% boost::detail::shared_count::shared_count (inline) 50ms 0.64% 76.48% 64ms 0.82% malloc_consolidate 61ms 0.78% 77.26% 61ms 0.78% __memcpy_avx_unaligned_erms 46ms 0.59% 77.85% 58ms 0.74% AbstractElement::GetNodeGlobalIndex 0 0% 77.85% 56ms 0.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.85% 56ms 0.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 56ms 0.71% 78.56% 56ms 0.71% boost::shared_ptr::operator-> (inline) 0 0% 78.56% 55ms 0.7% std::_Rb_tree::_M_destroy_node (inline) 3ms 0.038% 78.60% 55ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.60% 55ms 0.7% std::__new_allocator::destroy (inline) 0 0% 78.60% 55ms 0.7% std::allocator_traits::destroy (inline) 0 0% 78.60% 53ms 0.68% std::vector::vector (inline) 6ms 0.076% 78.68% 51ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 3ms 0.038% 78.71% 50ms 0.64% Node::ConstructNodeAttributes (inline) 0 0% 78.71% 49ms 0.62% Node::ClearAppliedForce 3ms 0.038% 78.75% 49ms 0.62% std::_Vector_base::_M_deallocate (inline) 0 0% 78.75% 49ms 0.62% std::map::map (inline) 49ms 0.62% 79.38% 49ms 0.62% std::vector::size (inline) 48ms 0.61% 79.99% 48ms 0.61% [libchaste_mesh.so] 0 0% 79.99% 48ms 0.61% std::_Vector_base::_Vector_base (inline) 47ms 0.6% 80.59% 47ms 0.6% counterclockwise 0 0% 80.59% 47ms 0.6% std::_Vector_base::_M_create_storage (inline) 0 0% 80.59% 46ms 0.59% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 80.59% 44ms 0.56% boost::numeric::ublas::norm_2 (inline) 13ms 0.17% 80.75% 44ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.025% 80.78% 44ms 0.56% std::__new_allocator::construct (inline) 0 0% 80.78% 44ms 0.56% std::allocator_traits::construct (inline) 0 0% 80.78% 43ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 80.78% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 24ms 0.31% 81.08% 43ms 0.55% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 81.08% 42ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 42ms 0.54% 81.62% 42ms 0.54% boost::numeric::ublas::c_vector::operator() 1ms 0.013% 81.63% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 81.63% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 33ms 0.42% 82.05% 41ms 0.52% std::num_put::do_put 0 0% 82.05% 40ms 0.51% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11]