File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6523ms, 84.08% of 7758ms total Dropped 561 nodes (cum <= 38.79ms) flat flat% sum% cum cum% 0 0% 0% 7722ms 99.54% __libc_start_call_main 0 0% 0% 7722ms 99.54% __libc_start_main_impl 0 0% 0% 7722ms 99.54% _start 0 0% 0% 7705ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7705ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7705ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7705ms 99.32% main 0 0% 0% 7663ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7663ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7663ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7661ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0% 3336ms 43.00% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2936ms 37.84% MeshBasedCellPopulation::Update 0 0% 0% 2782ms 35.86% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.013% 1536ms 19.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 1454ms 18.74% MutableMesh::ReMesh 0 0% 0.013% 1425ms 18.37% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.026% 0.039% 1372ms 17.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.052% 0.09% 1290ms 16.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 36ms 0.46% 0.55% 1223ms 15.76% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.46% 2.01% 982ms 12.66% TetrahedralMesh::EdgeIterator::operator++ 235ms 3.03% 5.04% 936ms 12.06% __dynamic_cast 4ms 0.052% 5.09% 911ms 11.74% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 5.09% 883ms 11.38% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.12% 5.21% 883ms 11.38% CellPropertyCollection::GetPropertiesType (inline) 414ms 5.34% 10.54% 871ms 11.23% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.12% 10.66% 848ms 10.93% CellPopulationElementWriter::Visit 30ms 0.39% 11.05% 774ms 9.98% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.039% 11.09% 774ms 9.98% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.026% 11.11% 733ms 9.45% AbstractCellProperty::IsSubType (inline) 25ms 0.32% 11.43% 720ms 9.28% AbstractCellPopulation::GetCellUsingLocationIndex 13ms 0.17% 11.60% 720ms 9.28% TetrahedralMesh::ImportFromMesher 0 0% 11.60% 591ms 7.62% std::ostream::operator<< (inline) 93ms 1.20% 12.80% 590ms 7.61% std::ostream::_M_insert 5ms 0.064% 12.86% 575ms 7.41% triangulate 34ms 0.44% 13.30% 551ms 7.10% operator new 542ms 6.99% 20.29% 542ms 6.99% __strcmp_avx2 6ms 0.077% 20.37% 531ms 6.84% std::set::insert (inline) 14ms 0.18% 20.55% 525ms 6.77% std::_Rb_tree::_M_insert_unique 2ms 0.026% 20.57% 524ms 6.75% LegacyCellProliferativeTypesWriter::VisitCell 49ms 0.63% 21.20% 518ms 6.68% std::map::operator[] (partial-inline) 168ms 2.17% 23.37% 505ms 6.51% __GI___libc_malloc 244ms 3.15% 26.51% 503ms 6.48% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.51% 501ms 6.46% delaunay 1ms 0.013% 26.53% 500ms 6.44% divconqdelaunay 15ms 0.19% 26.72% 495ms 6.38% std::__new_allocator::allocate (inline) 13ms 0.17% 26.89% 491ms 6.33% std::_Rb_tree::find (inline) 4ms 0.052% 26.94% 490ms 6.32% Cell::GetCellProliferativeType 0 0% 26.94% 488ms 6.29% std::allocator_traits::allocate (inline) 0 0% 26.94% 459ms 5.92% std::set::count (inline) 40ms 0.52% 27.46% 456ms 5.88% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.46% 420ms 5.41% std::_Rb_tree::lower_bound (inline) 0 0% 27.46% 420ms 5.41% std::map::lower_bound (inline) 90ms 1.16% 28.62% 413ms 5.32% std::_Rb_tree::_M_erase 0 0% 28.62% 410ms 5.28% std::set::~set (inline) 0 0% 28.62% 399ms 5.14% std::_Rb_tree::_M_create_node (inline) 2ms 0.026% 28.64% 395ms 5.09% Cell::GetMutationState 5ms 0.064% 28.71% 391ms 5.04% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.71% 381ms 4.91% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.71% 365ms 4.70% std::_Rb_tree::_M_get_node (inline) 11ms 0.14% 28.85% 358ms 4.61% std::less::operator() (inline) 0 0% 28.85% 352ms 4.54% NodeLocationWriter::Visit 347ms 4.47% 33.32% 347ms 4.47% std::operator< (inline) 7ms 0.09% 33.41% 343ms 4.42% Element::Element 29ms 0.37% 33.78% 341ms 4.40% std::_Rb_tree::_Rb_tree (partial-inline) 25ms 0.32% 34.11% 319ms 4.11% std::num_put::_M_insert_float 0 0% 34.11% 316ms 4.07% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.11% 316ms 4.07% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 34.11% 313ms 4.03% OutputFileHandler::OpenOutputFile 2ms 0.026% 34.13% 309ms 3.98% MeshBasedCellPopulation::GetDampingConstant 20ms 0.26% 34.39% 309ms 3.98% std::_Rb_tree::_M_insert_ (inline) 94ms 1.21% 35.60% 308ms 3.97% __GI___libc_free 3ms 0.039% 35.64% 307ms 3.96% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 35.64% 305ms 3.93% std::_Rb_tree::_M_drop_node (inline) 6ms 0.077% 35.72% 304ms 3.92% std::set::set (inline) 6ms 0.077% 35.80% 297ms 3.83% std::__new_allocator::deallocate (inline) 0 0% 35.80% 293ms 3.78% std::allocator_traits::deallocate (inline) 36ms 0.46% 36.26% 281ms 3.62% std::_Rb_tree::_M_copy (inline) 7ms 0.09% 36.35% 271ms 3.49% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.077% 36.43% 267ms 3.44% divconqrecurse 6ms 0.077% 36.50% 265ms 3.42% std::__cxx11::collate::do_transform 62ms 0.8% 37.30% 256ms 3.30% mergehulls 3ms 0.039% 37.34% 255ms 3.29% Cell::ReadyToDivide 3ms 0.039% 37.38% 250ms 3.22% ___vsnprintf 161ms 2.08% 39.46% 250ms 3.22% _int_malloc 1ms 0.013% 39.47% 247ms 3.18% __vsnprintf_internal (inline) 38ms 0.49% 39.96% 244ms 3.15% __printf_buffer 0 0% 39.96% 244ms 3.15% std::_Rb_tree::_M_put_node (inline) 61ms 0.79% 40.75% 238ms 3.07% std::_Rb_tree::_M_clone_node (inline) 235ms 3.03% 43.77% 235ms 3.03% std::_Rb_tree::_S_right (inline) 2ms 0.026% 43.80% 219ms 2.82% CellProliferativeTypesWriter::VisitCell 4ms 0.052% 43.85% 216ms 2.78% Element::RegisterWithNodes (inline) 183ms 2.36% 46.21% 213ms 2.75% _int_free 5ms 0.064% 46.27% 208ms 2.68% Node::AddElement 9ms 0.12% 46.39% 202ms 2.60% MeshBasedCellPopulation::SpringsEnd (inline) 65ms 0.84% 47.23% 202ms 2.60% std::_Rb_tree::_M_get_insert_unique_pos (inline) 6ms 0.077% 47.31% 200ms 2.58% CellPropertyCollection::HasProperty 0 0% 47.31% 199ms 2.57% Cell::HasCellProperty (inline) 3ms 0.039% 47.34% 191ms 2.46% __printf_fp_l_buffer 0 0% 47.34% 191ms 2.46% __printf_fp_spec (inline) 8ms 0.1% 47.45% 190ms 2.45% AbstractCellProperty::IsType (inline) 7ms 0.09% 47.54% 186ms 2.40% AbstractPhaseBasedCellCycleModel::ReadyToDivide 94ms 1.21% 48.75% 180ms 2.32% __printf_fp_buffer_1 7ms 0.09% 48.84% 178ms 2.29% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 48.94% 173ms 2.23% AbstractTetrahedralElement::CalculateJacobian 5ms 0.064% 49.01% 170ms 2.19% boost::numeric::ublas::vector_assign (inline) 6ms 0.077% 49.08% 167ms 2.15% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 49.08% 162ms 2.09% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 49.10% 161ms 2.08% std::basic_filebuf::close 0 0% 49.10% 160ms 2.06% AbstractCellBasedWriter::CloseFile 0 0% 49.10% 160ms 2.06% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 49.10% 160ms 2.06% std::basic_ofstream::close (inline) 2ms 0.026% 49.12% 156ms 2.01% std::basic_ofstream::open (inline) 8ms 0.1% 49.23% 155ms 2.00% TetrahedralMesh::Clear 2ms 0.026% 49.25% 153ms 1.97% alternateaxes 2ms 0.026% 49.28% 153ms 1.97% std::basic_filebuf::open 139ms 1.79% 51.07% 150ms 1.93% vertexmedian 32ms 0.41% 51.48% 149ms 1.92% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 51.50% 145ms 1.87% TetrahedralMesh::RefreshJacobianCachedData 19ms 0.24% 51.74% 141ms 1.82% MeshBasedCellPopulation::SpringIterator::SpringIterator 10ms 0.13% 51.87% 136ms 1.75% boost::detail::shared_count::~shared_count (inline) 0 0% 51.87% 136ms 1.75% boost::shared_ptr::~shared_ptr (inline) 26ms 0.34% 52.20% 134ms 1.73% AbstractCellProperty::IsSame 7ms 0.09% 52.29% 131ms 1.69% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.039% 52.33% 129ms 1.66% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 52.33% 129ms 1.66% std::__basic_file::open 1ms 0.013% 52.35% 128ms 1.65% _IO_new_file_fopen 0 0% 52.35% 128ms 1.65% _IO_new_fopen 0 0% 52.35% 128ms 1.65% __fopen_internal (inline) 49ms 0.63% 52.98% 127ms 1.64% std::__ostream_insert 1ms 0.013% 52.99% 126ms 1.62% __GI__IO_file_open 126ms 1.62% 54.61% 126ms 1.62% incircle 14ms 0.18% 54.80% 125ms 1.61% AbstractTetrahedralElement::RefreshJacobian 0 0% 54.80% 124ms 1.60% FilesystemPermissions::SetFilePermissions (inline) 124ms 1.60% 56.39% 124ms 1.60% __GI_fchmodat 0 0% 56.39% 124ms 1.60% std::filesystem::permissions 84ms 1.08% 57.48% 123ms 1.59% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 57.48% 123ms 1.59% std::_Vector_base::_M_allocate (inline) 40ms 0.52% 57.99% 122ms 1.57% boost::numeric::ublas::indexing_vector_assign 33ms 0.43% 58.42% 119ms 1.53% std::num_put::_M_insert_int 4ms 0.052% 58.47% 119ms 1.53% std::vector::push_back (inline) 0 0% 58.47% 115ms 1.48% std::basic_filebuf::_M_terminate_output 1ms 0.013% 58.48% 115ms 1.48% std::basic_filebuf::overflow 111ms 1.43% 59.91% 114ms 1.47% boost::detail::sp_counted_base::release 1ms 0.013% 59.93% 114ms 1.47% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 59.94% 113ms 1.46% std::__basic_file::xsputn 0 0% 59.94% 111ms 1.43% OutputFileHandler::CommonConstructor 0 0% 59.94% 111ms 1.43% OutputFileHandler::OutputFileHandler 111ms 1.43% 61.37% 111ms 1.43% __GI___libc_write 16ms 0.21% 61.58% 110ms 1.42% std::vector::_M_realloc_insert 10ms 0.13% 61.70% 108ms 1.39% std::type_info::operator== (inline) 0 0% 61.70% 107ms 1.38% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 61.70% 105ms 1.35% std::operator<< (inline) 51ms 0.66% 62.36% 104ms 1.34% boost::shared_ptr::shared_ptr (inline) 14ms 0.18% 62.54% 102ms 1.31% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 62.55% 101ms 1.30% AbstractCellPopulation::Iterator::operator++ (inline) 100ms 1.29% 63.84% 101ms 1.30% __libc_open64 99ms 1.28% 65.12% 99ms 1.28% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 2ms 0.026% 65.15% 95ms 1.22% Node::~Node 95ms 1.22% 66.37% 95ms 1.22% std::_Rb_tree_insert_and_rebalance 36ms 0.46% 66.83% 90ms 1.16% AbstractElement::GetNodeLocation 90ms 1.16% 67.99% 90ms 1.16% [libchaste_cell_based.so] 7ms 0.09% 68.08% 87ms 1.12% std::_Rb_tree_const_iterator::operator++ (inline) 53ms 0.68% 68.77% 86ms 1.11% std::basic_filebuf::xsputn 85ms 1.10% 69.86% 85ms 1.10% std::_Rb_tree_increment 7ms 0.09% 69.95% 84ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 69.95% 77ms 0.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 69.95% 76ms 0.98% tcache_get (inline) 76ms 0.98% 70.93% 76ms 0.98% tcache_get_n (inline) 63ms 0.81% 71.75% 73ms 0.94% malloc_consolidate 43ms 0.55% 72.30% 72ms 0.93% boost::numeric::ublas::c_matrix::operator() (partial-inline) 3ms 0.039% 72.34% 71ms 0.92% Cell::GetCellId 3ms 0.039% 72.38% 69ms 0.89% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.026% 72.40% 68ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 72.40% 68ms 0.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.40% 68ms 0.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.40% 68ms 0.88% std::vector::vector (inline) 67ms 0.86% 73.27% 67ms 0.86% __GI___fstatat64 2ms 0.026% 73.29% 67ms 0.86% std::filesystem::status 61ms 0.79% 74.08% 65ms 0.84% vertexsort 64ms 0.82% 74.90% 64ms 0.82% boost::numeric::ublas::c_vector::operator() (partial-inline) 53ms 0.68% 75.59% 64ms 0.82% std::num_put::do_put 64ms 0.82% 76.41% 64ms 0.82% std::vector::size (inline) 0 0% 76.41% 63ms 0.81% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 63ms 0.81% 77.22% 63ms 0.81% counterclockwise 0 0% 77.22% 63ms 0.81% std::filesystem::create_directory 9ms 0.12% 77.34% 62ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.34% 61ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.34% 61ms 0.79% std::__new_allocator::destroy (inline) 0 0% 77.34% 61ms 0.79% std::allocator_traits::destroy (inline) 6ms 0.077% 77.42% 60ms 0.77% Node::ConstructNodeAttributes (inline) 0 0% 77.42% 59ms 0.76% std::_Vector_base::_Vector_base (inline) 0 0% 77.42% 58ms 0.75% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 57ms 0.73% 78.15% 57ms 0.73% [libchaste_mesh.so] 0 0% 78.15% 57ms 0.73% std::_Vector_base::_M_create_storage (inline) 0 0% 78.15% 56ms 0.72% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 78.15% 56ms 0.72% Node::ClearAppliedForce 56ms 0.72% 78.87% 56ms 0.72% Node::GetIndex 12ms 0.15% 79.03% 53ms 0.68% Determinant (inline) 53ms 0.68% 79.71% 53ms 0.68% [libstdc++.so.6.0.33] 52ms 0.67% 80.38% 53ms 0.68% boost::detail::shared_count::shared_count (inline) 36ms 0.46% 80.85% 53ms 0.68% std::basic_streambuf::xsputn 29ms 0.37% 81.22% 52ms 0.67% hack_digit 3ms 0.039% 81.26% 50ms 0.64% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 81.27% 49ms 0.63% BoundaryNodeWriter::Visit 49ms 0.63% 81.90% 49ms 0.63% __memcpy_avx_unaligned_erms 4ms 0.052% 81.95% 49ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.95% 48ms 0.62% AbstractCentreBasedCellPopulation::CreateCellPair 4ms 0.052% 82.01% 48ms 0.62% CellPropertyCollection::AddProperty 48ms 0.62% 82.62% 48ms 0.62% boost::shared_ptr::operator-> (inline) 0 0% 82.62% 46ms 0.59% std::map::~map (inline) 31ms 0.4% 83.02% 45ms 0.58% AbstractElement::GetNodeGlobalIndex 0 0% 83.02% 43ms 0.55% CellPropertyCollection::~CellPropertyCollection (inline) 43ms 0.55% 83.58% 43ms 0.55% Node::rGetLocation 0 0% 83.58% 43ms 0.55% std::map::map (inline) 19ms 0.24% 83.82% 42ms 0.54% AbstractTetrahedralMesh::GetElement 3ms 0.039% 83.86% 42ms 0.54% std::__basic_file::close 2ms 0.026% 83.89% 41ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 83.89% 41ms 0.53% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 1ms 0.013% 83.90% 41ms 0.53% NodeAttributes::NodeAttributes 0 0% 83.90% 41ms 0.53% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 84.08% 41ms 0.53% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 84.08% 39ms 0.5% CxxTest::RealWorldDescription::setUp 0 0% 84.08% 39ms 0.5% PetscInitialize 0 0% 84.08% 39ms 0.5% PetscSetup::setUpWorld 0 0% 84.08% 39ms 0.5% PetscSetupUtils::CommonSetup 0 0% 84.08% 39ms 0.5% PetscSetupUtils::InitialisePetsc 0 0% 84.08% 39ms 0.5% _IO_new_fclose 0 0% 84.08% 39ms 0.5% _dl_init 0 0% 84.08% 39ms 0.5% call_init (inline) 0 0% 84.08% 39ms 0.5% std::__new_allocator::construct (inline) 0 0% 84.08% 39ms 0.5% std::allocator_traits::construct (inline)