File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6950ms, 85.98% of 8083ms total Dropped 557 nodes (cum <= 40.41ms) flat flat% sum% cum cum% 0 0% 0% 8043ms 99.51% __libc_start_call_main 0 0% 0% 8043ms 99.51% __libc_start_main_impl 0 0% 0% 8043ms 99.51% _start 0 0% 0% 8024ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8024ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8024ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8024ms 99.27% main 0 0% 0% 7978ms 98.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7978ms 98.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7978ms 98.70% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7975ms 98.66% AbstractCellBasedSimulation::Solve 0 0% 0% 3438ms 42.53% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2980ms 36.87% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.037% 2953ms 36.53% MeshBasedCellPopulation::Update 0 0% 0.037% 1549ms 19.16% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.037% 1460ms 18.06% MutableMesh::ReMesh 3ms 0.037% 0.074% 1452ms 17.96% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.074% 1384ms 17.12% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.11% 0.19% 1337ms 16.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.17% 0.36% 1250ms 15.46% MeshBasedCellPopulation::SpringIterator::operator++ 110ms 1.36% 1.72% 1024ms 12.67% TetrahedralMesh::EdgeIterator::operator++ 412ms 5.10% 6.82% 988ms 12.22% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.037% 6.85% 952ms 11.78% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 6.88% 950ms 11.75% AbstractTwoBodyInteractionForce::AddForceContribution 266ms 3.29% 10.17% 946ms 11.70% __dynamic_cast 15ms 0.19% 10.36% 916ms 11.33% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.087% 10.44% 910ms 11.26% CellPopulationElementWriter::Visit 36ms 0.45% 10.89% 848ms 10.49% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.074% 10.96% 805ms 9.96% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.37% 11.33% 746ms 9.23% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.049% 11.38% 728ms 9.01% AbstractCellProperty::IsSubType (inline) 14ms 0.17% 11.56% 709ms 8.77% TetrahedralMesh::ImportFromMesher 1ms 0.012% 11.57% 597ms 7.39% std::ostream::operator<< (inline) 42ms 0.52% 12.09% 596ms 7.37% std::map::operator[] (partial-inline) 98ms 1.21% 13.30% 591ms 7.31% std::ostream::_M_insert 37ms 0.46% 13.76% 561ms 6.94% operator new 4ms 0.049% 13.81% 557ms 6.89% triangulate 4ms 0.049% 13.86% 555ms 6.87% Cell::GetCellProliferativeType 553ms 6.84% 20.70% 553ms 6.84% __strcmp_avx2 15ms 0.19% 20.88% 531ms 6.57% std::_Rb_tree::find (inline) 187ms 2.31% 23.20% 523ms 6.47% __GI___libc_malloc 13ms 0.16% 23.36% 513ms 6.35% std::set::insert (inline) 4ms 0.049% 23.41% 509ms 6.30% LegacyCellProliferativeTypesWriter::VisitCell 7ms 0.087% 23.49% 500ms 6.19% std::_Rb_tree::_M_insert_unique 18ms 0.22% 23.72% 499ms 6.17% std::__new_allocator::allocate (inline) 0 0% 23.72% 496ms 6.14% std::allocator_traits::allocate (inline) 0 0% 23.72% 492ms 6.09% std::_Rb_tree::lower_bound (inline) 0 0% 23.72% 492ms 6.09% std::map::lower_bound (inline) 1ms 0.012% 23.73% 485ms 6.00% delaunay 1ms 0.012% 23.74% 483ms 5.98% divconqdelaunay 0 0% 23.74% 483ms 5.98% std::set::count (inline) 7ms 0.087% 23.83% 470ms 5.81% AbstractCellBasedSimulation::DoCellBirth 45ms 0.56% 24.38% 468ms 5.79% std::_Rb_tree::~_Rb_tree (inline) 205ms 2.54% 26.92% 467ms 5.78% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.92% 440ms 5.44% std::set::~set (inline) 91ms 1.13% 28.05% 421ms 5.21% std::_Rb_tree::_M_erase 0 0% 28.05% 415ms 5.13% std::_Rb_tree::_M_create_node (inline) 0 0% 28.05% 389ms 4.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.05% 386ms 4.78% std::_Rb_tree::_M_get_node (inline) 6ms 0.074% 28.12% 361ms 4.47% std::less::operator() (inline) 355ms 4.39% 32.51% 355ms 4.39% std::operator< (inline) 3ms 0.037% 32.55% 354ms 4.38% Cell::GetMutationState 1ms 0.012% 32.56% 344ms 4.26% NodeLocationWriter::Visit 343ms 4.24% 36.81% 343ms 4.24% std::_Rb_tree::_S_right (inline) 101ms 1.25% 38.06% 340ms 4.21% __GI___libc_free 0 0% 38.06% 339ms 4.19% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.06% 338ms 4.18% AbstractCellBasedWriter::OpenOutputFileForAppend 14ms 0.17% 38.23% 336ms 4.16% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 38.23% 332ms 4.11% OutputFileHandler::OpenOutputFile 7ms 0.087% 38.31% 318ms 3.93% AbstractCellPopulation::IsCellAttachedToLocationIndex 23ms 0.28% 38.60% 316ms 3.91% std::_Rb_tree::_M_insert_ (inline) 0 0% 38.60% 314ms 3.88% std::_Rb_tree::_M_drop_node (inline) 4ms 0.049% 38.65% 312ms 3.86% Cell::ReadyToDivide 4ms 0.049% 38.70% 300ms 3.71% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 38.70% 300ms 3.71% MeshBasedCellPopulation::GetDampingConstant 14ms 0.17% 38.87% 299ms 3.70% std::__new_allocator::deallocate (inline) 1ms 0.012% 38.88% 298ms 3.69% std::set::set (inline) 0 0% 38.88% 297ms 3.67% std::allocator_traits::deallocate (inline) 22ms 0.27% 39.16% 294ms 3.64% std::num_put::_M_insert_float 32ms 0.4% 39.55% 291ms 3.60% std::_Rb_tree::_M_copy (inline) 3ms 0.037% 39.59% 281ms 3.48% Element::Element 11ms 0.14% 39.73% 277ms 3.43% divconqrecurse 170ms 2.10% 41.83% 265ms 3.28% _int_malloc 0 0% 41.83% 263ms 3.25% std::_Rb_tree::_M_put_node (inline) 80ms 0.99% 42.82% 257ms 3.18% mergehulls 2ms 0.025% 42.84% 254ms 3.14% CellProliferativeTypesWriter::VisitCell 73ms 0.9% 43.75% 253ms 3.13% std::_Rb_tree::_M_clone_node (inline) 7ms 0.087% 43.83% 242ms 2.99% CellPropertyCollection::HasProperty 5ms 0.062% 43.89% 242ms 2.99% std::__cxx11::collate::do_transform 0 0% 43.89% 239ms 2.96% Cell::HasCellProperty (inline) 202ms 2.50% 46.39% 237ms 2.93% _int_free 3ms 0.037% 46.43% 234ms 2.89% AbstractCellProperty::IsType (inline) 10ms 0.12% 46.55% 223ms 2.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.012% 46.57% 222ms 2.75% ___vsnprintf 0 0% 46.57% 221ms 2.73% __vsnprintf_internal (inline) 15ms 0.19% 46.75% 218ms 2.70% TetrahedralMesh::Clear 27ms 0.33% 47.09% 217ms 2.68% __printf_buffer 7ms 0.087% 47.17% 211ms 2.61% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.099% 47.27% 188ms 2.33% MeshBasedCellPopulation::SpringsEnd (inline) 51ms 0.63% 47.90% 177ms 2.19% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.025% 47.93% 176ms 2.18% AbstractCellPopulation::CloseRoundRobinWritersFiles 4ms 0.049% 47.98% 176ms 2.18% Element::RegisterWithNodes (inline) 11ms 0.14% 48.11% 175ms 2.17% AbstractTetrahedralElement::CalculateJacobian 1ms 0.012% 48.13% 174ms 2.15% AbstractCellBasedWriter::CloseFile 0 0% 48.13% 174ms 2.15% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.099% 48.22% 174ms 2.15% __printf_fp_l_buffer 0 0% 48.22% 174ms 2.15% __printf_fp_spec (inline) 2ms 0.025% 48.25% 173ms 2.14% std::basic_filebuf::close 0 0% 48.25% 173ms 2.14% std::basic_ofstream::close (inline) 6ms 0.074% 48.32% 171ms 2.12% Node::AddElement 39ms 0.48% 48.81% 169ms 2.09% AbstractCellProperty::IsSame 12ms 0.15% 48.95% 168ms 2.08% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.012% 48.97% 168ms 2.08% OutputFileHandler::CommonConstructor 0 0% 48.97% 168ms 2.08% OutputFileHandler::OutputFileHandler 68ms 0.84% 49.81% 163ms 2.02% __printf_fp_buffer_1 1ms 0.012% 49.82% 160ms 1.98% OutputFileHandler::MakeFoldersAndReturnFullPath 39ms 0.48% 50.30% 160ms 1.98% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.30% 158ms 1.95% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.30% 155ms 1.92% std::basic_ofstream::open (inline) 1ms 0.012% 50.32% 154ms 1.91% std::basic_filebuf::open 0 0% 50.32% 141ms 1.74% FilesystemPermissions::SetFilePermissions (inline) 141ms 1.74% 52.06% 141ms 1.74% __GI_fchmodat 0 0% 52.06% 141ms 1.74% std::filesystem::permissions 23ms 0.28% 52.34% 138ms 1.71% AbstractTetrahedralElement::RefreshJacobian 34ms 0.42% 52.77% 135ms 1.67% std::num_put::_M_insert_int 54ms 0.67% 53.43% 133ms 1.65% std::__ostream_insert 5ms 0.062% 53.49% 130ms 1.61% Node::~Node 5ms 0.062% 53.56% 130ms 1.61% boost::numeric::ublas::vector_assign (inline) 27ms 0.33% 53.89% 130ms 1.61% std::type_info::operator== (inline) 3ms 0.037% 53.93% 128ms 1.58% alternateaxes 22ms 0.27% 54.20% 126ms 1.56% AbstractCellPopulation::Iterator::IsRealCell (inline) 120ms 1.48% 55.68% 125ms 1.55% vertexmedian 0 0% 55.68% 124ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.025% 55.71% 124ms 1.53% std::__basic_file::open 0 0% 55.71% 123ms 1.52% _IO_new_fopen 0 0% 55.71% 123ms 1.52% __fopen_internal (inline) 0 0% 55.71% 122ms 1.51% std::basic_filebuf::_M_terminate_output 1ms 0.012% 55.72% 121ms 1.50% _IO_new_file_fopen 6ms 0.074% 55.80% 121ms 1.50% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 55.80% 121ms 1.50% std::__basic_file::xsputn 0 0% 55.80% 121ms 1.50% std::basic_filebuf::_M_convert_to_external 0 0% 55.80% 121ms 1.50% std::basic_filebuf::overflow 0 0% 55.80% 120ms 1.48% __GI__IO_file_open 120ms 1.48% 57.28% 120ms 1.48% __GI___libc_write 117ms 1.45% 58.73% 117ms 1.45% [libchaste_cell_based.so] 11ms 0.14% 58.86% 114ms 1.41% boost::detail::shared_count::~shared_count (inline) 0 0% 58.86% 114ms 1.41% boost::shared_ptr::~shared_ptr (inline) 5ms 0.062% 58.93% 112ms 1.39% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.12% 59.05% 111ms 1.37% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 59.05% 110ms 1.36% std::_Vector_base::_M_allocate (inline) 75ms 0.93% 59.98% 108ms 1.34% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 108ms 1.34% 61.31% 108ms 1.34% incircle 50ms 0.62% 61.93% 106ms 1.31% boost::shared_ptr::shared_ptr (inline) 0 0% 61.93% 106ms 1.31% std::operator<< (inline) 102ms 1.26% 63.19% 102ms 1.26% __libc_open64 102ms 1.26% 64.46% 102ms 1.26% std::_Rb_tree_insert_and_rebalance 4ms 0.049% 64.51% 102ms 1.26% std::vector::push_back (inline) 99ms 1.22% 65.73% 99ms 1.22% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 33ms 0.41% 66.14% 98ms 1.21% boost::numeric::ublas::indexing_vector_assign 4ms 0.049% 66.19% 97ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 31ms 0.38% 66.57% 95ms 1.18% AbstractElement::GetNodeLocation 89ms 1.10% 67.67% 94ms 1.16% boost::detail::sp_counted_base::release 10ms 0.12% 67.80% 94ms 1.16% std::_Rb_tree_const_iterator::operator++ (inline) 9ms 0.11% 67.91% 92ms 1.14% std::vector::_M_realloc_insert 0 0% 67.91% 89ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 88ms 1.09% 69.00% 88ms 1.09% __GI___fstatat64 88ms 1.09% 70.09% 88ms 1.09% std::_Rb_tree_increment 0 0% 70.09% 87ms 1.08% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.09% 87ms 1.08% std::filesystem::create_directory 57ms 0.71% 70.79% 86ms 1.06% std::basic_filebuf::xsputn 1ms 0.012% 70.80% 86ms 1.06% std::filesystem::status 2ms 0.025% 70.83% 82ms 1.01% AbstractCellPopulation::GetLocationIndexUsingCell 7ms 0.087% 70.91% 80ms 0.99% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 70.91% 78ms 0.96% Cell::GetCellId 50ms 0.62% 71.53% 76ms 0.94% malloc_consolidate 72ms 0.89% 72.42% 72ms 0.89% std::vector::size (inline) 68ms 0.84% 73.26% 72ms 0.89% vertexsort 70ms 0.87% 74.13% 70ms 0.87% Node::GetIndex 52ms 0.64% 74.77% 67ms 0.83% std::num_put::do_put 27ms 0.33% 75.11% 66ms 0.82% AbstractTetrahedralMesh::GetElement 65ms 0.8% 75.91% 65ms 0.8% counterclockwise 52ms 0.64% 76.56% 64ms 0.79% AbstractElement::GetNodeGlobalIndex 64ms 0.79% 77.35% 64ms 0.79% boost::shared_ptr::operator-> (inline) 36ms 0.45% 77.79% 64ms 0.79% hack_digit 63ms 0.78% 78.57% 63ms 0.78% __memcpy_avx_unaligned_erms 2ms 0.025% 78.60% 62ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.049% 78.65% 61ms 0.75% CellPropertyCollection::AddProperty 3ms 0.037% 78.68% 61ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 78.68% 61ms 0.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.68% 61ms 0.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 78.68% 60ms 0.74% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 78.68% 59ms 0.73% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 78.68% 59ms 0.73% tcache_get (inline) 59ms 0.73% 79.41% 59ms 0.73% tcache_get_n (inline) 56ms 0.69% 80.11% 56ms 0.69% boost::detail::shared_count::shared_count (inline) 0 0% 80.11% 53ms 0.66% AbstractCentreBasedCellPopulation::CreateCellPair 53ms 0.66% 80.76% 53ms 0.66% [libchaste_mesh.so] 53ms 0.66% 81.42% 53ms 0.66% [libstdc++.so.6.0.33] 34ms 0.42% 81.84% 53ms 0.66% std::basic_streambuf::xsputn 0 0% 81.84% 53ms 0.66% std::vector::vector (inline) 18ms 0.22% 82.06% 51ms 0.63% Determinant (inline) 51ms 0.63% 82.69% 51ms 0.63% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.69% 51ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.69% 51ms 0.63% std::__new_allocator::destroy (inline) 0 0% 82.69% 51ms 0.63% std::allocator_traits::destroy (inline) 49ms 0.61% 83.30% 49ms 0.61% Node::rGetLocation 25ms 0.31% 83.61% 49ms 0.61% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.012% 83.62% 48ms 0.59% _IO_new_fclose 0 0% 83.62% 47ms 0.58% std::__basic_file::close 8ms 0.099% 83.72% 47ms 0.58% std::__copy_move::__copy_m (inline) 0 0% 83.72% 47ms 0.58% std::__copy_move_a (inline) 0 0% 83.72% 47ms 0.58% std::__copy_move_a1 (inline) 0 0% 83.72% 47ms 0.58% std::__copy_move_a2 (inline) 0 0% 83.72% 47ms 0.58% std::copy (inline) 47ms 0.58% 84.30% 47ms 0.58% std::ostream::sentry::sentry 46ms 0.57% 84.87% 46ms 0.57% __GI___mkdir 0 0% 84.87% 45ms 0.56% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 3ms 0.037% 84.91% 45ms 0.56% Node::ConstructNodeAttributes (inline) 0 0% 84.91% 45ms 0.56% boost::numeric::ublas::norm_2 (inline) 17ms 0.21% 85.12% 45ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 20ms 0.25% 85.36% 44ms 0.54% AbstractCellCycleModel::GetAge 0 0% 85.36% 44ms 0.54% BoundaryNodeWriter::Visit 1ms 0.012% 85.38% 44ms 0.54% std::_Vector_base::_M_create_storage (inline) 0 0% 85.38% 44ms 0.54% std::_Vector_base::_Vector_base (inline) 0 0% 85.38% 43ms 0.53% Node::ClearAppliedForce 2ms 0.025% 85.40% 43ms 0.53% _IO_new_file_close_it 0 0% 85.40% 43ms 0.53% std::map::find (inline) 6ms 0.074% 85.48% 42ms 0.52% Inverse 0 0% 85.48% 42ms 0.52% _dl_init 0 0% 85.48% 42ms 0.52% call_init (inline) 0 0% 85.48% 41ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.48% 41ms 0.51% CxxTest::RealWorldDescription::setUp 0 0% 85.48% 41ms 0.51% PetscSetup::setUpWorld 0 0% 85.48% 41ms 0.51% PetscSetupUtils::CommonSetup 41ms 0.51% 85.98% 41ms 0.51% __GI___close_nocancel 0 0% 85.98% 41ms 0.51% std::map::map (inline)