File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6904ms, 85.26% of 8098ms total Dropped 563 nodes (cum <= 40.49ms) flat flat% sum% cum cum% 0 0% 0% 8060ms 99.53% __libc_start_call_main 0 0% 0% 8060ms 99.53% __libc_start_main_impl 0 0% 0% 8060ms 99.53% _start 0 0% 0% 8046ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8046ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8046ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8046ms 99.36% main 0 0% 0% 8010ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 8010ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 8010ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 8009ms 98.90% AbstractCellBasedSimulation::Solve 0 0% 0.012% 3325ms 41.06% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.025% 2895ms 35.75% MeshBasedCellPopulation::Update 0 0% 0.025% 2890ms 35.69% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.025% 1784ms 22.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.062% 0.086% 1640ms 20.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.012% 0.099% 1590ms 19.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.099% 1460ms 18.03% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.012% 0.11% 1389ms 17.15% MutableMesh::ReMesh 16ms 0.2% 0.31% 1292ms 15.95% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.074% 0.38% 1209ms 14.93% AbstractTwoBodyInteractionForce::AddForceContribution 55ms 0.68% 1.06% 1083ms 13.37% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 7ms 0.086% 1.15% 1069ms 13.20% CellPopulationElementWriter::Visit 128ms 1.58% 2.73% 1057ms 13.05% TetrahedralMesh::EdgeIterator::operator++ 13ms 0.16% 2.89% 1046ms 12.92% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 427ms 5.27% 8.16% 1003ms 12.39% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.25% 8.41% 929ms 11.47% AbstractCellPopulation::GetCellUsingLocationIndex 253ms 3.12% 11.53% 925ms 11.42% __dynamic_cast 5ms 0.062% 11.60% 845ms 10.43% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.12% 11.72% 845ms 10.43% MeshBasedCellPopulation::AcceptCellWriter 12ms 0.15% 11.87% 736ms 9.09% TetrahedralMesh::ImportFromMesher 44ms 0.54% 12.41% 706ms 8.72% operator new 5ms 0.062% 12.47% 678ms 8.37% AbstractCellProperty::IsSubType (inline) 235ms 2.90% 15.37% 648ms 8.00% __GI___libc_malloc 6ms 0.074% 15.45% 644ms 7.95% std::ostream::operator<< (inline) 78ms 0.96% 16.41% 640ms 7.90% std::map::operator[] (partial-inline) 25ms 0.31% 16.72% 635ms 7.84% std::__new_allocator::allocate (inline) 94ms 1.16% 17.88% 633ms 7.82% std::ostream::_M_insert 0 0% 17.88% 631ms 7.79% std::allocator_traits::allocate (inline) 10ms 0.12% 18.00% 628ms 7.76% std::set::insert (inline) 24ms 0.3% 18.30% 618ms 7.63% std::_Rb_tree::_M_insert_unique 1ms 0.012% 18.31% 565ms 6.98% LegacyCellProliferativeTypesWriter::VisitCell 24ms 0.3% 18.61% 537ms 6.63% std::_Rb_tree::find (inline) 535ms 6.61% 25.22% 535ms 6.61% __strcmp_evex 71ms 0.88% 26.09% 532ms 6.57% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.09% 517ms 6.38% std::_Rb_tree::lower_bound (inline) 0 0% 26.09% 517ms 6.38% std::map::lower_bound (inline) 2ms 0.025% 26.12% 510ms 6.30% Cell::GetCellProliferativeType 0 0% 26.12% 504ms 6.22% std::set::~set (inline) 1ms 0.012% 26.13% 497ms 6.14% triangulate 0 0% 26.13% 494ms 6.10% std::_Rb_tree::_M_create_node (inline) 0 0% 26.13% 491ms 6.06% std::set::count (inline) 0 0% 26.13% 473ms 5.84% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.13% 473ms 5.84% std::_Rb_tree::_M_get_node (inline) 199ms 2.46% 28.59% 464ms 5.73% __cxxabiv1::__si_class_type_info::__do_dyncast 60ms 0.74% 29.33% 457ms 5.64% std::_Rb_tree::_M_erase 21ms 0.26% 29.59% 441ms 5.45% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.59% 438ms 5.41% delaunay 3ms 0.037% 29.62% 436ms 5.38% divconqdelaunay 2ms 0.025% 29.65% 429ms 5.30% std::set::set (inline) 1ms 0.012% 29.66% 420ms 5.19% AbstractCellBasedSimulation::DoCellBirth 43ms 0.53% 30.19% 395ms 4.88% std::_Rb_tree::_M_copy (inline) 34ms 0.42% 30.61% 394ms 4.87% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.61% 384ms 4.74% std::_Rb_tree::_M_drop_node (inline) 0 0% 30.61% 358ms 4.42% NodeLocationWriter::Visit 9ms 0.11% 30.72% 351ms 4.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.012% 30.74% 350ms 4.32% Cell::GetMutationState 130ms 1.61% 32.34% 341ms 4.21% std::_Rb_tree::_M_clone_node (inline) 4ms 0.049% 32.39% 334ms 4.12% Element::Element 69ms 0.85% 33.24% 323ms 3.99% __GI___libc_free 315ms 3.89% 37.13% 315ms 3.89% std::_Rb_tree::_S_right (inline) 13ms 0.16% 37.29% 311ms 3.84% std::less::operator() (inline) 29ms 0.36% 37.65% 311ms 3.84% std::num_put::_M_insert_float 8ms 0.099% 37.75% 304ms 3.75% boost::detail::shared_count::~shared_count (inline) 0 0% 37.75% 304ms 3.75% boost::shared_ptr::~shared_ptr (inline) 298ms 3.68% 41.43% 298ms 3.68% std::operator< (inline) 1ms 0.012% 41.44% 296ms 3.66% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 41.44% 296ms 3.66% MeshBasedCellPopulation::GetDampingConstant 196ms 2.42% 43.86% 295ms 3.64% _int_malloc 9ms 0.11% 43.97% 287ms 3.54% std::__new_allocator::deallocate (inline) 273ms 3.37% 47.35% 282ms 3.48% boost::detail::sp_counted_base::release 0 0% 47.35% 274ms 3.38% std::allocator_traits::deallocate (inline) 265ms 3.27% 50.62% 265ms 3.27% [libchaste_cell_based.so] 7ms 0.086% 50.70% 265ms 3.27% divconqrecurse 21ms 0.26% 50.96% 264ms 3.26% AbstractCellProperty::IsType (inline) 0 0% 50.96% 260ms 3.21% Cell::ReadyToDivide 6ms 0.074% 51.04% 255ms 3.15% std::__cxx11::collate::do_transform 80ms 0.99% 52.03% 252ms 3.11% mergehulls 5ms 0.062% 52.09% 249ms 3.07% CellPropertyCollection::HasProperty 2ms 0.025% 52.11% 248ms 3.06% Cell::HasCellProperty (inline) 6ms 0.074% 52.19% 246ms 3.04% Element::RegisterWithNodes (inline) 220ms 2.72% 54.90% 244ms 3.01% _int_free 2ms 0.025% 54.93% 240ms 2.96% ___vsnprintf 2ms 0.025% 54.95% 239ms 2.95% __vsnprintf_internal (inline) 0 0% 54.95% 239ms 2.95% std::_Rb_tree::_M_put_node (inline) 5ms 0.062% 55.01% 238ms 2.94% Node::AddElement 30ms 0.37% 55.38% 233ms 2.88% __printf_buffer 0 0% 55.38% 221ms 2.73% CellProliferativeTypesWriter::VisitCell 75ms 0.93% 56.31% 200ms 2.47% std::_Rb_tree::_M_get_insert_unique_pos (inline) 8ms 0.099% 56.41% 186ms 2.30% __printf_fp_l_buffer 0 0% 56.41% 186ms 2.30% __printf_fp_spec (inline) 3ms 0.037% 56.45% 185ms 2.28% boost::numeric::ublas::vector_assign (inline) 2ms 0.025% 56.47% 184ms 2.27% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 56.47% 183ms 2.26% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 56.47% 183ms 2.26% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 7ms 0.086% 56.56% 182ms 2.25% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 85ms 1.05% 57.61% 182ms 2.25% std::__ostream_insert 0 0% 57.61% 181ms 2.24% OutputFileHandler::OpenOutputFile 6ms 0.074% 57.68% 172ms 2.12% boost::numeric::ublas::c_vector::c_vector (inline) 41ms 0.51% 58.19% 172ms 2.12% std::num_put::_M_insert_int 5ms 0.062% 58.25% 169ms 2.09% TetrahedralMesh::Clear 87ms 1.07% 59.32% 165ms 2.04% __printf_fp_buffer_1 46ms 0.57% 59.89% 164ms 2.03% AbstractCellProperty::IsSame 2ms 0.025% 59.92% 164ms 2.03% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.012% 59.93% 159ms 1.96% std::_Vector_base::_M_allocate (inline) 0 0% 59.93% 145ms 1.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 59.93% 145ms 1.79% std::__new_allocator::destroy (inline) 0 0% 59.93% 145ms 1.79% std::allocator_traits::destroy (inline) 0 0% 59.93% 143ms 1.77% std::operator<< (inline) 1ms 0.012% 59.94% 138ms 1.70% TetrahedralMesh::RefreshJacobianCachedData 9ms 0.11% 60.05% 132ms 1.63% AbstractTetrahedralElement::CalculateJacobian 5ms 0.062% 60.11% 128ms 1.58% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.049% 60.16% 128ms 1.58% std::vector::push_back (inline) 31ms 0.38% 60.55% 127ms 1.57% TetrahedralMesh::EdgesEnd (partial-inline) 123ms 1.52% 62.06% 123ms 1.52% [libchaste_mesh.so] 28ms 0.35% 62.41% 123ms 1.52% boost::numeric::ublas::indexing_vector_assign 1ms 0.012% 62.42% 118ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 18ms 0.22% 62.65% 118ms 1.46% std::type_info::operator== (inline) 5ms 0.062% 62.71% 118ms 1.46% std::vector::_M_realloc_insert 12ms 0.15% 62.86% 117ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.037% 62.89% 111ms 1.37% alternateaxes 8ms 0.099% 62.99% 110ms 1.36% MeshBasedCellPopulation::SpringIterator::SpringIterator 97ms 1.20% 64.19% 106ms 1.31% vertexmedian 105ms 1.30% 65.49% 105ms 1.30% incircle 104ms 1.28% 66.77% 104ms 1.28% [libstdc++.so.6.0.33] 0 0% 66.77% 103ms 1.27% Node::~Node 0 0% 66.77% 101ms 1.25% Cell::GetCellId 0 0% 66.77% 101ms 1.25% tcache_get (inline) 101ms 1.25% 68.02% 101ms 1.25% tcache_get_n (inline) 0 0% 68.02% 99ms 1.22% std::basic_ofstream::basic_ofstream (inline) 1ms 0.012% 68.03% 97ms 1.20% std::basic_ofstream::open (inline) 0 0% 68.03% 96ms 1.19% std::basic_filebuf::open 95ms 1.17% 69.20% 95ms 1.17% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 69.21% 94ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 73ms 0.9% 70.12% 94ms 1.16% malloc_consolidate 64ms 0.79% 70.91% 94ms 1.16% std::basic_streambuf::xsputn 8ms 0.099% 71.01% 92ms 1.14% CellPropertyCollection::AddProperty 3ms 0.037% 71.04% 91ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 88ms 1.09% 72.13% 88ms 1.09% std::_Rb_tree::_S_left (inline) 1ms 0.012% 72.14% 87ms 1.07% AbstractTetrahedralElement::AbstractTetrahedralElement 12ms 0.15% 72.29% 87ms 1.07% AbstractTetrahedralElement::RefreshJacobian 61ms 0.75% 73.04% 86ms 1.06% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 66ms 0.82% 73.86% 84ms 1.04% std::basic_filebuf::xsputn 0 0% 73.86% 83ms 1.02% OutputFileHandler::CommonConstructor 0 0% 73.86% 83ms 1.02% OutputFileHandler::OutputFileHandler 9ms 0.11% 73.97% 83ms 1.02% std::_Rb_tree_const_iterator::operator++ (inline) 80ms 0.99% 74.96% 80ms 0.99% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 74.96% 78ms 0.96% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 74.98% 75ms 0.93% Node::ConstructNodeAttributes (inline) 0 0% 74.98% 74ms 0.91% std::vector::vector (inline) 0 0% 74.98% 73ms 0.9% AbstractCellBasedWriter::CloseFile 0 0% 74.98% 73ms 0.9% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 74.98% 73ms 0.9% Node::ClearAppliedForce 1ms 0.012% 74.99% 73ms 0.9% std::basic_ofstream::close (inline) 1ms 0.012% 75.01% 72ms 0.89% std::basic_filebuf::close 2ms 0.025% 75.03% 71ms 0.88% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.03% 71ms 0.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.03% 71ms 0.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.03% 69ms 0.85% std::_Vector_base::_Vector_base (inline) 55ms 0.68% 75.71% 68ms 0.84% std::num_put::do_put 67ms 0.83% 76.54% 67ms 0.83% std::_Rb_tree_increment 8ms 0.099% 76.64% 66ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.012% 76.65% 65ms 0.8% std::_Vector_base::_M_create_storage (inline) 0 0% 76.65% 63ms 0.78% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 40ms 0.49% 77.14% 61ms 0.75% AbstractElement::GetNodeLocation 0 0% 77.14% 58ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 58ms 0.72% 77.86% 58ms 0.72% __memcpy_evex_unaligned_erms 39ms 0.48% 78.34% 57ms 0.7% boost::shared_ptr::shared_ptr (inline) 1ms 0.012% 78.35% 57ms 0.7% std::__basic_file::xsputn 0 0% 78.35% 57ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 78.35% 57ms 0.7% std::basic_filebuf::_M_terminate_output 0 0% 78.35% 57ms 0.7% std::basic_filebuf::overflow 0 0% 78.35% 56ms 0.69% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 78.35% 56ms 0.69% NodeAttributes::NodeAttributes 7ms 0.086% 78.44% 56ms 0.69% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 78.44% 56ms 0.69% _IO_new_fopen 56ms 0.69% 79.13% 56ms 0.69% __GI___libc_write 0 0% 79.13% 56ms 0.69% __fopen_internal (inline) 0 0% 79.13% 56ms 0.69% std::__basic_file::open 0 0% 79.13% 54ms 0.67% _IO_new_file_fopen 22ms 0.27% 79.40% 53ms 0.65% Determinant (inline) 53ms 0.65% 80.06% 53ms 0.65% counterclockwise 0 0% 80.06% 52ms 0.64% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 80.06% 52ms 0.64% __GI__IO_file_open 29ms 0.36% 80.41% 52ms 0.64% hack_digit 39ms 0.48% 80.90% 51ms 0.63% CellPropertyCollection::GetProperty 0 0% 80.90% 50ms 0.62% AbstractCentreBasedCellPopulation::IsMarkedSpring 30ms 0.37% 81.27% 50ms 0.62% AbstractElement::GetNodeGlobalIndex 49ms 0.61% 81.87% 49ms 0.61% boost::numeric::ublas::c_vector::operator() 39ms 0.48% 82.35% 48ms 0.59% vertexsort 0 0% 82.35% 46ms 0.57% BoundaryNodeWriter::Visit 0 0% 82.35% 46ms 0.57% FilesystemPermissions::SetFilePermissions (inline) 46ms 0.57% 82.92% 46ms 0.57% Node::GetIndex 1ms 0.012% 82.93% 46ms 0.57% std::filesystem::permissions 46ms 0.57% 83.50% 46ms 0.57% std::vector::size (inline) 18ms 0.22% 83.72% 45ms 0.56% AbstractTetrahedralMesh::GetElement 45ms 0.56% 84.28% 45ms 0.56% __GI_fchmodat 5ms 0.062% 84.34% 45ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 43ms 0.53% 84.87% 44ms 0.54% __libc_open64 25ms 0.31% 85.18% 44ms 0.54% boost::numeric::ublas::c_matrix::operator() 6ms 0.074% 85.26% 43ms 0.53% Inverse