File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6456ms, 85.82% of 7523ms total Dropped 553 nodes (cum <= 37.62ms) flat flat% sum% cum cum% 0 0% 0% 7492ms 99.59% __libc_start_call_main 0 0% 0% 7492ms 99.59% __libc_start_main_impl 0 0% 0% 7492ms 99.59% _start 0 0% 0% 7478ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7478ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7478ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7478ms 99.40% main 0 0% 0% 7447ms 98.99% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7447ms 98.99% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7447ms 98.99% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7444ms 98.95% AbstractCellBasedSimulation::Solve 0 0% 0% 3296ms 43.81% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2836ms 37.70% MeshBasedCellPopulation::Update 1ms 0.013% 0.027% 2529ms 33.62% AbstractCellPopulation::WriteResultsToFiles 2ms 0.027% 0.053% 1615ms 21.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.04% 0.093% 1455ms 19.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.11% 1422ms 18.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.11% 1394ms 18.53% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.11% 1384ms 18.40% MutableMesh::ReMesh 7ms 0.093% 0.2% 1204ms 16.00% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.093% 0.29% 1024ms 13.61% AbstractTwoBodyInteractionForce::AddForceContribution 120ms 1.60% 1.89% 1011ms 13.44% TetrahedralMesh::EdgeIterator::operator++ 15ms 0.2% 2.09% 953ms 12.67% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 250ms 3.32% 5.41% 952ms 12.65% __dynamic_cast 43ms 0.57% 5.98% 921ms 12.24% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.08% 6.06% 876ms 11.64% CellPropertyCollection::GetPropertiesType (inline) 379ms 5.04% 11.10% 868ms 11.54% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.11% 11.21% 850ms 11.30% CellPopulationElementWriter::Visit 25ms 0.33% 11.54% 827ms 10.99% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.12% 11.66% 787ms 10.46% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.093% 11.75% 749ms 9.96% TetrahedralMesh::ImportFromMesher 7ms 0.093% 11.84% 735ms 9.77% AbstractCellProperty::IsSubType (inline) 36ms 0.48% 12.32% 699ms 9.29% operator new 250ms 3.32% 15.65% 647ms 8.60% __GI___libc_malloc 38ms 0.51% 16.15% 619ms 8.23% std::__new_allocator::allocate (inline) 0 0% 16.15% 615ms 8.17% std::allocator_traits::allocate (inline) 10ms 0.13% 16.28% 610ms 8.11% std::set::insert (inline) 13ms 0.17% 16.46% 600ms 7.98% std::_Rb_tree::_M_insert_unique 73ms 0.97% 17.43% 560ms 7.44% std::map::operator[] (partial-inline) 3ms 0.04% 17.47% 556ms 7.39% Cell::GetCellProliferativeType 79ms 1.05% 18.52% 552ms 7.34% std::_Rb_tree::~_Rb_tree (inline) 0 0% 18.52% 535ms 7.11% std::ostream::operator<< (inline) 108ms 1.44% 19.95% 528ms 7.02% std::ostream::_M_insert 0 0% 19.95% 521ms 6.93% std::set::~set (inline) 512ms 6.81% 26.76% 512ms 6.81% __strcmp_evex 3ms 0.04% 26.80% 506ms 6.73% LegacyCellProliferativeTypesWriter::VisitCell 226ms 3.00% 29.80% 504ms 6.70% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 29.80% 491ms 6.53% std::_Rb_tree::_M_create_node (inline) 18ms 0.24% 30.04% 476ms 6.33% std::_Rb_tree::find (inline) 0 0% 30.04% 476ms 6.33% triangulate 56ms 0.74% 30.79% 469ms 6.23% std::_Rb_tree::_M_erase 0 0% 30.79% 469ms 6.23% std::_Rb_tree::_M_get_node (inline) 0 0% 30.79% 462ms 6.14% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.013% 30.80% 447ms 5.94% AbstractCellBasedSimulation::DoCellBirth 0 0% 30.80% 444ms 5.90% std::set::count (inline) 0 0% 30.80% 434ms 5.77% std::_Rb_tree::lower_bound (inline) 0 0% 30.80% 434ms 5.77% std::map::lower_bound (inline) 0 0% 30.80% 426ms 5.66% delaunay 1ms 0.013% 30.81% 425ms 5.65% divconqdelaunay 28ms 0.37% 31.18% 413ms 5.49% std::_Rb_tree::_M_insert_ (inline) 12ms 0.16% 31.34% 407ms 5.41% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 31.34% 404ms 5.37% std::_Rb_tree::_M_drop_node (inline) 3ms 0.04% 31.38% 379ms 5.04% std::set::set (inline) 46ms 0.61% 32.00% 375ms 4.98% std::_Rb_tree::_M_copy (inline) 2ms 0.027% 32.02% 374ms 4.97% Cell::GetMutationState 1ms 0.013% 32.04% 345ms 4.59% Element::Element 0 0% 32.04% 333ms 4.43% NodeLocationWriter::Visit 74ms 0.98% 33.02% 324ms 4.31% __GI___libc_free 127ms 1.69% 34.71% 314ms 4.17% std::_Rb_tree::_M_clone_node (inline) 10ms 0.13% 34.84% 313ms 4.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 34.84% 303ms 4.03% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 34.84% 303ms 4.03% MeshBasedCellPopulation::GetDampingConstant 13ms 0.17% 35.01% 300ms 3.99% boost::detail::shared_count::~shared_count (inline) 0 0% 35.01% 300ms 3.99% boost::shared_ptr::~shared_ptr (inline) 204ms 2.71% 37.72% 299ms 3.97% _int_malloc 11ms 0.15% 37.87% 295ms 3.92% std::__new_allocator::deallocate (inline) 4ms 0.053% 37.92% 288ms 3.83% Cell::ReadyToDivide 0 0% 37.92% 287ms 3.81% std::allocator_traits::deallocate (inline) 8ms 0.11% 38.03% 284ms 3.78% std::less::operator() (inline) 276ms 3.67% 41.70% 276ms 3.67% std::operator< (inline) 274ms 3.64% 45.34% 275ms 3.66% boost::detail::sp_counted_base::release 19ms 0.25% 45.59% 273ms 3.63% std::num_put::_M_insert_float 251ms 3.34% 48.93% 251ms 3.34% std::_Rb_tree::_S_right (inline) 4ms 0.053% 48.98% 244ms 3.24% Element::RegisterWithNodes (inline) 0 0% 48.98% 244ms 3.24% std::_Rb_tree::_M_put_node (inline) 207ms 2.75% 51.73% 240ms 3.19% _int_free 9ms 0.12% 51.85% 240ms 3.19% divconqrecurse 3ms 0.04% 51.89% 236ms 3.14% Node::AddElement 234ms 3.11% 55.00% 234ms 3.11% [libchaste_cell_based.so] 7ms 0.093% 55.10% 231ms 3.07% std::__cxx11::collate::do_transform 4ms 0.053% 55.15% 229ms 3.04% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.013% 55.16% 227ms 3.02% CellProliferativeTypesWriter::VisitCell 58ms 0.77% 55.94% 220ms 2.92% mergehulls 3ms 0.04% 55.98% 217ms 2.88% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 55.98% 212ms 2.82% ___vsnprintf 1ms 0.013% 55.99% 212ms 2.82% __vsnprintf_internal (inline) 14ms 0.19% 56.17% 209ms 2.78% __printf_buffer 9ms 0.12% 56.29% 188ms 2.50% __printf_fp_l_buffer 0 0% 56.29% 188ms 2.50% __printf_fp_spec (inline) 7ms 0.093% 56.39% 180ms 2.39% AbstractCellProperty::IsType (inline) 4ms 0.053% 56.44% 178ms 2.37% CellPropertyCollection::HasProperty 0 0% 56.44% 176ms 2.34% Cell::HasCellProperty (inline) 0 0% 56.44% 174ms 2.31% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 60ms 0.8% 57.24% 174ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 57.24% 173ms 2.30% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 57.25% 172ms 2.29% OutputFileHandler::OpenOutputFile 86ms 1.14% 58.39% 166ms 2.21% __printf_fp_buffer_1 0 0% 58.39% 160ms 2.13% std::_Rb_tree::_M_destroy_node (inline) 0 0% 58.39% 160ms 2.13% std::__new_allocator::destroy (inline) 0 0% 58.39% 160ms 2.13% std::allocator_traits::destroy (inline) 0 0% 58.39% 159ms 2.11% boost::numeric::ublas::vector_assign (inline) 14ms 0.19% 58.58% 157ms 2.09% MeshBasedCellPopulation::SpringsEnd (inline) 13ms 0.17% 58.75% 149ms 1.98% AbstractTetrahedralElement::CalculateJacobian 0 0% 58.75% 146ms 1.94% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 58.77% 145ms 1.93% TetrahedralMesh::Clear 1ms 0.013% 58.78% 141ms 1.87% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.027% 58.81% 139ms 1.85% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.027% 58.83% 137ms 1.82% std::vector::push_back (inline) 135ms 1.79% 60.63% 135ms 1.79% [libchaste_mesh.so] 7ms 0.093% 60.72% 131ms 1.74% std::vector::_M_realloc_insert 15ms 0.2% 60.92% 128ms 1.70% AbstractCellProperty::IsSame 5ms 0.066% 60.99% 125ms 1.66% AbstractTetrahedralElement::CalculateInverseJacobian 31ms 0.41% 61.40% 125ms 1.66% TetrahedralMesh::EdgesEnd (partial-inline) 53ms 0.7% 62.10% 122ms 1.62% std::__ostream_insert 0 0% 62.10% 120ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 119ms 1.58% 63.68% 119ms 1.58% std::_Rb_tree_insert_and_rebalance 13ms 0.17% 63.86% 118ms 1.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.31% 64.16% 113ms 1.50% std::type_info::operator== (inline) 109ms 1.45% 65.61% 109ms 1.45% [libstdc++.so.6.0.33] 0 0% 65.61% 106ms 1.41% alternateaxes 3ms 0.04% 65.65% 105ms 1.40% AbstractTetrahedralElement::AbstractTetrahedralElement 89ms 1.18% 66.84% 105ms 1.40% vertexmedian 21ms 0.28% 67.11% 101ms 1.34% boost::numeric::ublas::indexing_vector_assign 25ms 0.33% 67.45% 101ms 1.34% std::num_put::_M_insert_int 8ms 0.11% 67.55% 100ms 1.33% AbstractTetrahedralElement::RefreshJacobian 20ms 0.27% 67.82% 98ms 1.30% MeshBasedCellPopulation::SpringIterator::SpringIterator 98ms 1.30% 69.12% 98ms 1.30% incircle 92ms 1.22% 70.34% 92ms 1.22% std::_Rb_tree::_S_left (inline) 1ms 0.013% 70.36% 92ms 1.22% std::operator<< (inline) 3ms 0.04% 70.40% 90ms 1.20% Node::~Node 3ms 0.04% 70.44% 89ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.04% 70.48% 87ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.48% 84ms 1.12% std::basic_ofstream::basic_ofstream (inline) 17ms 0.23% 70.70% 83ms 1.10% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.70% 82ms 1.09% OutputFileHandler::CommonConstructor 0 0% 70.70% 82ms 1.09% OutputFileHandler::OutputFileHandler 0 0% 70.70% 79ms 1.05% std::basic_filebuf::open 0 0% 70.70% 79ms 1.05% std::basic_ofstream::open (inline) 5ms 0.066% 70.77% 78ms 1.04% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 70.77% 78ms 1.04% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 70.77% 77ms 1.02% Cell::GetCellId 61ms 0.81% 71.58% 77ms 1.02% malloc_consolidate 60ms 0.8% 72.38% 76ms 1.01% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 72.38% 76ms 1.01% tcache_get (inline) 76ms 1.01% 73.39% 76ms 1.01% tcache_get_n (inline) 47ms 0.62% 74.01% 75ms 1% AbstractElement::GetNodeLocation 0 0% 74.01% 75ms 1% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.027% 74.04% 74ms 0.98% Node::ClearAppliedForce 0 0% 74.04% 72ms 0.96% Node::ConstructNodeAttributes (inline) 15ms 0.2% 74.24% 71ms 0.94% TetrahedralMesh::EdgeIterator::GetNodeB 63ms 0.84% 75.08% 71ms 0.94% vertexsort 0 0% 75.08% 70ms 0.93% std::basic_filebuf::close 0 0% 75.08% 69ms 0.92% AbstractCellBasedWriter::CloseFile 0 0% 75.08% 69ms 0.92% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 75.08% 69ms 0.92% std::basic_ofstream::close (inline) 3ms 0.04% 75.12% 67ms 0.89% CellPropertyCollection::AddProperty 61ms 0.81% 75.93% 61ms 0.81% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 40ms 0.53% 76.46% 60ms 0.8% std::basic_streambuf::xsputn 0 0% 76.46% 56ms 0.74% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.027% 76.49% 55ms 0.73% std::filesystem::permissions 30ms 0.4% 76.88% 54ms 0.72% AbstractElement::GetNodeGlobalIndex 0 0% 76.88% 54ms 0.72% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 34ms 0.45% 77.34% 53ms 0.7% boost::numeric::ublas::c_matrix::operator() 53ms 0.7% 78.04% 53ms 0.7% counterclockwise 2ms 0.027% 78.07% 53ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 53ms 0.7% 78.77% 53ms 0.7% std::_Rb_tree_increment 52ms 0.69% 79.46% 52ms 0.69% __GI_fchmodat 51ms 0.68% 80.14% 51ms 0.68% Node::GetIndex 10ms 0.13% 80.27% 51ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 80.27% 51ms 0.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 80.27% 51ms 0.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.027% 80.30% 50ms 0.66% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 80.30% 50ms 0.66% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 2ms 0.027% 80.33% 49ms 0.65% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 2ms 0.027% 80.35% 49ms 0.65% NodeAttributes::NodeAttributes 0 0% 80.35% 49ms 0.65% std::__basic_file::open 1ms 0.013% 80.37% 49ms 0.65% std::basic_filebuf::_M_terminate_output 0 0% 80.37% 48ms 0.64% _IO_new_fopen 0 0% 80.37% 48ms 0.64% __fopen_internal (inline) 48ms 0.64% 81.00% 48ms 0.64% __memcpy_evex_unaligned_erms 29ms 0.39% 81.39% 48ms 0.64% hack_digit 1ms 0.013% 81.40% 48ms 0.64% std::basic_filebuf::overflow 37ms 0.49% 81.90% 47ms 0.62% CellPropertyCollection::GetProperty 30ms 0.4% 82.29% 47ms 0.62% boost::shared_ptr::shared_ptr (inline) 0 0% 82.29% 47ms 0.62% std::__basic_file::xsputn 0 0% 82.29% 47ms 0.62% std::basic_filebuf::_M_convert_to_external 37ms 0.49% 82.79% 47ms 0.62% std::basic_filebuf::xsputn 46ms 0.61% 83.40% 46ms 0.61% __GI___libc_write 0 0% 83.40% 46ms 0.61% std::vector::vector (inline) 16ms 0.21% 83.61% 45ms 0.6% Determinant (inline) 10ms 0.13% 83.74% 45ms 0.6% Inverse 1ms 0.013% 83.76% 45ms 0.6% _IO_new_file_fopen 0 0% 83.76% 44ms 0.58% __GI__IO_file_open 35ms 0.47% 84.22% 44ms 0.58% std::num_put::do_put 0 0% 84.22% 43ms 0.57% std::_Vector_base::_Vector_base (inline) 43ms 0.57% 84.79% 43ms 0.57% std::vector::size (inline) 1ms 0.013% 84.81% 41ms 0.54% std::_Vector_base::_M_create_storage (inline) 0 0% 84.81% 40ms 0.53% BoundaryNodeWriter::Visit 38ms 0.51% 85.31% 40ms 0.53% __libc_open64 38ms 0.51% 85.82% 38ms 0.51% boost::numeric::ublas::c_vector::operator()