File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6538ms, 86.25% of 7580ms total Dropped 564 nodes (cum <= 37.90ms) flat flat% sum% cum cum% 0 0% 0% 7547ms 99.56% __libc_start_call_main 0 0% 0% 7547ms 99.56% __libc_start_main_impl 0 0% 0% 7547ms 99.56% _start 0 0% 0% 7533ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7533ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7533ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7533ms 99.38% main 0 0% 0% 7501ms 98.96% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7501ms 98.96% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7501ms 98.96% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7499ms 98.93% AbstractCellBasedSimulation::Solve 0 0% 0% 3308ms 43.64% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.026% 2838ms 37.44% MeshBasedCellPopulation::Update 1ms 0.013% 0.04% 2612ms 34.46% AbstractCellPopulation::WriteResultsToFiles 3ms 0.04% 0.079% 1574ms 20.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.053% 0.13% 1441ms 19.01% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.04% 0.17% 1413ms 18.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.026% 0.2% 1368ms 18.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.21% 1334ms 17.60% MutableMesh::ReMesh 13ms 0.17% 0.38% 1237ms 16.32% MeshBasedCellPopulation::SpringIterator::operator++ 105ms 1.39% 1.77% 1031ms 13.60% TetrahedralMesh::EdgeIterator::operator++ 11ms 0.15% 1.91% 1005ms 13.26% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.026% 1.94% 995ms 13.13% AbstractTwoBodyInteractionForce::AddForceContribution 404ms 5.33% 7.27% 925ms 12.20% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.04% 7.31% 911ms 12.02% CellPropertyCollection::GetPropertiesType (inline) 242ms 3.19% 10.50% 911ms 12.02% __dynamic_cast 42ms 0.55% 11.06% 907ms 11.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 6ms 0.079% 11.13% 863ms 11.39% CellPopulationElementWriter::Visit 25ms 0.33% 11.46% 832ms 10.98% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.16% 11.62% 820ms 10.82% MeshBasedCellPopulation::AcceptCellWriter 11ms 0.15% 11.77% 740ms 9.76% AbstractCellProperty::IsSubType (inline) 11ms 0.15% 11.91% 715ms 9.43% TetrahedralMesh::ImportFromMesher 47ms 0.62% 12.53% 678ms 8.94% operator new 19ms 0.25% 12.78% 625ms 8.25% std::__new_allocator::allocate (inline) 0 0% 12.78% 617ms 8.14% std::allocator_traits::allocate (inline) 242ms 3.19% 15.98% 615ms 8.11% __GI___libc_malloc 10ms 0.13% 16.11% 602ms 7.94% std::set::insert (inline) 11ms 0.15% 16.25% 592ms 7.81% std::_Rb_tree::_M_insert_unique 2ms 0.026% 16.28% 566ms 7.47% Cell::GetCellProliferativeType 79ms 1.04% 17.32% 564ms 7.44% std::map::operator[] (partial-inline) 24ms 0.32% 17.64% 556ms 7.34% std::_Rb_tree::find (inline) 3ms 0.04% 17.68% 537ms 7.08% std::ostream::operator<< (inline) 94ms 1.24% 18.92% 531ms 7.01% std::ostream::_M_insert 79ms 1.04% 19.96% 527ms 6.95% std::_Rb_tree::~_Rb_tree (inline) 0 0% 19.96% 521ms 6.87% std::set::count (inline) 0 0% 19.96% 516ms 6.81% std::_Rb_tree::_M_create_node (inline) 3ms 0.04% 20.00% 512ms 6.75% LegacyCellProliferativeTypesWriter::VisitCell 510ms 6.73% 26.73% 510ms 6.73% __strcmp_evex 0 0% 26.73% 502ms 6.62% std::set::~set (inline) 0 0% 26.73% 498ms 6.57% std::_Rb_tree::_M_get_node (inline) 0 0% 26.73% 480ms 6.33% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.013% 26.74% 469ms 6.19% triangulate 0 0% 26.74% 460ms 6.07% AbstractCellBasedSimulation::DoCellBirth 191ms 2.52% 29.26% 457ms 6.03% __cxxabiv1::__si_class_type_info::__do_dyncast 57ms 0.75% 30.01% 444ms 5.86% std::_Rb_tree::_M_erase 7ms 0.092% 30.11% 426ms 5.62% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 30.11% 425ms 5.61% std::_Rb_tree::lower_bound (inline) 0 0% 30.11% 425ms 5.61% std::map::lower_bound (inline) 0 0% 30.11% 414ms 5.46% delaunay 2ms 0.026% 30.13% 414ms 5.46% divconqdelaunay 3ms 0.04% 30.17% 400ms 5.28% std::set::set (inline) 41ms 0.54% 30.71% 392ms 5.17% std::_Rb_tree::_M_copy (inline) 33ms 0.44% 31.15% 390ms 5.15% std::_Rb_tree::_M_insert_ (inline) 4ms 0.053% 31.20% 389ms 5.13% Cell::GetMutationState 0 0% 31.20% 380ms 5.01% std::_Rb_tree::_M_drop_node (inline) 2ms 0.026% 31.23% 334ms 4.41% Element::Element 126ms 1.66% 32.89% 334ms 4.41% std::_Rb_tree::_M_clone_node (inline) 15ms 0.2% 33.09% 328ms 4.33% boost::detail::shared_count::~shared_count (inline) 0 0% 33.09% 328ms 4.33% boost::shared_ptr::~shared_ptr (inline) 10ms 0.13% 33.22% 312ms 4.12% std::less::operator() (inline) 1ms 0.013% 33.23% 309ms 4.08% NodeLocationWriter::Visit 6ms 0.079% 33.31% 308ms 4.06% AbstractCellPopulation::IsCellAttachedToLocationIndex 302ms 3.98% 37.30% 302ms 3.98% std::operator< (inline) 66ms 0.87% 38.17% 301ms 3.97% __GI___libc_free 297ms 3.92% 42.08% 301ms 3.97% boost::detail::sp_counted_base::release 1ms 0.013% 42.10% 286ms 3.77% MeshBasedCellPopulation::GetDampingConstant 286ms 3.77% 45.87% 286ms 3.77% std::_Rb_tree::_S_right (inline) 2ms 0.026% 45.90% 285ms 3.76% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.053% 45.95% 282ms 3.72% Cell::ReadyToDivide 16ms 0.21% 46.16% 273ms 3.60% std::num_put::_M_insert_float 9ms 0.12% 46.28% 272ms 3.59% std::__new_allocator::deallocate (inline) 0 0% 46.28% 264ms 3.48% std::allocator_traits::deallocate (inline) 188ms 2.48% 48.76% 262ms 3.46% _int_malloc 2ms 0.026% 48.79% 255ms 3.36% Element::RegisterWithNodes (inline) 3ms 0.04% 48.83% 249ms 3.28% Node::AddElement 1ms 0.013% 48.84% 248ms 3.27% CellProliferativeTypesWriter::VisitCell 6ms 0.079% 48.92% 247ms 3.26% divconqrecurse 233ms 3.07% 51.99% 233ms 3.07% [libchaste_cell_based.so] 63ms 0.83% 52.82% 232ms 3.06% mergehulls 213ms 2.81% 55.63% 231ms 3.05% _int_free 0 0% 55.63% 228ms 3.01% std::_Rb_tree::_M_put_node (inline) 4ms 0.053% 55.69% 227ms 2.99% std::__cxx11::collate::do_transform 5ms 0.066% 55.75% 221ms 2.92% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.04% 55.79% 213ms 2.81% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 55.79% 211ms 2.78% ___vsnprintf 0 0% 55.79% 211ms 2.78% __vsnprintf_internal (inline) 24ms 0.32% 56.11% 209ms 2.76% __printf_buffer 0 0% 56.11% 193ms 2.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 56.11% 192ms 2.53% AbstractCellBasedWriter::OpenOutputFileForAppend 56ms 0.74% 56.85% 191ms 2.52% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 56.85% 189ms 2.49% OutputFileHandler::OpenOutputFile 7ms 0.092% 56.94% 174ms 2.30% AbstractCellProperty::IsType (inline) 2ms 0.026% 56.97% 167ms 2.20% boost::numeric::ublas::vector_assign (inline) 2ms 0.026% 56.99% 164ms 2.16% TetrahedralMesh::Clear 14ms 0.18% 57.18% 164ms 2.16% __printf_fp_l_buffer 0 0% 57.18% 164ms 2.16% __printf_fp_spec (inline) 2ms 0.026% 57.20% 163ms 2.15% Cell::HasCellProperty (inline) 2ms 0.026% 57.23% 163ms 2.15% CellPropertyCollection::HasProperty 13ms 0.17% 57.40% 163ms 2.15% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.026% 57.43% 154ms 2.03% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 57.43% 152ms 2.01% std::_Rb_tree::_M_destroy_node (inline) 0 0% 57.43% 152ms 2.01% std::__new_allocator::destroy (inline) 0 0% 57.43% 152ms 2.01% std::allocator_traits::destroy (inline) 77ms 1.02% 58.44% 144ms 1.90% __printf_fp_buffer_1 10ms 0.13% 58.58% 133ms 1.75% AbstractTetrahedralElement::CalculateJacobian 0 0% 58.58% 133ms 1.75% TetrahedralMesh::RefreshJacobianCachedData 45ms 0.59% 59.17% 133ms 1.75% std::num_put::_M_insert_int 21ms 0.28% 59.45% 126ms 1.66% TetrahedralMesh::EdgesEnd (partial-inline) 7ms 0.092% 59.54% 124ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 65ms 0.86% 60.40% 124ms 1.64% std::__ostream_insert 1ms 0.013% 60.41% 120ms 1.58% std::_Vector_base::_M_allocate (inline) 9ms 0.12% 60.53% 117ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 20ms 0.26% 60.79% 117ms 1.54% AbstractCellProperty::IsSame 32ms 0.42% 61.21% 116ms 1.53% boost::numeric::ublas::indexing_vector_assign 2ms 0.026% 61.24% 115ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.053% 61.29% 113ms 1.49% alternateaxes 110ms 1.45% 62.74% 110ms 1.45% [libchaste_mesh.so] 101ms 1.33% 64.08% 108ms 1.42% vertexmedian 15ms 0.2% 64.27% 107ms 1.41% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.066% 64.34% 106ms 1.40% std::vector::push_back (inline) 103ms 1.36% 65.70% 103ms 1.36% incircle 2ms 0.026% 65.73% 97ms 1.28% Node::~Node 23ms 0.3% 66.03% 97ms 1.28% std::type_info::operator== (inline) 2ms 0.026% 66.06% 97ms 1.28% std::vector::_M_realloc_insert 0 0% 66.06% 97ms 1.28% tcache_get (inline) 97ms 1.28% 67.34% 97ms 1.28% tcache_get_n (inline) 0 0% 67.34% 96ms 1.27% std::operator<< (inline) 93ms 1.23% 68.56% 93ms 1.23% [libstdc++.so.6.0.33] 10ms 0.13% 68.69% 91ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 91ms 1.20% 69.89% 91ms 1.20% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 69.91% 90ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 10ms 0.13% 70.04% 90ms 1.19% AbstractTetrahedralElement::RefreshJacobian 69ms 0.91% 70.95% 88ms 1.16% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.066% 71.02% 85ms 1.12% CellPropertyCollection::AddProperty 0 0% 71.02% 85ms 1.12% std::basic_ofstream::basic_ofstream (inline) 0 0% 71.02% 84ms 1.11% std::basic_filebuf::open 0 0% 71.02% 84ms 1.11% std::basic_ofstream::open (inline) 11ms 0.15% 71.16% 82ms 1.08% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 71.17% 80ms 1.06% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 71.19% 80ms 1.06% OutputFileHandler::OutputFileHandler 1ms 0.013% 71.20% 79ms 1.04% OutputFileHandler::CommonConstructor 78ms 1.03% 72.23% 78ms 1.03% std::_Rb_tree::_S_left (inline) 77ms 1.02% 73.25% 77ms 1.02% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 73.25% 76ms 1.00% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 73.26% 75ms 0.99% std::basic_filebuf::close 1ms 0.013% 73.27% 75ms 0.99% std::basic_ofstream::close (inline) 0 0% 73.27% 74ms 0.98% AbstractCellBasedWriter::CloseFile 0 0% 73.27% 73ms 0.96% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 73.28% 71ms 0.94% Cell::GetCellId 0 0% 73.28% 70ms 0.92% FilesystemPermissions::SetFilePermissions (inline) 70ms 0.92% 74.21% 70ms 0.92% __GI_fchmodat 0 0% 74.21% 70ms 0.92% std::filesystem::permissions 40ms 0.53% 74.74% 68ms 0.9% AbstractElement::GetNodeLocation 0 0% 74.74% 66ms 0.87% CellPropertyCollection::~CellPropertyCollection (inline) 7ms 0.092% 74.83% 65ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 74.84% 64ms 0.84% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.013% 74.85% 62ms 0.82% Node::ClearAppliedForce 2ms 0.026% 74.88% 62ms 0.82% Node::ConstructNodeAttributes (inline) 0 0% 74.88% 62ms 0.82% _IO_new_fopen 0 0% 74.88% 62ms 0.82% __fopen_internal (inline) 0 0% 74.88% 62ms 0.82% std::__basic_file::open 4ms 0.053% 74.93% 60ms 0.79% TetrahedralMesh::EdgeIterator::GetNodeA 2ms 0.026% 74.96% 60ms 0.79% std::_Rb_tree::_M_emplace_hint_unique 59ms 0.78% 75.74% 59ms 0.78% counterclockwise 43ms 0.57% 76.31% 59ms 0.78% std::basic_filebuf::xsputn 0 0% 76.31% 58ms 0.77% _IO_new_file_fopen 1ms 0.013% 76.32% 58ms 0.77% std::basic_filebuf::_M_terminate_output 57ms 0.75% 77.07% 57ms 0.75% std::_Rb_tree_increment 2ms 0.026% 77.10% 57ms 0.75% std::basic_filebuf::_M_convert_to_external 0 0% 77.10% 57ms 0.75% std::basic_filebuf::overflow 1ms 0.013% 77.11% 56ms 0.74% __GI__IO_file_open 37ms 0.49% 77.60% 56ms 0.74% boost::shared_ptr::shared_ptr (inline) 53ms 0.7% 78.30% 55ms 0.73% __GI___libc_write 0 0% 78.30% 55ms 0.73% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.30% 55ms 0.73% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 78.30% 55ms 0.73% std::__basic_file::xsputn 55ms 0.73% 79.02% 55ms 0.73% std::vector::size (inline) 0 0% 79.02% 54ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.013% 79.04% 53ms 0.7% BoundaryNodeWriter::Visit 47ms 0.62% 79.66% 53ms 0.7% malloc_consolidate 39ms 0.51% 80.17% 53ms 0.7% std::basic_streambuf::xsputn 52ms 0.69% 80.86% 52ms 0.69% __memcpy_evex_unaligned_erms 39ms 0.51% 81.37% 51ms 0.67% std::num_put::do_put 3ms 0.04% 81.41% 50ms 0.66% NodeAttributes::NodeAttributes 49ms 0.65% 82.06% 49ms 0.65% __libc_open64 24ms 0.32% 82.37% 45ms 0.59% AbstractTetrahedralMesh::GetElement 15ms 0.2% 82.57% 45ms 0.59% Determinant (inline) 0 0% 82.57% 45ms 0.59% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 38ms 0.5% 83.07% 45ms 0.59% vertexsort 43ms 0.57% 83.64% 43ms 0.57% Node::GetIndex 21ms 0.28% 83.92% 42ms 0.55% AbstractElement::GetNodeGlobalIndex 41ms 0.54% 84.46% 41ms 0.54% boost::numeric::ublas::same_impl_ex 41ms 0.54% 85.00% 41ms 0.54% boost::shared_ptr::operator-> (inline) 34ms 0.45% 85.45% 39ms 0.51% CellPropertyCollection::GetProperty 2ms 0.026% 85.47% 39ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 21ms 0.28% 85.75% 39ms 0.51% hack_digit 0 0% 85.75% 38ms 0.5% AbstractCentreBasedCellPopulation::CreateCellPair 38ms 0.5% 86.25% 38ms 0.5% boost::numeric::ublas::c_vector::operator()