File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6427ms, 84.30% of 7624ms total Dropped 572 nodes (cum <= 38.12ms) flat flat% sum% cum cum% 0 0% 0% 7587ms 99.51% __libc_start_call_main 0 0% 0% 7587ms 99.51% __libc_start_main_impl 0 0% 0% 7587ms 99.51% _start 0 0% 0% 7571ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7571ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7571ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7571ms 99.30% main 0 0% 0% 7535ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7535ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7535ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7533ms 98.81% AbstractCellBasedSimulation::Solve 0 0% 0% 3243ms 42.54% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2807ms 36.82% MeshBasedCellPopulation::Update 0 0% 0.013% 2692ms 35.31% AbstractCellPopulation::WriteResultsToFiles 3ms 0.039% 0.052% 1589ms 20.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.066% 1434ms 18.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.079% 1392ms 18.26% MutableMesh::ReMesh 5ms 0.066% 0.14% 1367ms 17.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 3ms 0.039% 0.18% 1352ms 17.73% MeshBasedCellPopulation::UpdateNodePairs 19ms 0.25% 0.43% 1187ms 15.57% MeshBasedCellPopulation::SpringIterator::operator++ 120ms 1.57% 2.01% 980ms 12.85% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.013% 2.02% 945ms 12.40% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 2.02% 920ms 12.07% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 12ms 0.16% 2.18% 902ms 11.83% CellPropertyCollection::GetPropertiesType (inline) 399ms 5.23% 7.41% 895ms 11.74% std::_Rb_tree::_M_lower_bound (inline) 250ms 3.28% 10.69% 861ms 11.29% __dynamic_cast 7ms 0.092% 10.78% 834ms 10.94% CellPopulationElementWriter::Visit 37ms 0.49% 11.27% 832ms 10.91% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.052% 11.32% 782ms 10.26% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.13% 11.45% 706ms 9.26% TetrahedralMesh::ImportFromMesher 36ms 0.47% 11.92% 704ms 9.23% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.079% 12.00% 691ms 9.06% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.01% 639ms 8.38% std::ostream::operator<< (inline) 79ms 1.04% 13.05% 637ms 8.36% std::ostream::_M_insert 37ms 0.49% 13.54% 598ms 7.84% operator new 51ms 0.67% 14.21% 578ms 7.58% std::__new_allocator::allocate (inline) 0 0% 14.21% 575ms 7.54% std::allocator_traits::allocate (inline) 5ms 0.066% 14.27% 557ms 7.31% std::set::insert (inline) 9ms 0.12% 14.39% 552ms 7.24% std::_Rb_tree::_M_insert_unique 188ms 2.47% 16.85% 551ms 7.23% __GI___libc_malloc 46ms 0.6% 17.46% 548ms 7.19% std::map::operator[] (partial-inline) 5ms 0.066% 17.52% 519ms 6.81% Cell::GetCellProliferativeType 2ms 0.026% 17.55% 510ms 6.69% triangulate 3ms 0.039% 17.59% 502ms 6.58% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 17.59% 496ms 6.51% std::_Rb_tree::_M_create_node (inline) 0 0% 17.59% 474ms 6.22% std::_Rb_tree::_Alloc_node::operator() (inline) 16ms 0.21% 17.80% 472ms 6.19% std::_Rb_tree::find (inline) 464ms 6.09% 23.89% 464ms 6.09% __strcmp_avx2 0 0% 23.89% 455ms 5.97% std::_Rb_tree::_M_get_node (inline) 0 0% 23.89% 451ms 5.92% std::_Rb_tree::lower_bound (inline) 0 0% 23.89% 451ms 5.92% std::map::lower_bound (inline) 217ms 2.85% 26.73% 449ms 5.89% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.73% 439ms 5.76% delaunay 2ms 0.026% 26.76% 439ms 5.76% divconqdelaunay 0 0% 26.76% 425ms 5.57% std::set::count (inline) 3ms 0.039% 26.80% 418ms 5.48% NodeLocationWriter::Visit 3ms 0.039% 26.84% 415ms 5.44% AbstractCellBasedSimulation::DoCellBirth 4ms 0.052% 26.89% 390ms 5.12% Cell::GetMutationState 15ms 0.2% 27.09% 376ms 4.93% std::_Rb_tree::_Rb_tree (partial-inline) 27ms 0.35% 27.44% 367ms 4.81% std::num_put::_M_insert_float 32ms 0.42% 27.86% 366ms 4.80% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.17% 28.03% 358ms 4.70% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.03% 350ms 4.59% std::set::~set (inline) 2ms 0.026% 28.06% 333ms 4.37% MeshBasedCellPopulation::GetDampingConstant 31ms 0.41% 28.46% 333ms 4.37% std::_Rb_tree::_M_copy (inline) 4ms 0.052% 28.52% 332ms 4.35% std::set::set (inline) 0 0% 28.52% 331ms 4.34% AbstractCentreBasedCellPopulation::GetDampingConstant 72ms 0.94% 29.46% 325ms 4.26% std::_Rb_tree::_M_erase 14ms 0.18% 29.64% 317ms 4.16% std::less::operator() (inline) 314ms 4.12% 33.76% 314ms 4.12% std::_Rb_tree::_S_right (inline) 303ms 3.97% 37.74% 303ms 3.97% std::operator< (inline) 73ms 0.96% 38.69% 298ms 3.91% std::_Rb_tree::_M_clone_node (inline) 3ms 0.039% 38.73% 289ms 3.79% Element::Element 12ms 0.16% 38.89% 287ms 3.76% std::__cxx11::collate::do_transform 2ms 0.026% 38.92% 283ms 3.71% Cell::ReadyToDivide 193ms 2.53% 41.45% 283ms 3.71% _int_malloc 5ms 0.066% 41.51% 282ms 3.70% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.052% 41.57% 267ms 3.50% ___vsnprintf 0 0% 41.57% 263ms 3.45% __vsnprintf_internal (inline) 14ms 0.18% 41.75% 261ms 3.42% divconqrecurse 73ms 0.96% 42.71% 256ms 3.36% __GI___libc_free 28ms 0.37% 43.07% 256ms 3.36% __printf_buffer 2ms 0.026% 43.10% 236ms 3.10% CellProliferativeTypesWriter::VisitCell 62ms 0.81% 43.91% 236ms 3.10% mergehulls 0 0% 43.91% 234ms 3.07% std::_Rb_tree::_M_drop_node (inline) 4ms 0.052% 43.97% 225ms 2.95% std::__new_allocator::deallocate (inline) 0 0% 43.97% 222ms 2.91% std::allocator_traits::deallocate (inline) 8ms 0.1% 44.07% 220ms 2.89% AbstractCellProperty::IsType (inline) 5ms 0.066% 44.14% 205ms 2.69% CellPropertyCollection::HasProperty 0 0% 44.14% 203ms 2.66% Cell::HasCellProperty (inline) 5ms 0.066% 44.20% 203ms 2.66% Element::RegisterWithNodes (inline) 1ms 0.013% 44.22% 201ms 2.64% __printf_fp_spec (inline) 12ms 0.16% 44.37% 200ms 2.62% __printf_fp_l_buffer 3ms 0.039% 44.41% 197ms 2.58% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.079% 44.49% 193ms 2.53% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.039% 44.53% 192ms 2.52% Node::AddElement 57ms 0.75% 45.28% 186ms 2.44% std::_Rb_tree::_M_get_insert_unique_pos (inline) 154ms 2.02% 47.30% 183ms 2.40% _int_free 0 0% 47.30% 183ms 2.40% std::_Rb_tree::_M_put_node (inline) 16ms 0.21% 47.51% 182ms 2.39% TetrahedralMesh::Clear 100ms 1.31% 48.82% 177ms 2.32% __printf_fp_buffer_1 3ms 0.039% 48.86% 172ms 2.26% boost::numeric::ublas::vector_assign (inline) 8ms 0.1% 48.96% 171ms 2.24% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.079% 49.04% 170ms 2.23% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 49.06% 164ms 2.15% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 49.06% 162ms 2.12% AbstractCellBasedWriter::OpenOutputFileForAppend 44ms 0.58% 49.63% 162ms 2.12% AbstractCellProperty::IsSame 0 0% 49.63% 159ms 2.09% OutputFileHandler::OpenOutputFile 0 0% 49.63% 157ms 2.06% std::basic_ofstream::basic_ofstream (inline) 70ms 0.92% 50.55% 153ms 2.01% std::__ostream_insert 29ms 0.38% 50.93% 152ms 1.99% TetrahedralMesh::EdgesEnd (partial-inline) 12ms 0.16% 51.09% 150ms 1.97% AbstractTetrahedralElement::CalculateJacobian 2ms 0.026% 51.11% 150ms 1.97% std::basic_ofstream::open (inline) 2ms 0.026% 51.14% 148ms 1.94% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.026% 51.17% 148ms 1.94% std::basic_filebuf::open 1ms 0.013% 51.18% 143ms 1.88% OutputFileHandler::OutputFileHandler 0 0% 51.18% 142ms 1.86% OutputFileHandler::CommonConstructor 42ms 0.55% 51.73% 139ms 1.82% std::num_put::_M_insert_int 48ms 0.63% 52.36% 138ms 1.81% boost::numeric::ublas::indexing_vector_assign 2ms 0.026% 52.39% 137ms 1.80% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.066% 52.45% 133ms 1.74% std::vector::push_back (inline) 6ms 0.079% 52.53% 130ms 1.71% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.53% 126ms 1.65% AbstractCellPopulation::CloseRoundRobinWritersFiles 5ms 0.066% 52.60% 126ms 1.65% std::operator<< (inline) 0 0% 52.60% 125ms 1.64% AbstractCellBasedWriter::CloseFile 3ms 0.039% 52.64% 125ms 1.64% std::basic_filebuf::close 0 0% 52.64% 125ms 1.64% std::basic_ofstream::close (inline) 3ms 0.039% 52.68% 123ms 1.61% std::_Vector_base::_M_allocate (inline) 15ms 0.2% 52.87% 123ms 1.61% std::vector::_M_realloc_insert 13ms 0.17% 53.04% 121ms 1.59% boost::detail::shared_count::~shared_count (inline) 0 0% 53.04% 121ms 1.59% boost::shared_ptr::~shared_ptr (inline) 10ms 0.13% 53.17% 120ms 1.57% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 53.17% 119ms 1.56% _IO_new_fopen 0 0% 53.17% 119ms 1.56% __fopen_internal (inline) 1ms 0.013% 53.19% 119ms 1.56% std::__basic_file::open 0 0% 53.19% 118ms 1.55% _IO_new_file_fopen 32ms 0.42% 53.61% 118ms 1.55% std::type_info::operator== (inline) 1ms 0.013% 53.62% 117ms 1.53% __GI__IO_file_open 4ms 0.052% 53.67% 117ms 1.53% alternateaxes 117ms 1.53% 55.21% 117ms 1.53% std::_Rb_tree_increment 7ms 0.092% 55.30% 116ms 1.52% Node::~Node 84ms 1.10% 56.40% 113ms 1.48% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 103ms 1.35% 57.75% 113ms 1.48% vertexmedian 16ms 0.21% 57.96% 111ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 57.96% 108ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 14ms 0.18% 58.15% 108ms 1.42% MeshBasedCellPopulation::SpringIterator::SpringIterator 106ms 1.39% 59.54% 107ms 1.40% __libc_open64 105ms 1.38% 60.91% 106ms 1.39% boost::detail::sp_counted_base::release 105ms 1.38% 62.29% 105ms 1.38% incircle 21ms 0.28% 62.57% 102ms 1.34% AbstractTetrahedralElement::RefreshJacobian 49ms 0.64% 63.21% 102ms 1.34% boost::shared_ptr::shared_ptr (inline) 102ms 1.34% 64.55% 102ms 1.34% std::_Rb_tree_insert_and_rebalance 0 0% 64.55% 91ms 1.19% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 64.55% 90ms 1.18% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 64.55% 90ms 1.18% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 64.55% 88ms 1.15% std::__basic_file::xsputn 0 0% 64.55% 88ms 1.15% std::basic_filebuf::_M_convert_to_external 0 0% 64.55% 88ms 1.15% std::basic_filebuf::overflow 87ms 1.14% 65.69% 87ms 1.14% __GI___libc_write 0 0% 65.69% 87ms 1.14% std::basic_filebuf::_M_terminate_output 1ms 0.013% 65.70% 80ms 1.05% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 53ms 0.7% 66.40% 79ms 1.04% std::basic_streambuf::xsputn 0 0% 66.40% 79ms 1.04% std::filesystem::create_directory 78ms 1.02% 67.42% 78ms 1.02% [libchaste_cell_based.so] 47ms 0.62% 68.04% 75ms 0.98% std::basic_filebuf::xsputn 74ms 0.97% 69.01% 74ms 0.97% Node::GetIndex 2ms 0.026% 69.03% 73ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 69.05% 72ms 0.94% Cell::GetCellId 0 0% 69.05% 72ms 0.94% tcache_get (inline) 72ms 0.94% 69.99% 72ms 0.94% tcache_get_n (inline) 7ms 0.092% 70.08% 71ms 0.93% CellPropertyCollection::AddProperty 0 0% 70.08% 70ms 0.92% boost::numeric::ublas::norm_2 (inline) 23ms 0.3% 70.38% 70ms 0.92% boost::numeric::ublas::vector_norm_2::apply (inline) 54ms 0.71% 71.09% 69ms 0.91% AbstractElement::GetNodeGlobalIndex 30ms 0.39% 71.48% 69ms 0.91% AbstractElement::GetNodeLocation 69ms 0.91% 72.39% 69ms 0.91% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 68ms 0.89% 73.28% 68ms 0.89% __GI___fstatat64 1ms 0.013% 73.29% 68ms 0.89% std::filesystem::status 53ms 0.7% 73.99% 68ms 0.89% std::num_put::do_put 67ms 0.88% 74.87% 67ms 0.88% counterclockwise 0 0% 74.87% 65ms 0.85% AbstractCellPopulation::GetLocationIndexUsingCell 65ms 0.85% 75.72% 65ms 0.85% boost::numeric::ublas::c_vector::operator() (partial-inline) 47ms 0.62% 76.34% 65ms 0.85% malloc_consolidate 62ms 0.81% 77.15% 62ms 0.81% [libchaste_mesh.so] 8ms 0.1% 77.26% 61ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeB 36ms 0.47% 77.73% 61ms 0.8% boost::numeric::ublas::c_matrix::operator() (partial-inline) 5ms 0.066% 77.79% 59ms 0.77% Node::ConstructNodeAttributes (inline) 59ms 0.77% 78.57% 59ms 0.77% std::vector::size (inline) 2ms 0.026% 78.59% 58ms 0.76% Node::ClearAppliedForce 58ms 0.76% 79.35% 58ms 0.76% __memcpy_avx_unaligned_erms 52ms 0.68% 80.04% 53ms 0.7% boost::detail::shared_count::shared_count (inline) 19ms 0.25% 80.29% 51ms 0.67% Determinant (inline) 0 0% 80.29% 51ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 3ms 0.039% 80.33% 51ms 0.67% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.33% 51ms 0.67% std::__new_allocator::destroy (inline) 0 0% 80.33% 51ms 0.67% std::allocator_traits::destroy (inline) 46ms 0.6% 80.93% 51ms 0.67% vertexsort 1ms 0.013% 80.94% 50ms 0.66% TetrahedralMesh::EdgeIterator::GetNodeA 30ms 0.39% 81.34% 50ms 0.66% hack_digit 0 0% 81.34% 50ms 0.66% std::map::map (inline) 0 0% 81.34% 48ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 22ms 0.29% 81.62% 46ms 0.6% AbstractTetrahedralMesh::GetElement 45ms 0.59% 82.21% 45ms 0.59% [libstdc++.so.6.0.33] 7ms 0.092% 82.31% 45ms 0.59% std::_Vector_base::_M_deallocate (inline) 0 0% 82.31% 45ms 0.59% std::__new_allocator::construct (inline) 0 0% 82.31% 45ms 0.59% std::allocator_traits::construct (inline) 0 0% 82.31% 43ms 0.56% BoundaryNodeWriter::Visit 4ms 0.052% 82.36% 43ms 0.56% NodeAttributes::NodeAttributes 43ms 0.56% 82.92% 43ms 0.56% __GI___mkdir 19ms 0.25% 83.17% 42ms 0.55% AbstractCellCycleModel::GetAge 42ms 0.55% 83.72% 42ms 0.55% boost::numeric::ublas::same_impl_ex 4ms 0.052% 83.77% 41ms 0.54% Inverse 0 0% 83.77% 41ms 0.54% std::_Rb_tree::_M_construct_node (inline) 0 0% 83.77% 41ms 0.54% std::vector::vector (inline) 40ms 0.52% 84.30% 40ms 0.52% boost::shared_ptr::operator-> (inline) 0 0% 84.30% 40ms 0.52% std::map::find (inline) 0 0% 84.30% 39ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair