File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6729ms, 84.31% of 7981ms total Dropped 577 nodes (cum <= 39.91ms) flat flat% sum% cum cum% 0 0% 0% 7945ms 99.55% __libc_start_call_main 0 0% 0% 7945ms 99.55% __libc_start_main_impl 0 0% 0% 7945ms 99.55% _start 0 0% 0% 7927ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7927ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7927ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7927ms 99.32% main 0 0% 0% 7885ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7885ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7885ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7881ms 98.75% AbstractCellBasedSimulation::Solve 0 0% 0% 3482ms 43.63% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2980ms 37.34% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2841ms 35.60% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.038% 1553ms 19.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1480ms 18.54% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.038% 1448ms 18.14% MutableMesh::ReMesh 0 0% 0.038% 1407ms 17.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.063% 0.1% 1349ms 16.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.34% 1279ms 16.03% MeshBasedCellPopulation::SpringIterator::operator++ 123ms 1.54% 1.88% 1034ms 12.96% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.90% 972ms 12.18% AbstractTwoBodyInteractionForce::AddForceContribution 256ms 3.21% 5.11% 962ms 12.05% __dynamic_cast 409ms 5.12% 10.24% 923ms 11.56% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 10.26% 918ms 11.50% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.05% 10.31% 902ms 11.30% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.075% 10.39% 884ms 11.08% CellPopulationElementWriter::Visit 34ms 0.43% 10.81% 868ms 10.88% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.063% 10.88% 770ms 9.65% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.33% 11.20% 764ms 9.57% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 11.24% 730ms 9.15% AbstractCellProperty::IsSubType (inline) 13ms 0.16% 11.40% 712ms 8.92% TetrahedralMesh::ImportFromMesher 36ms 0.45% 11.85% 596ms 7.47% operator new 1ms 0.013% 11.87% 580ms 7.27% std::ostream::operator<< (inline) 83ms 1.04% 12.91% 576ms 7.22% std::ostream::_M_insert 55ms 0.69% 13.59% 569ms 7.13% std::map::operator[] (partial-inline) 184ms 2.31% 15.90% 559ms 7.00% __GI___libc_malloc 3ms 0.038% 15.94% 555ms 6.95% triangulate 536ms 6.72% 22.65% 536ms 6.72% __strcmp_avx2 27ms 0.34% 22.99% 532ms 6.67% std::__new_allocator::allocate (inline) 0 0% 22.99% 525ms 6.58% std::allocator_traits::allocate (inline) 25ms 0.31% 23.31% 523ms 6.55% std::_Rb_tree::find (inline) 3ms 0.038% 23.34% 521ms 6.53% Cell::GetCellProliferativeType 6ms 0.075% 23.42% 515ms 6.45% std::set::insert (inline) 8ms 0.1% 23.52% 509ms 6.38% std::_Rb_tree::_M_insert_unique 250ms 3.13% 26.65% 494ms 6.19% __cxxabiv1::__si_class_type_info::__do_dyncast 8ms 0.1% 26.75% 492ms 6.16% AbstractCellBasedSimulation::DoCellBirth 4ms 0.05% 26.80% 492ms 6.16% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.80% 490ms 6.14% delaunay 1ms 0.013% 26.81% 489ms 6.13% divconqdelaunay 0 0% 26.81% 456ms 5.71% std::set::count (inline) 0 0% 26.81% 454ms 5.69% std::_Rb_tree::lower_bound (inline) 0 0% 26.81% 454ms 5.69% std::map::lower_bound (inline) 41ms 0.51% 27.33% 446ms 5.59% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.33% 438ms 5.49% std::_Rb_tree::_M_create_node (inline) 0 0% 27.33% 426ms 5.34% std::set::~set (inline) 0 0% 27.33% 410ms 5.14% std::_Rb_tree::_M_get_node (inline) 0 0% 27.33% 408ms 5.11% std::_Rb_tree::_Alloc_node::operator() (inline) 102ms 1.28% 28.61% 397ms 4.97% std::_Rb_tree::_M_erase 25ms 0.31% 28.92% 386ms 4.84% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.05% 28.97% 359ms 4.50% Cell::GetMutationState 3ms 0.038% 29.01% 356ms 4.46% std::set::set (inline) 9ms 0.11% 29.12% 354ms 4.44% std::less::operator() (inline) 345ms 4.32% 33.44% 345ms 4.32% std::operator< (inline) 39ms 0.49% 33.93% 328ms 4.11% std::_Rb_tree::_M_copy (inline) 0 0% 33.93% 324ms 4.06% NodeLocationWriter::Visit 23ms 0.29% 34.22% 320ms 4.01% std::_Rb_tree::_M_insert_ (inline) 8ms 0.1% 34.32% 318ms 3.98% Cell::ReadyToDivide 0 0% 34.32% 317ms 3.97% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 34.32% 316ms 3.96% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 34.33% 311ms 3.90% OutputFileHandler::OpenOutputFile 7ms 0.088% 34.42% 305ms 3.82% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 34.44% 305ms 3.82% MeshBasedCellPopulation::GetDampingConstant 5ms 0.063% 34.51% 303ms 3.80% AbstractCentreBasedCellPopulation::GetDampingConstant 291ms 3.65% 38.15% 291ms 3.65% std::_Rb_tree::_S_right (inline) 4ms 0.05% 38.20% 290ms 3.63% Element::Element 21ms 0.26% 38.47% 290ms 3.63% std::num_put::_M_insert_float 85ms 1.07% 39.53% 288ms 3.61% __GI___libc_free 188ms 2.36% 41.89% 287ms 3.60% _int_malloc 6ms 0.075% 41.96% 286ms 3.58% divconqrecurse 76ms 0.95% 42.91% 277ms 3.47% std::_Rb_tree::_M_clone_node (inline) 0 0% 42.91% 273ms 3.42% std::_Rb_tree::_M_drop_node (inline) 84ms 1.05% 43.97% 271ms 3.40% mergehulls 6ms 0.075% 44.04% 253ms 3.17% std::__new_allocator::deallocate (inline) 0 0% 44.04% 249ms 3.12% std::allocator_traits::deallocate (inline) 5ms 0.063% 44.10% 247ms 3.09% CellProliferativeTypesWriter::VisitCell 4ms 0.05% 44.15% 244ms 3.06% CellPropertyCollection::HasProperty 0 0% 44.15% 239ms 2.99% Cell::HasCellProperty (inline) 6ms 0.075% 44.23% 236ms 2.96% std::__cxx11::collate::do_transform 5ms 0.063% 44.29% 234ms 2.93% AbstractCellProperty::IsType (inline) 2ms 0.025% 44.32% 222ms 2.78% ___vsnprintf 0 0% 44.32% 221ms 2.77% __vsnprintf_internal (inline) 28ms 0.35% 44.67% 219ms 2.74% __printf_buffer 13ms 0.16% 44.83% 214ms 2.68% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 44.83% 212ms 2.66% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 44.87% 205ms 2.57% AbstractPhaseBasedCellCycleModel::ReadyToDivide 18ms 0.23% 45.09% 202ms 2.53% TetrahedralMesh::Clear 175ms 2.19% 47.29% 202ms 2.53% _int_free 4ms 0.05% 47.34% 198ms 2.48% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 24ms 0.3% 47.64% 185ms 2.32% AbstractTetrahedralElement::CalculateJacobian 44ms 0.55% 48.19% 185ms 2.32% TetrahedralMesh::EdgesEnd (partial-inline) 59ms 0.74% 48.93% 181ms 2.27% std::_Rb_tree::_M_get_insert_unique_pos (inline) 54ms 0.68% 49.61% 180ms 2.26% AbstractCellProperty::IsSame 11ms 0.14% 49.74% 178ms 2.23% __printf_fp_l_buffer 0 0% 49.74% 178ms 2.23% __printf_fp_spec (inline) 3ms 0.038% 49.78% 174ms 2.18% Element::RegisterWithNodes (inline) 7ms 0.088% 49.87% 169ms 2.12% Node::AddElement 0 0% 49.87% 167ms 2.09% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 49.88% 166ms 2.08% AbstractCellBasedWriter::CloseFile 2ms 0.025% 49.91% 166ms 2.08% std::basic_filebuf::close 0 0% 49.91% 165ms 2.07% std::basic_ofstream::close (inline) 77ms 0.96% 50.87% 155ms 1.94% __printf_fp_buffer_1 0 0% 50.87% 153ms 1.92% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.87% 150ms 1.88% OutputFileHandler::CommonConstructor 0 0% 50.87% 150ms 1.88% OutputFileHandler::OutputFileHandler 40ms 0.5% 51.37% 150ms 1.88% std::num_put::_M_insert_int 0 0% 51.37% 148ms 1.85% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.37% 147ms 1.84% std::basic_ofstream::open (inline) 0 0% 51.37% 146ms 1.83% std::basic_filebuf::open 3ms 0.038% 51.41% 144ms 1.80% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 51.42% 144ms 1.80% OutputFileHandler::MakeFoldersAndReturnFullPath 16ms 0.2% 51.62% 143ms 1.79% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 51.62% 143ms 1.79% AbstractCellPopulation::Iterator::operator++ (inline) 99ms 1.24% 52.86% 138ms 1.73% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 52.86% 134ms 1.68% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 52.88% 134ms 1.68% std::filesystem::permissions 133ms 1.67% 54.54% 133ms 1.67% __GI_fchmodat 6ms 0.075% 54.62% 127ms 1.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 127ms 1.59% 56.21% 127ms 1.59% incircle 30ms 0.38% 56.58% 126ms 1.58% std::type_info::operator== (inline) 4ms 0.05% 56.63% 125ms 1.57% Node::~Node 12ms 0.15% 56.78% 123ms 1.54% AbstractTetrahedralElement::RefreshJacobian 12ms 0.15% 56.94% 122ms 1.53% boost::detail::shared_count::~shared_count (inline) 0 0% 56.94% 122ms 1.53% boost::shared_ptr::~shared_ptr (inline) 43ms 0.54% 57.47% 121ms 1.52% std::__ostream_insert 3ms 0.038% 57.51% 120ms 1.50% std::basic_filebuf::overflow 1ms 0.013% 57.52% 118ms 1.48% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 57.52% 118ms 1.48% std::basic_filebuf::_M_terminate_output 0 0% 57.52% 117ms 1.47% std::__basic_file::xsputn 0 0% 57.52% 117ms 1.47% std::basic_filebuf::_M_convert_to_external 3ms 0.038% 57.56% 116ms 1.45% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 57.57% 116ms 1.45% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 57.60% 116ms 1.45% std::__basic_file::open 114ms 1.43% 59.03% 115ms 1.44% __GI___libc_write 0 0% 59.03% 115ms 1.44% std::_Vector_base::_M_allocate (inline) 0 0% 59.03% 114ms 1.43% _IO_new_fopen 0 0% 59.03% 114ms 1.43% __fopen_internal (inline) 3ms 0.038% 59.07% 114ms 1.43% alternateaxes 2ms 0.025% 59.09% 112ms 1.40% _IO_new_file_fopen 3ms 0.038% 59.13% 112ms 1.40% boost::numeric::ublas::vector_assign (inline) 103ms 1.29% 60.42% 111ms 1.39% vertexmedian 7ms 0.088% 60.51% 110ms 1.38% std::vector::push_back (inline) 0 0% 60.51% 109ms 1.37% __GI__IO_file_open 0 0% 60.51% 104ms 1.30% std::operator<< (inline) 2ms 0.025% 60.53% 101ms 1.27% boost::numeric::ublas::c_vector::c_vector (inline) 55ms 0.69% 61.22% 101ms 1.27% boost::shared_ptr::shared_ptr (inline) 101ms 1.27% 62.49% 101ms 1.27% std::_Rb_tree_insert_and_rebalance 92ms 1.15% 63.64% 99ms 1.24% boost::detail::sp_counted_base::release 5ms 0.063% 63.70% 99ms 1.24% std::_Rb_tree_const_iterator::operator++ (inline) 99ms 1.24% 64.94% 99ms 1.24% std::_Rb_tree_increment 5ms 0.063% 65.00% 99ms 1.24% std::vector::_M_realloc_insert 98ms 1.23% 66.23% 98ms 1.23% __libc_open64 41ms 0.51% 66.75% 95ms 1.19% AbstractElement::GetNodeLocation 95ms 1.19% 67.94% 95ms 1.19% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 67.95% 94ms 1.18% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.95% 94ms 1.18% Cell::GetCellId 92ms 1.15% 69.10% 92ms 1.15% [libchaste_cell_based.so] 90ms 1.13% 70.23% 90ms 1.13% Node::GetIndex 81ms 1.01% 71.24% 81ms 1.01% __GI___fstatat64 1ms 0.013% 71.26% 81ms 1.01% std::filesystem::status 75ms 0.94% 72.20% 81ms 1.01% vertexsort 0 0% 72.20% 79ms 0.99% tcache_get (inline) 79ms 0.99% 73.19% 79ms 0.99% tcache_get_n (inline) 20ms 0.25% 73.44% 78ms 0.98% boost::numeric::ublas::indexing_vector_assign 53ms 0.66% 74.10% 78ms 0.98% malloc_consolidate 39ms 0.49% 74.59% 76ms 0.95% std::basic_filebuf::xsputn 74ms 0.93% 75.52% 74ms 0.93% __memcpy_avx_unaligned_erms 1ms 0.013% 75.53% 73ms 0.91% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 43ms 0.54% 76.07% 73ms 0.91% std::basic_streambuf::xsputn 1ms 0.013% 76.08% 72ms 0.9% std::filesystem::create_directory 2ms 0.025% 76.11% 70ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 48ms 0.6% 76.71% 70ms 0.88% boost::numeric::ublas::c_matrix::operator() (partial-inline) 54ms 0.68% 77.38% 66ms 0.83% std::num_put::do_put 6ms 0.075% 77.46% 65ms 0.81% CellPropertyCollection::AddProperty 3ms 0.038% 77.50% 64ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 77.50% 64ms 0.8% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.50% 64ms 0.8% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 52ms 0.65% 78.15% 62ms 0.78% AbstractElement::GetNodeGlobalIndex 0 0% 78.15% 61ms 0.76% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.15% 61ms 0.76% std::__new_allocator::destroy (inline) 0 0% 78.15% 61ms 0.76% std::allocator_traits::destroy (inline) 61ms 0.76% 78.91% 61ms 0.76% std::vector::size (inline) 24ms 0.3% 79.21% 59ms 0.74% AbstractTetrahedralMesh::GetElement 59ms 0.74% 79.95% 59ms 0.74% counterclockwise 3ms 0.038% 79.99% 59ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.99% 56ms 0.7% std::map::find (inline) 0 0% 79.99% 55ms 0.69% AbstractCentreBasedCellPopulation::IsMarkedSpring 55ms 0.69% 80.68% 55ms 0.69% [libchaste_mesh.so] 0 0% 80.68% 55ms 0.69% std::vector::vector (inline) 0 0% 80.68% 54ms 0.68% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 53ms 0.66% 81.34% 53ms 0.66% boost::shared_ptr::operator-> (inline) 0 0% 81.34% 52ms 0.65% boost::numeric::ublas::norm_2 (inline) 17ms 0.21% 81.56% 52ms 0.65% boost::numeric::ublas::vector_norm_2::apply (inline) 10ms 0.13% 81.68% 51ms 0.64% Determinant (inline) 0 0% 81.68% 51ms 0.64% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.68% 48ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.013% 81.69% 48ms 0.6% Node::ConstructNodeAttributes (inline) 26ms 0.33% 82.02% 48ms 0.6% hack_digit 0 0% 82.02% 48ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 82.02% 47ms 0.59% Node::ClearAppliedForce 45ms 0.56% 82.58% 46ms 0.58% boost::detail::shared_count::shared_count (inline) 0 0% 82.58% 45ms 0.56% std::_Vector_base::_M_create_storage (inline) 0 0% 82.58% 44ms 0.55% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 43ms 0.54% 83.12% 43ms 0.54% Node::IsDeleted 43ms 0.54% 83.66% 43ms 0.54% Node::rGetLocation 4ms 0.05% 83.71% 42ms 0.53% Inverse 1ms 0.013% 83.72% 42ms 0.53% std::__basic_file::close 0 0% 83.72% 41ms 0.51% _IO_new_fclose 0 0% 83.72% 40ms 0.5% CellPropertyCollection::~CellPropertyCollection (inline) 4ms 0.05% 83.77% 40ms 0.5% Element::~Element 0 0% 83.77% 40ms 0.5% _dl_init 0 0% 83.77% 40ms 0.5% call_init (inline) 3ms 0.038% 83.81% 40ms 0.5% std::_Vector_base::_M_deallocate (inline) 40ms 0.5% 84.31% 40ms 0.5% std::ostream::sentry::sentry