File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6793ms, 85.07% of 7985ms total Dropped 546 nodes (cum <= 39.92ms) flat flat% sum% cum cum% 0 0% 0% 7949ms 99.55% __libc_start_call_main 0 0% 0% 7949ms 99.55% __libc_start_main_impl 0 0% 0% 7949ms 99.55% _start 0 0% 0% 7931ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7931ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7931ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7931ms 99.32% main 0 0% 0% 7888ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7888ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7888ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7886ms 98.76% AbstractCellBasedSimulation::Solve 0 0% 0% 3451ms 43.22% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 3001ms 37.58% MeshBasedCellPopulation::Update 0 0% 0% 2873ms 35.98% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.013% 1556ms 19.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.038% 0.05% 1483ms 18.57% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.05% 1456ms 18.23% MutableMesh::ReMesh 1ms 0.013% 0.063% 1408ms 17.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.063% 0.13% 1332ms 16.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 31ms 0.39% 0.51% 1293ms 16.19% MeshBasedCellPopulation::SpringIterator::operator++ 121ms 1.52% 2.03% 1042ms 13.05% TetrahedralMesh::EdgeIterator::operator++ 259ms 3.24% 5.27% 985ms 12.34% __dynamic_cast 419ms 5.25% 10.52% 985ms 12.34% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 10.54% 973ms 12.19% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.013% 10.56% 951ms 11.91% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.18% 10.73% 921ms 11.53% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.38% 11.11% 867ms 10.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.063% 11.17% 859ms 10.76% CellPopulationElementWriter::Visit 6ms 0.075% 11.25% 839ms 10.51% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.025% 11.27% 765ms 9.58% AbstractCellProperty::IsSubType (inline) 25ms 0.31% 11.58% 745ms 9.33% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 11.70% 728ms 9.12% TetrahedralMesh::ImportFromMesher 64ms 0.8% 12.50% 621ms 7.78% std::map::operator[] (partial-inline) 595ms 7.45% 19.95% 595ms 7.45% __strcmp_avx2 3ms 0.038% 19.99% 576ms 7.21% triangulate 3ms 0.038% 20.03% 561ms 7.03% Cell::GetCellProliferativeType 1ms 0.013% 20.04% 558ms 6.99% std::ostream::operator<< (inline) 105ms 1.31% 21.35% 556ms 6.96% std::ostream::_M_insert 1ms 0.013% 21.37% 539ms 6.75% LegacyCellProliferativeTypesWriter::VisitCell 25ms 0.31% 21.68% 536ms 6.71% std::_Rb_tree::find (inline) 37ms 0.46% 22.14% 525ms 6.57% operator new 6ms 0.075% 22.22% 510ms 6.39% std::set::insert (inline) 1ms 0.013% 22.23% 506ms 6.34% delaunay 0 0% 22.23% 506ms 6.34% std::_Rb_tree::lower_bound (inline) 0 0% 22.23% 506ms 6.34% std::map::lower_bound (inline) 8ms 0.1% 22.33% 504ms 6.31% std::_Rb_tree::_M_insert_unique 2ms 0.025% 22.35% 503ms 6.30% divconqdelaunay 229ms 2.87% 25.22% 501ms 6.27% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 25.22% 488ms 6.11% std::set::count (inline) 149ms 1.87% 27.09% 483ms 6.05% __GI___libc_malloc 22ms 0.28% 27.36% 459ms 5.75% std::__new_allocator::allocate (inline) 0 0% 27.36% 455ms 5.70% std::allocator_traits::allocate (inline) 37ms 0.46% 27.83% 446ms 5.59% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.038% 27.86% 438ms 5.49% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.86% 420ms 5.26% std::set::~set (inline) 71ms 0.89% 28.75% 400ms 5.01% std::_Rb_tree::_M_erase 9ms 0.11% 28.87% 386ms 4.83% std::less::operator() (inline) 377ms 4.72% 33.59% 377ms 4.72% std::operator< (inline) 7ms 0.088% 33.68% 373ms 4.67% Cell::GetMutationState 0 0% 33.68% 368ms 4.61% std::_Rb_tree::_M_create_node (inline) 0 0% 33.68% 347ms 4.35% NodeLocationWriter::Visit 0 0% 33.68% 345ms 4.32% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 33.68% 343ms 4.30% std::_Rb_tree::_M_get_node (inline) 24ms 0.3% 33.98% 334ms 4.18% std::_Rb_tree::_Rb_tree (partial-inline) 331ms 4.15% 38.12% 331ms 4.15% std::_Rb_tree::_S_right (inline) 0 0% 38.12% 321ms 4.02% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.12% 320ms 4.01% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.12% 317ms 3.97% OutputFileHandler::OpenOutputFile 0 0% 38.12% 308ms 3.86% std::_Rb_tree::_M_drop_node (inline) 103ms 1.29% 39.41% 307ms 3.84% __GI___libc_free 2ms 0.025% 39.44% 304ms 3.81% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 39.44% 304ms 3.81% MeshBasedCellPopulation::GetDampingConstant 7ms 0.088% 39.52% 301ms 3.77% Cell::ReadyToDivide 4ms 0.05% 39.57% 299ms 3.74% std::set::set (inline) 26ms 0.33% 39.90% 295ms 3.69% std::num_put::_M_insert_float 12ms 0.15% 40.05% 294ms 3.68% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 40.06% 292ms 3.66% Element::Element 19ms 0.24% 40.30% 287ms 3.59% std::_Rb_tree::_M_insert_ (inline) 13ms 0.16% 40.46% 287ms 3.59% std::__new_allocator::deallocate (inline) 0 0% 40.46% 284ms 3.56% std::allocator_traits::deallocate (inline) 9ms 0.11% 40.58% 279ms 3.49% divconqrecurse 42ms 0.53% 41.10% 277ms 3.47% std::_Rb_tree::_M_copy (inline) 176ms 2.20% 43.31% 266ms 3.33% _int_malloc 74ms 0.93% 44.23% 263ms 3.29% mergehulls 1ms 0.013% 44.25% 261ms 3.27% CellProliferativeTypesWriter::VisitCell 7ms 0.088% 44.33% 249ms 3.12% CellPropertyCollection::HasProperty 8ms 0.1% 44.43% 248ms 3.11% AbstractCellProperty::IsType (inline) 0 0% 44.43% 248ms 3.11% Cell::HasCellProperty (inline) 0 0% 44.43% 242ms 3.03% std::_Rb_tree::_M_put_node (inline) 10ms 0.13% 44.56% 237ms 2.97% std::__cxx11::collate::do_transform 63ms 0.79% 45.35% 229ms 2.87% std::_Rb_tree::_M_clone_node (inline) 3ms 0.038% 45.39% 218ms 2.73% ___vsnprintf 12ms 0.15% 45.54% 215ms 2.69% TetrahedralMesh::Clear 0 0% 45.54% 215ms 2.69% __vsnprintf_internal (inline) 7ms 0.088% 45.62% 212ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 28ms 0.35% 45.97% 211ms 2.64% __printf_buffer 78ms 0.98% 46.95% 209ms 2.62% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.063% 47.01% 204ms 2.55% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 183ms 2.29% 49.30% 204ms 2.55% _int_free 39ms 0.49% 49.79% 193ms 2.42% AbstractCellProperty::IsSame 7ms 0.088% 49.88% 184ms 2.30% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.075% 49.96% 181ms 2.27% Element::RegisterWithNodes (inline) 5ms 0.063% 50.02% 173ms 2.17% __printf_fp_l_buffer 0 0% 50.02% 173ms 2.17% __printf_fp_spec (inline) 6ms 0.075% 50.09% 172ms 2.15% Node::AddElement 0 0% 50.09% 161ms 2.02% OutputFileHandler::CommonConstructor 0 0% 50.09% 161ms 2.02% OutputFileHandler::OutputFileHandler 89ms 1.11% 51.21% 161ms 2.02% __printf_fp_buffer_1 62ms 0.78% 51.98% 159ms 1.99% std::__ostream_insert 0 0% 51.98% 158ms 1.98% OutputFileHandler::MakeFoldersAndReturnFullPath 14ms 0.18% 52.16% 155ms 1.94% AbstractTetrahedralElement::CalculateJacobian 37ms 0.46% 52.62% 154ms 1.93% std::type_info::operator== (inline) 0 0% 52.62% 152ms 1.90% std::basic_ofstream::basic_ofstream (inline) 0 0% 52.62% 151ms 1.89% std::basic_ofstream::open (inline) 1ms 0.013% 52.64% 150ms 1.88% std::basic_filebuf::open 2ms 0.025% 52.66% 147ms 1.84% alternateaxes 8ms 0.1% 52.76% 145ms 1.82% Node::~Node 129ms 1.62% 54.38% 143ms 1.79% vertexmedian 0 0% 54.38% 140ms 1.75% FilesystemPermissions::SetFilePermissions (inline) 6ms 0.075% 54.45% 139ms 1.74% boost::numeric::ublas::vector_assign (inline) 2ms 0.025% 54.48% 139ms 1.74% std::filesystem::permissions 32ms 0.4% 54.88% 137ms 1.72% TetrahedralMesh::EdgesEnd (partial-inline) 137ms 1.72% 56.59% 137ms 1.72% __GI_fchmodat 1ms 0.013% 56.61% 135ms 1.69% AbstractCellPopulation::CloseRoundRobinWritersFiles 6ms 0.075% 56.68% 135ms 1.69% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 56.68% 134ms 1.68% TetrahedralMesh::RefreshJacobianCachedData 0 0% 56.68% 132ms 1.65% AbstractCellBasedWriter::CloseFile 1ms 0.013% 56.69% 132ms 1.65% std::basic_filebuf::close 0 0% 56.69% 132ms 1.65% std::basic_ofstream::close (inline) 0 0% 56.69% 131ms 1.64% std::operator<< (inline) 3ms 0.038% 56.73% 129ms 1.62% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.18% 56.91% 127ms 1.59% boost::detail::shared_count::~shared_count (inline) 0 0% 56.91% 127ms 1.59% boost::shared_ptr::~shared_ptr (inline) 14ms 0.18% 57.08% 123ms 1.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 118ms 1.48% 58.56% 118ms 1.48% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 117ms 1.47% 60.03% 117ms 1.47% incircle 3ms 0.038% 60.06% 116ms 1.45% std::vector::push_back (inline) 3ms 0.038% 60.10% 115ms 1.44% std::_Vector_base::_M_allocate (inline) 3ms 0.038% 60.14% 114ms 1.43% AbstractTetrahedralElement::AbstractTetrahedralElement 110ms 1.38% 61.52% 110ms 1.38% [libchaste_cell_based.so] 5ms 0.063% 61.58% 110ms 1.38% std::vector::_M_realloc_insert 11ms 0.14% 61.72% 108ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 61.72% 108ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 19ms 0.24% 61.95% 108ms 1.35% AbstractTetrahedralElement::RefreshJacobian 69ms 0.86% 62.82% 107ms 1.34% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 62.82% 107ms 1.34% _IO_new_file_fopen 0 0% 62.82% 107ms 1.34% _IO_new_fopen 2ms 0.025% 62.84% 107ms 1.34% __GI__IO_file_open 0 0% 62.84% 107ms 1.34% __fopen_internal (inline) 0 0% 62.84% 107ms 1.34% std::__basic_file::open 27ms 0.34% 63.18% 103ms 1.29% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 63.19% 101ms 1.26% std::basic_filebuf::_M_terminate_output 98ms 1.23% 64.42% 100ms 1.25% boost::detail::sp_counted_base::release 1ms 0.013% 64.43% 100ms 1.25% std::basic_filebuf::overflow 23ms 0.29% 64.72% 100ms 1.25% std::num_put::_M_insert_int 1ms 0.013% 64.73% 99ms 1.24% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 64.75% 98ms 1.23% std::__basic_file::xsputn 44ms 0.55% 65.30% 97ms 1.21% boost::shared_ptr::shared_ptr (inline) 97ms 1.21% 66.51% 97ms 1.21% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 66.54% 96ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 94ms 1.18% 67.71% 96ms 1.20% __GI___libc_write 91ms 1.14% 68.85% 91ms 1.14% __libc_open64 1ms 0.013% 68.87% 87ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 68.88% 85ms 1.06% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.013% 68.89% 84ms 1.05% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 68.89% 83ms 1.04% std::filesystem::create_directory 2ms 0.025% 68.92% 83ms 1.04% std::filesystem::status 0 0% 68.92% 82ms 1.03% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 68.92% 82ms 1.03% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 40ms 0.5% 69.42% 82ms 1.03% std::basic_filebuf::xsputn 81ms 1.01% 70.43% 81ms 1.01% __GI___fstatat64 7ms 0.088% 70.52% 76ms 0.95% std::_Rb_tree_const_iterator::operator++ (inline) 75ms 0.94% 71.46% 75ms 0.94% __memcpy_avx_unaligned_erms 1ms 0.013% 71.47% 74ms 0.93% Cell::GetCellId 33ms 0.41% 71.88% 71ms 0.89% AbstractElement::GetNodeLocation 71ms 0.89% 72.77% 71ms 0.89% std::_Rb_tree_increment 3ms 0.038% 72.81% 70ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 64ms 0.8% 73.61% 70ms 0.88% vertexsort 3ms 0.038% 73.65% 69ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 73.65% 68ms 0.85% tcache_get (inline) 68ms 0.85% 74.50% 68ms 0.85% tcache_get_n (inline) 67ms 0.84% 75.34% 67ms 0.84% counterclockwise 42ms 0.53% 75.87% 67ms 0.84% malloc_consolidate 0 0% 75.87% 66ms 0.83% boost::numeric::ublas::norm_2 (inline) 21ms 0.26% 76.13% 66ms 0.83% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.13% 66ms 0.83% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.13% 66ms 0.83% std::__new_allocator::destroy (inline) 0 0% 76.13% 66ms 0.83% std::allocator_traits::destroy (inline) 46ms 0.58% 76.71% 63ms 0.79% AbstractElement::GetNodeGlobalIndex 63ms 0.79% 77.50% 63ms 0.79% Node::GetIndex 0 0% 77.50% 59ms 0.74% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 77.50% 59ms 0.74% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 59ms 0.74% 78.23% 59ms 0.74% [libchaste_mesh.so] 33ms 0.41% 78.65% 56ms 0.7% std::basic_streambuf::xsputn 56ms 0.7% 79.35% 56ms 0.7% std::vector::size (inline) 50ms 0.63% 79.97% 53ms 0.66% boost::detail::shared_count::shared_count (inline) 32ms 0.4% 80.38% 52ms 0.65% boost::numeric::ublas::c_matrix::operator() (partial-inline) 7ms 0.088% 80.46% 51ms 0.64% CellPropertyCollection::AddProperty 2ms 0.025% 80.49% 51ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 45ms 0.56% 81.05% 51ms 0.64% std::num_put::do_put 21ms 0.26% 81.31% 50ms 0.63% AbstractTetrahedralMesh::GetElement 27ms 0.34% 81.65% 49ms 0.61% AbstractCellCycleModel::GetAge 0 0% 81.65% 49ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.65% 48ms 0.6% CellPropertyCollection::~CellPropertyCollection (inline) 48ms 0.6% 82.25% 48ms 0.6% __GI___mkdir 0 0% 82.25% 48ms 0.6% std::vector::vector (inline) 15ms 0.19% 82.44% 47ms 0.59% Determinant (inline) 5ms 0.063% 82.50% 46ms 0.58% std::_Vector_base::_M_deallocate (inline) 45ms 0.56% 83.07% 45ms 0.56% boost::shared_ptr::operator-> (inline) 29ms 0.36% 83.43% 45ms 0.56% hack_digit 1ms 0.013% 83.44% 44ms 0.55% BoundaryNodeWriter::Visit 44ms 0.55% 83.99% 44ms 0.55% [libstdc++.so.6.0.33] 0 0% 83.99% 43ms 0.54% Node::ClearAppliedForce 0 0% 83.99% 43ms 0.54% Node::ConstructNodeAttributes (inline) 2ms 0.025% 84.02% 42ms 0.53% std::__copy_move::__copy_m (inline) 0 0% 84.02% 42ms 0.53% std::__copy_move_a (inline) 0 0% 84.02% 42ms 0.53% std::__copy_move_a1 (inline) 0 0% 84.02% 42ms 0.53% std::__copy_move_a2 (inline) 1ms 0.013% 84.03% 42ms 0.53% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 84.03% 42ms 0.53% std::copy (inline) 1ms 0.013% 84.05% 41ms 0.51% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 41ms 0.51% 84.56% 41ms 0.51% boost::numeric::ublas::same_impl_ex 0 0% 84.56% 41ms 0.51% std::map::find (inline) 1ms 0.013% 84.57% 40ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 84.57% 40ms 0.5% CxxTest::RealWorldDescription::setUp 0 0% 84.57% 40ms 0.5% PetscInitialize 0 0% 84.57% 40ms 0.5% PetscSetup::setUpWorld 0 0% 84.57% 40ms 0.5% PetscSetupUtils::CommonSetup 0 0% 84.57% 40ms 0.5% PetscSetupUtils::InitialisePetsc 0 0% 84.57% 40ms 0.5% std::_Vector_base::_Vector_base (inline) 40ms 0.5% 85.07% 40ms 0.5% std::ostream::sentry::sentry