File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52507ms, 87.29% of 60153ms total Dropped 856 nodes (cum <= 300.76ms) flat flat% sum% cum cum% 0 0% 0% 60097ms 99.91% __libc_start_call_main 0 0% 0% 60097ms 99.91% __libc_start_main_impl 0 0% 0% 60097ms 99.91% _start 0 0% 0% 60082ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60082ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60082ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60082ms 99.88% main 0 0% 0% 60047ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60047ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60047ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 59779ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 50806ms 84.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50759ms 84.38% MeshBasedCellPopulation::Update 0 0% 0% 29579ms 49.17% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 29578ms 49.17% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 210ms 0.35% 0.35% 25942ms 43.13% VertexMesh::VertexMesh 0 0% 0.35% 17282ms 28.73% MutableMesh::ReMesh 0 0% 0.35% 12699ms 21.11% tetgen::tetrahedralize 2ms 0.0033% 0.35% 12568ms 20.89% tetgen::tetgenmesh::delaunizevertices 10ms 0.017% 0.37% 12560ms 20.88% tetgen::tetgenmesh::incrflipdelaunay 584ms 0.97% 1.34% 12004ms 19.96% TetrahedralMesh::EdgeIterator::operator++ 563ms 0.94% 2.28% 11113ms 18.47% tetgen::tetgenmesh::lawson 28ms 0.047% 2.32% 10586ms 17.60% std::set::insert (inline) 232ms 0.39% 2.71% 10067ms 16.74% std::_Rb_tree::_M_insert_unique 405ms 0.67% 3.38% 9466ms 15.74% VertexElement::AddFace 3045ms 5.06% 8.44% 8813ms 14.65% std::_Rb_tree::_M_lower_bound (inline) 210ms 0.35% 8.79% 8277ms 13.76% std::_Rb_tree::find (inline) 0 0% 8.79% 7752ms 12.89% std::set::count (inline) 280ms 0.47% 9.26% 6002ms 9.98% std::_Rb_tree::_M_insert_ (inline) 107ms 0.18% 9.44% 5656ms 9.40% std::less::operator() (inline) 5608ms 9.32% 18.76% 5608ms 9.32% std::operator< (inline) 208ms 0.35% 19.10% 5493ms 9.13% operator new 0 0% 19.10% 5274ms 8.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 1120ms 1.86% 20.97% 5203ms 8.65% __GI___libc_malloc 5145ms 8.55% 29.52% 5145ms 8.55% std::_Rb_tree_increment 0 0% 29.52% 5141ms 8.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.005% 29.52% 5113ms 8.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 58ms 0.096% 29.62% 4615ms 7.67% std::__new_allocator::allocate (inline) 0 0% 29.62% 4593ms 7.64% std::allocator_traits::allocate (inline) 7ms 0.012% 29.63% 4454ms 7.40% std::_Rb_tree::~_Rb_tree (inline) 1692ms 2.81% 32.45% 4443ms 7.39% std::_Rb_tree::_M_erase 0 0% 32.45% 4393ms 7.30% std::set::~set (inline) 0 0% 32.45% 4229ms 7.03% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.012% 32.46% 4223ms 7.02% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1258ms 2.09% 34.55% 4149ms 6.90% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.0033% 34.55% 4102ms 6.82% std::set_intersection (inline) 259ms 0.43% 34.98% 4100ms 6.82% std::__set_intersection 1263ms 2.10% 37.08% 4093ms 6.80% __GI___libc_free 10ms 0.017% 37.10% 4086ms 6.79% MeshBasedCellPopulation::SpringIterator::operator++ 22ms 0.037% 37.14% 4074ms 6.77% Node::AddElement 2774ms 4.61% 41.75% 3754ms 6.24% _int_malloc 0 0% 41.75% 3744ms 6.22% std::_Rb_tree::_M_create_node (inline) 0 0% 41.75% 3722ms 6.19% std::_Rb_tree::_Alloc_node::operator() (inline) 21ms 0.035% 41.78% 3707ms 6.16% TetrahedralMesh::ImportFromMesher 0 0% 41.78% 3697ms 6.15% std::_Rb_tree::_M_get_node (inline) 0 0% 41.78% 3666ms 6.09% VertexMesh::~VertexMesh 137ms 0.23% 42.01% 3582ms 5.95% std::__new_allocator::deallocate (inline) 0 0% 42.01% 3560ms 5.92% std::allocator_traits::deallocate (inline) 0 0% 42.01% 3558ms 5.91% AbstractCellPopulation::WriteResultsToFiles 111ms 0.18% 42.19% 3441ms 5.72% tetgen::tetgenmesh::insphere_sos 3438ms 5.72% 47.91% 3438ms 5.72% std::_Rb_tree::_S_right (inline) 214ms 0.36% 48.27% 3325ms 5.53% std::_Rb_tree_const_iterator::operator++ (inline) 3051ms 5.07% 53.34% 3314ms 5.51% tetgen::insphere 73ms 0.12% 53.46% 3050ms 5.07% MutableElement::AddNode 1219ms 2.03% 55.49% 2828ms 4.70% _int_free 175ms 0.29% 55.78% 2610ms 4.34% Node::~Node 198ms 0.33% 56.11% 2607ms 4.33% tetgen::tetgenmesh::flip23 209ms 0.35% 56.45% 2383ms 3.96% VertexMesh::Clear 2ms 0.0033% 56.46% 2356ms 3.92% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 199ms 0.33% 56.79% 2334ms 3.88% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0017% 56.79% 2144ms 3.56% std::_Rb_tree_iterator::operator++ (inline) 2074ms 3.45% 60.24% 2074ms 3.45% std::_Rb_tree_insert_and_rebalance 0 0% 60.24% 2024ms 3.36% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.24% 2010ms 3.34% std::_Rb_tree::_M_put_node (inline) 164ms 0.27% 60.51% 1899ms 3.16% tetgen::tetgenmesh::flip32 1ms 0.0017% 60.51% 1820ms 3.03% Element::Element 1642ms 2.73% 63.24% 1642ms 2.73% Node::GetIndex 1072ms 1.78% 65.02% 1594ms 2.65% malloc_consolidate 16ms 0.027% 65.05% 1566ms 2.60% std::_Vector_base::_M_deallocate (inline) 5ms 0.0083% 65.06% 1507ms 2.51% Element::RegisterWithNodes (inline) 202ms 0.34% 65.39% 1482ms 2.46% TetrahedralMesh::Clear 0 0% 65.39% 1461ms 2.43% std::vector::~vector (inline) 0 0% 65.39% 1389ms 2.31% std::_Vector_base::~_Vector_base (inline) 1288ms 2.14% 67.53% 1386ms 2.30% tetgen::orient3d 4ms 0.0066% 67.54% 1353ms 2.25% _int_free_maybe_consolidate 172ms 0.29% 67.83% 1309ms 2.18% tetgen::tetgenmesh::enqueueflipface 42ms 0.07% 67.90% 1248ms 2.07% tetgen::tetgenmesh::locate 1221ms 2.03% 69.93% 1221ms 2.03% unlink_chunk 112ms 0.19% 70.11% 1156ms 1.92% tetgen::tetgenmesh::preciselocate 60ms 0.1% 70.21% 1127ms 1.87% std::vector::_M_realloc_insert 0 0% 70.21% 1047ms 1.74% VertexMesh::GenerateVerticesFromElementCircumcentres 59ms 0.098% 70.31% 1031ms 1.71% std::map::operator[] 0 0% 70.31% 959ms 1.59% VoronoiDataWriter::Visit 795ms 1.32% 71.63% 940ms 1.56% AbstractElement::GetNodeGlobalIndex 924ms 1.54% 73.17% 924ms 1.54% tetgen::tetgenmesh::triface::triface 0 0% 73.17% 914ms 1.52% std::_Rb_tree::lower_bound (inline) 0 0% 73.17% 914ms 1.52% std::map::lower_bound (inline) 5ms 0.0083% 73.18% 901ms 1.50% std::_Vector_base::_M_allocate (inline) 89ms 0.15% 73.32% 894ms 1.49% std::vector::push_back (inline) 0 0% 73.32% 853ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 426ms 0.71% 74.03% 797ms 1.32% tetgen::tetgenmesh::fnextself 5ms 0.0083% 74.04% 761ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.022% 74.06% 734ms 1.22% boost::numeric::ublas::vector_assign (inline) 3ms 0.005% 74.07% 717ms 1.19% AbstractTwoBodyInteractionForce::AddForceContribution 323ms 0.54% 74.60% 709ms 1.18% AbstractElement::GetNodeLocation 709ms 1.18% 75.78% 709ms 1.18% tetgen::tetgenmesh::oppo 16ms 0.027% 75.81% 699ms 1.16% AbstractTetrahedralElement::CalculateJacobian 13ms 0.022% 75.83% 683ms 1.14% boost::numeric::ublas::c_vector::c_vector (inline) 19ms 0.032% 75.86% 670ms 1.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 665ms 1.11% 76.97% 665ms 1.11% [libchaste_mesh.so] 41ms 0.068% 77.04% 647ms 1.08% __atan2 625ms 1.04% 78.08% 625ms 1.04% Node::rGetLocation 606ms 1.01% 79.08% 606ms 1.01% AbstractElement::IsDeleted 474ms 0.79% 79.87% 606ms 1.01% __ieee754_atan2_fma 570ms 0.95% 80.82% 570ms 0.95% tetgen::tetgenmesh::triface::operator= 21ms 0.035% 80.85% 533ms 0.89% Element::CalculateCircumsphere 44ms 0.073% 80.93% 529ms 0.88% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.93% 523ms 0.87% std::insert_iterator::operator= (inline) 0 0% 80.93% 521ms 0.87% std::set::find (inline) 510ms 0.85% 81.77% 510ms 0.85% std::vector::size (inline) 0 0% 81.77% 499ms 0.83% boost::numeric::ublas::inner_prod (inline) 118ms 0.2% 81.97% 498ms 0.83% boost::numeric::ublas::indexing_vector_assign 1ms 0.0017% 81.97% 498ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 37ms 0.062% 82.03% 497ms 0.83% boost::numeric::ublas::vector_scalar_binary::evaluate 44ms 0.073% 82.11% 497ms 0.83% tetgen::tetgenmesh::enextfnext 481ms 0.8% 82.91% 481ms 0.8% boost::numeric::ublas::c_vector::operator() 35ms 0.058% 82.97% 476ms 0.79% tetgen::tetgenmesh::enext2fnext 23ms 0.038% 83.00% 469ms 0.78% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.00% 468ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 25ms 0.042% 83.04% 431ms 0.72% tetgen::tetgenmesh::queue::push 1ms 0.0017% 83.05% 419ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 278ms 0.46% 83.51% 410ms 0.68% tetgen::tetgenmesh::sym 213ms 0.35% 83.86% 405ms 0.67% AbstractTetrahedralMesh::GetElement 291ms 0.48% 84.35% 404ms 0.67% tetgen::tetgenmesh::link::add 27ms 0.045% 84.39% 401ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 159ms 0.26% 84.66% 400ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.66% 392ms 0.65% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0017% 84.66% 373ms 0.62% Cell::GetCellId 5ms 0.0083% 84.67% 372ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 82ms 0.14% 84.80% 369ms 0.61% __dynamic_cast 355ms 0.59% 85.39% 355ms 0.59% tetgen::tetgenmesh::org 254ms 0.42% 85.81% 354ms 0.59% tetgen::tetgenmesh::bond 353ms 0.59% 86.40% 353ms 0.59% std::_Rb_tree_decrement 16ms 0.027% 86.43% 345ms 0.57% std::vector::insert (inline) 0 0% 86.43% 339ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 7ms 0.012% 86.44% 334ms 0.56% VertexElement::~VertexElement 53ms 0.088% 86.53% 332ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 133ms 0.22% 86.75% 331ms 0.55% Inverse 7ms 0.012% 86.76% 319ms 0.53% VertexMesh::GetVolumeOfElement 0 0% 86.76% 315ms 0.52% tcache_get (inline) 315ms 0.52% 87.28% 315ms 0.52% tcache_get_n (inline) 3ms 0.005% 87.29% 312ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement