File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51457ms, 87.32% of 58926ms total Dropped 846 nodes (cum <= 294.63ms) flat flat% sum% cum cum% 0 0% 0% 58865ms 99.90% __libc_start_call_main 0 0% 0% 58865ms 99.90% __libc_start_main_impl 0 0% 0% 58865ms 99.90% _start 0 0% 0% 58849ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58849ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58849ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58849ms 99.87% main 0 0% 0% 58813ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58813ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58813ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 58556ms 99.37% AbstractCellBasedSimulation::Solve 1ms 0.0017% 0.0017% 48072ms 81.58% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0017% 48031ms 81.51% MeshBasedCellPopulation::Update 0 0% 0.0017% 27278ms 46.29% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0017% 27277ms 46.29% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 233ms 0.4% 0.4% 24028ms 40.78% VertexMesh::VertexMesh 0 0% 0.4% 16652ms 28.26% MutableMesh::ReMesh 0 0% 0.4% 12769ms 21.67% tetgen::tetrahedralize 2ms 0.0034% 0.4% 12633ms 21.44% tetgen::tetgenmesh::delaunizevertices 17ms 0.029% 0.43% 12625ms 21.43% tetgen::tetgenmesh::incrflipdelaunay 556ms 0.94% 1.37% 12431ms 21.10% TetrahedralMesh::EdgeIterator::operator++ 549ms 0.93% 2.30% 11240ms 19.07% tetgen::tetgenmesh::lawson 3078ms 5.22% 7.53% 10162ms 17.25% std::_Rb_tree::_M_lower_bound (inline) 254ms 0.43% 7.96% 9393ms 15.94% std::_Rb_tree::find (inline) 26ms 0.044% 8.00% 9368ms 15.90% std::set::insert (inline) 361ms 0.61% 8.62% 8993ms 15.26% VertexElement::AddFace 197ms 0.33% 8.95% 8876ms 15.06% std::_Rb_tree::_M_insert_unique 0 0% 8.95% 8804ms 14.94% std::set::count (inline) 115ms 0.2% 9.15% 6706ms 11.38% std::less::operator() (inline) 6657ms 11.30% 20.44% 6657ms 11.30% std::operator< (inline) 5923ms 10.05% 30.49% 5923ms 10.05% std::_Rb_tree_increment 0 0% 30.49% 5489ms 9.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.49% 5355ms 9.09% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0034% 30.50% 5328ms 9.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 264ms 0.45% 30.95% 5249ms 8.91% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.95% 4857ms 8.24% AbstractCellPopulation::WriteResultsToFiles 206ms 0.35% 31.30% 4703ms 7.98% operator new 1ms 0.0017% 31.30% 4429ms 7.52% MeshBasedCellPopulation::UpdateNodePairs 1037ms 1.76% 33.06% 4412ms 7.49% __GI___libc_malloc 6ms 0.01% 33.07% 4376ms 7.43% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.025% 33.09% 4298ms 7.29% MeshBasedCellPopulation::SpringIterator::operator++ 39ms 0.066% 33.16% 4036ms 6.85% std::__new_allocator::allocate (inline) 7ms 0.012% 33.17% 4033ms 6.84% std::_Rb_tree::~_Rb_tree (inline) 1632ms 2.77% 35.94% 4023ms 6.83% std::_Rb_tree::_M_erase 0 0% 35.94% 4014ms 6.81% std::allocator_traits::allocate (inline) 0 0% 35.94% 3973ms 6.74% std::set::~set (inline) 220ms 0.37% 36.31% 3769ms 6.40% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1176ms 2.00% 38.31% 3729ms 6.33% std::_Rb_tree::_M_get_insert_unique_pos 102ms 0.17% 38.48% 3599ms 6.11% tetgen::tetgenmesh::insphere_sos 3ms 0.0051% 38.49% 3567ms 6.05% std::_Rb_tree_iterator::operator++ (inline) 7ms 0.012% 38.50% 3501ms 5.94% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 957ms 1.62% 40.12% 3483ms 5.91% __GI___libc_free 3178ms 5.39% 45.52% 3481ms 5.91% tetgen::insphere 7ms 0.012% 45.53% 3299ms 5.60% std::set_intersection (inline) 207ms 0.35% 45.88% 3292ms 5.59% std::__set_intersection 0 0% 45.88% 3271ms 5.55% VertexMesh::~VertexMesh 27ms 0.046% 45.93% 3255ms 5.52% Node::AddElement 3240ms 5.50% 51.42% 3240ms 5.50% std::_Rb_tree::_S_right (inline) 0 0% 51.42% 3199ms 5.43% std::_Rb_tree::_M_create_node (inline) 0 0% 51.42% 3168ms 5.38% std::_Rb_tree::_M_get_node (inline) 0 0% 51.42% 3156ms 5.36% std::_Rb_tree::_Alloc_node::operator() (inline) 141ms 0.24% 51.66% 3152ms 5.35% std::__new_allocator::deallocate (inline) 0 0% 51.66% 3131ms 5.31% std::allocator_traits::deallocate (inline) 4ms 0.0068% 51.67% 3107ms 5.27% TetrahedralMesh::ImportFromMesher 2339ms 3.97% 55.64% 3042ms 5.16% _int_malloc 199ms 0.34% 55.98% 2701ms 4.58% tetgen::tetgenmesh::flip23 181ms 0.31% 56.28% 2655ms 4.51% std::_Rb_tree_const_iterator::operator++ (inline) 1133ms 1.92% 58.21% 2522ms 4.28% _int_free 82ms 0.14% 58.35% 2350ms 3.99% MutableElement::AddNode 133ms 0.23% 58.57% 2251ms 3.82% Node::~Node 182ms 0.31% 58.88% 2174ms 3.69% VertexMesh::Clear 1906ms 3.23% 62.12% 1906ms 3.23% std::_Rb_tree_insert_and_rebalance 0 0% 62.12% 1784ms 3.03% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.12% 1769ms 3.00% std::_Rb_tree::_M_put_node (inline) 1ms 0.0017% 62.12% 1744ms 2.96% Element::Element 180ms 0.31% 62.42% 1744ms 2.96% tetgen::tetgenmesh::flip32 1572ms 2.67% 65.09% 1572ms 2.67% Node::GetIndex 1304ms 2.21% 67.30% 1391ms 2.36% tetgen::orient3d 861ms 1.46% 68.76% 1388ms 2.36% malloc_consolidate 5ms 0.0085% 68.77% 1387ms 2.35% Element::RegisterWithNodes (inline) 12ms 0.02% 68.79% 1374ms 2.33% std::_Vector_base::_M_deallocate (inline) 56ms 0.095% 68.89% 1344ms 2.28% std::map::operator[] 0 0% 68.89% 1322ms 2.24% std::vector::~vector (inline) 174ms 0.3% 69.18% 1274ms 2.16% tetgen::tetgenmesh::enqueueflipface 0 0% 69.18% 1208ms 2.05% std::_Rb_tree::lower_bound (inline) 0 0% 69.18% 1208ms 2.05% std::map::lower_bound (inline) 4ms 0.0068% 69.19% 1204ms 2.04% std::_Vector_base::~_Vector_base (inline) 1ms 0.0017% 69.19% 1192ms 2.02% _int_free_maybe_consolidate 36ms 0.061% 69.25% 1161ms 1.97% tetgen::tetgenmesh::locate 1ms 0.0017% 69.25% 1126ms 1.91% VoronoiDataWriter::Visit 87ms 0.15% 69.40% 1082ms 1.84% tetgen::tetgenmesh::preciselocate 101ms 0.17% 69.57% 1078ms 1.83% TetrahedralMesh::Clear 76ms 0.13% 69.70% 1053ms 1.79% std::vector::_M_realloc_insert 4ms 0.0068% 69.71% 970ms 1.65% VertexMesh::GenerateVerticesFromElementCircumcentres 933ms 1.58% 71.29% 933ms 1.58% unlink_chunk 114ms 0.19% 71.49% 865ms 1.47% std::vector::push_back (inline) 5ms 0.0085% 71.49% 851ms 1.44% std::_Vector_base::_M_allocate (inline) 801ms 1.36% 72.85% 801ms 1.36% tetgen::tetgenmesh::triface::triface 456ms 0.77% 73.63% 764ms 1.30% tetgen::tetgenmesh::fnextself 1ms 0.0017% 73.63% 762ms 1.29% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 73.63% 760ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 723ms 1.23% 74.86% 723ms 1.23% tetgen::tetgenmesh::oppo 16ms 0.027% 74.88% 710ms 1.20% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.014% 74.90% 705ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.031% 74.93% 700ms 1.19% boost::numeric::ublas::vector_assign (inline) 18ms 0.031% 74.96% 675ms 1.15% AbstractTetrahedralElement::CalculateJacobian 543ms 0.92% 75.88% 672ms 1.14% AbstractElement::GetNodeGlobalIndex 266ms 0.45% 76.33% 663ms 1.13% AbstractElement::GetNodeLocation 12ms 0.02% 76.35% 661ms 1.12% boost::numeric::ublas::c_vector::c_vector (inline) 651ms 1.10% 77.46% 651ms 1.10% [libchaste_mesh.so] 65ms 0.11% 77.57% 627ms 1.06% __atan2 595ms 1.01% 78.58% 595ms 1.01% tetgen::tetgenmesh::triface::operator= 586ms 0.99% 79.57% 586ms 0.99% Node::rGetLocation 0 0% 79.57% 586ms 0.99% std::set::find (inline) 437ms 0.74% 80.31% 562ms 0.95% __ieee754_atan2_fma 22ms 0.037% 80.35% 506ms 0.86% Element::CalculateCircumsphere 0 0% 80.35% 500ms 0.85% std::insert_iterator::operator= (inline) 39ms 0.066% 80.42% 498ms 0.85% AbstractTetrahedralElement::RefreshJacobian 30ms 0.051% 80.47% 493ms 0.84% tetgen::tetgenmesh::enextfnext 0 0% 80.47% 485ms 0.82% boost::numeric::ublas::inner_prod (inline) 43ms 0.073% 80.54% 485ms 0.82% tetgen::tetgenmesh::enext2fnext 10ms 0.017% 80.56% 483ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 30ms 0.051% 80.61% 473ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 298ms 0.51% 81.11% 444ms 0.75% tetgen::tetgenmesh::sym 0 0% 81.11% 439ms 0.75% std::_Rb_tree::_M_insert_unique_ (inline) 115ms 0.2% 81.31% 431ms 0.73% boost::numeric::ublas::indexing_vector_assign 429ms 0.73% 82.04% 429ms 0.73% std::vector::size (inline) 15ms 0.025% 82.06% 418ms 0.71% std::_Rb_tree_iterator::operator-- (inline) 170ms 0.29% 82.35% 400ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 299ms 0.51% 82.86% 399ms 0.68% tetgen::tetgenmesh::bond 4ms 0.0068% 82.86% 394ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 392ms 0.67% 83.53% 392ms 0.67% boost::numeric::ublas::c_vector::operator() 2ms 0.0034% 83.53% 390ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 101ms 0.17% 83.70% 388ms 0.66% __dynamic_cast 384ms 0.65% 84.36% 384ms 0.65% std::_Rb_tree_decrement 0 0% 84.36% 383ms 0.65% VertexMeshWriter::WriteVtkUsingMesh 24ms 0.041% 84.40% 375ms 0.64% tetgen::tetgenmesh::queue::push 1ms 0.0017% 84.40% 373ms 0.63% Cell::GetCellId 209ms 0.35% 84.75% 370ms 0.63% AbstractTetrahedralMesh::GetElement 3ms 0.0051% 84.76% 356ms 0.6% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.027% 84.79% 356ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 351ms 0.6% 85.38% 351ms 0.6% AbstractElement::IsDeleted 257ms 0.44% 85.82% 350ms 0.59% tetgen::tetgenmesh::link::add 23ms 0.039% 85.86% 340ms 0.58% std::vector::insert (inline) 338ms 0.57% 86.43% 338ms 0.57% tetgen::tetgenmesh::org 6ms 0.01% 86.44% 334ms 0.57% VertexElement::~VertexElement 127ms 0.22% 86.66% 325ms 0.55% Inverse 54ms 0.092% 86.75% 322ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.0051% 86.75% 316ms 0.54% AbstractCellProperty::IsSubType (inline) 37ms 0.063% 86.82% 303ms 0.51% tetgen::insphereadapt 1ms 0.0017% 86.82% 300ms 0.51% tcache_get (inline) 299ms 0.51% 87.32% 299ms 0.51% tcache_get_n (inline) 0 0% 87.32% 297ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)