File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 59194ms, 88.34% of 67008ms total Dropped 879 nodes (cum <= 335.04ms) flat flat% sum% cum cum% 0 0% 0% 66947ms 99.91% __libc_start_call_main 0 0% 0% 66947ms 99.91% __libc_start_main_impl 0 0% 0% 66947ms 99.91% _start 0 0% 0% 66931ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66931ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66931ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66931ms 99.89% main 0 0% 0% 66892ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66892ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66892ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66613ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 55710ms 83.14% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55661ms 83.07% MeshBasedCellPopulation::Update 0 0% 0% 33420ms 49.87% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 33420ms 49.87% MeshBasedCellPopulation::TessellateIfNeeded 268ms 0.4% 0.4% 29110ms 43.44% VertexMesh::VertexMesh 0 0% 0.4% 17839ms 26.62% MutableMesh::ReMesh 562ms 0.84% 1.24% 13606ms 20.31% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0015% 1.24% 12840ms 19.16% tetgen::tetrahedralize 2ms 0.003% 1.24% 12702ms 18.96% tetgen::tetgenmesh::delaunizevertices 7ms 0.01% 1.25% 12697ms 18.95% tetgen::tetgenmesh::incrflipdelaunay 24ms 0.036% 1.29% 11311ms 16.88% std::set::insert (inline) 576ms 0.86% 2.15% 11226ms 16.75% tetgen::tetgenmesh::lawson 178ms 0.27% 2.41% 10812ms 16.14% std::_Rb_tree::_M_insert_unique 3051ms 4.55% 6.97% 10496ms 15.66% std::_Rb_tree::_M_lower_bound (inline) 436ms 0.65% 7.62% 9981ms 14.90% VertexElement::AddFace 220ms 0.33% 7.95% 9688ms 14.46% std::_Rb_tree::find (inline) 0 0% 7.95% 9124ms 13.62% std::set::count (inline) 7226ms 10.78% 18.73% 7226ms 10.78% std::_Rb_tree_increment 108ms 0.16% 18.89% 7024ms 10.48% std::less::operator() (inline) 6968ms 10.40% 29.29% 6968ms 10.40% std::operator< (inline) 282ms 0.42% 29.71% 6386ms 9.53% std::_Rb_tree::_M_insert_ (inline) 218ms 0.33% 30.04% 6083ms 9.08% operator new 0 0% 30.04% 5883ms 8.78% OffLatticeSimulation::UpdateCellLocationsAndTopology 1025ms 1.53% 31.57% 5768ms 8.61% __GI___libc_malloc 0 0% 31.57% 5725ms 8.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.009% 31.58% 5702ms 8.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 46ms 0.069% 31.64% 5041ms 7.52% std::__new_allocator::allocate (inline) 0 0% 31.64% 5012ms 7.48% std::allocator_traits::allocate (inline) 4ms 0.006% 31.65% 4923ms 7.35% std::set_intersection (inline) 293ms 0.44% 32.09% 4919ms 7.34% std::__set_intersection 0 0% 32.09% 4850ms 7.24% AbstractCellPopulation::WriteResultsToFiles 6ms 0.009% 32.10% 4845ms 7.23% std::_Rb_tree::~_Rb_tree (inline) 2084ms 3.11% 35.21% 4839ms 7.22% std::_Rb_tree::_M_erase 0 0% 35.21% 4776ms 7.13% std::set::~set (inline) 0 0% 35.21% 4762ms 7.11% MeshBasedCellPopulation::UpdateNodePairs 29ms 0.043% 35.25% 4759ms 7.10% Node::AddElement 4ms 0.006% 35.26% 4725ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.009% 35.26% 4586ms 6.84% MeshBasedCellPopulation::SpringIterator::operator++ 1205ms 1.80% 37.06% 4573ms 6.82% std::_Rb_tree::_M_get_insert_unique_pos 1207ms 1.80% 38.86% 4384ms 6.54% __GI___libc_free 4379ms 6.54% 45.40% 4379ms 6.54% std::_Rb_tree::_S_right (inline) 3214ms 4.80% 50.20% 4353ms 6.50% _int_malloc 0 0% 50.20% 4350ms 6.49% VertexMesh::~VertexMesh 173ms 0.26% 50.45% 4123ms 6.15% std::_Rb_tree_const_iterator::operator++ (inline) 10ms 0.015% 50.47% 4057ms 6.05% TetrahedralMesh::ImportFromMesher 0 0% 50.47% 4027ms 6.01% std::_Rb_tree::_M_create_node (inline) 0 0% 50.47% 3994ms 5.96% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.47% 3978ms 5.94% std::_Rb_tree::_M_get_node (inline) 126ms 0.19% 50.66% 3798ms 5.67% std::__new_allocator::deallocate (inline) 0 0% 50.66% 3777ms 5.64% std::allocator_traits::deallocate (inline) 74ms 0.11% 50.77% 3620ms 5.40% MutableElement::AddNode 249ms 0.37% 51.14% 3603ms 5.38% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 169ms 0.25% 51.39% 3501ms 5.22% tetgen::tetgenmesh::insphere_sos 1ms 0.0015% 51.39% 3376ms 5.04% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 51.39% 3370ms 5.03% std::_Rb_tree_iterator::operator++ (inline) 3024ms 4.51% 55.91% 3315ms 4.95% tetgen::insphere 1229ms 1.83% 57.74% 3175ms 4.74% _int_free 202ms 0.3% 58.04% 2990ms 4.46% Node::~Node 255ms 0.38% 58.42% 2776ms 4.14% VertexMesh::Clear 190ms 0.28% 58.70% 2651ms 3.96% tetgen::tetgenmesh::flip23 2203ms 3.29% 61.99% 2203ms 3.29% std::_Rb_tree_insert_and_rebalance 2044ms 3.05% 65.04% 2044ms 3.05% Node::GetIndex 7ms 0.01% 65.05% 2031ms 3.03% Element::Element 1309ms 1.95% 67.01% 1962ms 2.93% malloc_consolidate 0 0% 67.01% 1909ms 2.85% std::_Rb_tree::_M_drop_node (inline) 19ms 0.028% 67.04% 1899ms 2.83% std::_Vector_base::_M_deallocate (inline) 0 0% 67.04% 1897ms 2.83% std::_Rb_tree::_M_put_node (inline) 156ms 0.23% 67.27% 1891ms 2.82% tetgen::tetgenmesh::flip32 0 0% 67.27% 1755ms 2.62% std::vector::~vector (inline) 9ms 0.013% 67.28% 1699ms 2.54% _int_free_maybe_consolidate 1ms 0.0015% 67.28% 1698ms 2.53% std::_Vector_base::~_Vector_base (inline) 6ms 0.009% 67.29% 1687ms 2.52% Element::RegisterWithNodes (inline) 241ms 0.36% 67.65% 1593ms 2.38% TetrahedralMesh::Clear 1353ms 2.02% 69.67% 1449ms 2.16% tetgen::orient3d 1433ms 2.14% 71.81% 1433ms 2.14% unlink_chunk 56ms 0.084% 71.89% 1334ms 1.99% std::map::operator[] 160ms 0.24% 72.13% 1310ms 1.95% tetgen::tetgenmesh::enqueueflipface 55ms 0.082% 72.21% 1269ms 1.89% std::vector::_M_realloc_insert 4ms 0.006% 72.22% 1250ms 1.87% VertexMesh::GenerateVerticesFromElementCircumcentres 40ms 0.06% 72.28% 1236ms 1.84% tetgen::tetgenmesh::locate 0 0% 72.28% 1213ms 1.81% VoronoiDataWriter::Visit 0 0% 72.28% 1203ms 1.80% std::_Rb_tree::lower_bound (inline) 0 0% 72.28% 1203ms 1.80% std::map::lower_bound (inline) 102ms 0.15% 72.43% 1147ms 1.71% tetgen::tetgenmesh::preciselocate 937ms 1.40% 73.83% 1067ms 1.59% AbstractElement::GetNodeGlobalIndex 10ms 0.015% 73.84% 1044ms 1.56% std::_Vector_base::_M_allocate (inline) 131ms 0.2% 74.04% 1035ms 1.54% std::vector::push_back (inline) 1ms 0.0015% 74.04% 915ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 882ms 1.32% 75.36% 882ms 1.32% tetgen::tetgenmesh::triface::triface 852ms 1.27% 76.63% 852ms 1.27% Node::rGetLocation 335ms 0.5% 77.13% 816ms 1.22% AbstractElement::GetNodeLocation 7ms 0.01% 77.14% 803ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 425ms 0.63% 77.77% 762ms 1.14% tetgen::tetgenmesh::fnextself 0 0% 77.77% 749ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.016% 77.79% 746ms 1.11% AbstractTetrahedralElement::CalculateJacobian 711ms 1.06% 78.85% 711ms 1.06% AbstractElement::IsDeleted 704ms 1.05% 79.90% 704ms 1.05% tetgen::tetgenmesh::oppo 16ms 0.024% 79.93% 698ms 1.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 14ms 0.021% 79.95% 691ms 1.03% boost::numeric::ublas::vector_assign (inline) 668ms 1% 80.94% 668ms 1% [libchaste_mesh.so] 45ms 0.067% 81.01% 649ms 0.97% __atan2 5ms 0.0075% 81.02% 630ms 0.94% boost::numeric::ublas::c_vector::c_vector (inline) 12ms 0.018% 81.04% 607ms 0.91% Element::CalculateCircumsphere 491ms 0.73% 81.77% 603ms 0.9% __ieee754_atan2_fma 35ms 0.052% 81.82% 565ms 0.84% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.82% 564ms 0.84% std::set::find (inline) 554ms 0.83% 82.65% 554ms 0.83% tetgen::tetgenmesh::triface::operator= 525ms 0.78% 83.43% 525ms 0.78% std::vector::size (inline) 46ms 0.069% 83.50% 511ms 0.76% tetgen::tetgenmesh::enextfnext 0 0% 83.50% 505ms 0.75% std::insert_iterator::operator= (inline) 0 0% 83.50% 468ms 0.7% boost::numeric::ublas::inner_prod (inline) 5ms 0.0075% 83.51% 463ms 0.69% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.022% 83.53% 461ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 19ms 0.028% 83.56% 458ms 0.68% boost::numeric::ublas::vector_scalar_binary::evaluate 33ms 0.049% 83.61% 457ms 0.68% tetgen::tetgenmesh::enext2fnext 316ms 0.47% 84.08% 457ms 0.68% tetgen::tetgenmesh::sym 0 0% 84.08% 453ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 31ms 0.046% 84.13% 452ms 0.67% tetgen::tetgenmesh::queue::push 125ms 0.19% 84.31% 442ms 0.66% boost::numeric::ublas::indexing_vector_assign 2ms 0.003% 84.32% 422ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.0075% 84.32% 420ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 287ms 0.43% 84.75% 418ms 0.62% tetgen::tetgenmesh::link::add 201ms 0.3% 85.05% 409ms 0.61% AbstractTetrahedralMesh::GetElement 107ms 0.16% 85.21% 406ms 0.61% __dynamic_cast 0 0% 85.21% 404ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 23ms 0.034% 85.25% 404ms 0.6% std::vector::insert (inline) 0 0% 85.25% 396ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 27ms 0.04% 85.29% 394ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.0045% 85.29% 386ms 0.58% Cell::GetCellId 192ms 0.29% 85.58% 383ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 374ms 0.56% 86.13% 374ms 0.56% boost::numeric::ublas::c_vector::operator() 369ms 0.55% 86.69% 369ms 0.55% tetgen::tetgenmesh::org 354ms 0.53% 87.21% 354ms 0.53% std::_Rb_tree_decrement 0 0% 87.21% 347ms 0.52% tcache_get (inline) 347ms 0.52% 87.73% 347ms 0.52% tcache_get_n (inline) 142ms 0.21% 87.94% 341ms 0.51% Inverse 248ms 0.37% 88.31% 340ms 0.51% tetgen::tetgenmesh::bond 5ms 0.0075% 88.32% 339ms 0.51% AbstractCellProperty::IsSubType (inline) 2ms 0.003% 88.32% 337ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.015% 88.34% 336ms 0.5% VertexElement::~VertexElement