File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53088ms, 87.78% of 60481ms total Dropped 746 nodes (cum <= 302.40ms) flat flat% sum% cum cum% 0 0% 0% 60423ms 99.90% __libc_start_call_main 0 0% 0% 60423ms 99.90% __libc_start_main_impl 0 0% 0% 60423ms 99.90% _start 0 0% 0% 60409ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60409ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60409ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60409ms 99.88% main 0 0% 0% 60371ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60371ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60371ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60119ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 51643ms 85.39% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51594ms 85.31% MeshBasedCellPopulation::Update 0 0% 0% 30749ms 50.84% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 30749ms 50.84% MeshBasedCellPopulation::TessellateIfNeeded 237ms 0.39% 0.39% 26817ms 44.34% VertexMesh::VertexMesh 0 0% 0.39% 16962ms 28.05% MutableMesh::ReMesh 0 0% 0.39% 12691ms 20.98% tetgen::tetrahedralize 2ms 0.0033% 0.4% 12549ms 20.75% tetgen::tetgenmesh::delaunizevertices 6ms 0.0099% 0.41% 12544ms 20.74% tetgen::tetgenmesh::incrflipdelaunay 568ms 0.94% 1.34% 11935ms 19.73% TetrahedralMesh::EdgeIterator::operator++ 516ms 0.85% 2.20% 11096ms 18.35% tetgen::tetgenmesh::lawson 27ms 0.045% 2.24% 10538ms 17.42% std::set::insert (inline) 204ms 0.34% 2.58% 10046ms 16.61% std::_Rb_tree::_M_insert_unique 434ms 0.72% 3.30% 9830ms 16.25% VertexElement::AddFace 3111ms 5.14% 8.44% 8922ms 14.75% std::_Rb_tree::_M_lower_bound (inline) 257ms 0.42% 8.87% 8321ms 13.76% std::_Rb_tree::find (inline) 0 0% 8.87% 7785ms 12.87% std::set::count (inline) 287ms 0.47% 9.34% 5973ms 9.88% std::_Rb_tree::_M_insert_ (inline) 110ms 0.18% 9.52% 5647ms 9.34% std::less::operator() (inline) 5598ms 9.26% 18.78% 5598ms 9.26% std::operator< (inline) 202ms 0.33% 19.11% 5482ms 9.06% operator new 5395ms 8.92% 28.03% 5395ms 8.92% std::_Rb_tree_increment 2ms 0.0033% 28.04% 5254ms 8.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 1097ms 1.81% 29.85% 5185ms 8.57% __GI___libc_malloc 0 0% 29.85% 5127ms 8.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 29.85% 5100ms 8.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 10ms 0.017% 29.87% 4580ms 7.57% std::_Rb_tree::~_Rb_tree (inline) 53ms 0.088% 29.95% 4573ms 7.56% std::__new_allocator::allocate (inline) 1763ms 2.91% 32.87% 4569ms 7.55% std::_Rb_tree::_M_erase 0 0% 32.87% 4552ms 7.53% std::allocator_traits::allocate (inline) 0 0% 32.87% 4527ms 7.48% std::set::~set (inline) 6ms 0.0099% 32.88% 4341ms 7.18% std::set_intersection (inline) 260ms 0.43% 33.31% 4335ms 7.17% std::__set_intersection 0 0% 33.31% 4240ms 7.01% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.005% 33.31% 4214ms 6.97% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1257ms 2.08% 35.39% 4175ms 6.90% std::_Rb_tree::_M_get_insert_unique_pos 1218ms 2.01% 37.41% 4168ms 6.89% __GI___libc_free 17ms 0.028% 37.43% 4102ms 6.78% MeshBasedCellPopulation::SpringIterator::operator++ 26ms 0.043% 37.48% 3985ms 6.59% Node::AddElement 0 0% 37.48% 3949ms 6.53% VertexMesh::~VertexMesh 2734ms 4.52% 42.00% 3748ms 6.20% _int_malloc 137ms 0.23% 42.22% 3739ms 6.18% std::__new_allocator::deallocate (inline) 0 0% 42.22% 3723ms 6.16% std::_Rb_tree::_M_create_node (inline) 0 0% 42.22% 3711ms 6.14% std::allocator_traits::deallocate (inline) 0 0% 42.22% 3698ms 6.11% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.22% 3675ms 6.08% std::_Rb_tree::_M_get_node (inline) 184ms 0.3% 42.53% 3588ms 5.93% std::_Rb_tree_const_iterator::operator++ (inline) 3565ms 5.89% 48.42% 3565ms 5.89% std::_Rb_tree::_S_right (inline) 113ms 0.19% 48.61% 3477ms 5.75% tetgen::tetgenmesh::insphere_sos 7ms 0.012% 48.62% 3415ms 5.65% TetrahedralMesh::ImportFromMesher 3046ms 5.04% 53.66% 3351ms 5.54% tetgen::insphere 67ms 0.11% 53.77% 3113ms 5.15% MutableElement::AddNode 0 0% 53.77% 3066ms 5.07% AbstractCellPopulation::WriteResultsToFiles 1223ms 2.02% 55.79% 2944ms 4.87% _int_free 175ms 0.29% 56.08% 2693ms 4.45% Node::~Node 212ms 0.35% 56.43% 2666ms 4.41% tetgen::tetgenmesh::flip23 244ms 0.4% 56.83% 2528ms 4.18% VertexMesh::Clear 195ms 0.32% 57.16% 2258ms 3.73% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0066% 57.16% 2086ms 3.45% std::_Rb_tree_iterator::operator++ (inline) 2073ms 3.43% 60.59% 2073ms 3.43% std::_Rb_tree_insert_and_rebalance 0 0% 60.59% 2039ms 3.37% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.59% 2026ms 3.35% std::_Rb_tree::_M_put_node (inline) 1ms 0.0017% 60.59% 1974ms 3.26% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 139ms 0.23% 60.82% 1827ms 3.02% tetgen::tetgenmesh::flip32 1225ms 2.03% 62.85% 1733ms 2.87% malloc_consolidate 1718ms 2.84% 65.69% 1718ms 2.84% Node::GetIndex 15ms 0.025% 65.71% 1700ms 2.81% std::_Vector_base::_M_deallocate (inline) 7ms 0.012% 65.72% 1668ms 2.76% Element::Element 0 0% 65.72% 1591ms 2.63% std::vector::~vector (inline) 1ms 0.0017% 65.73% 1531ms 2.53% std::_Vector_base::~_Vector_base (inline) 4ms 0.0066% 65.73% 1499ms 2.48% _int_free_maybe_consolidate 1340ms 2.22% 67.95% 1421ms 2.35% tetgen::orient3d 190ms 0.31% 68.26% 1401ms 2.32% TetrahedralMesh::Clear 7ms 0.012% 68.27% 1368ms 2.26% Element::RegisterWithNodes (inline) 34ms 0.056% 68.33% 1244ms 2.06% tetgen::tetgenmesh::locate 188ms 0.31% 68.64% 1238ms 2.05% tetgen::tetgenmesh::enqueueflipface 1208ms 2.00% 70.64% 1208ms 2.00% unlink_chunk 2ms 0.0033% 70.64% 1185ms 1.96% VertexMesh::GenerateVerticesFromElementCircumcentres 93ms 0.15% 70.80% 1162ms 1.92% tetgen::tetgenmesh::preciselocate 58ms 0.096% 70.89% 1161ms 1.92% std::map::operator[] 66ms 0.11% 71.00% 1143ms 1.89% std::vector::_M_realloc_insert 0 0% 71.00% 1039ms 1.72% std::_Rb_tree::lower_bound (inline) 0 0% 71.00% 1039ms 1.72% std::map::lower_bound (inline) 820ms 1.36% 72.36% 959ms 1.59% AbstractElement::GetNodeGlobalIndex 10ms 0.017% 72.37% 887ms 1.47% std::_Vector_base::_M_allocate (inline) 81ms 0.13% 72.51% 885ms 1.46% std::vector::push_back (inline) 1ms 0.0017% 72.51% 873ms 1.44% VoronoiDataWriter::Visit 857ms 1.42% 73.93% 857ms 1.42% tetgen::tetgenmesh::triface::triface 0 0% 73.93% 832ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 402ms 0.66% 74.59% 742ms 1.23% tetgen::tetgenmesh::fnextself 7ms 0.012% 74.60% 720ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 74.60% 711ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 294ms 0.49% 75.09% 682ms 1.13% AbstractElement::GetNodeLocation 676ms 1.12% 76.21% 676ms 1.12% AbstractElement::IsDeleted 8ms 0.013% 76.22% 672ms 1.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.028% 76.25% 670ms 1.11% boost::numeric::ublas::vector_assign (inline) 657ms 1.09% 77.33% 657ms 1.09% Node::rGetLocation 15ms 0.025% 77.36% 655ms 1.08% boost::numeric::ublas::c_vector::c_vector (inline) 652ms 1.08% 78.44% 652ms 1.08% [libchaste_mesh.so] 644ms 1.06% 79.50% 644ms 1.06% tetgen::tetgenmesh::triface::operator= 21ms 0.035% 79.54% 625ms 1.03% AbstractTetrahedralElement::CalculateJacobian 53ms 0.088% 79.62% 608ms 1.01% __atan2 588ms 0.97% 80.60% 588ms 0.97% tetgen::tetgenmesh::oppo 432ms 0.71% 81.31% 555ms 0.92% __ieee754_atan2_fma 546ms 0.9% 82.21% 546ms 0.9% std::vector::size (inline) 13ms 0.021% 82.23% 543ms 0.9% Element::CalculateCircumsphere 0 0% 82.23% 531ms 0.88% std::set::find (inline) 0 0% 82.23% 530ms 0.88% boost::numeric::ublas::inner_prod (inline) 3ms 0.005% 82.24% 527ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.056% 82.30% 524ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 44ms 0.073% 82.37% 513ms 0.85% tetgen::tetgenmesh::enext2fnext 316ms 0.52% 82.89% 495ms 0.82% tetgen::tetgenmesh::sym 0 0% 82.89% 478ms 0.79% std::insert_iterator::operator= (inline) 45ms 0.074% 82.96% 464ms 0.77% tetgen::tetgenmesh::enextfnext 33ms 0.055% 83.02% 452ms 0.75% AbstractTetrahedralElement::RefreshJacobian 9ms 0.015% 83.03% 436ms 0.72% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.005% 83.04% 435ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 192ms 0.32% 83.36% 428ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 110ms 0.18% 83.54% 425ms 0.7% boost::numeric::ublas::indexing_vector_assign 28ms 0.046% 83.58% 419ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 12ms 0.02% 83.60% 411ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 1ms 0.0017% 83.61% 406ms 0.67% Cell::GetCellId 396ms 0.65% 84.26% 396ms 0.65% boost::numeric::ublas::c_vector::operator() 102ms 0.17% 84.43% 385ms 0.64% __dynamic_cast 283ms 0.47% 84.90% 378ms 0.62% tetgen::tetgenmesh::bond 5ms 0.0083% 84.91% 375ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 369ms 0.61% 85.52% 369ms 0.61% tetgen::tetgenmesh::org 202ms 0.33% 85.85% 367ms 0.61% AbstractTetrahedralMesh::GetElement 14ms 0.023% 85.87% 363ms 0.6% std::vector::insert (inline) 354ms 0.59% 86.46% 354ms 0.59% std::_Rb_tree_decrement 4ms 0.0066% 86.47% 339ms 0.56% AbstractCellProperty::IsSubType (inline) 0 0% 86.47% 337ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 23ms 0.038% 86.50% 333ms 0.55% tetgen::tetgenmesh::queue::push 146ms 0.24% 86.74% 326ms 0.54% Inverse 61ms 0.1% 86.85% 323ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 224ms 0.37% 87.22% 309ms 0.51% tetgen::tetgenmesh::link::add 0 0% 87.22% 306ms 0.51% tcache_get (inline) 306ms 0.51% 87.72% 306ms 0.51% tcache_get_n (inline) 33ms 0.055% 87.78% 305ms 0.5% tetgen::insphereadapt