File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54234ms, 87.12% of 62253ms total Dropped 907 nodes (cum <= 311.26ms) flat flat% sum% cum cum% 0 0% 0% 62181ms 99.88% __libc_start_call_main 0 0% 0% 62181ms 99.88% __libc_start_main_impl 0 0% 0% 62181ms 99.88% _start 0 0% 0% 62167ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62167ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62167ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62167ms 99.86% main 0 0% 0% 62128ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62128ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62128ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61857ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 52867ms 84.92% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52827ms 84.86% MeshBasedCellPopulation::Update 0 0% 0% 31337ms 50.34% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 31335ms 50.33% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 214ms 0.34% 0.34% 27261ms 43.79% VertexMesh::VertexMesh 0 0% 0.34% 17537ms 28.17% MutableMesh::ReMesh 0 0% 0.34% 13020ms 20.91% tetgen::tetrahedralize 0 0% 0.34% 12887ms 20.70% tetgen::tetgenmesh::delaunizevertices 6ms 0.0096% 0.35% 12878ms 20.69% tetgen::tetgenmesh::incrflipdelaunay 594ms 0.95% 1.31% 12232ms 19.65% TetrahedralMesh::EdgeIterator::operator++ 547ms 0.88% 2.19% 11527ms 18.52% tetgen::tetgenmesh::lawson 31ms 0.05% 2.24% 10792ms 17.34% std::set::insert (inline) 233ms 0.37% 2.61% 10277ms 16.51% std::_Rb_tree::_M_insert_unique 429ms 0.69% 3.30% 9619ms 15.45% VertexElement::AddFace 3034ms 4.87% 8.17% 8963ms 14.40% std::_Rb_tree::_M_lower_bound (inline) 260ms 0.42% 8.59% 8427ms 13.54% std::_Rb_tree::find (inline) 0 0% 8.59% 7851ms 12.61% std::set::count (inline) 280ms 0.45% 9.04% 6027ms 9.68% std::_Rb_tree::_M_insert_ (inline) 123ms 0.2% 9.24% 5770ms 9.27% std::less::operator() (inline) 5689ms 9.14% 18.38% 5689ms 9.14% std::operator< (inline) 5632ms 9.05% 27.42% 5632ms 9.05% std::_Rb_tree_increment 205ms 0.33% 27.75% 5563ms 8.94% operator new 0 0% 27.75% 5332ms 8.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 1097ms 1.76% 29.52% 5287ms 8.49% __GI___libc_malloc 0 0% 29.52% 5189ms 8.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.011% 29.53% 5170ms 8.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0032% 29.53% 4691ms 7.54% std::_Rb_tree::~_Rb_tree (inline) 1863ms 2.99% 32.52% 4688ms 7.53% std::_Rb_tree::_M_erase 52ms 0.084% 32.61% 4634ms 7.44% std::__new_allocator::allocate (inline) 0 0% 32.61% 4621ms 7.42% std::set::~set (inline) 0 0% 32.61% 4608ms 7.40% std::allocator_traits::allocate (inline) 3ms 0.0048% 32.61% 4583ms 7.36% std::set_intersection (inline) 273ms 0.44% 33.05% 4580ms 7.36% std::__set_intersection 1361ms 2.19% 35.24% 4436ms 7.13% __GI___libc_free 1260ms 2.02% 37.26% 4334ms 6.96% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 37.26% 4307ms 6.92% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 37.27% 4280ms 6.88% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 27ms 0.043% 37.31% 4266ms 6.85% Node::AddElement 16ms 0.026% 37.34% 4151ms 6.67% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 37.34% 4106ms 6.60% VertexMesh::~VertexMesh 2822ms 4.53% 41.87% 3863ms 6.21% _int_malloc 140ms 0.22% 42.10% 3852ms 6.19% std::__new_allocator::deallocate (inline) 0 0% 42.10% 3826ms 6.15% std::allocator_traits::deallocate (inline) 197ms 0.32% 42.41% 3803ms 6.11% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 42.41% 3782ms 6.08% std::_Rb_tree::_M_create_node (inline) 0 0% 42.41% 3753ms 6.03% std::_Rb_tree::_Alloc_node::operator() (inline) 3742ms 6.01% 48.42% 3742ms 6.01% std::_Rb_tree::_S_right (inline) 0 0% 48.42% 3737ms 6.00% std::_Rb_tree::_M_get_node (inline) 12ms 0.019% 48.44% 3621ms 5.82% TetrahedralMesh::ImportFromMesher 0 0% 48.44% 3494ms 5.61% AbstractCellPopulation::WriteResultsToFiles 114ms 0.18% 48.63% 3477ms 5.59% tetgen::tetgenmesh::insphere_sos 85ms 0.14% 48.76% 3377ms 5.42% MutableElement::AddNode 3083ms 4.95% 53.72% 3346ms 5.37% tetgen::insphere 1233ms 1.98% 55.70% 3072ms 4.93% _int_free 189ms 0.3% 56.00% 2839ms 4.56% tetgen::tetgenmesh::flip23 180ms 0.29% 56.29% 2802ms 4.50% Node::~Node 208ms 0.33% 56.62% 2608ms 4.19% VertexMesh::Clear 205ms 0.33% 56.95% 2293ms 3.68% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0032% 56.96% 2288ms 3.68% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0016% 56.96% 2104ms 3.38% std::_Rb_tree_iterator::operator++ (inline) 2085ms 3.35% 60.31% 2085ms 3.35% std::_Rb_tree_insert_and_rebalance 0 0% 60.31% 2034ms 3.27% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.31% 2024ms 3.25% std::_Rb_tree::_M_put_node (inline) 151ms 0.24% 60.55% 1929ms 3.10% tetgen::tetgenmesh::flip32 26ms 0.042% 60.59% 1828ms 2.94% std::_Vector_base::_M_deallocate (inline) 1222ms 1.96% 62.55% 1795ms 2.88% malloc_consolidate 4ms 0.0064% 62.56% 1730ms 2.78% Element::Element 0 0% 62.56% 1680ms 2.70% std::vector::~vector (inline) 1663ms 2.67% 65.23% 1663ms 2.67% Node::GetIndex 2ms 0.0032% 65.24% 1627ms 2.61% std::_Vector_base::~_Vector_base (inline) 9ms 0.014% 65.25% 1575ms 2.53% _int_free_maybe_consolidate 209ms 0.34% 65.59% 1508ms 2.42% TetrahedralMesh::Clear 1334ms 2.14% 67.73% 1427ms 2.29% tetgen::orient3d 184ms 0.3% 68.02% 1410ms 2.26% tetgen::tetgenmesh::enqueueflipface 3ms 0.0048% 68.03% 1403ms 2.25% Element::RegisterWithNodes (inline) 1342ms 2.16% 70.18% 1342ms 2.16% unlink_chunk 5ms 0.008% 70.19% 1175ms 1.89% VertexMesh::GenerateVerticesFromElementCircumcentres 28ms 0.045% 70.24% 1149ms 1.85% tetgen::tetgenmesh::locate 51ms 0.082% 70.32% 1120ms 1.80% std::vector::_M_realloc_insert 58ms 0.093% 70.41% 1106ms 1.78% std::map::operator[] 78ms 0.13% 70.54% 1066ms 1.71% tetgen::tetgenmesh::preciselocate 862ms 1.38% 71.92% 1005ms 1.61% AbstractElement::GetNodeGlobalIndex 0 0% 71.92% 981ms 1.58% std::_Rb_tree::lower_bound (inline) 0 0% 71.92% 981ms 1.58% std::map::lower_bound (inline) 0 0% 71.92% 963ms 1.55% VoronoiDataWriter::Visit 956ms 1.54% 73.46% 956ms 1.54% tetgen::tetgenmesh::triface::triface 116ms 0.19% 73.64% 894ms 1.44% std::vector::push_back (inline) 8ms 0.013% 73.66% 878ms 1.41% std::_Vector_base::_M_allocate (inline) 1ms 0.0016% 73.66% 871ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 425ms 0.68% 74.34% 758ms 1.22% tetgen::tetgenmesh::fnextself 7ms 0.011% 74.35% 751ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 339ms 0.54% 74.90% 749ms 1.20% AbstractElement::GetNodeLocation 721ms 1.16% 76.06% 721ms 1.16% AbstractElement::IsDeleted 2ms 0.0032% 76.06% 717ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 709ms 1.14% 77.20% 709ms 1.14% tetgen::tetgenmesh::oppo 686ms 1.10% 78.30% 686ms 1.10% Node::rGetLocation 13ms 0.021% 78.32% 679ms 1.09% AbstractTetrahedralElement::CalculateJacobian 23ms 0.037% 78.36% 674ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.018% 78.38% 673ms 1.08% boost::numeric::ublas::vector_assign (inline) 55ms 0.088% 78.46% 667ms 1.07% __atan2 667ms 1.07% 79.54% 667ms 1.07% tetgen::tetgenmesh::triface::operator= 655ms 1.05% 80.59% 655ms 1.05% [libchaste_mesh.so] 9ms 0.014% 80.60% 642ms 1.03% boost::numeric::ublas::c_vector::c_vector (inline) 490ms 0.79% 81.39% 611ms 0.98% __ieee754_atan2_fma 19ms 0.031% 81.42% 593ms 0.95% Element::CalculateCircumsphere 0 0% 81.42% 574ms 0.92% std::set::find (inline) 524ms 0.84% 82.26% 524ms 0.84% std::vector::size (inline) 37ms 0.059% 82.32% 512ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.32% 504ms 0.81% std::insert_iterator::operator= (inline) 46ms 0.074% 82.39% 504ms 0.81% tetgen::tetgenmesh::enextfnext 0 0% 82.39% 494ms 0.79% boost::numeric::ublas::inner_prod (inline) 6ms 0.0096% 82.40% 492ms 0.79% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.055% 82.46% 486ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 37ms 0.059% 82.52% 471ms 0.76% tetgen::tetgenmesh::enext2fnext 1ms 0.0016% 82.52% 456ms 0.73% std::_Rb_tree::_M_insert_unique_ (inline) 278ms 0.45% 82.97% 450ms 0.72% tetgen::tetgenmesh::sym 24ms 0.039% 83.00% 445ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 436ms 0.7% 83.71% 436ms 0.7% boost::numeric::ublas::c_vector::operator() 32ms 0.051% 83.76% 425ms 0.68% tetgen::tetgenmesh::queue::push 226ms 0.36% 84.12% 424ms 0.68% AbstractTetrahedralMesh::GetElement 121ms 0.19% 84.31% 419ms 0.67% boost::numeric::ublas::indexing_vector_assign 188ms 0.3% 84.62% 412ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 29ms 0.047% 84.66% 397ms 0.64% std::_Rb_tree_iterator::operator-- (inline) 281ms 0.45% 85.11% 392ms 0.63% tetgen::tetgenmesh::link::add 0 0% 85.11% 387ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.008% 85.12% 386ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 273ms 0.44% 85.56% 382ms 0.61% tetgen::tetgenmesh::bond 6ms 0.0096% 85.57% 377ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 89ms 0.14% 85.71% 375ms 0.6% __dynamic_cast 371ms 0.6% 86.31% 371ms 0.6% tetgen::tetgenmesh::org 0 0% 86.31% 368ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 7ms 0.011% 86.32% 366ms 0.59% Cell::GetCellId 10ms 0.016% 86.34% 363ms 0.58% std::vector::insert (inline) 348ms 0.56% 86.90% 348ms 0.56% std::_Rb_tree_decrement 134ms 0.22% 87.11% 341ms 0.55% Inverse 4ms 0.0064% 87.12% 336ms 0.54% VertexElement::~VertexElement 1ms 0.0016% 87.12% 324ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement