File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 57636ms, 87.50% of 65867ms total Dropped 872 nodes (cum <= 329.33ms) flat flat% sum% cum cum% 0 0% 0% 65791ms 99.88% __libc_start_call_main 0 0% 0% 65791ms 99.88% __libc_start_main_impl 0 0% 0% 65791ms 99.88% _start 0 0% 0% 65775ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65775ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65775ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65775ms 99.86% main 0 0% 0% 65739ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65739ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65739ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65459ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 56449ms 85.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 56407ms 85.64% MeshBasedCellPopulation::Update 0 0% 0% 34704ms 52.69% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 34704ms 52.69% MeshBasedCellPopulation::TessellateIfNeeded 289ms 0.44% 0.44% 30004ms 45.55% VertexMesh::VertexMesh 0 0% 0.44% 17656ms 26.81% MutableMesh::ReMesh 1ms 0.0015% 0.44% 12800ms 19.43% tetgen::tetrahedralize 1ms 0.0015% 0.44% 12664ms 19.23% tetgen::tetgenmesh::delaunizevertices 7ms 0.011% 0.45% 12659ms 19.22% tetgen::tetgenmesh::incrflipdelaunay 556ms 0.84% 1.30% 12607ms 19.14% TetrahedralMesh::EdgeIterator::operator++ 20ms 0.03% 1.33% 11730ms 17.81% std::set::insert (inline) 567ms 0.86% 2.19% 11257ms 17.09% tetgen::tetgenmesh::lawson 211ms 0.32% 2.51% 11236ms 17.06% std::_Rb_tree::_M_insert_unique 504ms 0.77% 3.27% 10426ms 15.83% VertexElement::AddFace 3128ms 4.75% 8.02% 9134ms 13.87% std::_Rb_tree::_M_lower_bound (inline) 245ms 0.37% 8.39% 8509ms 12.92% std::_Rb_tree::find (inline) 0 0% 8.39% 7920ms 12.02% std::set::count (inline) 275ms 0.42% 8.81% 6537ms 9.92% std::_Rb_tree::_M_insert_ (inline) 6248ms 9.49% 18.30% 6248ms 9.49% std::_Rb_tree_increment 255ms 0.39% 18.68% 6211ms 9.43% operator new 1122ms 1.70% 20.39% 5883ms 8.93% __GI___libc_malloc 124ms 0.19% 20.58% 5765ms 8.75% std::less::operator() (inline) 5700ms 8.65% 29.23% 5700ms 8.65% std::operator< (inline) 0 0% 29.23% 5489ms 8.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0046% 29.23% 5444ms 8.27% std::set_intersection (inline) 299ms 0.45% 29.69% 5441ms 8.26% std::__set_intersection 1ms 0.0015% 29.69% 5333ms 8.10% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.0076% 29.70% 5312ms 8.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 42ms 0.064% 29.76% 5037ms 7.65% std::__new_allocator::allocate (inline) 0 0% 29.76% 5006ms 7.60% std::allocator_traits::allocate (inline) 28ms 0.043% 29.80% 4991ms 7.58% Node::AddElement 9ms 0.014% 29.82% 4988ms 7.57% std::_Rb_tree::~_Rb_tree (inline) 2015ms 3.06% 32.88% 4977ms 7.56% std::_Rb_tree::_M_erase 0 0% 32.88% 4912ms 7.46% std::set::~set (inline) 1257ms 1.91% 34.79% 4788ms 7.27% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 34.79% 4736ms 7.19% VertexMesh::~VertexMesh 1309ms 1.99% 36.77% 4678ms 7.10% __GI___libc_free 195ms 0.3% 37.07% 4631ms 7.03% std::_Rb_tree_const_iterator::operator++ (inline) 3286ms 4.99% 42.06% 4458ms 6.77% _int_malloc 1ms 0.0015% 42.06% 4430ms 6.73% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0076% 42.07% 4421ms 6.71% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4365ms 6.63% 48.69% 4365ms 6.63% std::_Rb_tree::_S_right (inline) 11ms 0.017% 48.71% 4262ms 6.47% MeshBasedCellPopulation::SpringIterator::operator++ 144ms 0.22% 48.93% 4178ms 6.34% std::__new_allocator::deallocate (inline) 0 0% 48.93% 4157ms 6.31% std::allocator_traits::deallocate (inline) 0 0% 48.93% 4102ms 6.23% std::_Rb_tree::_M_create_node (inline) 0 0% 48.93% 4063ms 6.17% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.93% 4045ms 6.14% std::_Rb_tree::_M_get_node (inline) 84ms 0.13% 49.06% 3932ms 5.97% MutableElement::AddNode 9ms 0.014% 49.07% 3885ms 5.90% TetrahedralMesh::ImportFromMesher 110ms 0.17% 49.24% 3518ms 5.34% tetgen::tetgenmesh::insphere_sos 3104ms 4.71% 53.95% 3392ms 5.15% tetgen::insphere 1221ms 1.85% 55.80% 3364ms 5.11% _int_free 0 0% 55.80% 3336ms 5.06% AbstractCellPopulation::WriteResultsToFiles 237ms 0.36% 56.16% 3143ms 4.77% Node::~Node 240ms 0.36% 56.53% 2921ms 4.43% VertexMesh::Clear 193ms 0.29% 56.82% 2601ms 3.95% tetgen::tetgenmesh::flip23 2305ms 3.50% 60.32% 2305ms 3.50% std::_Rb_tree_insert_and_rebalance 3ms 0.0046% 60.32% 2173ms 3.30% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1500ms 2.28% 62.60% 2159ms 3.28% malloc_consolidate 2154ms 3.27% 65.87% 2154ms 3.27% Node::GetIndex 30ms 0.046% 65.92% 2152ms 3.27% std::_Vector_base::_M_deallocate (inline) 212ms 0.32% 66.24% 2121ms 3.22% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 66.24% 2046ms 3.11% std::_Rb_tree::_M_drop_node (inline) 0 0% 66.24% 2035ms 3.09% std::_Rb_tree::_M_put_node (inline) 0 0% 66.24% 2023ms 3.07% std::vector::~vector (inline) 1ms 0.0015% 66.24% 1975ms 3.00% std::_Vector_base::~_Vector_base (inline) 0 0% 66.24% 1929ms 2.93% std::_Rb_tree_iterator::operator++ (inline) 7ms 0.011% 66.25% 1910ms 2.90% _int_free_maybe_consolidate 6ms 0.0091% 66.26% 1883ms 2.86% Element::Element 163ms 0.25% 66.51% 1830ms 2.78% tetgen::tetgenmesh::flip32 4ms 0.0061% 66.51% 1573ms 2.39% Element::RegisterWithNodes (inline) 239ms 0.36% 66.88% 1570ms 2.38% TetrahedralMesh::Clear 1519ms 2.31% 69.18% 1519ms 2.31% unlink_chunk 1327ms 2.01% 71.20% 1430ms 2.17% tetgen::orient3d 4ms 0.0061% 71.20% 1382ms 2.10% VertexMesh::GenerateVerticesFromElementCircumcentres 195ms 0.3% 71.50% 1282ms 1.95% tetgen::tetgenmesh::enqueueflipface 1115ms 1.69% 73.19% 1249ms 1.90% AbstractElement::GetNodeGlobalIndex 52ms 0.079% 73.27% 1195ms 1.81% std::map::operator[] 41ms 0.062% 73.33% 1189ms 1.81% tetgen::tetgenmesh::locate 59ms 0.09% 73.42% 1170ms 1.78% std::vector::_M_realloc_insert 107ms 0.16% 73.59% 1107ms 1.68% tetgen::tetgenmesh::preciselocate 0 0% 73.59% 1054ms 1.60% std::_Rb_tree::lower_bound (inline) 0 0% 73.59% 1054ms 1.60% std::map::lower_bound (inline) 1ms 0.0015% 73.59% 962ms 1.46% std::_Vector_base::_M_allocate (inline) 1ms 0.0015% 73.59% 949ms 1.44% TetrahedralMesh::RefreshJacobianCachedData 105ms 0.16% 73.75% 928ms 1.41% std::vector::push_back (inline) 0 0% 73.75% 920ms 1.40% VoronoiDataWriter::Visit 854ms 1.30% 75.05% 854ms 1.30% AbstractElement::IsDeleted 385ms 0.58% 75.63% 804ms 1.22% AbstractElement::GetNodeLocation 7ms 0.011% 75.64% 775ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 769ms 1.17% 76.81% 769ms 1.17% tetgen::tetgenmesh::triface::triface 759ms 1.15% 77.96% 759ms 1.15% Node::rGetLocation 710ms 1.08% 79.04% 710ms 1.08% tetgen::tetgenmesh::oppo 13ms 0.02% 79.06% 707ms 1.07% AbstractTetrahedralElement::CalculateJacobian 0 0% 79.06% 701ms 1.06% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.02% 79.08% 691ms 1.05% boost::numeric::ublas::vector_assign (inline) 12ms 0.018% 79.10% 676ms 1.03% boost::numeric::ublas::c_vector::c_vector (inline) 17ms 0.026% 79.12% 659ms 1.00% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 21ms 0.032% 79.15% 639ms 0.97% Element::CalculateCircumsphere 414ms 0.63% 79.78% 637ms 0.97% tetgen::tetgenmesh::fnextself 632ms 0.96% 80.74% 632ms 0.96% [libchaste_mesh.so] 600ms 0.91% 81.65% 600ms 0.91% tetgen::tetgenmesh::triface::operator= 0 0% 81.65% 585ms 0.89% std::set::find (inline) 45ms 0.068% 81.72% 560ms 0.85% __atan2 43ms 0.065% 81.79% 542ms 0.82% AbstractTetrahedralElement::RefreshJacobian 541ms 0.82% 82.61% 542ms 0.82% std::vector::size (inline) 429ms 0.65% 83.26% 515ms 0.78% __ieee754_atan2_fma 0 0% 83.26% 498ms 0.76% std::insert_iterator::operator= (inline) 0 0% 83.26% 475ms 0.72% boost::numeric::ublas::inner_prod (inline) 4ms 0.0061% 83.26% 473ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 26ms 0.039% 83.30% 469ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.30% 454ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 292ms 0.44% 83.75% 448ms 0.68% tetgen::tetgenmesh::sym 40ms 0.061% 83.81% 447ms 0.68% tetgen::tetgenmesh::enext2fnext 128ms 0.19% 84.00% 444ms 0.67% boost::numeric::ublas::indexing_vector_assign 26ms 0.039% 84.04% 443ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 18ms 0.027% 84.07% 432ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 50ms 0.076% 84.15% 431ms 0.65% tetgen::tetgenmesh::enextfnext 0 0% 84.15% 410ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 9ms 0.014% 84.16% 408ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 404ms 0.61% 84.77% 404ms 0.61% std::_Rb_tree_decrement 22ms 0.033% 84.81% 402ms 0.61% tetgen::tetgenmesh::queue::push 0 0% 84.81% 398ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.003% 84.81% 385ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.011% 84.82% 385ms 0.58% VertexElement::~VertexElement 212ms 0.32% 85.14% 384ms 0.58% AbstractTetrahedralMesh::GetElement 170ms 0.26% 85.40% 381ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 95ms 0.14% 85.54% 379ms 0.58% __dynamic_cast 258ms 0.39% 85.94% 378ms 0.57% tetgen::tetgenmesh::link::add 377ms 0.57% 86.51% 377ms 0.57% boost::numeric::ublas::c_vector::operator() 377ms 0.57% 87.08% 377ms 0.57% tetgen::tetgenmesh::org 265ms 0.4% 87.48% 373ms 0.57% tetgen::tetgenmesh::bond 13ms 0.02% 87.50% 372ms 0.56% std::vector::insert (inline) 1ms 0.0015% 87.50% 365ms 0.55% Cell::GetCellId