File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48122ms, 86.69% of 55508ms total Dropped 876 nodes (cum <= 277.54ms) flat flat% sum% cum cum% 0 0% 0% 55447ms 99.89% __libc_start_call_main 0 0% 0% 55447ms 99.89% __libc_start_main_impl 0 0% 0% 55447ms 99.89% _start 0 0% 0% 55433ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 55433ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 55433ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 55433ms 99.86% main 0 0% 0% 55397ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55397ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 55397ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55144ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 46758ms 84.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46710ms 84.15% MeshBasedCellPopulation::Update 0 0% 0% 26188ms 47.18% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26185ms 47.17% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 191ms 0.34% 0.34% 23299ms 41.97% VertexMesh::VertexMesh 0 0% 0.34% 16925ms 30.49% MutableMesh::ReMesh 0 0% 0.34% 13121ms 23.64% tetgen::tetrahedralize 4ms 0.0072% 0.35% 12984ms 23.39% tetgen::tetgenmesh::delaunizevertices 4ms 0.0072% 0.36% 12974ms 23.37% tetgen::tetgenmesh::incrflipdelaunay 559ms 1.01% 1.37% 11591ms 20.88% tetgen::tetgenmesh::lawson 536ms 0.97% 2.33% 11045ms 19.90% TetrahedralMesh::EdgeIterator::operator++ 34ms 0.061% 2.39% 9507ms 17.13% std::set::insert (inline) 198ms 0.36% 2.75% 8992ms 16.20% std::_Rb_tree::_M_insert_unique 350ms 0.63% 3.38% 8876ms 15.99% VertexElement::AddFace 2922ms 5.26% 8.64% 8377ms 15.09% std::_Rb_tree::_M_lower_bound (inline) 195ms 0.35% 9.00% 7794ms 14.04% std::_Rb_tree::find (inline) 0 0% 9.00% 7248ms 13.06% std::set::count (inline) 276ms 0.5% 9.49% 5348ms 9.63% std::_Rb_tree::_M_insert_ (inline) 128ms 0.23% 9.72% 5331ms 9.60% std::less::operator() (inline) 5266ms 9.49% 19.21% 5266ms 9.49% std::operator< (inline) 1ms 0.0018% 19.21% 4920ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0018% 19.21% 4803ms 8.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0036% 19.22% 4787ms 8.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 200ms 0.36% 19.58% 4616ms 8.32% operator new 4464ms 8.04% 27.62% 4464ms 8.04% std::_Rb_tree_increment 1120ms 2.02% 29.64% 4358ms 7.85% __GI___libc_malloc 27ms 0.049% 29.69% 3982ms 7.17% std::__new_allocator::allocate (inline) 0 0% 29.69% 3959ms 7.13% std::allocator_traits::allocate (inline) 1ms 0.0018% 29.69% 3942ms 7.10% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.013% 29.70% 3921ms 7.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.022% 29.72% 3878ms 6.99% std::_Rb_tree::~_Rb_tree (inline) 1415ms 2.55% 32.27% 3863ms 6.96% std::_Rb_tree::_M_erase 0 0% 32.27% 3825ms 6.89% std::set::~set (inline) 7ms 0.013% 32.28% 3818ms 6.88% MeshBasedCellPopulation::SpringIterator::operator++ 1239ms 2.23% 34.52% 3758ms 6.77% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.0036% 34.52% 3542ms 6.38% std::set_intersection (inline) 260ms 0.47% 34.99% 3540ms 6.38% std::__set_intersection 1040ms 1.87% 36.86% 3509ms 6.32% __GI___libc_free 113ms 0.2% 37.06% 3421ms 6.16% tetgen::tetgenmesh::insphere_sos 0 0% 37.06% 3315ms 5.97% AbstractCellPopulation::WriteResultsToFiles 3002ms 5.41% 42.47% 3291ms 5.93% tetgen::insphere 0 0% 42.47% 3255ms 5.86% std::_Rb_tree::_M_create_node (inline) 0 0% 42.47% 3230ms 5.82% std::_Rb_tree::_M_get_node (inline) 0 0% 42.47% 3228ms 5.82% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.05% 42.52% 3165ms 5.70% Node::AddElement 10ms 0.018% 42.54% 3047ms 5.49% TetrahedralMesh::ImportFromMesher 102ms 0.18% 42.73% 3046ms 5.49% std::__new_allocator::deallocate (inline) 0 0% 42.73% 3028ms 5.46% std::allocator_traits::deallocate (inline) 2938ms 5.29% 48.02% 2938ms 5.29% std::_Rb_tree::_S_right (inline) 2190ms 3.95% 51.96% 2931ms 5.28% _int_malloc 0 0% 51.96% 2908ms 5.24% VertexMesh::~VertexMesh 237ms 0.43% 52.39% 2788ms 5.02% std::_Rb_tree_const_iterator::operator++ (inline) 217ms 0.39% 52.78% 2730ms 4.92% tetgen::tetgenmesh::flip23 72ms 0.13% 52.91% 2510ms 4.52% MutableElement::AddNode 1214ms 2.19% 55.10% 2468ms 4.45% _int_free 3ms 0.0054% 55.10% 2188ms 3.94% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 189ms 0.34% 55.44% 2177ms 3.92% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 153ms 0.28% 55.72% 2168ms 3.91% Node::~Node 0 0% 55.72% 2000ms 3.60% std::_Rb_tree_iterator::operator++ (inline) 177ms 0.32% 56.04% 1991ms 3.59% tetgen::tetgenmesh::flip32 158ms 0.28% 56.32% 1957ms 3.53% VertexMesh::Clear 1916ms 3.45% 59.78% 1916ms 3.45% std::_Rb_tree_insert_and_rebalance 0 0% 59.78% 1834ms 3.30% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.78% 1825ms 3.29% std::_Rb_tree::_M_put_node (inline) 4ms 0.0072% 59.78% 1467ms 2.64% Element::Element 1372ms 2.47% 62.25% 1455ms 2.62% tetgen::orient3d 1303ms 2.35% 64.60% 1303ms 2.35% Node::GetIndex 158ms 0.28% 64.89% 1292ms 2.33% TetrahedralMesh::Clear 195ms 0.35% 65.24% 1274ms 2.30% tetgen::tetgenmesh::enqueueflipface 808ms 1.46% 66.69% 1221ms 2.20% malloc_consolidate 14ms 0.025% 66.72% 1217ms 2.19% std::_Vector_base::_M_deallocate (inline) 28ms 0.05% 66.77% 1170ms 2.11% tetgen::tetgenmesh::locate 0 0% 66.77% 1122ms 2.02% std::vector::~vector (inline) 4ms 0.0072% 66.78% 1112ms 2.00% Element::RegisterWithNodes (inline) 97ms 0.17% 66.95% 1094ms 1.97% tetgen::tetgenmesh::preciselocate 5ms 0.009% 66.96% 1049ms 1.89% _int_free_maybe_consolidate 1ms 0.0018% 66.96% 1040ms 1.87% std::_Vector_base::~_Vector_base (inline) 52ms 0.094% 67.06% 1037ms 1.87% std::map::operator[] 74ms 0.13% 67.19% 974ms 1.75% std::vector::_M_realloc_insert 930ms 1.68% 68.86% 930ms 1.68% tetgen::tetgenmesh::triface::triface 0 0% 68.86% 922ms 1.66% std::_Rb_tree::lower_bound (inline) 0 0% 68.86% 922ms 1.66% std::map::lower_bound (inline) 898ms 1.62% 70.48% 898ms 1.62% unlink_chunk 0 0% 70.48% 897ms 1.62% VoronoiDataWriter::Visit 3ms 0.0054% 70.49% 842ms 1.52% VertexMesh::GenerateVerticesFromElementCircumcentres 649ms 1.17% 71.66% 816ms 1.47% AbstractElement::GetNodeGlobalIndex 428ms 0.77% 72.43% 791ms 1.43% tetgen::tetgenmesh::fnextself 775ms 1.40% 73.82% 775ms 1.40% tetgen::tetgenmesh::triface::operator= 101ms 0.18% 74.01% 774ms 1.39% std::vector::push_back (inline) 2ms 0.0036% 74.01% 733ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.0054% 74.01% 732ms 1.32% std::_Vector_base::_M_allocate (inline) 0 0% 74.01% 712ms 1.28% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.02% 74.03% 683ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 10ms 0.018% 74.05% 680ms 1.23% AbstractTetrahedralElement::CalculateJacobian 12ms 0.022% 74.07% 677ms 1.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 21ms 0.038% 74.11% 639ms 1.15% boost::numeric::ublas::vector_assign (inline) 627ms 1.13% 75.24% 627ms 1.13% [libchaste_mesh.so] 11ms 0.02% 75.26% 612ms 1.10% boost::numeric::ublas::c_vector::c_vector (inline) 242ms 0.44% 75.70% 609ms 1.10% AbstractElement::GetNodeLocation 44ms 0.079% 75.78% 600ms 1.08% __atan2 570ms 1.03% 76.80% 570ms 1.03% tetgen::tetgenmesh::oppo 434ms 0.78% 77.59% 556ms 1.00% __ieee754_atan2_fma 0 0% 77.59% 539ms 0.97% std::set::find (inline) 522ms 0.94% 78.53% 522ms 0.94% Node::rGetLocation 0 0% 78.53% 512ms 0.92% std::insert_iterator::operator= (inline) 50ms 0.09% 78.62% 507ms 0.91% tetgen::tetgenmesh::enext2fnext 49ms 0.088% 78.70% 501ms 0.9% tetgen::tetgenmesh::enextfnext 45ms 0.081% 78.79% 496ms 0.89% AbstractTetrahedralElement::RefreshJacobian 0 0% 78.79% 492ms 0.89% boost::numeric::ublas::inner_prod (inline) 6ms 0.011% 78.80% 490ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 485ms 0.87% 79.67% 485ms 0.87% std::vector::size (inline) 26ms 0.047% 79.72% 484ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 34ms 0.061% 79.78% 478ms 0.86% tetgen::tetgenmesh::queue::push 19ms 0.034% 79.81% 463ms 0.83% Element::CalculateCircumsphere 0 0% 79.81% 456ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 372ms 0.67% 80.48% 442ms 0.8% tetgen::tetgenmesh::link::add 426ms 0.77% 81.25% 426ms 0.77% AbstractElement::IsDeleted 273ms 0.49% 81.74% 419ms 0.75% tetgen::tetgenmesh::sym 223ms 0.4% 82.14% 418ms 0.75% AbstractTetrahedralMesh::GetElement 28ms 0.05% 82.19% 416ms 0.75% VertexMesh::CalculateUnitNormalToFaceWithArea 30ms 0.054% 82.25% 410ms 0.74% std::_Rb_tree_iterator::operator-- (inline) 173ms 0.31% 82.56% 406ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 112ms 0.2% 82.76% 405ms 0.73% boost::numeric::ublas::indexing_vector_assign 396ms 0.71% 83.47% 396ms 0.71% tetgen::tetgenmesh::org 90ms 0.16% 83.64% 384ms 0.69% __dynamic_cast 0 0% 83.64% 383ms 0.69% VertexMeshWriter::WriteVtkUsingMesh 8ms 0.014% 83.65% 380ms 0.68% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.013% 83.66% 377ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.0054% 83.67% 372ms 0.67% Cell::GetCellId 368ms 0.66% 84.33% 368ms 0.66% boost::numeric::ublas::c_vector::operator() 355ms 0.64% 84.97% 355ms 0.64% std::_Rb_tree_decrement 263ms 0.47% 85.45% 354ms 0.64% tetgen::tetgenmesh::bond 2ms 0.0036% 85.45% 351ms 0.63% AbstractTetrahedralElement::AbstractTetrahedralElement 96ms 0.17% 85.62% 350ms 0.63% tetgen::tetgenmesh::queue::pop 348ms 0.63% 86.25% 348ms 0.63% tetgen::tetgenmesh::pointmark 14ms 0.025% 86.27% 319ms 0.57% std::vector::insert (inline) 60ms 0.11% 86.38% 307ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 6ms 0.011% 86.39% 305ms 0.55% VertexElement::~VertexElement 2ms 0.0036% 86.40% 300ms 0.54% AbstractCellProperty::IsSubType (inline) 31ms 0.056% 86.45% 289ms 0.52% tetgen::insphereadapt 125ms 0.23% 86.68% 287ms 0.52% Inverse 9ms 0.016% 86.69% 283ms 0.51% VertexMesh::GetVolumeOfElement 0 0% 86.69% 282ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)