File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54516ms, 87.75% of 62129ms total Dropped 870 nodes (cum <= 310.64ms) flat flat% sum% cum cum% 0 0% 0% 62081ms 99.92% __libc_start_call_main 0 0% 0% 62081ms 99.92% __libc_start_main_impl 0 0% 0% 62081ms 99.92% _start 0 0% 0% 62065ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62065ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62065ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62065ms 99.90% main 0 0% 0% 62030ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62030ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62030ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61770ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 50942ms 81.99% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50889ms 81.91% MeshBasedCellPopulation::Update 0 0% 0% 29407ms 47.33% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 29407ms 47.33% MeshBasedCellPopulation::TessellateIfNeeded 216ms 0.35% 0.35% 25765ms 41.47% VertexMesh::VertexMesh 0 0% 0.35% 17272ms 27.80% MutableMesh::ReMesh 557ms 0.9% 1.24% 12936ms 20.82% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.24% 12748ms 20.52% tetgen::tetrahedralize 2ms 0.0032% 1.25% 12607ms 20.29% tetgen::tetgenmesh::delaunizevertices 6ms 0.0097% 1.26% 12600ms 20.28% tetgen::tetgenmesh::incrflipdelaunay 544ms 0.88% 2.13% 11234ms 18.08% tetgen::tetgenmesh::lawson 3079ms 4.96% 7.09% 10279ms 16.54% std::_Rb_tree::_M_lower_bound (inline) 34ms 0.055% 7.14% 10213ms 16.44% std::set::insert (inline) 217ms 0.35% 7.49% 9688ms 15.59% std::_Rb_tree::_M_insert_unique 231ms 0.37% 7.86% 9485ms 15.27% std::_Rb_tree::find (inline) 393ms 0.63% 8.50% 9269ms 14.92% VertexElement::AddFace 0 0% 8.50% 8937ms 14.38% std::set::count (inline) 113ms 0.18% 8.68% 6802ms 10.95% std::less::operator() (inline) 6752ms 10.87% 19.55% 6752ms 10.87% std::operator< (inline) 6385ms 10.28% 29.82% 6385ms 10.28% std::_Rb_tree_increment 277ms 0.45% 30.27% 5784ms 9.31% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.27% 5644ms 9.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.27% 5493ms 8.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0064% 30.28% 5467ms 8.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 214ms 0.34% 30.62% 5402ms 8.69% operator new 1123ms 1.81% 32.43% 5112ms 8.23% __GI___libc_malloc 0 0% 32.43% 5042ms 8.12% AbstractCellPopulation::WriteResultsToFiles 45ms 0.072% 32.50% 4566ms 7.35% std::__new_allocator::allocate (inline) 0 0% 32.50% 4545ms 7.32% std::allocator_traits::allocate (inline) 1ms 0.0016% 32.50% 4544ms 7.31% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.008% 32.51% 4544ms 7.31% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.024% 32.53% 4444ms 7.15% std::_Rb_tree::~_Rb_tree (inline) 1812ms 2.92% 35.45% 4427ms 7.13% std::_Rb_tree::_M_erase 16ms 0.026% 35.48% 4392ms 7.07% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 35.48% 4389ms 7.06% std::set::~set (inline) 1231ms 1.98% 37.46% 4023ms 6.48% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.032% 37.49% 3871ms 6.23% Node::AddElement 241ms 0.39% 37.88% 3825ms 6.16% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1142ms 1.84% 39.72% 3813ms 6.14% __GI___libc_free 1ms 0.0016% 39.72% 3794ms 6.11% std::set_intersection (inline) 225ms 0.36% 40.08% 3793ms 6.11% std::__set_intersection 3705ms 5.96% 46.04% 3705ms 5.96% std::_Rb_tree::_S_right (inline) 5ms 0.008% 46.05% 3691ms 5.94% TetrahedralMesh::ImportFromMesher 0 0% 46.05% 3668ms 5.90% VertexMesh::~VertexMesh 0 0% 46.05% 3643ms 5.86% std::_Rb_tree::_M_create_node (inline) 2702ms 4.35% 50.40% 3619ms 5.82% _int_malloc 0 0% 50.40% 3605ms 5.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.40% 3601ms 5.80% std::_Rb_tree::_M_get_node (inline) 1ms 0.0016% 50.40% 3595ms 5.79% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0032% 50.40% 3567ms 5.74% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 120ms 0.19% 50.60% 3438ms 5.53% tetgen::tetgenmesh::insphere_sos 134ms 0.22% 50.81% 3374ms 5.43% std::__new_allocator::deallocate (inline) 0 0% 50.81% 3356ms 5.40% std::allocator_traits::deallocate (inline) 3007ms 4.84% 55.65% 3299ms 5.31% tetgen::insphere 177ms 0.28% 55.94% 3064ms 4.93% std::_Rb_tree_const_iterator::operator++ (inline) 61ms 0.098% 56.04% 2806ms 4.52% MutableElement::AddNode 218ms 0.35% 56.39% 2710ms 4.36% tetgen::tetgenmesh::flip23 1114ms 1.79% 58.18% 2667ms 4.29% _int_free 185ms 0.3% 58.48% 2640ms 4.25% Node::~Node 193ms 0.31% 58.79% 2426ms 3.90% VertexMesh::Clear 1990ms 3.20% 61.99% 1990ms 3.20% std::_Rb_tree_insert_and_rebalance 149ms 0.24% 62.23% 1926ms 3.10% tetgen::tetgenmesh::flip32 5ms 0.008% 62.24% 1911ms 3.08% Element::Element 0 0% 62.24% 1867ms 3.01% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.24% 1857ms 2.99% std::_Rb_tree::_M_put_node (inline) 1690ms 2.72% 64.96% 1690ms 2.72% Node::GetIndex 970ms 1.56% 66.52% 1557ms 2.51% malloc_consolidate 4ms 0.0064% 66.53% 1543ms 2.48% Element::RegisterWithNodes (inline) 14ms 0.023% 66.55% 1513ms 2.44% std::_Vector_base::_M_deallocate (inline) 196ms 0.32% 66.87% 1438ms 2.31% tetgen::tetgenmesh::enqueueflipface 0 0% 66.87% 1435ms 2.31% std::vector::~vector (inline) 206ms 0.33% 67.20% 1413ms 2.27% TetrahedralMesh::Clear 1281ms 2.06% 69.26% 1355ms 2.18% tetgen::orient3d 7ms 0.011% 69.27% 1351ms 2.17% _int_free_maybe_consolidate 1ms 0.0016% 69.27% 1348ms 2.17% std::_Vector_base::~_Vector_base (inline) 49ms 0.079% 69.35% 1330ms 2.14% std::map::operator[] 1ms 0.0016% 69.35% 1219ms 1.96% VoronoiDataWriter::Visit 0 0% 69.35% 1212ms 1.95% std::_Rb_tree::lower_bound (inline) 0 0% 69.35% 1212ms 1.95% std::map::lower_bound (inline) 32ms 0.052% 69.40% 1155ms 1.86% tetgen::tetgenmesh::locate 1151ms 1.85% 71.26% 1151ms 1.85% unlink_chunk 64ms 0.1% 71.36% 1134ms 1.83% std::vector::_M_realloc_insert 110ms 0.18% 71.54% 1069ms 1.72% tetgen::tetgenmesh::preciselocate 6ms 0.0097% 71.55% 1042ms 1.68% VertexMesh::GenerateVerticesFromElementCircumcentres 11ms 0.018% 71.56% 955ms 1.54% std::_Vector_base::_M_allocate (inline) 132ms 0.21% 71.78% 934ms 1.50% std::vector::push_back (inline) 754ms 1.21% 72.99% 919ms 1.48% AbstractElement::GetNodeGlobalIndex 857ms 1.38% 74.37% 857ms 1.38% tetgen::tetgenmesh::triface::triface 1ms 0.0016% 74.37% 811ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0016% 74.37% 739ms 1.19% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.021% 74.39% 729ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 298ms 0.48% 74.87% 721ms 1.16% AbstractElement::GetNodeLocation 720ms 1.16% 76.03% 720ms 1.16% tetgen::tetgenmesh::oppo 10ms 0.016% 76.05% 697ms 1.12% AbstractTetrahedralElement::CalculateJacobian 385ms 0.62% 76.67% 691ms 1.11% tetgen::tetgenmesh::fnextself 22ms 0.035% 76.70% 689ms 1.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.031% 76.73% 684ms 1.10% boost::numeric::ublas::vector_assign (inline) 667ms 1.07% 77.81% 667ms 1.07% Node::rGetLocation 652ms 1.05% 78.86% 652ms 1.05% tetgen::tetgenmesh::triface::operator= 15ms 0.024% 78.88% 643ms 1.03% boost::numeric::ublas::c_vector::c_vector (inline) 636ms 1.02% 79.90% 636ms 1.02% [libchaste_mesh.so] 45ms 0.072% 79.98% 619ms 1% __atan2 469ms 0.75% 80.73% 574ms 0.92% __ieee754_atan2_fma 23ms 0.037% 80.77% 545ms 0.88% Element::CalculateCircumsphere 0 0% 80.77% 543ms 0.87% std::set::find (inline) 542ms 0.87% 81.64% 542ms 0.87% std::vector::size (inline) 0 0% 81.64% 530ms 0.85% std::insert_iterator::operator= (inline) 43ms 0.069% 81.71% 521ms 0.84% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.71% 501ms 0.81% boost::numeric::ublas::inner_prod (inline) 5ms 0.008% 81.72% 498ms 0.8% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 35ms 0.056% 81.78% 493ms 0.79% boost::numeric::ublas::vector_scalar_binary::evaluate 342ms 0.55% 82.33% 485ms 0.78% tetgen::tetgenmesh::sym 51ms 0.082% 82.41% 484ms 0.78% tetgen::tetgenmesh::enextfnext 0 0% 82.41% 471ms 0.76% std::_Rb_tree::_M_insert_unique_ (inline) 459ms 0.74% 83.15% 459ms 0.74% AbstractElement::IsDeleted 17ms 0.027% 83.17% 447ms 0.72% VertexMesh::CalculateUnitNormalToFaceWithArea 126ms 0.2% 83.38% 441ms 0.71% boost::numeric::ublas::indexing_vector_assign 40ms 0.064% 83.44% 435ms 0.7% tetgen::tetgenmesh::enext2fnext 234ms 0.38% 83.82% 428ms 0.69% AbstractTetrahedralMesh::GetElement 182ms 0.29% 84.11% 416ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 409ms 0.66% 84.77% 409ms 0.66% boost::numeric::ublas::c_vector::operator() 3ms 0.0048% 84.77% 395ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.77% 394ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0032% 84.78% 381ms 0.61% Cell::GetCellId 33ms 0.053% 84.83% 375ms 0.6% tetgen::tetgenmesh::queue::push 3ms 0.0048% 84.83% 371ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 20ms 0.032% 84.87% 365ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 6ms 0.0097% 84.88% 362ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 273ms 0.44% 85.32% 362ms 0.58% tetgen::tetgenmesh::bond 358ms 0.58% 85.89% 358ms 0.58% tetgen::tetgenmesh::org 90ms 0.14% 86.04% 355ms 0.57% __dynamic_cast 16ms 0.026% 86.06% 353ms 0.57% std::vector::insert (inline) 0 0% 86.06% 343ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 239ms 0.38% 86.45% 342ms 0.55% tetgen::tetgenmesh::link::add 11ms 0.018% 86.47% 341ms 0.55% VertexElement::~VertexElement 0 0% 86.47% 341ms 0.55% tcache_get (inline) 341ms 0.55% 87.01% 341ms 0.55% tcache_get_n (inline) 326ms 0.52% 87.54% 326ms 0.52% std::_Rb_tree_decrement 129ms 0.21% 87.75% 321ms 0.52% Inverse