File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52063ms, 87.44% of 59539ms total Dropped 823 nodes (cum <= 297.69ms) flat flat% sum% cum cum% 0 0% 0% 59475ms 99.89% __libc_start_call_main 0 0% 0% 59475ms 99.89% __libc_start_main_impl 0 0% 0% 59475ms 99.89% _start 0 0% 0% 59459ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 59459ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 59459ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 59459ms 99.87% main 0 0% 0% 59424ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 59424ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 59424ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 59162ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 48733ms 81.85% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48677ms 81.76% MeshBasedCellPopulation::Update 0 0% 0% 27580ms 46.32% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27580ms 46.32% MeshBasedCellPopulation::TessellateIfNeeded 226ms 0.38% 0.38% 24429ms 41.03% VertexMesh::VertexMesh 0 0% 0.38% 16977ms 28.51% MutableMesh::ReMesh 1ms 0.0017% 0.38% 12755ms 21.42% tetgen::tetrahedralize 0 0% 0.38% 12623ms 21.20% tetgen::tetgenmesh::delaunizevertices 4ms 0.0067% 0.39% 12622ms 21.20% tetgen::tetgenmesh::incrflipdelaunay 558ms 0.94% 1.33% 12497ms 20.99% TetrahedralMesh::EdgeIterator::operator++ 579ms 0.97% 2.30% 11218ms 18.84% tetgen::tetgenmesh::lawson 3036ms 5.10% 7.40% 10041ms 16.86% std::_Rb_tree::_M_lower_bound (inline) 21ms 0.035% 7.43% 9634ms 16.18% std::set::insert (inline) 236ms 0.4% 7.83% 9281ms 15.59% std::_Rb_tree::find (inline) 191ms 0.32% 8.15% 9123ms 15.32% std::_Rb_tree::_M_insert_unique 381ms 0.64% 8.79% 9092ms 15.27% VertexElement::AddFace 0 0% 8.79% 8744ms 14.69% std::set::count (inline) 109ms 0.18% 8.97% 6640ms 11.15% std::less::operator() (inline) 6578ms 11.05% 20.02% 6578ms 11.05% std::operator< (inline) 5817ms 9.77% 29.79% 5817ms 9.77% std::_Rb_tree_increment 0 0% 29.79% 5555ms 9.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 261ms 0.44% 30.23% 5482ms 9.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.23% 5422ms 9.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.0084% 30.24% 5395ms 9.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 215ms 0.36% 30.60% 5095ms 8.56% operator new 1082ms 1.82% 32.42% 4809ms 8.08% __GI___libc_malloc 0 0% 32.42% 4737ms 7.96% AbstractCellPopulation::WriteResultsToFiles 7ms 0.012% 32.43% 4442ms 7.46% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.43% 4438ms 7.45% MeshBasedCellPopulation::UpdateNodePairs 43ms 0.072% 32.50% 4327ms 7.27% std::__new_allocator::allocate (inline) 0 0% 32.50% 4311ms 7.24% std::allocator_traits::allocate (inline) 9ms 0.015% 32.51% 4305ms 7.23% MeshBasedCellPopulation::SpringIterator::operator++ 8ms 0.013% 32.53% 4035ms 6.78% std::_Rb_tree::~_Rb_tree (inline) 1564ms 2.63% 35.16% 4025ms 6.76% std::_Rb_tree::_M_erase 0 0% 35.16% 3988ms 6.70% std::set::~set (inline) 1133ms 1.90% 37.06% 3767ms 6.33% std::_Rb_tree::_M_get_insert_unique_pos 987ms 1.66% 38.72% 3611ms 6.06% __GI___libc_free 249ms 0.42% 39.13% 3579ms 6.01% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 104ms 0.17% 39.31% 3558ms 5.98% tetgen::tetgenmesh::insphere_sos 24ms 0.04% 39.35% 3474ms 5.83% Node::AddElement 3162ms 5.31% 44.66% 3447ms 5.79% tetgen::insphere 7ms 0.012% 44.67% 3442ms 5.78% std::set_intersection (inline) 208ms 0.35% 45.02% 3435ms 5.77% std::__set_intersection 0 0% 45.02% 3421ms 5.75% std::_Rb_tree::_M_create_node (inline) 6ms 0.01% 45.03% 3415ms 5.74% TetrahedralMesh::ImportFromMesher 0 0% 45.03% 3392ms 5.70% std::_Rb_tree::_M_get_node (inline) 0 0% 45.03% 3384ms 5.68% std::_Rb_tree::_Alloc_node::operator() (inline) 3375ms 5.67% 50.70% 3375ms 5.67% std::_Rb_tree::_S_right (inline) 2517ms 4.23% 54.93% 3360ms 5.64% _int_malloc 0 0% 54.93% 3337ms 5.60% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0034% 54.93% 3328ms 5.59% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 140ms 0.24% 55.17% 3201ms 5.38% std::__new_allocator::deallocate (inline) 0 0% 55.17% 3179ms 5.34% std::allocator_traits::deallocate (inline) 0 0% 55.17% 3178ms 5.34% VertexMesh::~VertexMesh 191ms 0.32% 55.49% 2782ms 4.67% std::_Rb_tree_const_iterator::operator++ (inline) 209ms 0.35% 55.84% 2644ms 4.44% tetgen::tetgenmesh::flip23 1163ms 1.95% 57.79% 2621ms 4.40% _int_free 66ms 0.11% 57.90% 2470ms 4.15% MutableElement::AddNode 116ms 0.19% 58.10% 2231ms 3.75% Node::~Node 140ms 0.24% 58.33% 2078ms 3.49% VertexMesh::Clear 1923ms 3.23% 61.56% 1923ms 3.23% std::_Rb_tree_insert_and_rebalance 163ms 0.27% 61.84% 1879ms 3.16% tetgen::tetgenmesh::flip32 0 0% 61.84% 1844ms 3.10% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.84% 1834ms 3.08% std::_Rb_tree::_M_put_node (inline) 7ms 0.012% 61.85% 1811ms 3.04% Element::Element 1681ms 2.82% 64.67% 1681ms 2.82% Node::GetIndex 2ms 0.0034% 64.67% 1477ms 2.48% Element::RegisterWithNodes (inline) 882ms 1.48% 66.15% 1439ms 2.42% malloc_consolidate 19ms 0.032% 66.19% 1364ms 2.29% std::_Vector_base::_M_deallocate (inline) 1272ms 2.14% 68.32% 1357ms 2.28% tetgen::orient3d 61ms 0.1% 68.43% 1317ms 2.21% std::map::operator[] 0 0% 68.43% 1310ms 2.20% std::vector::~vector (inline) 182ms 0.31% 68.73% 1296ms 2.18% tetgen::tetgenmesh::enqueueflipface 142ms 0.24% 68.97% 1247ms 2.09% TetrahedralMesh::Clear 11ms 0.018% 68.99% 1240ms 2.08% _int_free_maybe_consolidate 42ms 0.071% 69.06% 1204ms 2.02% tetgen::tetgenmesh::locate 1ms 0.0017% 69.06% 1191ms 2.00% std::_Vector_base::~_Vector_base (inline) 0 0% 69.06% 1179ms 1.98% std::_Rb_tree::lower_bound (inline) 0 0% 69.06% 1179ms 1.98% std::map::lower_bound (inline) 1ms 0.0017% 69.06% 1172ms 1.97% VoronoiDataWriter::Visit 66ms 0.11% 69.17% 1116ms 1.87% std::vector::_M_realloc_insert 79ms 0.13% 69.31% 1105ms 1.86% tetgen::tetgenmesh::preciselocate 1084ms 1.82% 71.13% 1084ms 1.82% unlink_chunk 5ms 0.0084% 71.13% 953ms 1.60% VertexMesh::GenerateVerticesFromElementCircumcentres 6ms 0.01% 71.14% 925ms 1.55% std::_Vector_base::_M_allocate (inline) 109ms 0.18% 71.33% 906ms 1.52% std::vector::push_back (inline) 878ms 1.47% 72.80% 878ms 1.47% tetgen::tetgenmesh::triface::triface 0 0% 72.80% 787ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 645ms 1.08% 73.89% 783ms 1.32% AbstractElement::GetNodeGlobalIndex 1ms 0.0017% 73.89% 763ms 1.28% AbstractTwoBodyInteractionForce::AddForceContribution 444ms 0.75% 74.63% 756ms 1.27% tetgen::tetgenmesh::fnextself 6ms 0.01% 74.64% 723ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 716ms 1.20% 75.85% 716ms 1.20% tetgen::tetgenmesh::oppo 8ms 0.013% 75.86% 713ms 1.20% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 686ms 1.15% 77.01% 686ms 1.15% [libchaste_mesh.so] 280ms 0.47% 77.48% 683ms 1.15% AbstractElement::GetNodeLocation 25ms 0.042% 77.52% 679ms 1.14% boost::numeric::ublas::vector_assign (inline) 18ms 0.03% 77.55% 677ms 1.14% AbstractTetrahedralElement::CalculateJacobian 611ms 1.03% 78.58% 611ms 1.03% Node::rGetLocation 46ms 0.077% 78.66% 609ms 1.02% __atan2 11ms 0.018% 78.68% 606ms 1.02% boost::numeric::ublas::c_vector::c_vector (inline) 592ms 0.99% 79.67% 592ms 0.99% tetgen::tetgenmesh::triface::operator= 462ms 0.78% 80.45% 562ms 0.94% __ieee754_atan2_fma 0 0% 80.45% 530ms 0.89% std::set::find (inline) 21ms 0.035% 80.48% 500ms 0.84% Element::CalculateCircumsphere 500ms 0.84% 81.32% 500ms 0.84% std::vector::size (inline) 40ms 0.067% 81.39% 499ms 0.84% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.39% 498ms 0.84% std::insert_iterator::operator= (inline) 41ms 0.069% 81.46% 488ms 0.82% tetgen::tetgenmesh::enext2fnext 0 0% 81.46% 486ms 0.82% boost::numeric::ublas::inner_prod (inline) 9ms 0.015% 81.47% 483ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 36ms 0.06% 81.53% 477ms 0.8% tetgen::tetgenmesh::enextfnext 38ms 0.064% 81.60% 474ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0017% 81.60% 449ms 0.75% std::_Rb_tree::_M_insert_unique_ (inline) 133ms 0.22% 81.82% 436ms 0.73% boost::numeric::ublas::indexing_vector_assign 12ms 0.02% 81.84% 434ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.005% 81.85% 428ms 0.72% CellPropertyCollection::GetPropertiesType (inline) 32ms 0.054% 81.90% 415ms 0.7% tetgen::tetgenmesh::queue::push 101ms 0.17% 82.07% 414ms 0.7% __dynamic_cast 17ms 0.029% 82.10% 409ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 1ms 0.0017% 82.10% 400ms 0.67% Cell::GetCellId 395ms 0.66% 82.76% 395ms 0.66% boost::numeric::ublas::c_vector::operator() 173ms 0.29% 83.05% 386ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 384ms 0.64% 83.70% 384ms 0.64% AbstractElement::IsDeleted 0 0% 83.70% 384ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 248ms 0.42% 84.12% 382ms 0.64% tetgen::tetgenmesh::sym 265ms 0.45% 84.56% 381ms 0.64% tetgen::tetgenmesh::link::add 192ms 0.32% 84.88% 366ms 0.61% AbstractTetrahedralMesh::GetElement 21ms 0.035% 84.92% 366ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 366ms 0.61% 85.53% 366ms 0.61% tetgen::tetgenmesh::org 249ms 0.42% 85.95% 358ms 0.6% tetgen::tetgenmesh::bond 2ms 0.0034% 85.96% 354ms 0.59% AbstractCellProperty::IsSubType (inline) 16ms 0.027% 85.98% 341ms 0.57% std::vector::insert (inline) 4ms 0.0067% 85.99% 328ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.017% 86.01% 327ms 0.55% VertexElement::~VertexElement 0 0% 86.01% 327ms 0.55% tcache_get (inline) 327ms 0.55% 86.56% 327ms 0.55% tcache_get_n (inline) 153ms 0.26% 86.81% 326ms 0.55% Inverse 325ms 0.55% 87.36% 325ms 0.55% std::_Rb_tree_decrement 0 0% 87.36% 314ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 51ms 0.086% 87.44% 302ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)