File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 41226ms, 85.68% of 48116ms total Dropped 854 nodes (cum <= 240.58ms) flat flat% sum% cum cum% 0 0% 0% 48063ms 99.89% __libc_start_call_main 0 0% 0% 48063ms 99.89% __libc_start_main_impl 0 0% 0% 48063ms 99.89% _start 0 0% 0% 48050ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 48050ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 48050ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 48050ms 99.86% main 0 0% 0% 48012ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 48012ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 48012ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 47797ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 40591ms 84.36% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 40555ms 84.29% MeshBasedCellPopulation::Update 0 0% 0% 21932ms 45.58% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 21932ms 45.58% MeshBasedCellPopulation::TessellateIfNeeded 170ms 0.35% 0.35% 19535ms 40.60% VertexMesh::VertexMesh 0 0% 0.35% 15455ms 32.12% MutableMesh::ReMesh 1ms 0.0021% 0.36% 12356ms 25.68% tetgen::tetrahedralize 2ms 0.0042% 0.36% 12239ms 25.44% tetgen::tetgenmesh::delaunizevertices 4ms 0.0083% 0.37% 12232ms 25.42% tetgen::tetgenmesh::incrflipdelaunay 381ms 0.79% 1.16% 10903ms 22.66% tetgen::tetgenmesh::lawson 465ms 0.97% 2.13% 9547ms 19.84% TetrahedralMesh::EdgeIterator::operator++ 21ms 0.044% 2.17% 7643ms 15.88% std::set::insert (inline) 284ms 0.59% 2.76% 7566ms 15.72% VertexElement::AddFace 185ms 0.38% 3.14% 7316ms 15.20% std::_Rb_tree::_M_insert_unique 2463ms 5.12% 8.26% 7128ms 14.81% std::_Rb_tree::_M_lower_bound (inline) 206ms 0.43% 8.69% 6685ms 13.89% std::_Rb_tree::find (inline) 0 0% 8.69% 6222ms 12.93% std::set::count (inline) 94ms 0.2% 8.89% 4480ms 9.31% std::less::operator() (inline) 4428ms 9.20% 18.09% 4428ms 9.20% std::operator< (inline) 237ms 0.49% 18.58% 4378ms 9.10% std::_Rb_tree::_M_insert_ (inline) 0 0% 18.58% 4255ms 8.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.58% 4149ms 8.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0042% 18.59% 4132ms 8.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 133ms 0.28% 18.86% 3967ms 8.24% operator new 3958ms 8.23% 27.09% 3958ms 8.23% std::_Rb_tree_increment 948ms 1.97% 29.06% 3772ms 7.84% __GI___libc_malloc 22ms 0.046% 29.10% 3453ms 7.18% std::__new_allocator::allocate (inline) 0 0% 29.10% 3451ms 7.17% MeshBasedCellPopulation::UpdateNodePairs 0 0% 29.10% 3433ms 7.13% std::allocator_traits::allocate (inline) 9ms 0.019% 29.12% 3406ms 7.08% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.0083% 29.13% 3365ms 6.99% std::_Rb_tree::~_Rb_tree (inline) 1154ms 2.40% 31.53% 3359ms 6.98% std::_Rb_tree::_M_erase 0 0% 31.53% 3339ms 6.94% std::set::~set (inline) 11ms 0.023% 31.55% 3321ms 6.90% MeshBasedCellPopulation::SpringIterator::operator++ 972ms 2.02% 33.57% 3091ms 6.42% __GI___libc_free 976ms 2.03% 35.60% 2960ms 6.15% std::_Rb_tree::_M_get_insert_unique_pos 86ms 0.18% 35.78% 2949ms 6.13% tetgen::tetgenmesh::insphere_sos 2ms 0.0042% 35.78% 2929ms 6.09% std::set_intersection (inline) 190ms 0.39% 36.18% 2927ms 6.08% std::__set_intersection 2615ms 5.43% 41.61% 2843ms 5.91% tetgen::insphere 0 0% 41.61% 2831ms 5.88% AbstractCellPopulation::WriteResultsToFiles 0 0% 41.61% 2792ms 5.80% std::_Rb_tree::_M_create_node (inline) 0 0% 41.61% 2773ms 5.76% std::_Rb_tree::_M_get_node (inline) 0 0% 41.61% 2764ms 5.74% std::_Rb_tree::_Alloc_node::operator() (inline) 98ms 0.2% 41.82% 2724ms 5.66% std::__new_allocator::deallocate (inline) 0 0% 41.82% 2711ms 5.63% std::allocator_traits::deallocate (inline) 123ms 0.26% 42.07% 2710ms 5.63% tetgen::tetgenmesh::flip23 1854ms 3.85% 45.93% 2551ms 5.30% _int_malloc 4ms 0.0083% 45.93% 2514ms 5.22% TetrahedralMesh::ImportFromMesher 2460ms 5.11% 51.05% 2460ms 5.11% std::_Rb_tree::_S_right (inline) 23ms 0.048% 51.10% 2451ms 5.09% Node::AddElement 0 0% 51.10% 2415ms 5.02% VertexMesh::~VertexMesh 128ms 0.27% 51.36% 2408ms 5.00% std::_Rb_tree_const_iterator::operator++ (inline) 1055ms 2.19% 53.55% 2114ms 4.39% _int_free 41ms 0.085% 53.64% 1974ms 4.10% MutableElement::AddNode 4ms 0.0083% 53.65% 1932ms 4.02% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 139ms 0.29% 53.94% 1907ms 3.96% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 89ms 0.18% 54.12% 1906ms 3.96% tetgen::tetgenmesh::flip32 107ms 0.22% 54.34% 1872ms 3.89% Node::~Node 0 0% 54.34% 1775ms 3.69% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.34% 1700ms 3.53% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.34% 1693ms 3.52% std::_Rb_tree::_M_put_node (inline) 118ms 0.25% 54.59% 1624ms 3.38% VertexMesh::Clear 173ms 0.36% 54.95% 1492ms 3.10% tetgen::tetgenmesh::enqueueflipface 1420ms 2.95% 57.90% 1420ms 2.95% std::_Rb_tree_insert_and_rebalance 1217ms 2.53% 60.43% 1276ms 2.65% tetgen::orient3d 1240ms 2.58% 63.01% 1240ms 2.58% Node::GetIndex 78ms 0.16% 63.17% 1155ms 2.40% TetrahedralMesh::Clear 3ms 0.0062% 63.17% 1121ms 2.33% Element::Element 23ms 0.048% 63.22% 1101ms 2.29% tetgen::tetgenmesh::locate 27ms 0.056% 63.28% 1045ms 2.17% std::_Vector_base::_M_deallocate (inline) 65ms 0.14% 63.41% 1036ms 2.15% tetgen::tetgenmesh::preciselocate 657ms 1.37% 64.78% 1030ms 2.14% malloc_consolidate 0 0% 64.78% 1008ms 2.09% std::vector::~vector (inline) 70ms 0.15% 64.92% 930ms 1.93% std::map::operator[] 2ms 0.0042% 64.93% 906ms 1.88% std::_Vector_base::~_Vector_base (inline) 5ms 0.01% 64.94% 870ms 1.81% _int_free_maybe_consolidate 2ms 0.0042% 64.94% 862ms 1.79% Element::RegisterWithNodes (inline) 47ms 0.098% 65.04% 852ms 1.77% std::vector::_M_realloc_insert 844ms 1.75% 66.79% 844ms 1.75% tetgen::tetgenmesh::oppo 838ms 1.74% 68.54% 838ms 1.74% unlink_chunk 0 0% 68.54% 796ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 68.54% 796ms 1.65% std::map::lower_bound (inline) 599ms 1.24% 69.78% 741ms 1.54% AbstractElement::GetNodeGlobalIndex 718ms 1.49% 71.27% 718ms 1.49% tetgen::tetgenmesh::triface::triface 0 0% 71.27% 706ms 1.47% VoronoiDataWriter::Visit 4ms 0.0083% 71.28% 664ms 1.38% std::_Vector_base::_M_allocate (inline) 88ms 0.18% 71.46% 664ms 1.38% std::vector::push_back (inline) 4ms 0.0083% 71.47% 645ms 1.34% VertexMesh::GenerateVerticesFromElementCircumcentres 636ms 1.32% 72.79% 636ms 1.32% [libchaste_mesh.so] 222ms 0.46% 73.26% 608ms 1.26% tetgen::tetgenmesh::sym 0 0% 73.26% 598ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 570ms 1.18% 74.44% 570ms 1.18% tetgen::tetgenmesh::triface::operator= 0 0% 74.44% 569ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.023% 74.46% 559ms 1.16% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.019% 74.48% 533ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.0083% 74.49% 496ms 1.03% boost::numeric::ublas::vector_assign (inline) 25ms 0.052% 74.54% 492ms 1.02% tetgen::tetgenmesh::queue::push 297ms 0.62% 75.16% 482ms 1.00% tetgen::tetgenmesh::fnextself 6ms 0.012% 75.17% 476ms 0.99% AbstractTetrahedralElement::CalculateJacobian 38ms 0.079% 75.25% 470ms 0.98% __atan2 284ms 0.59% 75.84% 467ms 0.97% tetgen::tetgenmesh::link::add 5ms 0.01% 75.85% 466ms 0.97% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 75.85% 463ms 0.96% std::set::find (inline) 187ms 0.39% 76.24% 453ms 0.94% tetgen::tetgenmesh::bond 56ms 0.12% 76.36% 451ms 0.94% tetgen::tetgenmesh::enext2fnext 50ms 0.1% 76.46% 442ms 0.92% tetgen::tetgenmesh::enextfnext 204ms 0.42% 76.89% 435ms 0.9% AbstractElement::GetNodeLocation 429ms 0.89% 77.78% 429ms 0.89% Node::rGetLocation 335ms 0.7% 78.47% 425ms 0.88% __ieee754_atan2_fma 408ms 0.85% 79.32% 408ms 0.85% tetgen::tetgenmesh::decode 0 0% 79.32% 395ms 0.82% boost::numeric::ublas::inner_prod (inline) 1ms 0.0021% 79.32% 393ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 41ms 0.085% 79.41% 392ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 391ms 0.81% 80.22% 391ms 0.81% std::vector::size (inline) 376ms 0.78% 81.00% 376ms 0.78% tetgen::tetgenmesh::pointmark 370ms 0.77% 81.77% 370ms 0.77% tetgen::tetgenmesh::org 369ms 0.77% 82.54% 369ms 0.77% AbstractElement::IsDeleted 173ms 0.36% 82.90% 352ms 0.73% AbstractTetrahedralMesh::GetElement 81ms 0.17% 83.07% 349ms 0.73% __dynamic_cast 0 0% 83.07% 347ms 0.72% std::insert_iterator::operator= (inline) 17ms 0.035% 83.10% 343ms 0.71% Element::CalculateCircumsphere 39ms 0.081% 83.18% 342ms 0.71% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0042% 83.19% 339ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0042% 83.19% 322ms 0.67% Cell::GetCellId 23ms 0.048% 83.24% 314ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 8ms 0.017% 83.26% 312ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.26% 310ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0042% 83.26% 304ms 0.63% VertexElement::~VertexElement 0 0% 83.26% 302ms 0.63% std::_Rb_tree::_M_insert_unique_ (inline) 126ms 0.26% 83.52% 297ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 17ms 0.035% 83.56% 297ms 0.62% std::vector::insert (inline) 68ms 0.14% 83.70% 296ms 0.62% boost::numeric::ublas::indexing_vector_assign 292ms 0.61% 84.30% 292ms 0.61% boost::numeric::ublas::c_vector::operator() 0 0% 84.30% 289ms 0.6% AbstractCellProperty::IsSubType (inline) 4ms 0.0083% 84.31% 284ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 277ms 0.58% 84.89% 277ms 0.58% std::_Rb_tree_decrement 88ms 0.18% 85.07% 272ms 0.57% Inverse 5ms 0.01% 85.08% 257ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.08% 256ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 253ms 0.53% 85.61% 253ms 0.53% tetgen::tetgenmesh::encode 1ms 0.0021% 85.61% 250ms 0.52% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 1ms 0.0021% 85.61% 250ms 0.52% Element::~Element 33ms 0.069% 85.68% 244ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)