File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51249ms, 87.51% of 58565ms total Dropped 820 nodes (cum <= 292.82ms) flat flat% sum% cum cum% 0 0% 0% 58499ms 99.89% __libc_start_call_main 0 0% 0% 58499ms 99.89% __libc_start_main_impl 0 0% 0% 58499ms 99.89% _start 0 0% 0% 58484ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58484ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58484ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58484ms 99.86% main 0 0% 0% 58447ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58447ms 99.80% CxxTest::TestRunner::runTest (inline) 1ms 0.0017% 0.0017% 58447ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0.0017% 58188ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0.0017% 48096ms 82.12% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0017% 48046ms 82.04% MeshBasedCellPopulation::Update 0 0% 0.0017% 27024ms 46.14% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0017% 27024ms 46.14% MeshBasedCellPopulation::TessellateIfNeeded 220ms 0.38% 0.38% 24067ms 41.09% VertexMesh::VertexMesh 0 0% 0.38% 17081ms 29.17% MutableMesh::ReMesh 0 0% 0.38% 13049ms 22.28% tetgen::tetrahedralize 1ms 0.0017% 0.38% 12908ms 22.04% tetgen::tetgenmesh::delaunizevertices 6ms 0.01% 0.39% 12904ms 22.03% tetgen::tetgenmesh::incrflipdelaunay 541ms 0.92% 1.31% 12044ms 20.57% TetrahedralMesh::EdgeIterator::operator++ 507ms 0.87% 2.18% 11450ms 19.55% tetgen::tetgenmesh::lawson 2967ms 5.07% 7.24% 9667ms 16.51% std::_Rb_tree::_M_lower_bound (inline) 28ms 0.048% 7.29% 9430ms 16.10% std::set::insert (inline) 186ms 0.32% 7.61% 8940ms 15.27% std::_Rb_tree::_M_insert_unique 337ms 0.58% 8.19% 8937ms 15.26% VertexElement::AddFace 247ms 0.42% 8.61% 8888ms 15.18% std::_Rb_tree::find (inline) 0 0% 8.61% 8311ms 14.19% std::set::count (inline) 104ms 0.18% 8.79% 6306ms 10.77% std::less::operator() (inline) 6260ms 10.69% 19.47% 6260ms 10.69% std::operator< (inline) 5713ms 9.75% 29.23% 5713ms 9.75% std::_Rb_tree_increment 0 0% 29.23% 5356ms 9.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 286ms 0.49% 29.72% 5354ms 9.14% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0017% 29.72% 5229ms 8.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 29.72% 5202ms 8.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 175ms 0.3% 30.02% 4811ms 8.21% operator new 0 0% 30.02% 4577ms 7.82% AbstractCellPopulation::WriteResultsToFiles 1056ms 1.80% 31.82% 4552ms 7.77% __GI___libc_malloc 6ms 0.01% 31.83% 4295ms 7.33% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.015% 31.85% 4292ms 7.33% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.015% 31.86% 4160ms 7.10% MeshBasedCellPopulation::SpringIterator::operator++ 37ms 0.063% 31.93% 4145ms 7.08% std::__new_allocator::allocate (inline) 0 0% 31.93% 4127ms 7.05% std::allocator_traits::allocate (inline) 6ms 0.01% 31.94% 3980ms 6.80% std::_Rb_tree::~_Rb_tree (inline) 1483ms 2.53% 34.47% 3972ms 6.78% std::_Rb_tree::_M_erase 0 0% 34.47% 3918ms 6.69% std::set::~set (inline) 1182ms 2.02% 36.49% 3714ms 6.34% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.0051% 36.49% 3508ms 5.99% std::set_intersection (inline) 234ms 0.4% 36.89% 3505ms 5.98% std::__set_intersection 119ms 0.2% 37.10% 3499ms 5.97% tetgen::tetgenmesh::insphere_sos 1007ms 1.72% 38.81% 3455ms 5.90% __GI___libc_free 239ms 0.41% 39.22% 3417ms 5.83% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 28ms 0.048% 39.27% 3379ms 5.77% Node::AddElement 3055ms 5.22% 44.49% 3365ms 5.75% tetgen::insphere 0 0% 44.49% 3291ms 5.62% std::_Rb_tree::_M_create_node (inline) 0 0% 44.49% 3259ms 5.56% std::_Rb_tree::_Alloc_node::operator() (inline) 3259ms 5.56% 50.05% 3259ms 5.56% std::_Rb_tree::_S_right (inline) 0 0% 50.05% 3244ms 5.54% std::_Rb_tree::_M_get_node (inline) 7ms 0.012% 50.06% 3240ms 5.53% TetrahedralMesh::ImportFromMesher 5ms 0.0085% 50.07% 3228ms 5.51% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0034% 50.08% 3185ms 5.44% std::_Rb_tree_iterator::operator++ (inline) 2355ms 4.02% 54.10% 3128ms 5.34% _int_malloc 115ms 0.2% 54.29% 3112ms 5.31% std::__new_allocator::deallocate (inline) 0 0% 54.29% 3093ms 5.28% std::allocator_traits::deallocate (inline) 0 0% 54.29% 2979ms 5.09% VertexMesh::~VertexMesh 191ms 0.33% 54.62% 2819ms 4.81% std::_Rb_tree_const_iterator::operator++ (inline) 195ms 0.33% 54.95% 2690ms 4.59% tetgen::tetgenmesh::flip23 1179ms 2.01% 56.97% 2445ms 4.17% _int_free 68ms 0.12% 57.08% 2424ms 4.14% MutableElement::AddNode 138ms 0.24% 57.32% 2143ms 3.66% Node::~Node 156ms 0.27% 57.58% 1976ms 3.37% VertexMesh::Clear 177ms 0.3% 57.89% 1975ms 3.37% tetgen::tetgenmesh::flip32 1886ms 3.22% 61.11% 1886ms 3.22% std::_Rb_tree_insert_and_rebalance 0 0% 61.11% 1844ms 3.15% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.11% 1830ms 3.12% std::_Rb_tree::_M_put_node (inline) 3ms 0.0051% 61.11% 1753ms 2.99% Element::Element 1550ms 2.65% 63.76% 1550ms 2.65% Node::GetIndex 1395ms 2.38% 66.14% 1488ms 2.54% tetgen::orient3d 3ms 0.0051% 66.15% 1410ms 2.41% Element::RegisterWithNodes (inline) 219ms 0.37% 66.52% 1324ms 2.26% tetgen::tetgenmesh::enqueueflipface 67ms 0.11% 66.63% 1281ms 2.19% std::map::operator[] 14ms 0.024% 66.66% 1277ms 2.18% std::_Vector_base::_M_deallocate (inline) 755ms 1.29% 67.95% 1267ms 2.16% malloc_consolidate 37ms 0.063% 68.01% 1245ms 2.13% tetgen::tetgenmesh::locate 0 0% 68.01% 1201ms 2.05% std::vector::~vector (inline) 154ms 0.26% 68.27% 1172ms 2.00% TetrahedralMesh::Clear 93ms 0.16% 68.43% 1168ms 1.99% tetgen::tetgenmesh::preciselocate 0 0% 68.43% 1152ms 1.97% std::_Rb_tree::lower_bound (inline) 0 0% 68.43% 1152ms 1.97% std::map::lower_bound (inline) 0 0% 68.43% 1108ms 1.89% VoronoiDataWriter::Visit 0 0% 68.43% 1098ms 1.87% std::_Vector_base::~_Vector_base (inline) 11ms 0.019% 68.45% 1087ms 1.86% _int_free_maybe_consolidate 64ms 0.11% 68.56% 1062ms 1.81% std::vector::_M_realloc_insert 958ms 1.64% 70.20% 958ms 1.64% tetgen::tetgenmesh::triface::triface 956ms 1.63% 71.83% 956ms 1.63% unlink_chunk 3ms 0.0051% 71.83% 906ms 1.55% VertexMesh::GenerateVerticesFromElementCircumcentres 125ms 0.21% 72.05% 898ms 1.53% std::vector::push_back (inline) 1ms 0.0017% 72.05% 884ms 1.51% std::_Vector_base::_M_allocate (inline) 1ms 0.0017% 72.05% 783ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 587ms 1.00% 73.05% 759ms 1.30% AbstractElement::GetNodeGlobalIndex 1ms 0.0017% 73.05% 740ms 1.26% AbstractTwoBodyInteractionForce::AddForceContribution 732ms 1.25% 74.30% 732ms 1.25% tetgen::tetgenmesh::triface::operator= 7ms 0.012% 74.32% 717ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 321ms 0.55% 74.86% 713ms 1.22% tetgen::tetgenmesh::fnextself 11ms 0.019% 74.88% 681ms 1.16% boost::numeric::ublas::vector_assign (inline) 7ms 0.012% 74.89% 680ms 1.16% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 18ms 0.031% 74.93% 668ms 1.14% AbstractTetrahedralElement::CalculateJacobian 13ms 0.022% 74.95% 642ms 1.10% boost::numeric::ublas::c_vector::c_vector (inline) 246ms 0.42% 75.37% 623ms 1.06% AbstractElement::GetNodeLocation 42ms 0.072% 75.44% 612ms 1.04% __atan2 607ms 1.04% 76.48% 607ms 1.04% [libchaste_mesh.so] 576ms 0.98% 77.46% 576ms 0.98% tetgen::tetgenmesh::oppo 0 0% 77.46% 571ms 0.97% std::set::find (inline) 475ms 0.81% 78.27% 570ms 0.97% __ieee754_atan2_fma 560ms 0.96% 79.23% 560ms 0.96% Node::rGetLocation 0 0% 79.23% 523ms 0.89% boost::numeric::ublas::inner_prod (inline) 5ms 0.0085% 79.24% 520ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 38ms 0.065% 79.30% 515ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 512ms 0.87% 80.17% 512ms 0.87% std::vector::size (inline) 55ms 0.094% 80.27% 501ms 0.86% tetgen::tetgenmesh::enext2fnext 24ms 0.041% 80.31% 491ms 0.84% Element::CalculateCircumsphere 342ms 0.58% 80.89% 490ms 0.84% tetgen::tetgenmesh::sym 43ms 0.073% 80.97% 484ms 0.83% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.97% 482ms 0.82% std::insert_iterator::operator= (inline) 115ms 0.2% 81.16% 451ms 0.77% boost::numeric::ublas::indexing_vector_assign 48ms 0.082% 81.24% 450ms 0.77% tetgen::tetgenmesh::enextfnext 1ms 0.0017% 81.25% 432ms 0.74% std::_Rb_tree::_M_insert_unique_ (inline) 175ms 0.3% 81.55% 422ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 419ms 0.72% 82.26% 419ms 0.72% boost::numeric::ublas::c_vector::operator() 226ms 0.39% 82.65% 403ms 0.69% AbstractTetrahedralMesh::GetElement 25ms 0.043% 82.69% 399ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 22ms 0.038% 82.73% 395ms 0.67% tetgen::tetgenmesh::queue::push 391ms 0.67% 83.39% 391ms 0.67% AbstractElement::IsDeleted 2ms 0.0034% 83.40% 391ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.40% 388ms 0.66% VertexMeshWriter::WriteVtkUsingMesh 380ms 0.65% 84.05% 380ms 0.65% tetgen::tetgenmesh::org 3ms 0.0051% 84.05% 377ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 11ms 0.019% 84.07% 375ms 0.64% std::_Rb_tree_iterator::operator-- (inline) 302ms 0.52% 84.59% 373ms 0.64% tetgen::tetgenmesh::link::add 3ms 0.0051% 84.59% 372ms 0.64% Cell::GetCellId 97ms 0.17% 84.76% 368ms 0.63% __dynamic_cast 269ms 0.46% 85.22% 346ms 0.59% tetgen::tetgenmesh::bond 5ms 0.0085% 85.22% 340ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 150ms 0.26% 85.48% 340ms 0.58% Inverse 336ms 0.57% 86.05% 336ms 0.57% std::_Rb_tree_decrement 0 0% 86.05% 328ms 0.56% tcache_get (inline) 328ms 0.56% 86.61% 328ms 0.56% tcache_get_n (inline) 328ms 0.56% 87.17% 328ms 0.56% tetgen::tetgenmesh::pointmark 61ms 0.1% 87.28% 323ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 7ms 0.012% 87.29% 310ms 0.53% VertexElement::~VertexElement 13ms 0.022% 87.31% 310ms 0.53% std::vector::insert (inline) 32ms 0.055% 87.37% 310ms 0.53% tetgen::insphereadapt 0 0% 87.37% 306ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.0017% 87.37% 301ms 0.51% AbstractCellProperty::IsSubType (inline) 81ms 0.14% 87.51% 298ms 0.51% tetgen::tetgenmesh::queue::pop