File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51198ms, 87.86% of 58275ms total Dropped 826 nodes (cum <= 291.38ms) flat flat% sum% cum cum% 0 0% 0% 58230ms 99.92% __libc_start_call_main 0 0% 0% 58230ms 99.92% __libc_start_main_impl 0 0% 0% 58230ms 99.92% _start 0 0% 0% 58216ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58216ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58216ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58216ms 99.90% main 0 0% 0% 58177ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58177ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58177ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57940ms 99.43% AbstractCellBasedSimulation::Solve 0 0% 0% 50288ms 86.29% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50247ms 86.22% MeshBasedCellPopulation::Update 0 0% 0% 29779ms 51.10% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 29778ms 51.10% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 198ms 0.34% 0.34% 25595ms 43.92% VertexMesh::VertexMesh 0 0% 0.34% 17011ms 29.19% MutableMesh::ReMesh 0 0% 0.34% 12642ms 21.69% tetgen::tetrahedralize 0 0% 0.34% 12525ms 21.49% tetgen::tetgenmesh::delaunizevertices 5ms 0.0086% 0.35% 12521ms 21.49% tetgen::tetgenmesh::incrflipdelaunay 398ms 0.68% 1.03% 11216ms 19.25% tetgen::tetgenmesh::lawson 498ms 0.85% 1.89% 10991ms 18.86% TetrahedralMesh::EdgeIterator::operator++ 24ms 0.041% 1.93% 10025ms 17.20% std::set::insert (inline) 163ms 0.28% 2.21% 9704ms 16.65% std::_Rb_tree::_M_insert_unique 391ms 0.67% 2.88% 8773ms 15.05% VertexElement::AddFace 2514ms 4.31% 7.19% 7590ms 13.02% std::_Rb_tree::_M_lower_bound (inline) 227ms 0.39% 7.58% 7128ms 12.23% std::_Rb_tree::find (inline) 0 0% 7.58% 6658ms 11.43% std::set::count (inline) 253ms 0.43% 8.02% 5739ms 9.85% std::_Rb_tree::_M_insert_ (inline) 5687ms 9.76% 17.77% 5687ms 9.76% std::_Rb_tree_increment 124ms 0.21% 17.99% 5579ms 9.57% operator new 992ms 1.70% 19.69% 5400ms 9.27% __GI___libc_malloc 92ms 0.16% 19.85% 4889ms 8.39% std::less::operator() (inline) 3ms 0.0051% 19.85% 4865ms 8.35% std::set_intersection (inline) 283ms 0.49% 20.34% 4862ms 8.34% std::__set_intersection 4842ms 8.31% 28.65% 4842ms 8.31% std::operator< (inline) 0 0% 28.65% 4675ms 8.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.65% 4540ms 7.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0069% 28.65% 4518ms 7.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 31ms 0.053% 28.71% 4496ms 7.72% std::__new_allocator::allocate (inline) 0 0% 28.71% 4479ms 7.69% std::allocator_traits::allocate (inline) 44ms 0.076% 28.78% 4378ms 7.51% Node::AddElement 1187ms 2.04% 30.82% 4281ms 7.35% __GI___libc_free 5ms 0.0086% 30.83% 4258ms 7.31% std::_Rb_tree::~_Rb_tree (inline) 1648ms 2.83% 33.66% 4252ms 7.30% std::_Rb_tree::_M_erase 0 0% 33.66% 4217ms 7.24% VertexMesh::~VertexMesh 133ms 0.23% 33.88% 4215ms 7.23% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 33.88% 4195ms 7.20% std::set::~set (inline) 3074ms 5.27% 39.16% 4150ms 7.12% _int_malloc 1164ms 2.00% 41.16% 3991ms 6.85% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.0051% 41.16% 3781ms 6.49% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0017% 41.16% 3772ms 6.47% MeshBasedCellPopulation::UpdateNodePairs 0 0% 41.16% 3712ms 6.37% std::_Rb_tree::_M_create_node (inline) 85ms 0.15% 41.31% 3707ms 6.36% std::__new_allocator::deallocate (inline) 0 0% 41.31% 3699ms 6.35% std::allocator_traits::deallocate (inline) 0 0% 41.31% 3683ms 6.32% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.31% 3664ms 6.29% std::_Rb_tree::_M_get_node (inline) 12ms 0.021% 41.33% 3638ms 6.24% MeshBasedCellPopulation::SpringIterator::operator++ 3552ms 6.10% 47.43% 3552ms 6.10% std::_Rb_tree::_S_right (inline) 5ms 0.0086% 47.43% 3533ms 6.06% TetrahedralMesh::ImportFromMesher 49ms 0.084% 47.52% 3233ms 5.55% MutableElement::AddNode 1113ms 1.91% 49.43% 3093ms 5.31% _int_free 83ms 0.14% 49.57% 3030ms 5.20% tetgen::tetgenmesh::insphere_sos 2694ms 4.62% 54.19% 2938ms 5.04% tetgen::insphere 0 0% 54.19% 2833ms 4.86% AbstractCellPopulation::WriteResultsToFiles 103ms 0.18% 54.37% 2793ms 4.79% tetgen::tetgenmesh::flip23 191ms 0.33% 54.70% 2755ms 4.73% Node::~Node 179ms 0.31% 55.00% 2555ms 4.38% VertexMesh::Clear 1425ms 2.45% 57.45% 2005ms 3.44% malloc_consolidate 103ms 0.18% 57.63% 1979ms 3.40% tetgen::tetgenmesh::flip32 19ms 0.033% 57.66% 1920ms 3.29% std::_Vector_base::_M_deallocate (inline) 1896ms 3.25% 60.91% 1896ms 3.25% Node::GetIndex 0 0% 60.91% 1878ms 3.22% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1859ms 3.19% 64.10% 1859ms 3.19% std::_Rb_tree_insert_and_rebalance 0 0% 64.10% 1840ms 3.16% std::vector::~vector (inline) 153ms 0.26% 64.37% 1836ms 3.15% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 64.37% 1808ms 3.10% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.37% 1798ms 3.09% std::_Rb_tree::_M_put_node (inline) 5ms 0.0086% 64.37% 1792ms 3.08% Element::Element 2ms 0.0034% 64.38% 1781ms 3.06% std::_Vector_base::~_Vector_base (inline) 7ms 0.012% 64.39% 1759ms 3.02% _int_free_maybe_consolidate 3ms 0.0051% 64.39% 1703ms 2.92% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0034% 64.40% 1525ms 2.62% Element::RegisterWithNodes (inline) 168ms 0.29% 64.69% 1438ms 2.47% tetgen::tetgenmesh::enqueueflipface 1394ms 2.39% 67.08% 1394ms 2.39% unlink_chunk 73ms 0.13% 67.20% 1322ms 2.27% TetrahedralMesh::Clear 1171ms 2.01% 69.21% 1232ms 2.11% tetgen::orient3d 1017ms 1.75% 70.96% 1205ms 2.07% AbstractElement::GetNodeGlobalIndex 1ms 0.0017% 70.96% 1184ms 2.03% VertexMesh::GenerateVerticesFromElementCircumcentres 26ms 0.045% 71.00% 1052ms 1.81% tetgen::tetgenmesh::locate 50ms 0.086% 71.09% 986ms 1.69% std::vector::_M_realloc_insert 80ms 0.14% 71.23% 979ms 1.68% tetgen::tetgenmesh::preciselocate 57ms 0.098% 71.33% 949ms 1.63% std::map::operator[] 858ms 1.47% 72.80% 858ms 1.47% tetgen::tetgenmesh::triface::triface 836ms 1.43% 74.23% 836ms 1.43% tetgen::tetgenmesh::oppo 106ms 0.18% 74.41% 834ms 1.43% std::vector::push_back (inline) 0 0% 74.41% 823ms 1.41% std::_Rb_tree::lower_bound (inline) 0 0% 74.41% 823ms 1.41% std::map::lower_bound (inline) 3ms 0.0051% 74.42% 818ms 1.40% std::_Vector_base::_M_allocate (inline) 0 0% 74.42% 808ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 781ms 1.34% 75.76% 781ms 1.34% AbstractElement::IsDeleted 1ms 0.0017% 75.76% 754ms 1.29% VoronoiDataWriter::Visit 382ms 0.66% 76.42% 745ms 1.28% AbstractElement::GetNodeLocation 5ms 0.0086% 76.43% 666ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 243ms 0.42% 76.84% 654ms 1.12% tetgen::tetgenmesh::sym 651ms 1.12% 77.96% 651ms 1.12% Node::rGetLocation 640ms 1.10% 79.06% 640ms 1.10% [libchaste_mesh.so] 15ms 0.026% 79.08% 625ms 1.07% AbstractTetrahedralElement::CalculateJacobian 3ms 0.0051% 79.09% 576ms 0.99% AbstractTwoBodyInteractionForce::AddForceContribution 562ms 0.96% 80.05% 562ms 0.96% std::vector::size (inline) 303ms 0.52% 80.57% 561ms 0.96% tetgen::tetgenmesh::fnextself 554ms 0.95% 81.52% 554ms 0.95% tetgen::tetgenmesh::triface::operator= 194ms 0.33% 81.86% 539ms 0.92% tetgen::tetgenmesh::bond 8ms 0.014% 81.87% 529ms 0.91% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 14ms 0.024% 81.89% 524ms 0.9% Element::CalculateCircumsphere 12ms 0.021% 81.92% 510ms 0.88% boost::numeric::ublas::vector_assign (inline) 9ms 0.015% 81.93% 509ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 44ms 0.076% 82.01% 492ms 0.84% tetgen::tetgenmesh::enextfnext 48ms 0.082% 82.09% 487ms 0.84% tetgen::tetgenmesh::enext2fnext 39ms 0.067% 82.16% 473ms 0.81% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.16% 465ms 0.8% std::set::find (inline) 26ms 0.045% 82.20% 450ms 0.77% tetgen::tetgenmesh::queue::push 37ms 0.063% 82.26% 448ms 0.77% __atan2 251ms 0.43% 82.69% 424ms 0.73% tetgen::tetgenmesh::link::add 416ms 0.71% 83.41% 416ms 0.71% tetgen::tetgenmesh::decode 331ms 0.57% 83.98% 410ms 0.7% __ieee754_atan2_fma 0 0% 83.98% 404ms 0.69% boost::numeric::ublas::inner_prod (inline) 36ms 0.062% 84.04% 404ms 0.69% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.04% 404ms 0.69% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 402ms 0.69% 84.73% 402ms 0.69% tetgen::tetgenmesh::org 28ms 0.048% 84.78% 386ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 9ms 0.015% 84.79% 355ms 0.61% VertexElement::~VertexElement 166ms 0.28% 85.08% 352ms 0.6% AbstractTetrahedralMesh::GetElement 19ms 0.033% 85.11% 348ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 345ms 0.59% 85.70% 345ms 0.59% tetgen::tetgenmesh::pointmark 0 0% 85.70% 339ms 0.58% std::insert_iterator::operator= (inline) 337ms 0.58% 86.28% 337ms 0.58% tetgen::tetgenmesh::encode 0 0% 86.28% 333ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.0086% 86.29% 329ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 141ms 0.24% 86.53% 319ms 0.55% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 86.53% 314ms 0.54% VertexMeshWriter::WriteVtkUsingMesh 73ms 0.13% 86.65% 314ms 0.54% __dynamic_cast 82ms 0.14% 86.80% 313ms 0.54% boost::numeric::ublas::indexing_vector_assign 313ms 0.54% 87.33% 313ms 0.54% std::_Rb_tree_decrement 3ms 0.0051% 87.34% 309ms 0.53% Cell::GetCellId 9ms 0.015% 87.35% 299ms 0.51% boost::numeric::ublas::c_vector::operator= (inline) 293ms 0.5% 87.86% 293ms 0.5% boost::numeric::ublas::c_vector::operator() 0 0% 87.86% 292ms 0.5% std::_Rb_tree::_M_insert_unique_ (inline)