File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 68445ms, 87.49% of 78235ms total Dropped 888 nodes (cum <= 391.18ms) flat flat% sum% cum cum% 0 0% 0% 78165ms 99.91% __libc_start_call_main 0 0% 0% 78165ms 99.91% __libc_start_main_impl 0 0% 0% 78165ms 99.91% _start 0 0% 0% 78147ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 78147ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 78147ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 78147ms 99.89% main 0 0% 0% 78108ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 78108ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 78108ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 77781ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 66714ms 85.27% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 66668ms 85.22% MeshBasedCellPopulation::Update 0 0% 0% 40091ms 51.24% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 40091ms 51.24% MeshBasedCellPopulation::TessellateIfNeeded 337ms 0.43% 0.43% 34822ms 44.51% VertexMesh::VertexMesh 0 0% 0.43% 21590ms 27.60% MutableMesh::ReMesh 1ms 0.0013% 0.43% 16210ms 20.72% tetgen::tetrahedralize 1ms 0.0013% 0.43% 16064ms 20.53% tetgen::tetgenmesh::delaunizevertices 8ms 0.01% 0.44% 16056ms 20.52% tetgen::tetgenmesh::incrflipdelaunay 615ms 0.79% 1.23% 15437ms 19.73% TetrahedralMesh::EdgeIterator::operator++ 496ms 0.63% 1.86% 14281ms 18.25% tetgen::tetgenmesh::lawson 40ms 0.051% 1.91% 12796ms 16.36% std::set::insert (inline) 234ms 0.3% 2.21% 12337ms 15.77% std::_Rb_tree::_M_insert_unique 487ms 0.62% 2.84% 11578ms 14.80% VertexElement::AddFace 3282ms 4.20% 7.03% 11362ms 14.52% std::_Rb_tree::_M_lower_bound (inline) 270ms 0.35% 7.38% 10536ms 13.47% std::_Rb_tree::find (inline) 0 0% 7.38% 9968ms 12.74% std::set::count (inline) 8317ms 10.63% 18.01% 8317ms 10.63% std::_Rb_tree_increment 108ms 0.14% 18.15% 7649ms 9.78% std::less::operator() (inline) 7603ms 9.72% 27.86% 7603ms 9.72% std::operator< (inline) 169ms 0.22% 28.08% 7221ms 9.23% operator new 321ms 0.41% 28.49% 7196ms 9.20% std::_Rb_tree::_M_insert_ (inline) 1340ms 1.71% 30.20% 6977ms 8.92% __GI___libc_malloc 2ms 0.0026% 30.21% 6535ms 8.35% std::set_intersection (inline) 337ms 0.43% 30.64% 6533ms 8.35% std::__set_intersection 0 0% 30.64% 6480ms 8.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.64% 6286ms 8.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0038% 30.64% 6268ms 8.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 50ms 0.064% 30.70% 5838ms 7.46% std::__new_allocator::allocate (inline) 0 0% 30.70% 5813ms 7.43% std::allocator_traits::allocate (inline) 191ms 0.24% 30.95% 5698ms 7.28% std::_Rb_tree_const_iterator::operator++ (inline) 62ms 0.079% 31.03% 5527ms 7.06% Node::AddElement 1438ms 1.84% 32.87% 5471ms 6.99% __GI___libc_free 7ms 0.0089% 32.87% 5372ms 6.87% std::_Rb_tree::~_Rb_tree (inline) 2114ms 2.70% 35.58% 5364ms 6.86% std::_Rb_tree::_M_erase 0 0% 35.58% 5332ms 6.82% MeshBasedCellPopulation::UpdateNodePairs 0 0% 35.58% 5330ms 6.81% VertexMesh::~VertexMesh 0 0% 35.58% 5301ms 6.78% std::set::~set (inline) 3851ms 4.92% 40.50% 5243ms 6.70% _int_malloc 6ms 0.0077% 40.51% 5234ms 6.69% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1425ms 1.82% 42.33% 5181ms 6.62% std::_Rb_tree::_M_get_insert_unique_pos 19ms 0.024% 42.35% 5140ms 6.57% MeshBasedCellPopulation::SpringIterator::operator++ 4883ms 6.24% 48.59% 4883ms 6.24% std::_Rb_tree::_S_right (inline) 0 0% 48.59% 4680ms 5.98% std::_Rb_tree::_M_create_node (inline) 117ms 0.15% 48.74% 4672ms 5.97% std::__new_allocator::deallocate (inline) 0 0% 48.74% 4659ms 5.96% std::allocator_traits::deallocate (inline) 0 0% 48.74% 4631ms 5.92% std::_Rb_tree::_M_get_node (inline) 0 0% 48.74% 4627ms 5.91% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.74% 4433ms 5.67% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0077% 48.75% 4325ms 5.53% TetrahedralMesh::ImportFromMesher 80ms 0.1% 48.85% 4200ms 5.37% MutableElement::AddNode 1395ms 1.78% 50.64% 4029ms 5.15% _int_free 109ms 0.14% 50.78% 3939ms 5.03% tetgen::tetgenmesh::insphere_sos 3525ms 4.51% 55.28% 3821ms 4.88% tetgen::insphere 139ms 0.18% 55.46% 3466ms 4.43% tetgen::tetgenmesh::flip23 224ms 0.29% 55.74% 3379ms 4.32% Node::~Node 199ms 0.25% 56.00% 3215ms 4.11% VertexMesh::Clear 207ms 0.26% 56.26% 3129ms 4.00% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 8ms 0.01% 56.27% 3039ms 3.88% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 56.27% 2939ms 3.76% std::_Rb_tree_iterator::operator++ (inline) 2903ms 3.71% 59.98% 2903ms 3.71% Node::GetIndex 1781ms 2.28% 62.26% 2615ms 3.34% malloc_consolidate 40ms 0.051% 62.31% 2443ms 3.12% std::_Vector_base::_M_deallocate (inline) 139ms 0.18% 62.49% 2443ms 3.12% tetgen::tetgenmesh::flip32 2356ms 3.01% 65.50% 2356ms 3.01% std::_Rb_tree_insert_and_rebalance 0 0% 65.50% 2353ms 3.01% std::vector::~vector (inline) 1ms 0.0013% 65.50% 2289ms 2.93% std::_Vector_base::~_Vector_base (inline) 3ms 0.0038% 65.51% 2283ms 2.92% _int_free_maybe_consolidate 0 0% 65.51% 2269ms 2.90% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.51% 2256ms 2.88% std::_Rb_tree::_M_put_node (inline) 3ms 0.0038% 65.51% 2217ms 2.83% Element::Element 208ms 0.27% 65.78% 1945ms 2.49% tetgen::tetgenmesh::enqueueflipface 6ms 0.0077% 65.78% 1846ms 2.36% Element::RegisterWithNodes (inline) 1806ms 2.31% 68.09% 1806ms 2.31% unlink_chunk 1571ms 2.01% 70.10% 1649ms 2.11% tetgen::orient3d 93ms 0.12% 70.22% 1632ms 2.09% TetrahedralMesh::Clear 3ms 0.0038% 70.22% 1580ms 2.02% VertexMesh::GenerateVerticesFromElementCircumcentres 1249ms 1.60% 71.82% 1470ms 1.88% AbstractElement::GetNodeGlobalIndex 58ms 0.074% 71.89% 1470ms 1.88% std::map::operator[] 39ms 0.05% 71.94% 1447ms 1.85% tetgen::tetgenmesh::locate 73ms 0.093% 72.04% 1377ms 1.76% std::vector::_M_realloc_insert 79ms 0.1% 72.14% 1363ms 1.74% tetgen::tetgenmesh::preciselocate 0 0% 72.14% 1309ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 72.14% 1309ms 1.67% std::map::lower_bound (inline) 1201ms 1.54% 73.67% 1201ms 1.54% tetgen::tetgenmesh::oppo 5ms 0.0064% 73.68% 1187ms 1.52% std::_Vector_base::_M_allocate (inline) 135ms 0.17% 73.85% 1157ms 1.48% std::vector::push_back (inline) 1ms 0.0013% 73.85% 1121ms 1.43% VoronoiDataWriter::Visit 1062ms 1.36% 75.21% 1062ms 1.36% Node::rGetLocation 0 0% 75.21% 1025ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 468ms 0.6% 75.81% 1011ms 1.29% AbstractElement::GetNodeLocation 979ms 1.25% 77.06% 979ms 1.25% AbstractElement::IsDeleted 959ms 1.23% 78.29% 959ms 1.23% tetgen::tetgenmesh::triface::triface 12ms 0.015% 78.30% 848ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.024% 78.33% 806ms 1.03% AbstractTetrahedralElement::CalculateJacobian 332ms 0.42% 78.75% 793ms 1.01% tetgen::tetgenmesh::sym 785ms 1.00% 79.75% 785ms 1.00% [libchaste_mesh.so] 0 0% 79.75% 781ms 1% AbstractTwoBodyInteractionForce::AddForceContribution 748ms 0.96% 80.71% 748ms 0.96% tetgen::tetgenmesh::triface::operator= 12ms 0.015% 80.72% 738ms 0.94% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 729ms 0.93% 81.66% 729ms 0.93% std::vector::size (inline) 20ms 0.026% 81.68% 691ms 0.88% Element::CalculateCircumsphere 42ms 0.054% 81.74% 690ms 0.88% tetgen::tetgenmesh::queue::push 388ms 0.5% 82.23% 648ms 0.83% tetgen::tetgenmesh::link::add 13ms 0.017% 82.25% 640ms 0.82% boost::numeric::ublas::c_vector::c_vector (inline) 48ms 0.061% 82.31% 627ms 0.8% AbstractTetrahedralElement::RefreshJacobian 354ms 0.45% 82.76% 623ms 0.8% tetgen::tetgenmesh::fnextself 56ms 0.072% 82.83% 621ms 0.79% __atan2 17ms 0.022% 82.86% 609ms 0.78% boost::numeric::ublas::vector_assign (inline) 52ms 0.066% 82.92% 584ms 0.75% tetgen::tetgenmesh::enextfnext 55ms 0.07% 82.99% 581ms 0.74% tetgen::tetgenmesh::enext2fnext 449ms 0.57% 83.57% 562ms 0.72% __ieee754_atan2_fma 0 0% 83.57% 562ms 0.72% std::set::find (inline) 199ms 0.25% 83.82% 555ms 0.71% tetgen::tetgenmesh::bond 0 0% 83.82% 533ms 0.68% boost::numeric::ublas::inner_prod (inline) 52ms 0.066% 83.89% 528ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.89% 528ms 0.67% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 83.89% 485ms 0.62% std::insert_iterator::operator= (inline) 477ms 0.61% 84.50% 477ms 0.61% tetgen::tetgenmesh::decode 11ms 0.014% 84.51% 464ms 0.59% VertexElement::~VertexElement 13ms 0.017% 84.53% 453ms 0.58% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.53% 452ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 451ms 0.58% 85.10% 451ms 0.58% tetgen::tetgenmesh::org 23ms 0.029% 85.13% 447ms 0.57% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0051% 85.14% 441ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 197ms 0.25% 85.39% 421ms 0.54% boost::numeric::ublas::vector_inner_prod::apply (inline) 417ms 0.53% 85.92% 417ms 0.53% boost::numeric::ublas::c_vector::operator() 0 0% 85.92% 414ms 0.53% std::_Rb_tree::_M_insert_unique_ (inline) 203ms 0.26% 86.18% 412ms 0.53% AbstractTetrahedralMesh::GetElement 3ms 0.0038% 86.19% 410ms 0.52% Cell::GetCellId 0 0% 86.19% 404ms 0.52% VertexMeshWriter::WriteVtkUsingMesh 98ms 0.13% 86.31% 400ms 0.51% __dynamic_cast 400ms 0.51% 86.82% 400ms 0.51% tetgen::tetgenmesh::pointmark 127ms 0.16% 86.99% 393ms 0.5% boost::numeric::ublas::indexing_vector_assign 392ms 0.5% 87.49% 392ms 0.5% std::_Rb_tree_decrement