File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 46122ms, 86.28% of 53457ms total Dropped 868 nodes (cum <= 267.29ms) flat flat% sum% cum cum% 0 0% 0% 53389ms 99.87% __libc_start_call_main 0 0% 0% 53389ms 99.87% __libc_start_main_impl 0 0% 0% 53389ms 99.87% _start 0 0% 0% 53375ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 53375ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 53375ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 53375ms 99.85% main 0 0% 0% 53339ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 53339ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 53339ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 53096ms 99.32% AbstractCellBasedSimulation::Solve 1ms 0.0019% 0.0019% 44583ms 83.40% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0019% 44539ms 83.32% MeshBasedCellPopulation::Update 0 0% 0.0019% 24729ms 46.26% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0019% 24729ms 46.26% MeshBasedCellPopulation::TessellateIfNeeded 200ms 0.37% 0.38% 22152ms 41.44% VertexMesh::VertexMesh 0 0% 0.38% 16173ms 30.25% MutableMesh::ReMesh 0 0% 0.38% 12787ms 23.92% tetgen::tetrahedralize 3ms 0.0056% 0.38% 12650ms 23.66% tetgen::tetgenmesh::delaunizevertices 10ms 0.019% 0.4% 12643ms 23.65% tetgen::tetgenmesh::incrflipdelaunay 565ms 1.06% 1.46% 11247ms 21.04% tetgen::tetgenmesh::lawson 569ms 1.06% 2.52% 11060ms 20.69% TetrahedralMesh::EdgeIterator::operator++ 22ms 0.041% 2.56% 8866ms 16.59% std::set::insert (inline) 309ms 0.58% 3.14% 8691ms 16.26% VertexElement::AddFace 2979ms 5.57% 8.71% 8557ms 16.01% std::_Rb_tree::_M_lower_bound (inline) 288ms 0.54% 9.25% 8375ms 15.67% std::_Rb_tree::_M_insert_unique 228ms 0.43% 9.68% 8072ms 15.10% std::_Rb_tree::find (inline) 0 0% 9.68% 7519ms 14.07% std::set::count (inline) 109ms 0.2% 9.88% 5436ms 10.17% std::less::operator() (inline) 5384ms 10.07% 19.95% 5384ms 10.07% std::operator< (inline) 268ms 0.5% 20.46% 4985ms 9.33% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.46% 4920ms 9.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0019% 20.46% 4803ms 8.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0037% 20.46% 4772ms 8.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 4311ms 8.06% 28.53% 4311ms 8.06% std::_Rb_tree_increment 213ms 0.4% 28.92% 4229ms 7.91% operator new 2ms 0.0037% 28.93% 3965ms 7.42% MeshBasedCellPopulation::UpdateNodePairs 1041ms 1.95% 30.88% 3956ms 7.40% __GI___libc_malloc 6ms 0.011% 30.89% 3927ms 7.35% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.026% 30.91% 3832ms 7.17% MeshBasedCellPopulation::SpringIterator::operator++ 40ms 0.075% 30.99% 3661ms 6.85% std::__new_allocator::allocate (inline) 11ms 0.021% 31.01% 3656ms 6.84% std::_Rb_tree::~_Rb_tree (inline) 1303ms 2.44% 33.45% 3643ms 6.81% std::_Rb_tree::_M_erase 0 0% 33.45% 3639ms 6.81% std::allocator_traits::allocate (inline) 0 0% 33.45% 3615ms 6.76% std::set::~set (inline) 94ms 0.18% 33.62% 3506ms 6.56% tetgen::tetgenmesh::insphere_sos 0 0% 33.62% 3460ms 6.47% AbstractCellPopulation::WriteResultsToFiles 1201ms 2.25% 35.87% 3413ms 6.38% std::_Rb_tree::_M_get_insert_unique_pos 3136ms 5.87% 41.73% 3394ms 6.35% tetgen::insphere 885ms 1.66% 43.39% 3220ms 6.02% __GI___libc_free 2ms 0.0037% 43.39% 3068ms 5.74% std::set_intersection (inline) 195ms 0.36% 43.76% 3066ms 5.74% std::__set_intersection 153ms 0.29% 44.04% 2972ms 5.56% std::__new_allocator::deallocate (inline) 0 0% 44.04% 2956ms 5.53% std::allocator_traits::deallocate (inline) 0 0% 44.04% 2940ms 5.50% std::_Rb_tree::_M_create_node (inline) 0 0% 44.04% 2922ms 5.47% std::_Rb_tree::_M_get_node (inline) 0 0% 44.04% 2911ms 5.45% std::_Rb_tree::_Alloc_node::operator() (inline) 27ms 0.051% 44.10% 2762ms 5.17% Node::AddElement 14ms 0.026% 44.12% 2665ms 4.99% TetrahedralMesh::ImportFromMesher 213ms 0.4% 44.52% 2661ms 4.98% tetgen::tetgenmesh::flip23 0 0% 44.52% 2589ms 4.84% VertexMesh::~VertexMesh 1971ms 3.69% 48.21% 2586ms 4.84% _int_malloc 2573ms 4.81% 53.02% 2573ms 4.81% std::_Rb_tree::_S_right (inline) 197ms 0.37% 53.39% 2448ms 4.58% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.0056% 53.39% 2374ms 4.44% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 223ms 0.42% 53.81% 2369ms 4.43% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1191ms 2.23% 56.04% 2331ms 4.36% _int_free 0 0% 56.04% 2162ms 4.04% std::_Rb_tree_iterator::operator++ (inline) 58ms 0.11% 56.15% 2064ms 3.86% MutableElement::AddNode 1869ms 3.50% 59.64% 1869ms 3.50% std::_Rb_tree_insert_and_rebalance 179ms 0.33% 59.98% 1860ms 3.48% tetgen::tetgenmesh::flip32 0 0% 59.98% 1836ms 3.43% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.98% 1821ms 3.41% std::_Rb_tree::_M_put_node (inline) 117ms 0.22% 60.20% 1801ms 3.37% Node::~Node 136ms 0.25% 60.45% 1722ms 3.22% VertexMesh::Clear 1370ms 2.56% 63.02% 1475ms 2.76% tetgen::orient3d 4ms 0.0075% 63.02% 1438ms 2.69% Element::Element 188ms 0.35% 63.37% 1296ms 2.42% tetgen::tetgenmesh::enqueueflipface 1259ms 2.36% 65.73% 1259ms 2.36% Node::GetIndex 33ms 0.062% 65.79% 1184ms 2.21% tetgen::tetgenmesh::locate 13ms 0.024% 65.82% 1148ms 2.15% std::_Vector_base::_M_deallocate (inline) 3ms 0.0056% 65.82% 1112ms 2.08% Element::RegisterWithNodes (inline) 84ms 0.16% 65.98% 1105ms 2.07% tetgen::tetgenmesh::preciselocate 674ms 1.26% 67.24% 1085ms 2.03% malloc_consolidate 0 0% 67.24% 1082ms 2.02% std::vector::~vector (inline) 63ms 0.12% 67.36% 1026ms 1.92% std::map::operator[] 0 0% 67.36% 979ms 1.83% std::_Vector_base::~_Vector_base (inline) 99ms 0.19% 67.54% 949ms 1.78% TetrahedralMesh::Clear 4ms 0.0075% 67.55% 945ms 1.77% _int_free_maybe_consolidate 40ms 0.075% 67.62% 917ms 1.72% std::vector::_M_realloc_insert 0 0% 67.62% 893ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 67.62% 893ms 1.67% std::map::lower_bound (inline) 0 0% 67.62% 871ms 1.63% VoronoiDataWriter::Visit 815ms 1.52% 69.15% 815ms 1.52% tetgen::tetgenmesh::triface::triface 5ms 0.0094% 69.16% 814ms 1.52% VertexMesh::GenerateVerticesFromElementCircumcentres 784ms 1.47% 70.62% 784ms 1.47% unlink_chunk 451ms 0.84% 71.47% 759ms 1.42% tetgen::tetgenmesh::fnextself 106ms 0.2% 71.67% 746ms 1.40% std::vector::push_back (inline) 3ms 0.0056% 71.67% 720ms 1.35% std::_Vector_base::_M_allocate (inline) 1ms 0.0019% 71.67% 708ms 1.32% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.0019% 71.68% 706ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 699ms 1.31% 72.98% 699ms 1.31% tetgen::tetgenmesh::oppo 674ms 1.26% 74.24% 674ms 1.26% [libchaste_mesh.so] 510ms 0.95% 75.20% 663ms 1.24% AbstractElement::GetNodeGlobalIndex 17ms 0.032% 75.23% 663ms 1.24% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.032% 75.26% 657ms 1.23% boost::numeric::ublas::vector_assign (inline) 6ms 0.011% 75.27% 651ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 47ms 0.088% 75.36% 629ms 1.18% __atan2 15ms 0.028% 75.39% 620ms 1.16% boost::numeric::ublas::c_vector::c_vector (inline) 19ms 0.036% 75.43% 619ms 1.16% AbstractTetrahedralElement::CalculateJacobian 612ms 1.14% 76.57% 612ms 1.14% tetgen::tetgenmesh::triface::operator= 473ms 0.88% 77.45% 580ms 1.08% __ieee754_atan2_fma 0 0% 77.45% 550ms 1.03% std::set::find (inline) 217ms 0.41% 77.86% 543ms 1.02% AbstractElement::GetNodeLocation 0 0% 77.86% 518ms 0.97% boost::numeric::ublas::inner_prod (inline) 4ms 0.0075% 77.87% 516ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 35ms 0.065% 77.93% 512ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.93% 505ms 0.94% std::insert_iterator::operator= (inline) 43ms 0.08% 78.01% 496ms 0.93% tetgen::tetgenmesh::enext2fnext 16ms 0.03% 78.04% 470ms 0.88% Element::CalculateCircumsphere 36ms 0.067% 78.11% 467ms 0.87% tetgen::tetgenmesh::enextfnext 53ms 0.099% 78.21% 458ms 0.86% AbstractTetrahedralElement::RefreshJacobian 0 0% 78.21% 437ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 426ms 0.8% 79.01% 426ms 0.8% Node::rGetLocation 420ms 0.79% 79.79% 420ms 0.79% std::vector::size (inline) 194ms 0.36% 80.16% 416ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 235ms 0.44% 80.60% 414ms 0.77% AbstractTetrahedralMesh::GetElement 6ms 0.011% 80.61% 409ms 0.77% CellPropertyCollection::GetPropertiesType (inline) 408ms 0.76% 81.37% 408ms 0.76% boost::numeric::ublas::c_vector::operator() (partial-inline) 3ms 0.0056% 81.38% 404ms 0.76% Cell::GetCellId 21ms 0.039% 81.41% 401ms 0.75% tetgen::tetgenmesh::queue::push 253ms 0.47% 81.89% 398ms 0.74% tetgen::tetgenmesh::sym 102ms 0.19% 82.08% 392ms 0.73% boost::numeric::ublas::indexing_vector_assign 20ms 0.037% 82.12% 391ms 0.73% std::_Rb_tree_iterator::operator-- (inline) 8ms 0.015% 82.13% 384ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 106ms 0.2% 82.33% 379ms 0.71% __dynamic_cast 0 0% 82.33% 376ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 261ms 0.49% 82.82% 376ms 0.7% tetgen::tetgenmesh::link::add 20ms 0.037% 82.86% 374ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 358ms 0.67% 83.53% 358ms 0.67% std::_Rb_tree_decrement 255ms 0.48% 84.00% 350ms 0.65% tetgen::tetgenmesh::bond 2ms 0.0037% 84.01% 328ms 0.61% AbstractCellProperty::IsSubType (inline) 58ms 0.11% 84.11% 328ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 324ms 0.61% 84.72% 324ms 0.61% tetgen::tetgenmesh::org 5ms 0.0094% 84.73% 323ms 0.6% AbstractTetrahedralElement::AbstractTetrahedralElement 314ms 0.59% 85.32% 314ms 0.59% AbstractElement::IsDeleted 13ms 0.024% 85.34% 301ms 0.56% std::vector::insert (inline) 10ms 0.019% 85.36% 291ms 0.54% VertexElement::~VertexElement 131ms 0.25% 85.61% 290ms 0.54% Inverse 0 0% 85.61% 288ms 0.54% tcache_get (inline) 288ms 0.54% 86.14% 288ms 0.54% tcache_get_n (inline) 72ms 0.13% 86.28% 279ms 0.52% tetgen::tetgenmesh::queue::pop 0 0% 86.28% 271ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)