File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48732ms, 86.59% of 56282ms total Dropped 876 nodes (cum <= 281.41ms) flat flat% sum% cum cum% 0 0% 0% 56228ms 99.90% __libc_start_call_main 0 0% 0% 56228ms 99.90% __libc_start_main_impl 0 0% 0% 56228ms 99.90% _start 0 0% 0% 56214ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56214ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56214ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56214ms 99.88% main 0 0% 0% 56177ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56177ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 56176ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55929ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 47150ms 83.77% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47092ms 83.67% MeshBasedCellPopulation::Update 0 0% 0% 26757ms 47.54% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 26757ms 47.54% MeshBasedCellPopulation::TessellateIfNeeded 185ms 0.33% 0.33% 23779ms 42.25% VertexMesh::VertexMesh 1ms 0.0018% 0.33% 16577ms 29.45% MutableMesh::ReMesh 0 0% 0.33% 12729ms 22.62% tetgen::tetrahedralize 1ms 0.0018% 0.33% 12593ms 22.37% tetgen::tetgenmesh::delaunizevertices 7ms 0.012% 0.34% 12585ms 22.36% tetgen::tetgenmesh::incrflipdelaunay 546ms 0.97% 1.31% 11402ms 20.26% TetrahedralMesh::EdgeIterator::operator++ 525ms 0.93% 2.25% 11111ms 19.74% tetgen::tetgenmesh::lawson 28ms 0.05% 2.30% 9589ms 17.04% std::set::insert (inline) 239ms 0.42% 2.72% 9098ms 16.17% std::_Rb_tree::_M_insert_unique 346ms 0.61% 3.34% 8971ms 15.94% VertexElement::AddFace 2964ms 5.27% 8.60% 8508ms 15.12% std::_Rb_tree::_M_lower_bound (inline) 246ms 0.44% 9.04% 8046ms 14.30% std::_Rb_tree::find (inline) 0 0% 9.04% 7517ms 13.36% std::set::count (inline) 137ms 0.24% 9.28% 5450ms 9.68% std::less::operator() (inline) 290ms 0.52% 9.80% 5412ms 9.62% std::_Rb_tree::_M_insert_ (inline) 5365ms 9.53% 19.33% 5365ms 9.53% std::operator< (inline) 0 0% 19.33% 5073ms 9.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.33% 4953ms 8.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0018% 19.33% 4930ms 8.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 4825ms 8.57% 27.91% 4825ms 8.57% std::_Rb_tree_increment 185ms 0.33% 28.23% 4632ms 8.23% operator new 1051ms 1.87% 30.10% 4391ms 7.80% __GI___libc_malloc 0 0% 30.10% 4110ms 7.30% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.0036% 30.11% 4059ms 7.21% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0018% 30.11% 4012ms 7.13% std::_Rb_tree::~_Rb_tree (inline) 1508ms 2.68% 32.79% 4008ms 7.12% std::_Rb_tree::_M_erase 48ms 0.085% 32.87% 3999ms 7.11% std::__new_allocator::allocate (inline) 0 0% 32.87% 3977ms 7.07% std::allocator_traits::allocate (inline) 16ms 0.028% 32.90% 3969ms 7.05% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 32.90% 3956ms 7.03% std::set::~set (inline) 1199ms 2.13% 35.03% 3745ms 6.65% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0018% 35.03% 3608ms 6.41% std::set_intersection (inline) 222ms 0.39% 35.43% 3607ms 6.41% std::__set_intersection 1055ms 1.87% 37.30% 3566ms 6.34% __GI___libc_free 0 0% 37.30% 3555ms 6.32% AbstractCellPopulation::WriteResultsToFiles 125ms 0.22% 37.52% 3490ms 6.20% tetgen::tetgenmesh::insphere_sos 21ms 0.037% 37.56% 3360ms 5.97% Node::AddElement 3045ms 5.41% 42.97% 3353ms 5.96% tetgen::insphere 0 0% 42.97% 3258ms 5.79% std::_Rb_tree::_M_create_node (inline) 0 0% 42.97% 3237ms 5.75% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.97% 3222ms 5.72% std::_Rb_tree::_M_get_node (inline) 156ms 0.28% 43.25% 3178ms 5.65% std::__new_allocator::deallocate (inline) 0 0% 43.25% 3159ms 5.61% std::allocator_traits::deallocate (inline) 10ms 0.018% 43.27% 3082ms 5.48% TetrahedralMesh::ImportFromMesher 3008ms 5.34% 48.61% 3008ms 5.34% std::_Rb_tree::_S_right (inline) 2224ms 3.95% 52.56% 2996ms 5.32% _int_malloc 0 0% 52.56% 2995ms 5.32% VertexMesh::~VertexMesh 178ms 0.32% 52.88% 2947ms 5.24% std::_Rb_tree_const_iterator::operator++ (inline) 169ms 0.3% 53.18% 2743ms 4.87% tetgen::tetgenmesh::flip23 68ms 0.12% 53.30% 2689ms 4.78% MutableElement::AddNode 1223ms 2.17% 55.47% 2511ms 4.46% _int_free 3ms 0.0053% 55.48% 2400ms 4.26% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 227ms 0.4% 55.88% 2373ms 4.22% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 145ms 0.26% 56.14% 2164ms 3.84% Node::~Node 0 0% 56.14% 2162ms 3.84% std::_Rb_tree_iterator::operator++ (inline) 183ms 0.33% 56.46% 2001ms 3.56% VertexMesh::Clear 1951ms 3.47% 59.93% 1951ms 3.47% std::_Rb_tree_insert_and_rebalance 0 0% 59.93% 1910ms 3.39% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.93% 1899ms 3.37% std::_Rb_tree::_M_put_node (inline) 146ms 0.26% 60.19% 1801ms 3.20% tetgen::tetgenmesh::flip32 4ms 0.0071% 60.20% 1482ms 2.63% Element::Element 1350ms 2.40% 62.60% 1423ms 2.53% tetgen::orient3d 1401ms 2.49% 65.08% 1401ms 2.49% Node::GetIndex 206ms 0.37% 65.45% 1334ms 2.37% tetgen::tetgenmesh::enqueueflipface 14ms 0.025% 65.48% 1274ms 2.26% std::_Vector_base::_M_deallocate (inline) 187ms 0.33% 65.81% 1271ms 2.26% TetrahedralMesh::Clear 822ms 1.46% 67.27% 1253ms 2.23% malloc_consolidate 30ms 0.053% 67.32% 1214ms 2.16% tetgen::tetgenmesh::locate 0 0% 67.32% 1185ms 2.11% std::vector::~vector (inline) 4ms 0.0071% 67.33% 1153ms 2.05% Element::RegisterWithNodes (inline) 92ms 0.16% 67.49% 1140ms 2.03% tetgen::tetgenmesh::preciselocate 3ms 0.0053% 67.50% 1107ms 1.97% std::_Vector_base::~_Vector_base (inline) 5ms 0.0089% 67.51% 1072ms 1.90% _int_free_maybe_consolidate 62ms 0.11% 67.62% 1025ms 1.82% std::vector::_M_realloc_insert 49ms 0.087% 67.70% 987ms 1.75% std::map::operator[] 935ms 1.66% 69.36% 935ms 1.66% unlink_chunk 2ms 0.0036% 69.37% 927ms 1.65% VoronoiDataWriter::Visit 904ms 1.61% 70.97% 904ms 1.61% tetgen::tetgenmesh::triface::triface 0 0% 70.97% 881ms 1.57% std::_Rb_tree::lower_bound (inline) 0 0% 70.97% 881ms 1.57% std::map::lower_bound (inline) 6ms 0.011% 70.99% 857ms 1.52% VertexMesh::GenerateVerticesFromElementCircumcentres 121ms 0.21% 71.20% 824ms 1.46% std::vector::push_back (inline) 667ms 1.19% 72.39% 808ms 1.44% AbstractElement::GetNodeGlobalIndex 7ms 0.012% 72.40% 762ms 1.35% std::_Vector_base::_M_allocate (inline) 418ms 0.74% 73.14% 762ms 1.35% tetgen::tetgenmesh::fnextself 0 0% 73.14% 748ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 714ms 1.27% 74.41% 714ms 1.27% tetgen::tetgenmesh::oppo 2ms 0.0036% 74.41% 710ms 1.26% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.025% 74.44% 709ms 1.26% boost::numeric::ublas::vector_assign (inline) 5ms 0.0089% 74.45% 692ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 677ms 1.20% 75.65% 677ms 1.20% [libchaste_mesh.so] 12ms 0.021% 75.67% 669ms 1.19% boost::numeric::ublas::c_vector::c_vector (inline) 14ms 0.025% 75.70% 665ms 1.18% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.023% 75.72% 646ms 1.15% AbstractTetrahedralElement::CalculateJacobian 215ms 0.38% 76.10% 601ms 1.07% AbstractElement::GetNodeLocation 39ms 0.069% 76.17% 598ms 1.06% __atan2 566ms 1.01% 77.18% 566ms 1.01% tetgen::tetgenmesh::triface::operator= 445ms 0.79% 77.97% 558ms 0.99% __ieee754_atan2_fma 539ms 0.96% 78.92% 539ms 0.96% Node::rGetLocation 0 0% 78.92% 525ms 0.93% std::set::find (inline) 0 0% 78.92% 511ms 0.91% boost::numeric::ublas::inner_prod (inline) 4ms 0.0071% 78.93% 510ms 0.91% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.057% 78.99% 506ms 0.9% boost::numeric::ublas::vector_scalar_binary::evaluate 49ms 0.087% 79.08% 503ms 0.89% tetgen::tetgenmesh::enextfnext 0 0% 79.08% 493ms 0.88% std::insert_iterator::operator= (inline) 44ms 0.078% 79.15% 480ms 0.85% tetgen::tetgenmesh::enext2fnext 469ms 0.83% 79.99% 469ms 0.83% std::vector::size (inline) 44ms 0.078% 80.06% 466ms 0.83% AbstractTetrahedralElement::RefreshJacobian 12ms 0.021% 80.09% 466ms 0.83% Element::CalculateCircumsphere 122ms 0.22% 80.30% 465ms 0.83% boost::numeric::ublas::indexing_vector_assign 462ms 0.82% 81.12% 462ms 0.82% boost::numeric::ublas::c_vector::operator() 443ms 0.79% 81.91% 443ms 0.79% AbstractElement::IsDeleted 15ms 0.027% 81.94% 441ms 0.78% VertexMesh::CalculateUnitNormalToFaceWithArea 11ms 0.02% 81.96% 435ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 81.96% 434ms 0.77% std::_Rb_tree::_M_insert_unique_ (inline) 267ms 0.47% 82.43% 413ms 0.73% tetgen::tetgenmesh::sym 188ms 0.33% 82.77% 412ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0053% 82.77% 410ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 98ms 0.17% 82.94% 408ms 0.72% __dynamic_cast 222ms 0.39% 83.34% 405ms 0.72% AbstractTetrahedralMesh::GetElement 2ms 0.0036% 83.34% 398ms 0.71% Cell::GetCellId 257ms 0.46% 83.80% 393ms 0.7% tetgen::tetgenmesh::bond 25ms 0.044% 83.84% 390ms 0.69% tetgen::tetgenmesh::queue::push 0 0% 83.84% 388ms 0.69% VertexMeshWriter::WriteVtkUsingMesh 252ms 0.45% 84.29% 363ms 0.64% tetgen::tetgenmesh::link::add 47ms 0.084% 84.38% 356ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 347ms 0.62% 84.99% 347ms 0.62% tetgen::tetgenmesh::org 23ms 0.041% 85.03% 346ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 11ms 0.02% 85.05% 345ms 0.61% std::vector::insert (inline) 2ms 0.0036% 85.06% 338ms 0.6% AbstractCellProperty::IsSubType (inline) 7ms 0.012% 85.07% 327ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 126ms 0.22% 85.29% 315ms 0.56% Inverse 311ms 0.55% 85.84% 311ms 0.55% std::_Rb_tree_decrement 36ms 0.064% 85.91% 308ms 0.55% tetgen::insphereadapt 0 0% 85.91% 306ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.91% 304ms 0.54% tcache_get (inline) 304ms 0.54% 86.45% 304ms 0.54% tcache_get_n (inline) 10ms 0.018% 86.47% 298ms 0.53% VertexMesh::GetVolumeOfElement 3ms 0.0053% 86.47% 293ms 0.52% VertexElement::~VertexElement 64ms 0.11% 86.59% 293ms 0.52% tetgen::tetgenmesh::queue::pop