File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50459ms, 86.85% of 58098ms total Dropped 855 nodes (cum <= 290.49ms) flat flat% sum% cum cum% 0 0% 0% 58023ms 99.87% __libc_start_call_main 0 0% 0% 58023ms 99.87% __libc_start_main_impl 0 0% 0% 58023ms 99.87% _start 0 0% 0% 58009ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58009ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58009ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58009ms 99.85% main 0 0% 0% 57974ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57974ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57974ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57713ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 49134ms 84.57% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 49091ms 84.50% MeshBasedCellPopulation::Update 0 0% 0% 27736ms 47.74% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27736ms 47.74% MeshBasedCellPopulation::TessellateIfNeeded 196ms 0.34% 0.34% 24381ms 41.97% VertexMesh::VertexMesh 0 0% 0.34% 17635ms 30.35% MutableMesh::ReMesh 0 0% 0.34% 13164ms 22.66% tetgen::tetrahedralize 1ms 0.0017% 0.34% 13027ms 22.42% tetgen::tetgenmesh::delaunizevertices 11ms 0.019% 0.36% 13020ms 22.41% tetgen::tetgenmesh::incrflipdelaunay 558ms 0.96% 1.32% 11570ms 19.91% tetgen::tetgenmesh::lawson 518ms 0.89% 2.21% 11318ms 19.48% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.052% 2.26% 10123ms 17.42% std::set::insert (inline) 250ms 0.43% 2.69% 9649ms 16.61% std::_Rb_tree::_M_insert_unique 357ms 0.61% 3.31% 9170ms 15.78% VertexElement::AddFace 2965ms 5.10% 8.41% 8438ms 14.52% std::_Rb_tree::_M_lower_bound (inline) 195ms 0.34% 8.75% 7898ms 13.59% std::_Rb_tree::find (inline) 0 0% 8.75% 7388ms 12.72% std::set::count (inline) 282ms 0.49% 9.23% 5751ms 9.90% std::_Rb_tree::_M_insert_ (inline) 103ms 0.18% 9.41% 5346ms 9.20% std::less::operator() (inline) 5304ms 9.13% 18.54% 5304ms 9.13% std::operator< (inline) 224ms 0.39% 18.92% 5152ms 8.87% operator new 0 0% 18.92% 5016ms 8.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0017% 18.92% 4896ms 8.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 1073ms 1.85% 20.77% 4871ms 8.38% __GI___libc_malloc 8ms 0.014% 20.79% 4869ms 8.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 4707ms 8.10% 28.89% 4707ms 8.10% std::_Rb_tree_increment 38ms 0.065% 28.95% 4393ms 7.56% std::__new_allocator::allocate (inline) 0 0% 28.95% 4371ms 7.52% std::allocator_traits::allocate (inline) 11ms 0.019% 28.97% 4363ms 7.51% std::_Rb_tree::~_Rb_tree (inline) 1725ms 2.97% 31.94% 4350ms 7.49% std::_Rb_tree::_M_erase 0 0% 31.94% 4295ms 7.39% std::set::~set (inline) 0 0% 31.94% 4065ms 7.00% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.012% 31.95% 3993ms 6.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1234ms 2.12% 34.08% 3943ms 6.79% std::_Rb_tree::_M_get_insert_unique_pos 13ms 0.022% 34.10% 3924ms 6.75% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.012% 34.11% 3774ms 6.50% std::set_intersection (inline) 1126ms 1.94% 36.05% 3772ms 6.49% __GI___libc_free 21ms 0.036% 36.09% 3768ms 6.49% Node::AddElement 290ms 0.5% 36.58% 3767ms 6.48% std::__set_intersection 22ms 0.038% 36.62% 3627ms 6.24% TetrahedralMesh::ImportFromMesher 0 0% 36.62% 3576ms 6.16% std::_Rb_tree::_M_create_node (inline) 0 0% 36.62% 3552ms 6.11% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.62% 3533ms 6.08% std::_Rb_tree::_M_get_node (inline) 116ms 0.2% 36.82% 3490ms 6.01% tetgen::tetgenmesh::insphere_sos 2670ms 4.60% 41.42% 3477ms 5.98% _int_malloc 0 0% 41.42% 3419ms 5.88% AbstractCellPopulation::WriteResultsToFiles 0 0% 41.42% 3382ms 5.82% VertexMesh::~VertexMesh 3058ms 5.26% 46.68% 3358ms 5.78% tetgen::insphere 137ms 0.24% 46.92% 3318ms 5.71% std::__new_allocator::deallocate (inline) 0 0% 46.92% 3301ms 5.68% std::allocator_traits::deallocate (inline) 3219ms 5.54% 52.46% 3219ms 5.54% std::_Rb_tree::_S_right (inline) 229ms 0.39% 52.85% 3000ms 5.16% std::_Rb_tree_const_iterator::operator++ (inline) 83ms 0.14% 52.99% 2815ms 4.85% MutableElement::AddNode 193ms 0.33% 53.33% 2732ms 4.70% tetgen::tetgenmesh::flip23 1224ms 2.11% 55.43% 2645ms 4.55% _int_free 160ms 0.28% 55.71% 2521ms 4.34% Node::~Node 175ms 0.3% 56.01% 2286ms 3.93% VertexMesh::Clear 1ms 0.0017% 56.01% 2259ms 3.89% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 227ms 0.39% 56.40% 2257ms 3.88% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0034% 56.41% 2044ms 3.52% std::_Rb_tree_iterator::operator++ (inline) 1987ms 3.42% 59.83% 1987ms 3.42% std::_Rb_tree_insert_and_rebalance 0 0% 59.83% 1917ms 3.30% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.83% 1910ms 3.29% std::_Rb_tree::_M_put_node (inline) 171ms 0.29% 60.12% 1899ms 3.27% tetgen::tetgenmesh::flip32 3ms 0.0052% 60.13% 1787ms 3.08% Element::Element 7ms 0.012% 60.14% 1455ms 2.50% Element::RegisterWithNodes (inline) 1360ms 2.34% 62.48% 1451ms 2.50% tetgen::orient3d 202ms 0.35% 62.83% 1433ms 2.47% TetrahedralMesh::Clear 19ms 0.033% 62.86% 1410ms 2.43% std::_Vector_base::_M_deallocate (inline) 945ms 1.63% 64.49% 1386ms 2.39% malloc_consolidate 1351ms 2.33% 66.81% 1351ms 2.33% Node::GetIndex 207ms 0.36% 67.17% 1305ms 2.25% tetgen::tetgenmesh::enqueueflipface 0 0% 67.17% 1296ms 2.23% std::vector::~vector (inline) 0 0% 67.17% 1205ms 2.07% std::_Vector_base::~_Vector_base (inline) 33ms 0.057% 67.22% 1200ms 2.07% tetgen::tetgenmesh::locate 4ms 0.0069% 67.23% 1187ms 2.04% _int_free_maybe_consolidate 99ms 0.17% 67.40% 1113ms 1.92% tetgen::tetgenmesh::preciselocate 58ms 0.1% 67.50% 1098ms 1.89% std::vector::_M_realloc_insert 987ms 1.70% 69.20% 987ms 1.70% unlink_chunk 61ms 0.1% 69.31% 982ms 1.69% std::map::operator[] 966ms 1.66% 70.97% 966ms 1.66% tetgen::tetgenmesh::triface::triface 745ms 1.28% 72.25% 945ms 1.63% AbstractElement::GetNodeGlobalIndex 1ms 0.0017% 72.25% 924ms 1.59% VoronoiDataWriter::Visit 112ms 0.19% 72.44% 888ms 1.53% std::vector::push_back (inline) 2ms 0.0034% 72.45% 878ms 1.51% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 72.45% 870ms 1.50% std::_Rb_tree::lower_bound (inline) 0 0% 72.45% 870ms 1.50% std::map::lower_bound (inline) 6ms 0.01% 72.46% 844ms 1.45% std::_Vector_base::_M_allocate (inline) 0 0% 72.46% 824ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 796ms 1.37% 73.83% 796ms 1.37% tetgen::tetgenmesh::triface::operator= 11ms 0.019% 73.85% 748ms 1.29% AbstractTetrahedralElement::CalculateInverseJacobian 291ms 0.5% 74.35% 734ms 1.26% tetgen::tetgenmesh::fnextself 0 0% 74.35% 715ms 1.23% AbstractTwoBodyInteractionForce::AddForceContribution 26ms 0.045% 74.39% 710ms 1.22% AbstractTetrahedralElement::CalculateJacobian 680ms 1.17% 75.56% 680ms 1.17% [libchaste_mesh.so] 19ms 0.033% 75.60% 680ms 1.17% boost::numeric::ublas::vector_assign (inline) 15ms 0.026% 75.62% 667ms 1.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 288ms 0.5% 76.12% 654ms 1.13% AbstractElement::GetNodeLocation 50ms 0.086% 76.20% 637ms 1.10% __atan2 16ms 0.028% 76.23% 631ms 1.09% boost::numeric::ublas::c_vector::c_vector (inline) 459ms 0.79% 77.02% 587ms 1.01% __ieee754_atan2_fma 553ms 0.95% 77.97% 553ms 0.95% std::vector::size (inline) 535ms 0.92% 78.89% 535ms 0.92% Node::rGetLocation 534ms 0.92% 79.81% 534ms 0.92% tetgen::tetgenmesh::oppo 53ms 0.091% 79.90% 524ms 0.9% AbstractTetrahedralElement::RefreshJacobian 0 0% 79.90% 516ms 0.89% boost::numeric::ublas::inner_prod (inline) 8ms 0.014% 79.92% 514ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 37ms 0.064% 79.98% 506ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.98% 503ms 0.87% std::set::find (inline) 43ms 0.074% 80.06% 492ms 0.85% tetgen::tetgenmesh::enext2fnext 489ms 0.84% 80.90% 489ms 0.84% AbstractElement::IsDeleted 56ms 0.096% 80.99% 478ms 0.82% tetgen::tetgenmesh::enextfnext 11ms 0.019% 81.01% 475ms 0.82% Element::CalculateCircumsphere 0 0% 81.01% 469ms 0.81% std::insert_iterator::operator= (inline) 34ms 0.059% 81.07% 464ms 0.8% tetgen::tetgenmesh::queue::push 284ms 0.49% 81.56% 452ms 0.78% tetgen::tetgenmesh::sym 119ms 0.2% 81.77% 438ms 0.75% boost::numeric::ublas::indexing_vector_assign 353ms 0.61% 82.37% 426ms 0.73% tetgen::tetgenmesh::link::add 233ms 0.4% 82.77% 422ms 0.73% AbstractTetrahedralMesh::GetElement 26ms 0.045% 82.82% 419ms 0.72% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.82% 418ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0034% 82.82% 400ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 171ms 0.29% 83.12% 395ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 393ms 0.68% 83.79% 393ms 0.68% boost::numeric::ublas::c_vector::operator() 0 0% 83.79% 391ms 0.67% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0052% 83.80% 381ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 68ms 0.12% 83.92% 379ms 0.65% __dynamic_cast 26ms 0.045% 83.96% 378ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 375ms 0.65% 84.61% 375ms 0.65% tetgen::tetgenmesh::pointmark 369ms 0.64% 85.24% 369ms 0.64% tetgen::tetgenmesh::org 6ms 0.01% 85.25% 365ms 0.63% Cell::GetCellId 16ms 0.028% 85.28% 349ms 0.6% std::vector::insert (inline) 338ms 0.58% 85.86% 338ms 0.58% std::_Rb_tree_decrement 2ms 0.0034% 85.86% 332ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.015% 85.88% 332ms 0.57% VertexElement::~VertexElement 255ms 0.44% 86.32% 323ms 0.56% tetgen::tetgenmesh::bond 4ms 0.0069% 86.32% 314ms 0.54% AbstractCellProperty::IsSubType (inline) 0 0% 86.32% 314ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 141ms 0.24% 86.57% 310ms 0.53% Inverse 69ms 0.12% 86.69% 305ms 0.52% tetgen::tetgenmesh::queue::pop 36ms 0.062% 86.75% 300ms 0.52% tetgen::insphereadapt 50ms 0.086% 86.83% 299ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline) 10ms 0.017% 86.85% 294ms 0.51% VertexMesh::GetVolumeOfElement