File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49051ms, 87.08% of 56329ms total Dropped 862 nodes (cum <= 281.64ms) flat flat% sum% cum cum% 0 0% 0% 56270ms 99.90% __libc_start_call_main 0 0% 0% 56270ms 99.90% __libc_start_main_impl 0 0% 0% 56270ms 99.90% _start 0 0% 0% 56256ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56256ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56256ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56256ms 99.87% main 0 0% 0% 56219ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56219ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 56219ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55960ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 47485ms 84.30% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47438ms 84.22% MeshBasedCellPopulation::Update 0 0% 0% 26561ms 47.15% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26559ms 47.15% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 209ms 0.37% 0.37% 23432ms 41.60% VertexMesh::VertexMesh 0 0% 0.37% 17188ms 30.51% MutableMesh::ReMesh 0 0% 0.37% 12755ms 22.64% tetgen::tetrahedralize 3ms 0.0053% 0.38% 12618ms 22.40% tetgen::tetgenmesh::delaunizevertices 7ms 0.012% 0.39% 12615ms 22.40% tetgen::tetgenmesh::incrflipdelaunay 535ms 0.95% 1.34% 11194ms 19.87% TetrahedralMesh::EdgeIterator::operator++ 551ms 0.98% 2.32% 11142ms 19.78% tetgen::tetgenmesh::lawson 29ms 0.051% 2.37% 9942ms 17.65% std::set::insert (inline) 246ms 0.44% 2.80% 9439ms 16.76% std::_Rb_tree::_M_insert_unique 325ms 0.58% 3.38% 8969ms 15.92% VertexElement::AddFace 3042ms 5.40% 8.78% 8459ms 15.02% std::_Rb_tree::_M_lower_bound (inline) 246ms 0.44% 9.22% 8000ms 14.20% std::_Rb_tree::find (inline) 0 0% 9.22% 7406ms 13.15% std::set::count (inline) 253ms 0.45% 9.67% 5673ms 10.07% std::_Rb_tree::_M_insert_ (inline) 114ms 0.2% 9.87% 5334ms 9.47% std::less::operator() (inline) 5281ms 9.38% 19.25% 5281ms 9.38% std::operator< (inline) 0 0% 19.25% 5043ms 8.95% OffLatticeSimulation::UpdateCellLocationsAndTopology 260ms 0.46% 19.71% 5026ms 8.92% operator new 0 0% 19.71% 4920ms 8.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0036% 19.71% 4887ms 8.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 1067ms 1.89% 21.61% 4691ms 8.33% __GI___libc_malloc 46ms 0.082% 21.69% 4364ms 7.75% std::__new_allocator::allocate (inline) 0 0% 21.69% 4345ms 7.71% std::allocator_traits::allocate (inline) 4312ms 7.66% 29.34% 4312ms 7.66% std::_Rb_tree_increment 7ms 0.012% 29.35% 4181ms 7.42% std::_Rb_tree::~_Rb_tree (inline) 1551ms 2.75% 32.11% 4172ms 7.41% std::_Rb_tree::_M_erase 0 0% 32.11% 4123ms 7.32% std::set::~set (inline) 1ms 0.0018% 32.11% 4037ms 7.17% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.012% 32.12% 4015ms 7.13% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.02% 32.14% 3898ms 6.92% MeshBasedCellPopulation::SpringIterator::operator++ 1303ms 2.31% 34.45% 3844ms 6.82% std::_Rb_tree::_M_get_insert_unique_pos 1223ms 2.17% 36.63% 3759ms 6.67% __GI___libc_free 20ms 0.036% 36.66% 3627ms 6.44% Node::AddElement 9ms 0.016% 36.68% 3614ms 6.42% TetrahedralMesh::ImportFromMesher 0 0% 36.68% 3547ms 6.30% std::_Rb_tree::_M_create_node (inline) 0 0% 36.68% 3517ms 6.24% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.68% 3514ms 6.24% std::_Rb_tree::_M_get_node (inline) 112ms 0.2% 36.88% 3451ms 6.13% tetgen::tetgenmesh::insphere_sos 5ms 0.0089% 36.89% 3394ms 6.03% std::set_intersection (inline) 241ms 0.43% 37.31% 3389ms 6.02% std::__set_intersection 3024ms 5.37% 42.68% 3322ms 5.90% tetgen::insphere 2545ms 4.52% 47.20% 3295ms 5.85% _int_malloc 0 0% 47.20% 3285ms 5.83% AbstractCellPopulation::WriteResultsToFiles 138ms 0.24% 47.44% 3265ms 5.80% std::__new_allocator::deallocate (inline) 0 0% 47.44% 3232ms 5.74% std::allocator_traits::deallocate (inline) 0 0% 47.44% 3153ms 5.60% VertexMesh::~VertexMesh 2952ms 5.24% 52.69% 2952ms 5.24% std::_Rb_tree::_S_right (inline) 207ms 0.37% 53.05% 2686ms 4.77% tetgen::tetgenmesh::flip23 205ms 0.36% 53.42% 2679ms 4.76% std::_Rb_tree_const_iterator::operator++ (inline) 72ms 0.13% 53.54% 2635ms 4.68% MutableElement::AddNode 1218ms 2.16% 55.71% 2532ms 4.50% _int_free 139ms 0.25% 55.95% 2380ms 4.23% Node::~Node 174ms 0.31% 56.26% 2171ms 3.85% VertexMesh::Clear 2ms 0.0036% 56.27% 2156ms 3.83% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 196ms 0.35% 56.61% 2127ms 3.78% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 56.61% 1988ms 3.53% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.61% 1980ms 3.52% std::_Rb_tree::_M_put_node (inline) 1965ms 3.49% 60.10% 1965ms 3.49% std::_Rb_tree_insert_and_rebalance 1ms 0.0018% 60.10% 1945ms 3.45% std::_Rb_tree_iterator::operator++ (inline) 157ms 0.28% 60.38% 1884ms 3.34% tetgen::tetgenmesh::flip32 7ms 0.012% 60.40% 1800ms 3.20% Element::Element 6ms 0.011% 60.41% 1503ms 2.67% Element::RegisterWithNodes (inline) 1369ms 2.43% 62.84% 1457ms 2.59% tetgen::orient3d 196ms 0.35% 63.18% 1441ms 2.56% TetrahedralMesh::Clear 169ms 0.3% 63.48% 1311ms 2.33% tetgen::tetgenmesh::enqueueflipface 24ms 0.043% 63.53% 1276ms 2.27% std::_Vector_base::_M_deallocate (inline) 843ms 1.50% 65.02% 1271ms 2.26% malloc_consolidate 24ms 0.043% 65.07% 1255ms 2.23% tetgen::tetgenmesh::locate 1239ms 2.20% 67.27% 1239ms 2.20% Node::GetIndex 0 0% 67.27% 1190ms 2.11% std::vector::~vector (inline) 90ms 0.16% 67.43% 1174ms 2.08% tetgen::tetgenmesh::preciselocate 1ms 0.0018% 67.43% 1097ms 1.95% std::_Vector_base::~_Vector_base (inline) 9ms 0.016% 67.44% 1082ms 1.92% _int_free_maybe_consolidate 40ms 0.071% 67.51% 1077ms 1.91% std::vector::_M_realloc_insert 58ms 0.1% 67.62% 1000ms 1.78% std::map::operator[] 941ms 1.67% 69.29% 941ms 1.67% tetgen::tetgenmesh::triface::triface 904ms 1.60% 70.89% 904ms 1.60% unlink_chunk 0 0% 70.89% 894ms 1.59% VoronoiDataWriter::Visit 0 0% 70.89% 872ms 1.55% std::_Rb_tree::lower_bound (inline) 0 0% 70.89% 872ms 1.55% std::map::lower_bound (inline) 6ms 0.011% 70.90% 837ms 1.49% std::_Vector_base::_M_allocate (inline) 2ms 0.0036% 70.91% 835ms 1.48% VertexMesh::GenerateVerticesFromElementCircumcentres 105ms 0.19% 71.09% 833ms 1.48% std::vector::push_back (inline) 668ms 1.19% 72.28% 823ms 1.46% AbstractElement::GetNodeGlobalIndex 0 0% 72.28% 795ms 1.41% TetrahedralMesh::RefreshJacobianCachedData 379ms 0.67% 72.95% 727ms 1.29% tetgen::tetgenmesh::fnextself 0 0% 72.95% 725ms 1.29% AbstractTwoBodyInteractionForce::AddForceContribution 718ms 1.27% 74.23% 718ms 1.27% tetgen::tetgenmesh::oppo 11ms 0.02% 74.25% 716ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.03% 74.28% 698ms 1.24% boost::numeric::ublas::vector_assign (inline) 688ms 1.22% 75.50% 688ms 1.22% [libchaste_mesh.so] 17ms 0.03% 75.53% 681ms 1.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.016% 75.54% 663ms 1.18% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.018% 75.56% 651ms 1.16% AbstractTetrahedralElement::CalculateJacobian 57ms 0.1% 75.66% 598ms 1.06% __atan2 273ms 0.48% 76.15% 592ms 1.05% AbstractElement::GetNodeLocation 0 0% 76.15% 589ms 1.05% std::set::find (inline) 559ms 0.99% 77.14% 559ms 0.99% tetgen::tetgenmesh::triface::operator= 438ms 0.78% 77.92% 541ms 0.96% __ieee754_atan2_fma 52ms 0.092% 78.01% 515ms 0.91% tetgen::tetgenmesh::enextfnext 502ms 0.89% 78.90% 502ms 0.89% AbstractElement::IsDeleted 0 0% 78.90% 498ms 0.88% std::insert_iterator::operator= (inline) 0 0% 78.90% 489ms 0.87% boost::numeric::ublas::inner_prod (inline) 488ms 0.87% 79.77% 488ms 0.87% Node::rGetLocation 7ms 0.012% 79.78% 486ms 0.86% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 335ms 0.59% 80.37% 484ms 0.86% tetgen::tetgenmesh::sym 483ms 0.86% 81.23% 483ms 0.86% std::vector::size (inline) 49ms 0.087% 81.32% 482ms 0.86% AbstractTetrahedralElement::RefreshJacobian 32ms 0.057% 81.38% 479ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 16ms 0.028% 81.40% 467ms 0.83% Element::CalculateCircumsphere 98ms 0.17% 81.58% 452ms 0.8% boost::numeric::ublas::indexing_vector_assign 42ms 0.075% 81.65% 451ms 0.8% tetgen::tetgenmesh::enext2fnext 0 0% 81.65% 447ms 0.79% std::_Rb_tree::_M_insert_unique_ (inline) 431ms 0.77% 82.42% 431ms 0.77% boost::numeric::ublas::c_vector::operator() 17ms 0.03% 82.45% 418ms 0.74% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0071% 82.45% 416ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 12ms 0.021% 82.48% 401ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 2ms 0.0036% 82.48% 398ms 0.71% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0018% 82.48% 396ms 0.7% Cell::GetCellId 0 0% 82.48% 394ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 96ms 0.17% 82.65% 392ms 0.7% __dynamic_cast 170ms 0.3% 82.95% 386ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 386ms 0.69% 83.64% 386ms 0.69% std::_Rb_tree_decrement 211ms 0.37% 84.01% 373ms 0.66% AbstractTetrahedralMesh::GetElement 31ms 0.055% 84.07% 373ms 0.66% tetgen::tetgenmesh::queue::push 15ms 0.027% 84.10% 371ms 0.66% std::vector::insert (inline) 371ms 0.66% 84.75% 371ms 0.66% tetgen::tetgenmesh::org 255ms 0.45% 85.21% 361ms 0.64% tetgen::tetgenmesh::bond 228ms 0.4% 85.61% 340ms 0.6% tetgen::tetgenmesh::link::add 5ms 0.0089% 85.62% 338ms 0.6% VertexElement::~VertexElement 52ms 0.092% 85.71% 323ms 0.57% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0018% 85.71% 314ms 0.56% AbstractCellProperty::IsSubType (inline) 142ms 0.25% 85.97% 306ms 0.54% Inverse 0 0% 85.97% 301ms 0.53% tcache_get (inline) 301ms 0.53% 86.50% 301ms 0.53% tcache_get_n (inline) 27ms 0.048% 86.55% 298ms 0.53% tetgen::insphereadapt 293ms 0.52% 87.07% 293ms 0.52% tetgen::tetgenmesh::pointmark 1ms 0.0018% 87.07% 291ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 87.07% 290ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.0089% 87.08% 284ms 0.5% VertexMesh::GetVolumeOfElement