File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47282ms, 86.51% of 54658ms total Dropped 855 nodes (cum <= 273.29ms) flat flat% sum% cum cum% 0 0% 0% 54610ms 99.91% __libc_start_call_main 0 0% 0% 54610ms 99.91% __libc_start_main_impl 0 0% 0% 54610ms 99.91% _start 0 0% 0% 54596ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54596ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54596ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54596ms 99.89% main 0 0% 0% 54562ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54562ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54562ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54316ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 45929ms 84.03% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45887ms 83.95% MeshBasedCellPopulation::Update 0 0% 0% 25582ms 46.80% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 25581ms 46.80% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 193ms 0.35% 0.35% 22687ms 41.51% VertexMesh::VertexMesh 0 0% 0.35% 16650ms 30.46% MutableMesh::ReMesh 0 0% 0.35% 12773ms 23.37% tetgen::tetrahedralize 2ms 0.0037% 0.36% 12639ms 23.12% tetgen::tetgenmesh::delaunizevertices 9ms 0.016% 0.37% 12634ms 23.11% tetgen::tetgenmesh::incrflipdelaunay 530ms 0.97% 1.34% 11227ms 20.54% tetgen::tetgenmesh::lawson 529ms 0.97% 2.31% 11070ms 20.25% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.055% 2.37% 9287ms 16.99% std::set::insert (inline) 340ms 0.62% 2.99% 8860ms 16.21% VertexElement::AddFace 228ms 0.42% 3.40% 8800ms 16.10% std::_Rb_tree::_M_insert_unique 3093ms 5.66% 9.06% 8552ms 15.65% std::_Rb_tree::_M_lower_bound (inline) 221ms 0.4% 9.47% 8039ms 14.71% std::_Rb_tree::find (inline) 0 0% 9.47% 7466ms 13.66% std::set::count (inline) 108ms 0.2% 9.67% 5337ms 9.76% std::less::operator() (inline) 282ms 0.52% 10.18% 5292ms 9.68% std::_Rb_tree::_M_insert_ (inline) 5278ms 9.66% 19.84% 5278ms 9.66% std::operator< (inline) 0 0% 19.84% 4949ms 9.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.84% 4840ms 8.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0037% 19.84% 4815ms 8.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 206ms 0.38% 20.22% 4529ms 8.29% operator new 1059ms 1.94% 22.16% 4250ms 7.78% __GI___libc_malloc 4213ms 7.71% 29.86% 4213ms 7.71% std::_Rb_tree_increment 9ms 0.016% 29.88% 4000ms 7.32% std::_Rb_tree::~_Rb_tree (inline) 39ms 0.071% 29.95% 3994ms 7.31% std::__new_allocator::allocate (inline) 3ms 0.0055% 29.96% 3993ms 7.31% MeshBasedCellPopulation::UpdateNodePairs 1550ms 2.84% 32.79% 3987ms 7.29% std::_Rb_tree::_M_erase 0 0% 32.79% 3978ms 7.28% std::allocator_traits::allocate (inline) 0 0% 32.79% 3960ms 7.25% std::set::~set (inline) 5ms 0.0091% 32.80% 3959ms 7.24% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.029% 32.83% 3856ms 7.05% MeshBasedCellPopulation::SpringIterator::operator++ 1226ms 2.24% 35.07% 3568ms 6.53% std::_Rb_tree::_M_get_insert_unique_pos 100ms 0.18% 35.26% 3410ms 6.24% tetgen::tetgenmesh::insphere_sos 1026ms 1.88% 37.13% 3363ms 6.15% __GI___libc_free 3016ms 5.52% 42.65% 3299ms 6.04% tetgen::insphere 0 0% 42.65% 3296ms 6.03% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.65% 3247ms 5.94% std::_Rb_tree::_M_create_node (inline) 4ms 0.0073% 42.66% 3221ms 5.89% std::set_intersection (inline) 250ms 0.46% 43.12% 3217ms 5.89% std::__set_intersection 0 0% 43.12% 3214ms 5.88% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.12% 3209ms 5.87% std::_Rb_tree::_M_get_node (inline) 7ms 0.013% 43.13% 3119ms 5.71% TetrahedralMesh::ImportFromMesher 24ms 0.044% 43.17% 3109ms 5.69% Node::AddElement 131ms 0.24% 43.41% 3008ms 5.50% std::__new_allocator::deallocate (inline) 0 0% 43.41% 2984ms 5.46% std::allocator_traits::deallocate (inline) 0 0% 43.41% 2909ms 5.32% VertexMesh::~VertexMesh 2178ms 3.98% 47.40% 2858ms 5.23% _int_malloc 2803ms 5.13% 52.53% 2803ms 5.13% std::_Rb_tree::_S_right (inline) 184ms 0.34% 52.86% 2797ms 5.12% tetgen::tetgenmesh::flip23 183ms 0.33% 53.20% 2528ms 4.63% std::_Rb_tree_const_iterator::operator++ (inline) 1174ms 2.15% 55.35% 2335ms 4.27% _int_free 66ms 0.12% 55.47% 2282ms 4.18% MutableElement::AddNode 132ms 0.24% 55.71% 2221ms 4.06% Node::~Node 2ms 0.0037% 55.71% 2213ms 4.05% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 201ms 0.37% 56.08% 2173ms 3.98% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 172ms 0.31% 56.39% 1998ms 3.66% VertexMesh::Clear 2ms 0.0037% 56.40% 1986ms 3.63% std::_Rb_tree_iterator::operator++ (inline) 151ms 0.28% 56.67% 1939ms 3.55% tetgen::tetgenmesh::flip32 1866ms 3.41% 60.09% 1866ms 3.41% std::_Rb_tree_insert_and_rebalance 0 0% 60.09% 1830ms 3.35% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.09% 1817ms 3.32% std::_Rb_tree::_M_put_node (inline) 2ms 0.0037% 60.09% 1587ms 2.90% Element::Element 1341ms 2.45% 62.55% 1435ms 2.63% tetgen::orient3d 163ms 0.3% 62.84% 1358ms 2.48% tetgen::tetgenmesh::enqueueflipface 1285ms 2.35% 65.19% 1285ms 2.35% Node::GetIndex 4ms 0.0073% 65.20% 1282ms 2.35% Element::RegisterWithNodes (inline) 162ms 0.3% 65.50% 1267ms 2.32% TetrahedralMesh::Clear 31ms 0.057% 65.55% 1191ms 2.18% tetgen::tetgenmesh::locate 19ms 0.035% 65.59% 1186ms 2.17% std::_Vector_base::_M_deallocate (inline) 739ms 1.35% 66.94% 1170ms 2.14% malloc_consolidate 0 0% 66.94% 1099ms 2.01% std::vector::~vector (inline) 93ms 0.17% 67.11% 1098ms 2.01% tetgen::tetgenmesh::preciselocate 58ms 0.11% 67.22% 1032ms 1.89% std::map::operator[] 51ms 0.093% 67.31% 1015ms 1.86% std::vector::_M_realloc_insert 1015ms 1.86% 69.17% 1015ms 1.86% tetgen::tetgenmesh::triface::triface 1ms 0.0018% 69.17% 1005ms 1.84% std::_Vector_base::~_Vector_base (inline) 7ms 0.013% 69.18% 989ms 1.81% _int_free_maybe_consolidate 0 0% 69.18% 904ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 69.18% 904ms 1.65% std::map::lower_bound (inline) 0 0% 69.18% 857ms 1.57% VoronoiDataWriter::Visit 854ms 1.56% 70.75% 854ms 1.56% unlink_chunk 412ms 0.75% 71.50% 833ms 1.52% tetgen::tetgenmesh::fnextself 100ms 0.18% 71.68% 824ms 1.51% std::vector::push_back (inline) 659ms 1.21% 72.89% 802ms 1.47% AbstractElement::GetNodeGlobalIndex 8ms 0.015% 72.90% 791ms 1.45% VertexMesh::GenerateVerticesFromElementCircumcentres 3ms 0.0055% 72.91% 772ms 1.41% std::_Vector_base::_M_allocate (inline) 1ms 0.0018% 72.91% 735ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.0055% 72.92% 706ms 1.29% AbstractTwoBodyInteractionForce::AddForceContribution 706ms 1.29% 74.21% 706ms 1.29% tetgen::tetgenmesh::oppo 20ms 0.037% 74.24% 684ms 1.25% boost::numeric::ublas::vector_assign (inline) 12ms 0.022% 74.27% 676ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 670ms 1.23% 75.49% 670ms 1.23% [libchaste_mesh.so] 14ms 0.026% 75.52% 653ms 1.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.024% 75.54% 649ms 1.19% boost::numeric::ublas::c_vector::c_vector (inline) 48ms 0.088% 75.63% 619ms 1.13% __atan2 16ms 0.029% 75.66% 597ms 1.09% AbstractTetrahedralElement::CalculateJacobian 449ms 0.82% 76.48% 571ms 1.04% __ieee754_atan2_fma 0 0% 76.48% 569ms 1.04% std::set::find (inline) 569ms 1.04% 77.52% 569ms 1.04% tetgen::tetgenmesh::triface::operator= 41ms 0.075% 77.60% 548ms 1.00% tetgen::tetgenmesh::enext2fnext 47ms 0.086% 77.68% 544ms 1% tetgen::tetgenmesh::enextfnext 221ms 0.4% 78.09% 535ms 0.98% AbstractElement::GetNodeLocation 0 0% 78.09% 471ms 0.86% std::insert_iterator::operator= (inline) 0 0% 78.09% 469ms 0.86% boost::numeric::ublas::inner_prod (inline) 4ms 0.0073% 78.09% 465ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 462ms 0.85% 78.94% 462ms 0.85% std::vector::size (inline) 34ms 0.062% 79.00% 461ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 22ms 0.04% 79.04% 455ms 0.83% Element::CalculateCircumsphere 42ms 0.077% 79.12% 443ms 0.81% AbstractTetrahedralElement::RefreshJacobian 26ms 0.048% 79.16% 441ms 0.81% tetgen::tetgenmesh::queue::push 438ms 0.8% 79.97% 438ms 0.8% Node::rGetLocation 430ms 0.79% 80.75% 430ms 0.79% boost::numeric::ublas::c_vector::operator() 96ms 0.18% 80.93% 427ms 0.78% boost::numeric::ublas::indexing_vector_assign 318ms 0.58% 81.51% 427ms 0.78% tetgen::tetgenmesh::sym 1ms 0.0018% 81.51% 425ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 291ms 0.53% 82.04% 409ms 0.75% tetgen::tetgenmesh::link::add 6ms 0.011% 82.06% 404ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 231ms 0.42% 82.48% 395ms 0.72% AbstractTetrahedralMesh::GetElement 96ms 0.18% 82.65% 386ms 0.71% __dynamic_cast 29ms 0.053% 82.71% 386ms 0.71% std::_Rb_tree_iterator::operator-- (inline) 0 0% 82.71% 385ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0091% 82.72% 382ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.035% 82.75% 379ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 158ms 0.29% 83.04% 367ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0018% 83.04% 366ms 0.67% Cell::GetCellId 352ms 0.64% 83.69% 352ms 0.64% AbstractElement::IsDeleted 346ms 0.63% 84.32% 346ms 0.63% tetgen::tetgenmesh::org 240ms 0.44% 84.76% 343ms 0.63% tetgen::tetgenmesh::bond 333ms 0.61% 85.37% 333ms 0.61% std::_Rb_tree_decrement 4ms 0.0073% 85.37% 319ms 0.58% VertexElement::~VertexElement 12ms 0.022% 85.40% 318ms 0.58% std::vector::insert (inline) 151ms 0.28% 85.67% 315ms 0.58% Inverse 3ms 0.0055% 85.68% 311ms 0.57% AbstractCellProperty::IsSubType (inline) 6ms 0.011% 85.69% 304ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 47ms 0.086% 85.78% 299ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.78% 292ms 0.53% tcache_get (inline) 292ms 0.53% 86.31% 292ms 0.53% tcache_get_n (inline) 69ms 0.13% 86.44% 285ms 0.52% tetgen::tetgenmesh::queue::pop 38ms 0.07% 86.51% 283ms 0.52% tetgen::insphereadapt 0 0% 86.51% 274ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)