File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52892ms, 86.40% of 61221ms total Dropped 864 nodes (cum <= 306.11ms) flat flat% sum% cum cum% 0 0% 0% 61180ms 99.93% __libc_start_call_main 0 0% 0% 61180ms 99.93% __libc_start_main_impl 0 0% 0% 61180ms 99.93% _start 0 0% 0% 61163ms 99.91% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61163ms 99.91% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61163ms 99.91% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61163ms 99.91% main 0 0% 0% 61133ms 99.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61133ms 99.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61133ms 99.86% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60919ms 99.51% AbstractCellBasedSimulation::Solve 0 0% 0% 50137ms 81.90% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50071ms 81.79% MeshBasedCellPopulation::Update 0 0% 0% 30965ms 50.58% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30963ms 50.58% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 243ms 0.4% 0.4% 27734ms 45.30% VertexMesh::VertexMesh 0 0% 0.4% 14659ms 23.94% MutableMesh::ReMesh 484ms 0.79% 1.19% 13946ms 22.78% TetrahedralMesh::EdgeIterator::operator++ 33ms 0.054% 1.24% 11427ms 18.67% std::set::insert (inline) 3967ms 6.48% 7.72% 11130ms 18.18% std::_Rb_tree::_M_lower_bound (inline) 146ms 0.24% 7.96% 10900ms 17.80% std::_Rb_tree::_M_insert_unique 0 0% 7.96% 10541ms 17.22% tetgen::tetrahedralize 179ms 0.29% 8.25% 10470ms 17.10% std::_Rb_tree::find (inline) 0 0% 8.25% 10434ms 17.04% tetgen::tetgenmesh::delaunizevertices 4ms 0.0065% 8.26% 10430ms 17.04% tetgen::tetgenmesh::incrflipdelaunay 247ms 0.4% 8.66% 9981ms 16.30% VertexElement::AddFace 0 0% 8.66% 9941ms 16.24% std::set::count (inline) 449ms 0.73% 9.40% 9189ms 15.01% tetgen::tetgenmesh::lawson 196ms 0.32% 9.72% 7338ms 11.99% operator new 266ms 0.43% 10.15% 7109ms 11.61% std::_Rb_tree::_M_insert_ (inline) 2402ms 3.92% 14.07% 7092ms 11.58% __GI___libc_malloc 6497ms 10.61% 24.69% 6497ms 10.61% std::_Rb_tree_increment 63ms 0.1% 24.79% 6289ms 10.27% std::__new_allocator::allocate (inline) 0 0% 24.79% 6268ms 10.24% std::allocator_traits::allocate (inline) 77ms 0.13% 24.91% 6218ms 10.16% std::less::operator() (inline) 6213ms 10.15% 35.06% 6213ms 10.15% std::operator< (inline) 0 0% 35.06% 5931ms 9.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 35.06% 5769ms 9.42% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0033% 35.07% 5753ms 9.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 35.07% 5096ms 8.32% std::_Rb_tree::_M_create_node (inline) 0 0% 35.07% 5070ms 8.28% std::_Rb_tree::_M_get_node (inline) 0 0% 35.07% 5060ms 8.27% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.07% 4753ms 7.76% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.015% 35.08% 4749ms 7.76% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 35.08% 4701ms 7.68% AbstractCellPopulation::WriteResultsToFiles 15ms 0.025% 35.11% 4621ms 7.55% MeshBasedCellPopulation::SpringIterator::operator++ 808ms 1.32% 36.43% 4520ms 7.38% __GI___libc_free 278ms 0.45% 36.88% 4442ms 7.26% std::__set_intersection 0 0% 36.88% 4442ms 7.26% std::set_intersection (inline) 3343ms 5.46% 42.34% 4236ms 6.92% _int_malloc 11ms 0.018% 42.36% 4025ms 6.57% std::_Rb_tree::~_Rb_tree (inline) 1201ms 1.96% 44.32% 3999ms 6.53% std::_Rb_tree::_M_erase 0 0% 44.32% 3978ms 6.50% std::set::~set (inline) 1280ms 2.09% 46.41% 3977ms 6.50% std::_Rb_tree::_M_get_insert_unique_pos 66ms 0.11% 46.52% 3974ms 6.49% Node::AddElement 71ms 0.12% 46.63% 3913ms 6.39% std::__new_allocator::deallocate (inline) 0 0% 46.63% 3892ms 6.36% std::allocator_traits::deallocate (inline) 3739ms 6.11% 52.74% 3739ms 6.11% std::_Rb_tree::_S_right (inline) 262ms 0.43% 53.17% 3699ms 6.04% std::_Rb_tree_iterator::operator++ (inline) 1835ms 3.00% 56.17% 3698ms 6.04% _int_free 1ms 0.0016% 56.17% 3678ms 6.01% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 246ms 0.4% 56.57% 3630ms 5.93% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.0082% 56.58% 3436ms 5.61% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 56.58% 3247ms 5.30% VertexMesh::~VertexMesh 3ms 0.0049% 56.58% 3230ms 5.28% TetrahedralMesh::ImportFromMesher 36ms 0.059% 56.64% 2873ms 4.69% MutableElement::AddNode 98ms 0.16% 56.80% 2786ms 4.55% tetgen::tetgenmesh::insphere_sos 2496ms 4.08% 60.88% 2660ms 4.34% tetgen::insphere 0 0% 60.88% 2335ms 3.81% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.88% 2314ms 3.78% std::_Rb_tree::_M_put_node (inline) 215ms 0.35% 61.23% 2219ms 3.62% tetgen::tetgenmesh::flip23 2044ms 3.34% 64.57% 2044ms 3.34% [libchaste_mesh.so] 35ms 0.057% 64.63% 2012ms 3.29% Node::~Node 39ms 0.064% 64.69% 1960ms 3.20% VertexMesh::Clear 4ms 0.0065% 64.70% 1924ms 3.14% Element::Element 1890ms 3.09% 67.78% 1890ms 3.09% std::_Rb_tree_insert_and_rebalance 997ms 1.63% 69.41% 1642ms 2.68% malloc_consolidate 23ms 0.038% 69.45% 1601ms 2.62% std::_Vector_base::_M_deallocate (inline) 2ms 0.0033% 69.45% 1600ms 2.61% Element::RegisterWithNodes (inline) 1435ms 2.34% 71.80% 1498ms 2.45% tetgen::orient3d 0 0% 71.80% 1485ms 2.43% std::vector::~vector (inline) 205ms 0.33% 72.13% 1473ms 2.41% tetgen::tetgenmesh::flip32 6ms 0.0098% 72.14% 1439ms 2.35% std::_Vector_base::~_Vector_base (inline) 5ms 0.0082% 72.15% 1416ms 2.31% _int_free_maybe_consolidate 44ms 0.072% 72.22% 1357ms 2.22% std::vector::_M_realloc_insert 78ms 0.13% 72.35% 1338ms 2.19% std::map::operator[] 1254ms 2.05% 74.40% 1254ms 2.05% Node::GetIndex 2ms 0.0033% 74.40% 1200ms 1.96% std::_Vector_base::_M_allocate (inline) 0 0% 74.40% 1165ms 1.90% std::_Rb_tree::lower_bound (inline) 0 0% 74.40% 1165ms 1.90% std::map::lower_bound (inline) 1137ms 1.86% 76.26% 1137ms 1.86% unlink_chunk 75ms 0.12% 76.38% 1080ms 1.76% std::vector::push_back (inline) 1ms 0.0016% 76.38% 1061ms 1.73% VertexMesh::GenerateVerticesFromElementCircumcentres 27ms 0.044% 76.43% 1052ms 1.72% tetgen::tetgenmesh::locate 1ms 0.0016% 76.43% 1050ms 1.72% VoronoiDataWriter::Visit 79ms 0.13% 76.56% 987ms 1.61% tetgen::tetgenmesh::preciselocate 183ms 0.3% 76.86% 970ms 1.58% tetgen::tetgenmesh::enqueueflipface 5ms 0.0082% 76.86% 948ms 1.55% TetrahedralMesh::Clear 1ms 0.0016% 76.87% 868ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 488ms 0.8% 77.66% 816ms 1.33% AbstractElement::GetNodeGlobalIndex 7ms 0.011% 77.67% 768ms 1.25% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 77.67% 747ms 1.22% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.015% 77.69% 710ms 1.16% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 683ms 1.12% 78.80% 683ms 1.12% Node::rGetLocation 10ms 0.016% 78.82% 650ms 1.06% AbstractTetrahedralElement::CalculateJacobian 6ms 0.0098% 78.83% 627ms 1.02% boost::numeric::ublas::vector_assign (inline) 2ms 0.0033% 78.83% 607ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 307ms 0.5% 79.34% 602ms 0.98% AbstractElement::GetNodeLocation 344ms 0.56% 79.90% 575ms 0.94% tetgen::tetgenmesh::sym 0 0% 79.90% 529ms 0.86% std::insert_iterator::operator= (inline) 34ms 0.056% 79.95% 528ms 0.86% __atan2 0 0% 79.95% 527ms 0.86% std::set::find (inline) 524ms 0.86% 80.81% 524ms 0.86% tetgen::tetgenmesh::oppo 100ms 0.16% 80.97% 504ms 0.82% std::_Rb_tree_iterator::operator-- (inline) 20ms 0.033% 81.00% 492ms 0.8% AbstractTetrahedralElement::RefreshJacobian 12ms 0.02% 81.02% 492ms 0.8% Element::CalculateCircumsphere 448ms 0.73% 81.76% 487ms 0.8% __ieee754_atan2_fma 486ms 0.79% 82.55% 486ms 0.79% std::vector::size (inline) 0 0% 82.55% 468ms 0.76% std::_Rb_tree::_M_insert_unique_ (inline) 9ms 0.015% 82.56% 420ms 0.69% CellPropertyCollection::GetPropertiesType (inline) 0 0% 82.56% 415ms 0.68% Cell::GetCellId 15ms 0.025% 82.59% 409ms 0.67% std::vector::insert (inline) 0 0% 82.59% 381ms 0.62% boost::numeric::ublas::inner_prod (inline) 148ms 0.24% 82.83% 380ms 0.62% Inverse 16ms 0.026% 82.86% 378ms 0.62% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.86% 378ms 0.62% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 377ms 0.62% 83.47% 377ms 0.62% std::_Rb_tree_decrement 1ms 0.0016% 83.47% 373ms 0.61% tcache_get (inline) 372ms 0.61% 84.08% 372ms 0.61% tcache_get_n (inline) 0 0% 84.08% 356ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 348ms 0.57% 84.65% 348ms 0.57% AbstractElement::IsDeleted 344ms 0.56% 85.21% 344ms 0.56% boost::numeric::ublas::c_vector::operator() 11ms 0.018% 85.23% 342ms 0.56% VertexMesh::CalculateUnitNormalToFaceWithArea 108ms 0.18% 85.41% 338ms 0.55% boost::numeric::ublas::vector_inner_prod::apply (inline) 84ms 0.14% 85.54% 332ms 0.54% __dynamic_cast 26ms 0.042% 85.59% 328ms 0.54% tetgen::tetgenmesh::enext2fnext 6ms 0.0098% 85.60% 327ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 4ms 0.0065% 85.60% 321ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 264ms 0.43% 86.03% 319ms 0.52% tetgen::tetgenmesh::fnextself 221ms 0.36% 86.40% 307ms 0.5% AbstractTetrahedralMesh::GetElement