File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49596ms, 86.88% of 57088ms total Dropped 889 nodes (cum <= 285.44ms) flat flat% sum% cum cum% 0 0% 0% 57032ms 99.90% __libc_start_call_main 0 0% 0% 57032ms 99.90% __libc_start_main_impl 0 0% 0% 57032ms 99.90% _start 0 0% 0% 57016ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57016ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57016ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57016ms 99.87% main 0 0% 0% 56977ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56977ms 99.81% CxxTest::TestRunner::runTest (inline) 1ms 0.0018% 0.0018% 56977ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0.0018% 56733ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0.0018% 48237ms 84.50% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0018% 48195ms 84.42% MeshBasedCellPopulation::Update 0 0% 0.0018% 27843ms 48.77% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0018% 27841ms 48.77% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 192ms 0.34% 0.34% 24529ms 42.97% VertexMesh::VertexMesh 0 0% 0.34% 16696ms 29.25% MutableMesh::ReMesh 0 0% 0.34% 12637ms 22.14% tetgen::tetrahedralize 1ms 0.0018% 0.34% 12501ms 21.90% tetgen::tetgenmesh::delaunizevertices 12ms 0.021% 0.36% 12496ms 21.89% tetgen::tetgenmesh::incrflipdelaunay 573ms 1.00% 1.36% 11378ms 19.93% TetrahedralMesh::EdgeIterator::operator++ 568ms 0.99% 2.36% 11008ms 19.28% tetgen::tetgenmesh::lawson 27ms 0.047% 2.41% 9908ms 17.36% std::set::insert (inline) 214ms 0.37% 2.78% 9411ms 16.49% std::_Rb_tree::_M_insert_unique 375ms 0.66% 3.44% 9033ms 15.82% VertexElement::AddFace 2910ms 5.10% 8.54% 8468ms 14.83% std::_Rb_tree::_M_lower_bound (inline) 215ms 0.38% 8.91% 7881ms 13.81% std::_Rb_tree::find (inline) 0 0% 8.91% 7310ms 12.80% std::set::count (inline) 276ms 0.48% 9.40% 5551ms 9.72% std::_Rb_tree::_M_insert_ (inline) 108ms 0.19% 9.59% 5419ms 9.49% std::less::operator() (inline) 5369ms 9.40% 18.99% 5369ms 9.40% std::operator< (inline) 0 0% 18.99% 4970ms 8.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 198ms 0.35% 19.34% 4917ms 8.61% operator new 4892ms 8.57% 27.91% 4892ms 8.57% std::_Rb_tree_increment 0 0% 27.91% 4847ms 8.49% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0035% 27.91% 4821ms 8.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 1092ms 1.91% 29.82% 4672ms 8.18% __GI___libc_malloc 49ms 0.086% 29.91% 4203ms 7.36% std::__new_allocator::allocate (inline) 0 0% 29.91% 4181ms 7.32% std::allocator_traits::allocate (inline) 9ms 0.016% 29.92% 4133ms 7.24% std::_Rb_tree::~_Rb_tree (inline) 1626ms 2.85% 32.77% 4121ms 7.22% std::_Rb_tree::_M_erase 0 0% 32.77% 4074ms 7.14% std::set::~set (inline) 0 0% 32.77% 4016ms 7.03% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.014% 32.79% 3953ms 6.92% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1252ms 2.19% 34.98% 3944ms 6.91% std::_Rb_tree::_M_get_insert_unique_pos 4ms 0.007% 34.99% 3871ms 6.78% std::set_intersection (inline) 13ms 0.023% 35.01% 3867ms 6.77% MeshBasedCellPopulation::SpringIterator::operator++ 249ms 0.44% 35.45% 3867ms 6.77% std::__set_intersection 1120ms 1.96% 37.41% 3711ms 6.50% __GI___libc_free 21ms 0.037% 37.44% 3567ms 6.25% Node::AddElement 111ms 0.19% 37.64% 3418ms 5.99% tetgen::tetgenmesh::insphere_sos 0 0% 37.64% 3399ms 5.95% std::_Rb_tree::_M_create_node (inline) 0 0% 37.64% 3369ms 5.90% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0018% 37.64% 3363ms 5.89% AbstractCellPopulation::WriteResultsToFiles 0 0% 37.64% 3362ms 5.89% std::_Rb_tree::_M_get_node (inline) 0 0% 37.64% 3326ms 5.83% VertexMesh::~VertexMesh 3008ms 5.27% 42.91% 3286ms 5.76% tetgen::insphere 11ms 0.019% 42.93% 3253ms 5.70% TetrahedralMesh::ImportFromMesher 140ms 0.25% 43.17% 3251ms 5.69% std::__new_allocator::deallocate (inline) 2406ms 4.21% 47.39% 3242ms 5.68% _int_malloc 0 0% 47.39% 3235ms 5.67% std::allocator_traits::deallocate (inline) 3163ms 5.54% 52.93% 3163ms 5.54% std::_Rb_tree::_S_right (inline) 176ms 0.31% 53.24% 3132ms 5.49% std::_Rb_tree_const_iterator::operator++ (inline) 71ms 0.12% 53.36% 2733ms 4.79% MutableElement::AddNode 186ms 0.33% 53.69% 2696ms 4.72% tetgen::tetgenmesh::flip23 1119ms 1.96% 55.65% 2589ms 4.54% _int_free 148ms 0.26% 55.91% 2365ms 4.14% Node::~Node 2ms 0.0035% 55.91% 2258ms 3.96% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 205ms 0.36% 56.27% 2233ms 3.91% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 186ms 0.33% 56.60% 2196ms 3.85% VertexMesh::Clear 0 0% 56.60% 2034ms 3.56% std::_Rb_tree_iterator::operator++ (inline) 1977ms 3.46% 60.06% 1977ms 3.46% std::_Rb_tree_insert_and_rebalance 167ms 0.29% 60.35% 1859ms 3.26% tetgen::tetgenmesh::flip32 0 0% 60.35% 1852ms 3.24% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.35% 1846ms 3.23% std::_Rb_tree::_M_put_node (inline) 5ms 0.0088% 60.36% 1589ms 2.78% Element::Element 1002ms 1.76% 62.11% 1428ms 2.50% malloc_consolidate 1418ms 2.48% 64.60% 1418ms 2.48% Node::GetIndex 16ms 0.028% 64.63% 1405ms 2.46% std::_Vector_base::_M_deallocate (inline) 1297ms 2.27% 66.90% 1383ms 2.42% tetgen::orient3d 181ms 0.32% 67.22% 1338ms 2.34% TetrahedralMesh::Clear 0 0% 67.22% 1313ms 2.30% std::vector::~vector (inline) 4ms 0.007% 67.22% 1300ms 2.28% Element::RegisterWithNodes (inline) 182ms 0.32% 67.54% 1272ms 2.23% tetgen::tetgenmesh::enqueueflipface 23ms 0.04% 67.58% 1260ms 2.21% tetgen::tetgenmesh::locate 8ms 0.014% 67.60% 1237ms 2.17% _int_free_maybe_consolidate 1ms 0.0018% 67.60% 1231ms 2.16% std::_Vector_base::~_Vector_base (inline) 110ms 0.19% 67.79% 1184ms 2.07% tetgen::tetgenmesh::preciselocate 88ms 0.15% 67.94% 1076ms 1.88% std::vector::_M_realloc_insert 65ms 0.11% 68.06% 1057ms 1.85% std::map::operator[] 1004ms 1.76% 69.82% 1004ms 1.76% unlink_chunk 0 0% 69.82% 923ms 1.62% std::_Rb_tree::lower_bound (inline) 0 0% 69.82% 923ms 1.62% std::map::lower_bound (inline) 1ms 0.0018% 69.82% 919ms 1.61% VertexMesh::GenerateVerticesFromElementCircumcentres 905ms 1.59% 71.40% 905ms 1.59% tetgen::tetgenmesh::triface::triface 106ms 0.19% 71.59% 895ms 1.57% std::vector::push_back (inline) 721ms 1.26% 72.85% 886ms 1.55% AbstractElement::GetNodeGlobalIndex 0 0% 72.85% 878ms 1.54% VoronoiDataWriter::Visit 8ms 0.014% 72.87% 827ms 1.45% std::_Vector_base::_M_allocate (inline) 0 0% 72.87% 779ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 392ms 0.69% 73.55% 749ms 1.31% tetgen::tetgenmesh::fnextself 0 0% 73.55% 708ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.028% 73.58% 700ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 685ms 1.20% 74.78% 685ms 1.20% [libchaste_mesh.so] 18ms 0.032% 74.81% 665ms 1.16% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 25ms 0.044% 74.86% 661ms 1.16% boost::numeric::ublas::vector_assign (inline) 14ms 0.025% 74.88% 626ms 1.10% boost::numeric::ublas::c_vector::c_vector (inline) 20ms 0.035% 74.92% 607ms 1.06% AbstractTetrahedralElement::CalculateJacobian 605ms 1.06% 75.98% 605ms 1.06% tetgen::tetgenmesh::oppo 586ms 1.03% 77.00% 586ms 1.03% tetgen::tetgenmesh::triface::operator= 255ms 0.45% 77.45% 578ms 1.01% AbstractElement::GetNodeLocation 50ms 0.088% 77.54% 578ms 1.01% __atan2 0 0% 77.54% 571ms 1.00% std::set::find (inline) 534ms 0.94% 78.47% 534ms 0.94% AbstractElement::IsDeleted 415ms 0.73% 79.20% 527ms 0.92% __ieee754_atan2_fma 520ms 0.91% 80.11% 520ms 0.91% Node::rGetLocation 46ms 0.081% 80.19% 519ms 0.91% tetgen::tetgenmesh::enext2fnext 0 0% 80.19% 507ms 0.89% boost::numeric::ublas::inner_prod (inline) 7ms 0.012% 80.20% 502ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 80.20% 498ms 0.87% std::insert_iterator::operator= (inline) 498ms 0.87% 81.07% 498ms 0.87% std::vector::size (inline) 40ms 0.07% 81.14% 495ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 21ms 0.037% 81.18% 481ms 0.84% Element::CalculateCircumsphere 52ms 0.091% 81.27% 478ms 0.84% tetgen::tetgenmesh::enextfnext 298ms 0.52% 81.79% 451ms 0.79% tetgen::tetgenmesh::sym 1ms 0.0018% 81.80% 446ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 34ms 0.06% 81.86% 429ms 0.75% AbstractTetrahedralElement::RefreshJacobian 422ms 0.74% 82.60% 422ms 0.74% boost::numeric::ublas::c_vector::operator() 112ms 0.2% 82.79% 409ms 0.72% boost::numeric::ublas::indexing_vector_assign 408ms 0.71% 83.51% 408ms 0.71% tetgen::tetgenmesh::org 161ms 0.28% 83.79% 405ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 20ms 0.035% 83.82% 399ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 27ms 0.047% 83.87% 398ms 0.7% tetgen::tetgenmesh::queue::push 230ms 0.4% 84.27% 392ms 0.69% AbstractTetrahedralMesh::GetElement 3ms 0.0053% 84.28% 390ms 0.68% Cell::GetCellId 2ms 0.0035% 84.28% 389ms 0.68% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.28% 389ms 0.68% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0088% 84.29% 377ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 17ms 0.03% 84.32% 374ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 259ms 0.45% 84.77% 368ms 0.64% tetgen::tetgenmesh::link::add 250ms 0.44% 85.21% 361ms 0.63% tetgen::tetgenmesh::bond 82ms 0.14% 85.36% 359ms 0.63% __dynamic_cast 343ms 0.6% 85.96% 343ms 0.6% std::_Rb_tree_decrement 63ms 0.11% 86.07% 326ms 0.57% boost::numeric::ublas::vector_reference::operator() (inline) 6ms 0.011% 86.08% 324ms 0.57% VertexElement::~VertexElement 142ms 0.25% 86.33% 318ms 0.56% Inverse 3ms 0.0053% 86.33% 311ms 0.54% AbstractCellProperty::IsSubType (inline) 0 0% 86.33% 308ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 11ms 0.019% 86.35% 307ms 0.54% std::vector::insert (inline) 0 0% 86.35% 298ms 0.52% tcache_get (inline) 298ms 0.52% 86.87% 298ms 0.52% tcache_get_n (inline) 2ms 0.0035% 86.88% 286ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement