File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 63991ms, 86.74% of 73772ms total Dropped 850 nodes (cum <= 368.86ms) flat flat% sum% cum cum% 0 0% 0% 73715ms 99.92% __libc_start_call_main 0 0% 0% 73715ms 99.92% __libc_start_main_impl 0 0% 0% 73715ms 99.92% _start 0 0% 0% 73700ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 73700ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 73700ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 73700ms 99.90% main 0 0% 0% 73661ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 73661ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 73661ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 73394ms 99.49% AbstractCellBasedSimulation::Solve 0 0% 0% 63750ms 86.41% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 63675ms 86.31% MeshBasedCellPopulation::Update 0 0% 0% 41192ms 55.84% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 41191ms 55.84% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 572ms 0.78% 0.78% 35973ms 48.76% VertexMesh::VertexMesh 0 0% 0.78% 18150ms 24.60% MutableMesh::ReMesh 575ms 0.78% 1.55% 13961ms 18.92% TetrahedralMesh::EdgeIterator::operator++ 33ms 0.045% 1.60% 13894ms 18.83% std::set::insert (inline) 203ms 0.28% 1.87% 13356ms 18.10% std::_Rb_tree::_M_insert_unique 0 0% 1.87% 12710ms 17.23% tetgen::tetrahedralize 3ms 0.0041% 1.88% 12546ms 17.01% tetgen::tetgenmesh::delaunizevertices 7ms 0.0095% 1.89% 12535ms 16.99% tetgen::tetgenmesh::incrflipdelaunay 437ms 0.59% 2.48% 12437ms 16.86% VertexElement::AddFace 598ms 0.81% 3.29% 11206ms 15.19% tetgen::tetgenmesh::lawson 2740ms 3.71% 7.01% 9958ms 13.50% std::_Rb_tree::_M_lower_bound (inline) 229ms 0.31% 7.32% 9699ms 13.15% operator new 270ms 0.37% 7.68% 9428ms 12.78% std::_Rb_tree::find (inline) 2952ms 4.00% 11.68% 9354ms 12.68% __GI___libc_malloc 0 0% 11.68% 8929ms 12.10% std::set::count (inline) 290ms 0.39% 12.08% 8763ms 11.88% std::_Rb_tree::_M_insert_ (inline) 79ms 0.11% 12.18% 7794ms 10.56% std::__new_allocator::allocate (inline) 0 0% 12.18% 7761ms 10.52% std::allocator_traits::allocate (inline) 7059ms 9.57% 21.75% 7059ms 9.57% std::_Rb_tree_increment 3ms 0.0041% 21.76% 6701ms 9.08% std::set_intersection (inline) 444ms 0.6% 22.36% 6698ms 9.08% std::__set_intersection 1125ms 1.52% 23.88% 6400ms 8.68% __GI___libc_free 0 0% 23.88% 6262ms 8.49% std::_Rb_tree::_M_create_node (inline) 0 0% 23.88% 6230ms 8.44% std::_Rb_tree::_M_get_node (inline) 0 0% 23.88% 6212ms 8.42% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 23.88% 6096ms 8.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 6084ms 8.25% 32.13% 6084ms 8.25% std::operator< (inline) 25ms 0.034% 32.16% 6029ms 8.17% std::less::operator() (inline) 4552ms 6.17% 38.33% 5969ms 8.09% _int_malloc 2ms 0.0027% 38.34% 5924ms 8.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0054% 38.34% 5894ms 7.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 27ms 0.037% 38.38% 5766ms 7.82% Node::AddElement 276ms 0.37% 38.75% 5669ms 7.68% std::_Rb_tree_const_iterator::operator++ (inline) 109ms 0.15% 38.90% 5437ms 7.37% std::__new_allocator::deallocate (inline) 0 0% 38.90% 5416ms 7.34% std::allocator_traits::deallocate (inline) 0 0% 38.90% 5257ms 7.13% VertexMesh::~VertexMesh 2068ms 2.80% 41.70% 5235ms 7.10% _int_free 5046ms 6.84% 48.54% 5046ms 6.84% std::_Rb_tree::_S_right (inline) 15ms 0.02% 48.56% 4907ms 6.65% std::_Rb_tree::~_Rb_tree (inline) 1479ms 2.00% 50.57% 4871ms 6.60% std::_Rb_tree::_M_erase 0 0% 50.57% 4843ms 6.56% std::set::~set (inline) 3ms 0.0041% 50.57% 4809ms 6.52% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1222ms 1.66% 52.23% 4726ms 6.41% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 52.23% 4700ms 6.37% MeshBasedCellPopulation::UpdateNodePairs 16ms 0.022% 52.25% 4523ms 6.13% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.015% 52.27% 4390ms 5.95% TetrahedralMesh::ImportFromMesher 67ms 0.091% 52.36% 4162ms 5.64% MutableElement::AddNode 0 0% 52.36% 3346ms 4.54% AbstractCellPopulation::WriteResultsToFiles 2098ms 2.84% 55.20% 2976ms 4.03% malloc_consolidate 252ms 0.34% 55.54% 2955ms 4.01% tetgen::tetgenmesh::flip23 98ms 0.13% 55.68% 2918ms 3.96% tetgen::tetgenmesh::insphere_sos 23ms 0.031% 55.71% 2845ms 3.86% std::_Vector_base::_M_deallocate (inline) 2822ms 3.83% 59.53% 2822ms 3.83% Node::GetIndex 2560ms 3.47% 63.00% 2801ms 3.80% tetgen::insphere 69ms 0.094% 63.10% 2778ms 3.77% VertexMesh::Clear 0 0% 63.10% 2653ms 3.60% std::vector::~vector (inline) 2ms 0.0027% 63.10% 2642ms 3.58% std::_Vector_base::~_Vector_base (inline) 9ms 0.012% 63.11% 2638ms 3.58% _int_free_maybe_consolidate 34ms 0.046% 63.16% 2635ms 3.57% Node::~Node 5ms 0.0068% 63.16% 2627ms 3.56% Element::Element 0 0% 63.16% 2620ms 3.55% std::_Rb_tree::_M_drop_node (inline) 0 0% 63.16% 2594ms 3.52% std::_Rb_tree::_M_put_node (inline) 2349ms 3.18% 66.35% 2349ms 3.18% std::_Rb_tree_insert_and_rebalance 2ms 0.0027% 66.35% 2253ms 3.05% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 8ms 0.011% 66.36% 2229ms 3.02% Element::RegisterWithNodes (inline) 62ms 0.084% 66.45% 2155ms 2.92% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 6ms 0.0081% 66.45% 2127ms 2.88% VertexMesh::GenerateVerticesFromElementCircumcentres 180ms 0.24% 66.70% 2124ms 2.88% std::_Rb_tree_iterator::operator++ (inline) 2034ms 2.76% 69.45% 2034ms 2.76% [libchaste_mesh.so] 187ms 0.25% 69.71% 2020ms 2.74% tetgen::tetgenmesh::flip32 1876ms 2.54% 72.25% 1876ms 2.54% unlink_chunk 57ms 0.077% 72.33% 1664ms 2.26% std::vector::_M_realloc_insert 3ms 0.0041% 72.33% 1534ms 2.08% std::_Vector_base::_M_allocate (inline) 159ms 0.22% 72.55% 1477ms 2.00% tetgen::tetgenmesh::enqueueflipface 1386ms 1.88% 74.43% 1438ms 1.95% tetgen::orient3d 76ms 0.1% 74.53% 1314ms 1.78% std::vector::push_back (inline) 83ms 0.11% 74.64% 1274ms 1.73% std::map::operator[] 995ms 1.35% 75.99% 1186ms 1.61% AbstractElement::GetNodeGlobalIndex 59ms 0.08% 76.07% 1147ms 1.55% TetrahedralMesh::Clear 26ms 0.035% 76.11% 1108ms 1.50% tetgen::tetgenmesh::locate 603ms 0.82% 76.92% 1098ms 1.49% AbstractElement::GetNodeLocation 0 0% 76.92% 1082ms 1.47% std::_Rb_tree::lower_bound (inline) 0 0% 76.92% 1082ms 1.47% std::map::lower_bound (inline) 1058ms 1.43% 78.36% 1058ms 1.43% Node::rGetLocation 12ms 0.016% 78.37% 1057ms 1.43% Element::CalculateCircumsphere 106ms 0.14% 78.52% 1050ms 1.42% tetgen::tetgenmesh::preciselocate 2ms 0.0027% 78.52% 1019ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 558ms 0.76% 79.28% 990ms 1.34% tetgen::tetgenmesh::sym 6ms 0.0081% 79.28% 913ms 1.24% boost::numeric::ublas::c_vector::c_vector (inline) 912ms 1.24% 80.52% 912ms 1.24% AbstractElement::IsDeleted 254ms 0.34% 80.87% 901ms 1.22% boost::numeric::ublas::vector_assign (inline) 1ms 0.0014% 80.87% 864ms 1.17% VoronoiDataWriter::Visit 2ms 0.0027% 80.87% 817ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.0041% 80.87% 813ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.012% 80.89% 805ms 1.09% AbstractTetrahedralElement::CalculateJacobian 19ms 0.026% 80.91% 761ms 1.03% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 49ms 0.066% 80.98% 678ms 0.92% AbstractTetrahedralElement::RefreshJacobian 628ms 0.85% 81.83% 628ms 0.85% tetgen::tetgenmesh::oppo 587ms 0.8% 82.62% 587ms 0.8% std::vector::size (inline) 554ms 0.75% 83.38% 554ms 0.75% tetgen::tetgenmesh::triface::triface 0 0% 83.38% 526ms 0.71% std::insert_iterator::operator= (inline) 31ms 0.042% 83.42% 520ms 0.7% __atan2 63ms 0.085% 83.50% 498ms 0.68% tetgen::tetgenmesh::enextfnext 0 0% 83.50% 497ms 0.67% std::set::find (inline) 21ms 0.028% 83.53% 497ms 0.67% std::vector::insert (inline) 406ms 0.55% 84.08% 495ms 0.67% tetgen::tetgenmesh::fnextself 42ms 0.057% 84.14% 491ms 0.67% tetgen::tetgenmesh::enext2fnext 435ms 0.59% 84.73% 484ms 0.66% __ieee754_atan2_fma 0 0% 84.73% 472ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 5ms 0.0068% 84.74% 462ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 54ms 0.073% 84.81% 462ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.0041% 84.81% 448ms 0.61% Cell::GetCellId 0 0% 84.81% 436ms 0.59% boost::numeric::ublas::inner_prod (inline) 2ms 0.0027% 84.82% 432ms 0.59% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 23ms 0.031% 84.85% 430ms 0.58% boost::numeric::ublas::vector_scalar_binary::evaluate 82ms 0.11% 84.96% 419ms 0.57% tetgen::tetgenmesh::queue::pop 0 0% 84.96% 418ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.96% 408ms 0.55% VertexMeshWriter::WriteVtkUsingMesh 17ms 0.023% 84.98% 404ms 0.55% tetgen::tetgenmesh::queue::push 105ms 0.14% 85.12% 398ms 0.54% __dynamic_cast 11ms 0.015% 85.14% 395ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 133ms 0.18% 85.32% 382ms 0.52% boost::numeric::ublas::vector_inner_prod::apply (inline) 381ms 0.52% 85.83% 381ms 0.52% std::_Rb_tree_decrement 1ms 0.0014% 85.84% 381ms 0.52% tcache_get (inline) 380ms 0.52% 86.35% 380ms 0.52% tcache_get_n (inline) 14ms 0.019% 86.37% 379ms 0.51% VertexMesh::CalculateUnitNormalToFaceWithArea 88ms 0.12% 86.49% 379ms 0.51% boost::numeric::ublas::indexing_vector_assign 186ms 0.25% 86.74% 375ms 0.51% tetgen::tetgenmesh::bond