File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 61622ms, 86.41% of 71315ms total Dropped 837 nodes (cum <= 356.57ms) flat flat% sum% cum cum% 0 0% 0% 71270ms 99.94% __libc_start_call_main 0 0% 0% 71270ms 99.94% __libc_start_main_impl 0 0% 0% 71270ms 99.94% _start 0 0% 0% 71255ms 99.92% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 71255ms 99.92% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 71255ms 99.92% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 71255ms 99.92% main 0 0% 0% 71222ms 99.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 71222ms 99.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 71222ms 99.87% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 70967ms 99.51% AbstractCellBasedSimulation::Solve 0 0% 0% 59662ms 83.66% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0014% 0.0014% 59599ms 83.57% MeshBasedCellPopulation::Update 0 0% 0.0014% 37165ms 52.11% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0014% 37165ms 52.11% MeshBasedCellPopulation::TessellateIfNeeded 370ms 0.52% 0.52% 32771ms 45.95% VertexMesh::VertexMesh 0 0% 0.52% 17731ms 24.86% MutableMesh::ReMesh 608ms 0.85% 1.37% 14620ms 20.50% TetrahedralMesh::EdgeIterator::operator++ 41ms 0.057% 1.43% 13311ms 18.67% std::set::insert (inline) 203ms 0.28% 1.71% 12728ms 17.85% std::_Rb_tree::_M_insert_unique 0 0% 1.71% 12674ms 17.77% tetgen::tetrahedralize 5ms 0.007% 1.72% 12501ms 17.53% tetgen::tetgenmesh::delaunizevertices 9ms 0.013% 1.73% 12489ms 17.51% tetgen::tetgenmesh::incrflipdelaunay 360ms 0.5% 2.24% 11287ms 15.83% VertexElement::AddFace 652ms 0.91% 3.15% 11129ms 15.61% tetgen::tetgenmesh::lawson 2973ms 4.17% 7.32% 11026ms 15.46% std::_Rb_tree::_M_lower_bound (inline) 231ms 0.32% 7.65% 10356ms 14.52% std::_Rb_tree::find (inline) 0 0% 7.65% 9876ms 13.85% std::set::count (inline) 260ms 0.36% 8.01% 9029ms 12.66% operator new 3028ms 4.25% 12.26% 8663ms 12.15% __GI___libc_malloc 306ms 0.43% 12.69% 8362ms 11.73% std::_Rb_tree::_M_insert_ (inline) 88ms 0.12% 12.81% 7427ms 10.41% std::__new_allocator::allocate (inline) 0 0% 12.81% 7391ms 10.36% std::allocator_traits::allocate (inline) 7387ms 10.36% 23.17% 7387ms 10.36% std::_Rb_tree_increment 6845ms 9.60% 32.77% 6845ms 9.60% std::operator< (inline) 20ms 0.028% 32.79% 6813ms 9.55% std::less::operator() (inline) 0 0% 32.79% 6372ms 8.94% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 32.79% 6203ms 8.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0042% 32.80% 6175ms 8.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 32.80% 5963ms 8.36% std::_Rb_tree::_M_create_node (inline) 0 0% 32.80% 5933ms 8.32% std::_Rb_tree::_M_get_node (inline) 0 0% 32.80% 5932ms 8.32% std::_Rb_tree::_Alloc_node::operator() (inline) 1048ms 1.47% 34.27% 5810ms 8.15% __GI___libc_free 3ms 0.0042% 34.27% 5678ms 7.96% std::set_intersection (inline) 323ms 0.45% 34.72% 5675ms 7.96% std::__set_intersection 38ms 0.053% 34.78% 5270ms 7.39% Node::AddElement 3826ms 5.36% 40.14% 5167ms 7.25% _int_malloc 2ms 0.0028% 40.15% 5034ms 7.06% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.007% 40.15% 5028ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4898ms 6.87% 47.02% 4898ms 6.87% std::_Rb_tree::_S_right (inline) 9ms 0.013% 47.03% 4875ms 6.84% MeshBasedCellPopulation::SpringIterator::operator++ 102ms 0.14% 47.18% 4843ms 6.79% std::__new_allocator::deallocate (inline) 0 0% 47.18% 4822ms 6.76% std::allocator_traits::deallocate (inline) 0 0% 47.18% 4755ms 6.67% AbstractCellPopulation::WriteResultsToFiles 284ms 0.4% 47.57% 4755ms 6.67% std::_Rb_tree_const_iterator::operator++ (inline) 12ms 0.017% 47.59% 4731ms 6.63% std::_Rb_tree::~_Rb_tree (inline) 2187ms 3.07% 50.66% 4710ms 6.60% _int_free 1310ms 1.84% 52.50% 4698ms 6.59% std::_Rb_tree::_M_erase 0 0% 52.50% 4669ms 6.55% std::set::~set (inline) 1156ms 1.62% 54.12% 4541ms 6.37% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 54.12% 4431ms 6.21% VertexMesh::~VertexMesh 13ms 0.018% 54.13% 4085ms 5.73% TetrahedralMesh::ImportFromMesher 64ms 0.09% 54.22% 3859ms 5.41% MutableElement::AddNode 76ms 0.11% 54.33% 3462ms 4.85% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 254ms 0.36% 54.69% 3415ms 4.79% std::_Rb_tree_iterator::operator++ (inline) 4ms 0.0056% 54.69% 3318ms 4.65% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 100ms 0.14% 54.83% 2925ms 4.10% tetgen::tetgenmesh::insphere_sos 241ms 0.34% 55.17% 2823ms 3.96% tetgen::tetgenmesh::flip23 2575ms 3.61% 58.78% 2806ms 3.93% tetgen::insphere 0 0% 58.78% 2675ms 3.75% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.78% 2637ms 3.70% std::_Rb_tree::_M_put_node (inline) 66ms 0.093% 58.87% 2580ms 3.62% VertexMesh::Clear 50ms 0.07% 58.94% 2497ms 3.50% Node::~Node 1ms 0.0014% 58.95% 2367ms 3.32% Element::Element 1612ms 2.26% 61.21% 2324ms 3.26% malloc_consolidate 22ms 0.031% 61.24% 2207ms 3.09% std::_Vector_base::_M_deallocate (inline) 2170ms 3.04% 64.28% 2170ms 3.04% std::_Rb_tree_insert_and_rebalance 0 0% 64.28% 2034ms 2.85% std::vector::~vector (inline) 3ms 0.0042% 64.28% 2010ms 2.82% std::_Vector_base::~_Vector_base (inline) 7ms 0.0098% 64.29% 2009ms 2.82% _int_free_maybe_consolidate 2ms 0.0028% 64.30% 1978ms 2.77% Element::RegisterWithNodes (inline) 197ms 0.28% 64.57% 1944ms 2.73% tetgen::tetgenmesh::flip32 1923ms 2.70% 67.27% 1923ms 2.70% [libchaste_mesh.so] 1851ms 2.60% 69.86% 1851ms 2.60% Node::GetIndex 1648ms 2.31% 72.18% 1648ms 2.31% unlink_chunk 6ms 0.0084% 72.18% 1634ms 2.29% VertexMesh::GenerateVerticesFromElementCircumcentres 63ms 0.088% 72.27% 1579ms 2.21% std::vector::_M_realloc_insert 1426ms 2.00% 74.27% 1486ms 2.08% tetgen::orient3d 1ms 0.0014% 74.27% 1459ms 2.05% std::_Vector_base::_M_allocate (inline) 177ms 0.25% 74.52% 1452ms 2.04% tetgen::tetgenmesh::enqueueflipface 86ms 0.12% 74.64% 1315ms 1.84% std::map::operator[] 105ms 0.15% 74.79% 1291ms 1.81% std::vector::push_back (inline) 55ms 0.077% 74.87% 1201ms 1.68% TetrahedralMesh::Clear 0 0% 74.87% 1188ms 1.67% VoronoiDataWriter::Visit 0 0% 74.87% 1153ms 1.62% std::_Rb_tree::lower_bound (inline) 0 0% 74.87% 1153ms 1.62% std::map::lower_bound (inline) 33ms 0.046% 74.91% 1134ms 1.59% tetgen::tetgenmesh::locate 90ms 0.13% 75.04% 1068ms 1.50% tetgen::tetgenmesh::preciselocate 867ms 1.22% 76.25% 1054ms 1.48% AbstractElement::GetNodeGlobalIndex 958ms 1.34% 77.60% 958ms 1.34% Node::rGetLocation 1ms 0.0014% 77.60% 941ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 549ms 0.77% 78.37% 921ms 1.29% tetgen::tetgenmesh::sym 195ms 0.27% 78.64% 911ms 1.28% boost::numeric::ublas::vector_assign (inline) 1ms 0.0014% 78.64% 879ms 1.23% AbstractTwoBodyInteractionForce::AddForceContribution 499ms 0.7% 79.34% 870ms 1.22% AbstractElement::GetNodeLocation 8ms 0.011% 79.35% 848ms 1.19% Element::CalculateCircumsphere 5ms 0.007% 79.36% 831ms 1.17% boost::numeric::ublas::c_vector::c_vector (inline) 16ms 0.022% 79.38% 818ms 1.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.011% 79.40% 815ms 1.14% AbstractTetrahedralElement::CalculateJacobian 3ms 0.0042% 79.40% 806ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 776ms 1.09% 80.49% 776ms 1.09% AbstractElement::IsDeleted 77ms 0.11% 80.60% 652ms 0.91% AbstractTetrahedralElement::RefreshJacobian 590ms 0.83% 81.42% 590ms 0.83% tetgen::tetgenmesh::oppo 0 0% 81.42% 571ms 0.8% std::insert_iterator::operator= (inline) 0 0% 81.42% 528ms 0.74% std::_Rb_tree::_M_insert_unique_ (inline) 37ms 0.052% 81.48% 523ms 0.73% __atan2 3ms 0.0042% 81.48% 498ms 0.7% Cell::GetCellId 498ms 0.7% 82.18% 498ms 0.7% tetgen::tetgenmesh::triface::triface 19ms 0.027% 82.20% 496ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 494ms 0.69% 82.90% 494ms 0.69% std::vector::size (inline) 437ms 0.61% 83.51% 481ms 0.67% __ieee754_atan2_fma 6ms 0.0084% 83.52% 477ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.52% 476ms 0.67% std::set::find (inline) 124ms 0.17% 83.69% 467ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 38ms 0.053% 83.75% 464ms 0.65% tetgen::tetgenmesh::enext2fnext 58ms 0.081% 83.83% 458ms 0.64% tetgen::tetgenmesh::enextfnext 359ms 0.5% 84.33% 458ms 0.64% tetgen::tetgenmesh::fnextself 17ms 0.024% 84.35% 448ms 0.63% std::vector::insert (inline) 105ms 0.15% 84.50% 439ms 0.62% boost::numeric::ublas::indexing_vector_assign 79ms 0.11% 84.61% 433ms 0.61% tetgen::tetgenmesh::queue::pop 0 0% 84.61% 407ms 0.57% tcache_get (inline) 407ms 0.57% 85.18% 407ms 0.57% tcache_get_n (inline) 0 0% 85.18% 405ms 0.57% VertexMeshWriter::WriteVtkUsingMesh 100ms 0.14% 85.32% 404ms 0.57% __dynamic_cast 0 0% 85.32% 403ms 0.57% boost::numeric::ublas::inner_prod (inline) 237ms 0.33% 85.66% 399ms 0.56% tetgen::tetgenmesh::bond 1ms 0.0014% 85.66% 397ms 0.56% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.017% 85.67% 396ms 0.56% boost::numeric::ublas::vector_scalar_binary::evaluate 24ms 0.034% 85.71% 396ms 0.56% tetgen::tetgenmesh::queue::push 0 0% 85.71% 391ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.0042% 85.71% 388ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.0098% 85.72% 376ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 121ms 0.17% 85.89% 369ms 0.52% boost::numeric::ublas::vector_inner_prod::apply (inline) 367ms 0.51% 86.41% 367ms 0.51% boost::numeric::ublas::c_vector::operator() 2ms 0.0028% 86.41% 362ms 0.51% VertexElement::~VertexElement