File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48246ms, 85.90% of 56167ms total Dropped 837 nodes (cum <= 280.83ms) flat flat% sum% cum cum% 0 0% 0% 56119ms 99.91% __libc_start_call_main 0 0% 0% 56119ms 99.91% __libc_start_main_impl 0 0% 0% 56119ms 99.91% _start 0 0% 0% 56103ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56103ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56103ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56103ms 99.89% main 0 0% 0% 56068ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56068ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 56068ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55859ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0% 46890ms 83.48% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0018% 0.0018% 46811ms 83.34% MeshBasedCellPopulation::Update 0 0% 0.0018% 28436ms 50.63% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0018% 28436ms 50.63% MeshBasedCellPopulation::TessellateIfNeeded 210ms 0.37% 0.38% 25242ms 44.94% VertexMesh::VertexMesh 0 0% 0.38% 14444ms 25.72% MutableMesh::ReMesh 494ms 0.88% 1.26% 12076ms 21.50% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.26% 10674ms 19.00% tetgen::tetrahedralize 32ms 0.057% 1.31% 10657ms 18.97% std::set::insert (inline) 2ms 0.0036% 1.32% 10570ms 18.82% tetgen::tetgenmesh::delaunizevertices 5ms 0.0089% 1.32% 10563ms 18.81% tetgen::tetgenmesh::incrflipdelaunay 150ms 0.27% 1.59% 10127ms 18.03% std::_Rb_tree::_M_insert_unique 266ms 0.47% 2.07% 10001ms 17.81% VertexElement::AddFace 467ms 0.83% 2.90% 9325ms 16.60% tetgen::tetgenmesh::lawson 3988ms 7.10% 10.00% 9285ms 16.53% std::_Rb_tree::_M_lower_bound (inline) 176ms 0.31% 10.31% 8901ms 15.85% std::_Rb_tree::find (inline) 0 0% 10.31% 8347ms 14.86% std::set::count (inline) 217ms 0.39% 10.70% 6923ms 12.33% operator new 270ms 0.48% 11.18% 6845ms 12.19% std::_Rb_tree::_M_insert_ (inline) 2463ms 4.39% 15.56% 6644ms 11.83% __GI___libc_malloc 64ms 0.11% 15.68% 6019ms 10.72% std::__new_allocator::allocate (inline) 0 0% 15.68% 5981ms 10.65% std::allocator_traits::allocate (inline) 0 0% 15.68% 5343ms 9.51% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 15.68% 5218ms 9.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.012% 15.69% 5198ms 9.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 15.69% 4894ms 8.71% std::_Rb_tree::_M_create_node (inline) 0 0% 15.69% 4874ms 8.68% std::_Rb_tree::_M_get_node (inline) 0 0% 15.69% 4858ms 8.65% std::_Rb_tree::_Alloc_node::operator() (inline) 4705ms 8.38% 24.07% 4705ms 8.38% std::_Rb_tree_increment 72ms 0.13% 24.19% 4646ms 8.27% std::less::operator() (inline) 4621ms 8.23% 32.42% 4621ms 8.23% std::operator< (inline) 783ms 1.39% 33.82% 4304ms 7.66% __GI___libc_free 1ms 0.0018% 33.82% 4240ms 7.55% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.012% 33.83% 4238ms 7.55% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.023% 33.85% 4125ms 7.34% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.02% 33.87% 3976ms 7.08% std::_Rb_tree::~_Rb_tree (inline) 1130ms 2.01% 35.88% 3948ms 7.03% std::_Rb_tree::_M_erase 0 0% 35.88% 3941ms 7.02% std::set::~set (inline) 1ms 0.0018% 35.89% 3793ms 6.75% std::set_intersection (inline) 237ms 0.42% 36.31% 3792ms 6.75% std::__set_intersection 70ms 0.12% 36.43% 3784ms 6.74% std::__new_allocator::deallocate (inline) 0 0% 36.43% 3774ms 6.72% std::allocator_traits::deallocate (inline) 3055ms 5.44% 41.87% 3744ms 6.67% _int_malloc 1934ms 3.44% 45.31% 3505ms 6.24% _int_free 0 0% 45.31% 3474ms 6.19% AbstractCellPopulation::WriteResultsToFiles 1285ms 2.29% 47.60% 3452ms 6.15% std::_Rb_tree::_M_get_insert_unique_pos 65ms 0.12% 47.72% 3300ms 5.88% Node::AddElement 0 0% 47.72% 3213ms 5.72% VertexMesh::~VertexMesh 253ms 0.45% 48.17% 3049ms 5.43% std::_Rb_tree_const_iterator::operator++ (inline) 2948ms 5.25% 53.42% 2948ms 5.25% std::_Rb_tree::_S_right (inline) 3ms 0.0053% 53.42% 2927ms 5.21% TetrahedralMesh::ImportFromMesher 81ms 0.14% 53.57% 2845ms 5.07% tetgen::tetgenmesh::insphere_sos 2541ms 4.52% 58.09% 2740ms 4.88% tetgen::insphere 45ms 0.08% 58.17% 2573ms 4.58% MutableElement::AddNode 239ms 0.43% 58.60% 2459ms 4.38% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0036% 58.60% 2446ms 4.35% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0018% 58.60% 2443ms 4.35% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 58.60% 2403ms 4.28% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.60% 2374ms 4.23% std::_Rb_tree::_M_put_node (inline) 235ms 0.42% 59.02% 2208ms 3.93% tetgen::tetgenmesh::flip23 27ms 0.048% 59.07% 2151ms 3.83% VertexMesh::Clear 2038ms 3.63% 62.70% 2038ms 3.63% [libchaste_mesh.so] 86ms 0.15% 62.85% 2025ms 3.61% Node::~Node 1777ms 3.16% 66.01% 1777ms 3.16% std::_Rb_tree_insert_and_rebalance 5ms 0.0089% 66.02% 1637ms 2.91% Element::Element 214ms 0.38% 66.40% 1545ms 2.75% tetgen::tetgenmesh::flip32 0 0% 66.40% 1466ms 2.61% std::vector::~vector (inline) 1411ms 2.51% 68.92% 1463ms 2.60% tetgen::orient3d 36ms 0.064% 68.98% 1436ms 2.56% std::_Vector_base::_M_deallocate (inline) 823ms 1.47% 70.45% 1349ms 2.40% malloc_consolidate 49ms 0.087% 70.53% 1329ms 2.37% std::vector::_M_realloc_insert 3ms 0.0053% 70.54% 1295ms 2.31% Element::RegisterWithNodes (inline) 1ms 0.0018% 70.54% 1223ms 2.18% std::_Vector_base::~_Vector_base (inline) 11ms 0.02% 70.56% 1189ms 2.12% _int_free_maybe_consolidate 1ms 0.0018% 70.56% 1108ms 1.97% std::_Vector_base::_M_allocate (inline) 85ms 0.15% 70.71% 1085ms 1.93% std::map::operator[] 21ms 0.037% 70.75% 1033ms 1.84% tetgen::tetgenmesh::locate 1029ms 1.83% 72.58% 1029ms 1.83% Node::GetIndex 185ms 0.33% 72.91% 1003ms 1.79% tetgen::tetgenmesh::enqueueflipface 78ms 0.14% 73.05% 980ms 1.74% tetgen::tetgenmesh::preciselocate 50ms 0.089% 73.14% 971ms 1.73% std::vector::push_back (inline) 4ms 0.0071% 73.15% 941ms 1.68% VertexMesh::GenerateVerticesFromElementCircumcentres 928ms 1.65% 74.80% 928ms 1.65% unlink_chunk 0 0% 74.80% 921ms 1.64% std::_Rb_tree::lower_bound (inline) 0 0% 74.80% 921ms 1.64% std::map::lower_bound (inline) 4ms 0.0071% 74.81% 913ms 1.63% TetrahedralMesh::Clear 0 0% 74.81% 832ms 1.48% VoronoiDataWriter::Visit 0 0% 74.81% 823ms 1.47% TetrahedralMesh::RefreshJacobianCachedData 493ms 0.88% 75.68% 803ms 1.43% AbstractElement::GetNodeGlobalIndex 3ms 0.0053% 75.69% 741ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.0053% 75.69% 740ms 1.32% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.018% 75.71% 709ms 1.26% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.0089% 75.72% 668ms 1.19% boost::numeric::ublas::vector_assign (inline) 13ms 0.023% 75.74% 635ms 1.13% AbstractTetrahedralElement::CalculateJacobian 8ms 0.014% 75.76% 625ms 1.11% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 75.76% 547ms 0.97% std::set::find (inline) 539ms 0.96% 76.72% 539ms 0.96% tetgen::tetgenmesh::oppo 318ms 0.57% 77.28% 532ms 0.95% tetgen::tetgenmesh::sym 277ms 0.49% 77.78% 522ms 0.93% AbstractElement::GetNodeLocation 0 0% 77.78% 521ms 0.93% std::insert_iterator::operator= (inline) 38ms 0.068% 77.84% 517ms 0.92% __atan2 506ms 0.9% 78.75% 506ms 0.9% Node::rGetLocation 491ms 0.87% 79.62% 491ms 0.87% std::vector::size (inline) 42ms 0.075% 79.69% 478ms 0.85% AbstractTetrahedralElement::RefreshJacobian 427ms 0.76% 80.45% 475ms 0.85% __ieee754_atan2_fma 4ms 0.0071% 80.46% 471ms 0.84% VertexElement::~VertexElement 14ms 0.025% 80.49% 469ms 0.84% Element::CalculateCircumsphere 15ms 0.027% 80.51% 464ms 0.83% std::vector::insert (inline) 0 0% 80.51% 457ms 0.81% std::_Rb_tree::_M_insert_unique_ (inline) 49ms 0.087% 80.60% 434ms 0.77% std::_Rb_tree_iterator::operator-- (inline) 9ms 0.016% 80.62% 412ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0071% 80.62% 393ms 0.7% Cell::GetCellId 168ms 0.3% 80.92% 386ms 0.69% Inverse 374ms 0.67% 81.59% 374ms 0.67% boost::numeric::ublas::c_vector::operator() 13ms 0.023% 81.61% 360ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 81.61% 358ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 352ms 0.63% 82.24% 352ms 0.63% std::_Rb_tree_decrement 0 0% 82.24% 351ms 0.62% boost::numeric::ublas::inner_prod (inline) 16ms 0.028% 82.27% 350ms 0.62% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.27% 350ms 0.62% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 82.27% 350ms 0.62% tcache_get (inline) 350ms 0.62% 82.89% 350ms 0.62% tcache_get_n (inline) 5ms 0.0089% 82.90% 348ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 104ms 0.19% 83.08% 346ms 0.62% __dynamic_cast 2ms 0.0036% 83.09% 339ms 0.6% AbstractTetrahedralElement::AbstractTetrahedralElement 34ms 0.061% 83.15% 329ms 0.59% tetgen::tetgenmesh::enext2fnext 97ms 0.17% 83.32% 317ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 171ms 0.3% 83.63% 317ms 0.56% tetgen::tetgenmesh::bond 61ms 0.11% 83.73% 313ms 0.56% boost::numeric::ublas::indexing_vector_assign 37ms 0.066% 83.80% 313ms 0.56% tetgen::tetgenmesh::queue::push 258ms 0.46% 84.26% 312ms 0.56% tetgen::tetgenmesh::fnextself 10ms 0.018% 84.28% 309ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 214ms 0.38% 84.66% 306ms 0.54% AbstractTetrahedralMesh::GetElement 32ms 0.057% 84.72% 300ms 0.53% tetgen::tetgenmesh::enextfnext 294ms 0.52% 85.24% 294ms 0.52% AbstractElement::IsDeleted 78ms 0.14% 85.38% 289ms 0.51% tetgen::tetgenmesh::queue::pop 288ms 0.51% 85.89% 288ms 0.51% tetgen::tetgenmesh::triface::triface 4ms 0.0071% 85.90% 286ms 0.51% AbstractCellProperty::IsSubType (inline)