File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 60824ms, 86.80% of 70077ms total Dropped 899 nodes (cum <= 350.38ms) flat flat% sum% cum cum% 0 0% 0% 70013ms 99.91% __libc_start_call_main 0 0% 0% 70013ms 99.91% __libc_start_main_impl 0 0% 0% 70013ms 99.91% _start 0 0% 0% 69993ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 69993ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 69993ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 69993ms 99.88% main 0 0% 0% 69950ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 69950ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 69950ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 69653ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 59046ms 84.26% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 59000ms 84.19% MeshBasedCellPopulation::Update 0 0% 0% 33441ms 47.72% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 33438ms 47.72% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 237ms 0.34% 0.34% 29409ms 41.97% VertexMesh::VertexMesh 0 0% 0.34% 20984ms 29.94% MutableMesh::ReMesh 1ms 0.0014% 0.34% 16286ms 23.24% tetgen::tetrahedralize 2ms 0.0029% 0.34% 16130ms 23.02% tetgen::tetgenmesh::delaunizevertices 9ms 0.013% 0.36% 16125ms 23.01% tetgen::tetgenmesh::incrflipdelaunay 518ms 0.74% 1.09% 14416ms 20.57% tetgen::tetgenmesh::lawson 625ms 0.89% 1.99% 14113ms 20.14% TetrahedralMesh::EdgeIterator::operator++ 32ms 0.046% 2.03% 11156ms 15.92% std::set::insert (inline) 251ms 0.36% 2.39% 10715ms 15.29% std::_Rb_tree::_M_insert_unique 3192ms 4.55% 6.95% 10598ms 15.12% std::_Rb_tree::_M_lower_bound (inline) 411ms 0.59% 7.53% 10445ms 14.91% VertexElement::AddFace 287ms 0.41% 7.94% 9921ms 14.16% std::_Rb_tree::find (inline) 0 0% 7.94% 9336ms 13.32% std::set::count (inline) 124ms 0.18% 8.12% 7058ms 10.07% std::less::operator() (inline) 6990ms 9.97% 18.09% 6990ms 9.97% std::operator< (inline) 6813ms 9.72% 27.82% 6813ms 9.72% std::_Rb_tree_increment 306ms 0.44% 28.25% 6269ms 8.95% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.25% 6096ms 8.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 172ms 0.25% 28.50% 6000ms 8.56% operator new 0 0% 28.50% 5939ms 8.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0029% 28.50% 5916ms 8.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 1134ms 1.62% 30.12% 5746ms 8.20% __GI___libc_malloc 34ms 0.049% 30.17% 4992ms 7.12% std::__new_allocator::allocate (inline) 0 0% 30.17% 4977ms 7.10% std::allocator_traits::allocate (inline) 5ms 0.0071% 30.17% 4950ms 7.06% std::set_intersection (inline) 1ms 0.0014% 30.18% 4945ms 7.06% MeshBasedCellPopulation::UpdateNodePairs 280ms 0.4% 30.57% 4945ms 7.06% std::__set_intersection 8ms 0.011% 30.59% 4939ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 20ms 0.029% 30.61% 4759ms 6.79% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.014% 30.63% 4700ms 6.71% std::_Rb_tree::~_Rb_tree (inline) 1754ms 2.50% 33.13% 4690ms 6.69% std::_Rb_tree::_M_erase 0 0% 33.13% 4637ms 6.62% std::set::~set (inline) 1244ms 1.78% 34.91% 4491ms 6.41% __GI___libc_free 1337ms 1.91% 36.82% 4453ms 6.35% std::_Rb_tree::_M_get_insert_unique_pos 52ms 0.074% 36.89% 4385ms 6.26% Node::AddElement 0 0% 36.89% 4353ms 6.21% AbstractCellPopulation::WriteResultsToFiles 3103ms 4.43% 41.32% 4218ms 6.02% _int_malloc 190ms 0.27% 41.59% 4204ms 6.00% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 41.59% 4065ms 5.80% VertexMesh::~VertexMesh 0 0% 41.59% 4022ms 5.74% std::_Rb_tree::_M_create_node (inline) 0 0% 41.59% 3976ms 5.67% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.59% 3972ms 5.67% std::_Rb_tree::_M_get_node (inline) 138ms 0.2% 41.79% 3972ms 5.67% std::__new_allocator::deallocate (inline) 0 0% 41.79% 3951ms 5.64% std::allocator_traits::deallocate (inline) 3943ms 5.63% 47.41% 3943ms 5.63% std::_Rb_tree::_S_right (inline) 142ms 0.2% 47.61% 3838ms 5.48% tetgen::tetgenmesh::insphere_sos 9ms 0.013% 47.63% 3777ms 5.39% TetrahedralMesh::ImportFromMesher 3392ms 4.84% 52.47% 3683ms 5.26% tetgen::insphere 112ms 0.16% 52.63% 3421ms 4.88% tetgen::tetgenmesh::flip23 78ms 0.11% 52.74% 3280ms 4.68% MutableElement::AddNode 1361ms 1.94% 54.68% 3242ms 4.63% _int_free 210ms 0.3% 54.98% 3118ms 4.45% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 9ms 0.013% 54.99% 3016ms 4.30% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0014% 55.00% 2926ms 4.18% std::_Rb_tree_iterator::operator++ (inline) 229ms 0.33% 55.32% 2796ms 3.99% Node::~Node 127ms 0.18% 55.50% 2626ms 3.75% tetgen::tetgenmesh::flip32 187ms 0.27% 55.77% 2556ms 3.65% VertexMesh::Clear 2189ms 3.12% 58.89% 2189ms 3.12% Node::GetIndex 0 0% 58.89% 2184ms 3.12% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.89% 2168ms 3.09% std::_Rb_tree::_M_put_node (inline) 2087ms 2.98% 61.87% 2087ms 2.98% std::_Rb_tree_insert_and_rebalance 5ms 0.0071% 61.88% 1949ms 2.78% Element::Element 208ms 0.3% 62.18% 1936ms 2.76% tetgen::tetgenmesh::enqueueflipface 1276ms 1.82% 64.00% 1908ms 2.72% malloc_consolidate 25ms 0.036% 64.03% 1807ms 2.58% std::_Vector_base::_M_deallocate (inline) 0 0% 64.03% 1712ms 2.44% std::vector::~vector (inline) 1565ms 2.23% 66.27% 1659ms 2.37% tetgen::orient3d 5ms 0.0071% 66.27% 1654ms 2.36% _int_free_maybe_consolidate 1ms 0.0014% 66.27% 1639ms 2.34% std::_Vector_base::~_Vector_base (inline) 3ms 0.0043% 66.28% 1614ms 2.30% Element::RegisterWithNodes (inline) 98ms 0.14% 66.42% 1417ms 2.02% TetrahedralMesh::Clear 37ms 0.053% 66.47% 1385ms 1.98% tetgen::tetgenmesh::locate 1356ms 1.94% 68.41% 1356ms 1.94% unlink_chunk 77ms 0.11% 68.52% 1350ms 1.93% std::map::operator[] 72ms 0.1% 68.62% 1304ms 1.86% tetgen::tetgenmesh::preciselocate 65ms 0.093% 68.71% 1229ms 1.75% std::vector::_M_realloc_insert 1002ms 1.43% 70.14% 1174ms 1.68% AbstractElement::GetNodeGlobalIndex 0 0% 70.14% 1168ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 70.14% 1168ms 1.67% std::map::lower_bound (inline) 3ms 0.0043% 70.15% 1163ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 70.15% 1077ms 1.54% VoronoiDataWriter::Visit 1045ms 1.49% 71.64% 1045ms 1.49% tetgen::tetgenmesh::oppo 132ms 0.19% 71.83% 1035ms 1.48% std::vector::push_back (inline) 3ms 0.0043% 71.83% 1008ms 1.44% std::_Vector_base::_M_allocate (inline) 928ms 1.32% 73.15% 928ms 1.32% tetgen::tetgenmesh::triface::triface 0 0% 73.15% 888ms 1.27% TetrahedralMesh::RefreshJacobianCachedData 314ms 0.45% 73.60% 871ms 1.24% tetgen::tetgenmesh::sym 843ms 1.20% 74.80% 843ms 1.20% [libchaste_mesh.so] 9ms 0.013% 74.82% 779ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 777ms 1.11% 75.93% 777ms 1.11% tetgen::tetgenmesh::triface::operator= 333ms 0.48% 76.40% 773ms 1.10% AbstractElement::GetNodeLocation 3ms 0.0043% 76.41% 748ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 736ms 1.05% 77.46% 736ms 1.05% AbstractElement::IsDeleted 727ms 1.04% 78.49% 727ms 1.04% Node::rGetLocation 26ms 0.037% 78.53% 714ms 1.02% AbstractTetrahedralElement::CalculateJacobian 17ms 0.024% 78.56% 698ms 1% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 248ms 0.35% 78.91% 667ms 0.95% tetgen::tetgenmesh::bond 48ms 0.068% 78.98% 613ms 0.87% tetgen::tetgenmesh::queue::push 50ms 0.071% 79.05% 612ms 0.87% __atan2 358ms 0.51% 79.56% 610ms 0.87% tetgen::tetgenmesh::fnextself 65ms 0.093% 79.65% 608ms 0.87% tetgen::tetgenmesh::enext2fnext 603ms 0.86% 80.51% 603ms 0.86% std::vector::size (inline) 42ms 0.06% 80.57% 594ms 0.85% boost::numeric::ublas::vector_assign (inline) 0 0% 80.57% 583ms 0.83% std::set::find (inline) 583ms 0.83% 81.40% 583ms 0.83% tetgen::tetgenmesh::decode 7ms 0.01% 81.41% 568ms 0.81% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.41% 564ms 0.8% boost::numeric::ublas::inner_prod (inline) 54ms 0.077% 81.49% 564ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.49% 564ms 0.8% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 329ms 0.47% 81.96% 564ms 0.8% tetgen::tetgenmesh::link::add 426ms 0.61% 82.57% 559ms 0.8% __ieee754_atan2_fma 20ms 0.029% 82.60% 554ms 0.79% Element::CalculateCircumsphere 61ms 0.087% 82.68% 554ms 0.79% tetgen::tetgenmesh::enextfnext 529ms 0.75% 83.44% 529ms 0.75% tetgen::tetgenmesh::org 40ms 0.057% 83.50% 518ms 0.74% AbstractTetrahedralElement::RefreshJacobian 485ms 0.69% 84.19% 485ms 0.69% tetgen::tetgenmesh::pointmark 0 0% 84.19% 467ms 0.67% std::insert_iterator::operator= (inline) 194ms 0.28% 84.47% 450ms 0.64% boost::numeric::ublas::vector_inner_prod::apply (inline) 9ms 0.013% 84.48% 437ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 32ms 0.046% 84.52% 435ms 0.62% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.0043% 84.53% 426ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 409ms 0.58% 85.11% 409ms 0.58% tetgen::tetgenmesh::encode 1ms 0.0014% 85.11% 404ms 0.58% std::_Rb_tree::_M_insert_unique_ (inline) 100ms 0.14% 85.26% 400ms 0.57% __dynamic_cast 4ms 0.0057% 85.26% 396ms 0.57% Cell::GetCellId 0 0% 85.26% 395ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 391ms 0.56% 85.82% 391ms 0.56% boost::numeric::ublas::c_vector::operator() 9ms 0.013% 85.83% 384ms 0.55% VertexElement::~VertexElement 0 0% 85.83% 380ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 183ms 0.26% 86.09% 378ms 0.54% AbstractTetrahedralMesh::GetElement 376ms 0.54% 86.63% 376ms 0.54% std::_Rb_tree_decrement 4ms 0.0057% 86.64% 373ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 90ms 0.13% 86.76% 368ms 0.53% boost::numeric::ublas::indexing_vector_assign 22ms 0.031% 86.80% 363ms 0.52% std::vector::insert (inline)