File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 28584ms, 86.40% of 33083ms total Dropped 761 nodes (cum <= 165.41ms) flat flat% sum% cum cum% 0 0% 0% 33038ms 99.86% __libc_start_call_main 0 0% 0% 33038ms 99.86% __libc_start_main_impl 0 0% 0% 33038ms 99.86% _start 0 0% 0% 33026ms 99.83% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33026ms 99.83% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33026ms 99.83% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33026ms 99.83% main 0 0% 0% 32995ms 99.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 32995ms 99.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 32995ms 99.73% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 32847ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 27397ms 82.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 27368ms 82.73% MeshBasedCellPopulation::Update 0 0% 0% 15230ms 46.04% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 15230ms 46.04% MeshBasedCellPopulation::TessellateIfNeeded 86ms 0.26% 0.26% 13715ms 41.46% VertexMesh::VertexMesh 0 0% 0.26% 9671ms 29.23% MutableMesh::ReMesh 0 0% 0.26% 8093ms 24.46% tetgen::tetrahedralize 0 0% 0.26% 8018ms 24.24% tetgen::tetgenmesh::delaunizevertices 11ms 0.033% 0.29% 8016ms 24.23% tetgen::tetgenmesh::incrflipdelaunay 386ms 1.17% 1.46% 7365ms 22.26% TetrahedralMesh::EdgeIterator::operator++ 285ms 0.86% 2.32% 7065ms 21.36% tetgen::tetgenmesh::lawson 2352ms 7.11% 9.43% 5836ms 17.64% std::_Rb_tree::_M_lower_bound (inline) 121ms 0.37% 9.80% 5614ms 16.97% VertexElement::AddFace 14ms 0.042% 9.84% 5600ms 16.93% std::set::insert (inline) 220ms 0.66% 10.50% 5524ms 16.70% std::_Rb_tree::find (inline) 121ms 0.37% 10.87% 5273ms 15.94% std::_Rb_tree::_M_insert_unique 0 0% 10.87% 5115ms 15.46% std::set::count (inline) 89ms 0.27% 11.14% 3392ms 10.25% std::less::operator() (inline) 3347ms 10.12% 21.26% 3347ms 10.12% std::operator< (inline) 191ms 0.58% 21.83% 3234ms 9.78% std::_Rb_tree::_M_insert_ (inline) 0 0% 21.83% 3200ms 9.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.83% 3133ms 9.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 21.83% 3116ms 9.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 126ms 0.38% 22.21% 3041ms 9.19% operator new 1170ms 3.54% 25.75% 2868ms 8.67% __GI___libc_malloc 0 0% 25.75% 2675ms 8.09% MeshBasedCellPopulation::UpdateNodePairs 33ms 0.1% 25.85% 2642ms 7.99% std::__new_allocator::allocate (inline) 0 0% 25.85% 2629ms 7.95% std::allocator_traits::allocate (inline) 2616ms 7.91% 33.76% 2616ms 7.91% std::_Rb_tree_increment 7ms 0.021% 33.78% 2600ms 7.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.018% 33.80% 2599ms 7.86% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 33.80% 2184ms 6.60% std::_Rb_tree::_M_create_node (inline) 0 0% 33.80% 2173ms 6.57% std::_Rb_tree::_M_get_node (inline) 0 0% 33.80% 2169ms 6.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 33.80% 2163ms 6.54% AbstractCellPopulation::WriteResultsToFiles 385ms 1.16% 34.96% 2162ms 6.54% __GI___libc_free 70ms 0.21% 35.17% 2127ms 6.43% tetgen::tetgenmesh::insphere_sos 19ms 0.057% 35.23% 2117ms 6.40% std::_Rb_tree::~_Rb_tree (inline) 842ms 2.55% 37.77% 2112ms 6.38% std::_Rb_tree::_M_get_insert_unique_pos 561ms 1.70% 39.47% 2098ms 6.34% std::_Rb_tree::_M_erase 0 0% 39.47% 2097ms 6.34% std::set::~set (inline) 1898ms 5.74% 45.21% 2051ms 6.20% tetgen::insphere 63ms 0.19% 45.40% 1978ms 5.98% std::__new_allocator::deallocate (inline) 0 0% 45.40% 1974ms 5.97% std::allocator_traits::deallocate (inline) 1ms 0.003% 45.40% 1918ms 5.80% std::set_intersection (inline) 153ms 0.46% 45.86% 1917ms 5.79% std::__set_intersection 1140ms 3.45% 49.31% 1777ms 5.37% _int_free 85ms 0.26% 49.57% 1634ms 4.94% tetgen::tetgenmesh::flip23 110ms 0.33% 49.90% 1599ms 4.83% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.003% 49.90% 1561ms 4.72% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 49.90% 1522ms 4.60% VertexMesh::~VertexMesh 3ms 0.0091% 49.91% 1495ms 4.52% std::_Rb_tree_iterator::operator++ (inline) 1205ms 3.64% 53.55% 1492ms 4.51% _int_malloc 171ms 0.52% 54.07% 1422ms 4.30% std::_Rb_tree_const_iterator::operator++ (inline) 23ms 0.07% 54.14% 1393ms 4.21% Node::AddElement 0 0% 54.14% 1353ms 4.09% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.14% 1335ms 4.04% std::_Rb_tree::_M_put_node (inline) 1250ms 3.78% 57.92% 1250ms 3.78% std::_Rb_tree::_S_right (inline) 3ms 0.0091% 57.93% 1220ms 3.69% TetrahedralMesh::ImportFromMesher 60ms 0.18% 58.11% 1109ms 3.35% tetgen::tetgenmesh::flip32 30ms 0.091% 58.20% 1098ms 3.32% MutableElement::AddNode 31ms 0.094% 58.29% 1041ms 3.15% VertexMesh::Clear 34ms 0.1% 58.40% 936ms 2.83% Node::~Node 879ms 2.66% 61.05% 928ms 2.81% tetgen::orient3d 899ms 2.72% 63.77% 899ms 2.72% std::_Rb_tree_insert_and_rebalance 82ms 0.25% 64.02% 820ms 2.48% tetgen::tetgenmesh::enqueueflipface 16ms 0.048% 64.07% 808ms 2.44% tetgen::tetgenmesh::locate 73ms 0.22% 64.29% 770ms 2.33% tetgen::tetgenmesh::preciselocate 1ms 0.003% 64.29% 719ms 2.17% Element::Element 51ms 0.15% 64.44% 688ms 2.08% std::map::operator[] 658ms 1.99% 66.43% 658ms 1.99% [libchaste_mesh.so] 10ms 0.03% 66.46% 649ms 1.96% std::_Vector_base::_M_deallocate (inline) 380ms 1.15% 67.61% 608ms 1.84% malloc_consolidate 1ms 0.003% 67.61% 607ms 1.83% std::vector::~vector (inline) 0 0% 67.61% 600ms 1.81% std::_Rb_tree::lower_bound (inline) 0 0% 67.61% 600ms 1.81% std::map::lower_bound (inline) 584ms 1.77% 69.38% 584ms 1.77% tetgen::tetgenmesh::oppo 34ms 0.1% 69.48% 572ms 1.73% std::vector::_M_realloc_insert 6ms 0.018% 69.50% 544ms 1.64% Element::RegisterWithNodes (inline) 1ms 0.003% 69.50% 544ms 1.64% std::_Vector_base::~_Vector_base (inline) 3ms 0.0091% 69.51% 527ms 1.59% _int_free_maybe_consolidate 299ms 0.9% 70.42% 514ms 1.55% tetgen::tetgenmesh::sym 2ms 0.006% 70.42% 480ms 1.45% VoronoiDataWriter::Visit 471ms 1.42% 71.85% 471ms 1.42% Node::GetIndex 322ms 0.97% 72.82% 467ms 1.41% AbstractElement::GetNodeGlobalIndex 52ms 0.16% 72.98% 466ms 1.41% std::vector::push_back (inline) 1ms 0.003% 72.98% 457ms 1.38% std::_Vector_base::_M_allocate (inline) 2ms 0.006% 72.99% 422ms 1.28% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.003% 72.99% 421ms 1.27% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 72.99% 408ms 1.23% std::set::find (inline) 11ms 0.033% 73.02% 406ms 1.23% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 375ms 1.13% 74.16% 375ms 1.13% unlink_chunk 14ms 0.042% 74.20% 374ms 1.13% __atan2 268ms 0.81% 75.01% 357ms 1.08% __ieee754_atan2_fma 0 0% 75.01% 355ms 1.07% TetrahedralMesh::RefreshJacobianCachedData 0 0% 75.01% 347ms 1.05% std::insert_iterator::operator= (inline) 8ms 0.024% 75.03% 345ms 1.04% TetrahedralMesh::Clear 5ms 0.015% 75.05% 335ms 1.01% boost::numeric::ublas::vector_assign (inline) 6ms 0.018% 75.07% 331ms 1.00% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.0091% 75.07% 328ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 325ms 0.98% 76.06% 325ms 0.98% std::vector::size (inline) 210ms 0.63% 76.69% 319ms 0.96% tetgen::tetgenmesh::fnextself 10ms 0.03% 76.72% 317ms 0.96% AbstractTetrahedralElement::CalculateJacobian 1ms 0.003% 76.73% 313ms 0.95% std::_Rb_tree::_M_insert_unique_ (inline) 309ms 0.93% 77.66% 309ms 0.93% tetgen::tetgenmesh::org 304ms 0.92% 78.58% 304ms 0.92% tetgen::tetgenmesh::triface::triface 36ms 0.11% 78.69% 285ms 0.86% std::_Rb_tree_iterator::operator-- (inline) 124ms 0.37% 79.06% 283ms 0.86% AbstractTetrahedralMesh::GetElement 276ms 0.83% 79.90% 276ms 0.83% tetgen::tetgenmesh::triface::operator= 36ms 0.11% 80.00% 274ms 0.83% tetgen::tetgenmesh::enext2fnext 263ms 0.79% 80.80% 263ms 0.79% boost::numeric::ublas::c_vector::operator() 122ms 0.37% 81.17% 251ms 0.76% AbstractElement::GetNodeLocation 15ms 0.045% 81.21% 249ms 0.75% tetgen::tetgenmesh::queue::push 241ms 0.73% 81.94% 241ms 0.73% std::_Rb_tree_decrement 0 0% 81.94% 231ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 148ms 0.45% 82.39% 229ms 0.69% tetgen::tetgenmesh::link::add 0 0% 82.39% 227ms 0.69% boost::numeric::ublas::inner_prod (inline) 1ms 0.003% 82.39% 226ms 0.68% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.003% 82.40% 225ms 0.68% Cell::GetCellId 11ms 0.033% 82.43% 225ms 0.68% boost::numeric::ublas::vector_scalar_binary::evaluate 143ms 0.43% 82.86% 225ms 0.68% tetgen::tetgenmesh::bond 4ms 0.012% 82.87% 219ms 0.66% Element::CalculateCircumsphere 34ms 0.1% 82.98% 210ms 0.63% tetgen::tetgenmesh::enextfnext 209ms 0.63% 83.61% 209ms 0.63% tetgen::tetgenmesh::decode 20ms 0.06% 83.67% 207ms 0.63% AbstractTetrahedralElement::RefreshJacobian 3ms 0.0091% 83.68% 200ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.012% 83.69% 199ms 0.6% boost::numeric::ublas::c_vector::operator= (inline) 49ms 0.15% 83.84% 198ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 10ms 0.03% 83.87% 197ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 50ms 0.15% 84.02% 194ms 0.59% boost::numeric::ublas::indexing_vector_assign 3ms 0.0091% 84.03% 192ms 0.58% VertexElement::~VertexElement 54ms 0.16% 84.19% 183ms 0.55% tetgen::tetgenmesh::queue::pop 149ms 0.45% 84.64% 182ms 0.55% boost::numeric::ublas::c_matrix::operator() 10ms 0.03% 84.67% 179ms 0.54% std::vector::insert (inline) 179ms 0.54% 85.21% 179ms 0.54% tetgen::tetgenmesh::pointmark 177ms 0.54% 85.75% 177ms 0.54% Node::rGetLocation 3ms 0.0091% 85.76% 174ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 45ms 0.14% 85.89% 171ms 0.52% __dynamic_cast 0 0% 85.89% 168ms 0.51% tcache_get (inline) 168ms 0.51% 86.40% 168ms 0.51% tcache_get_n (inline)