File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48268ms, 86.57% of 55757ms total Dropped 839 nodes (cum <= 278.79ms) flat flat% sum% cum cum% 0 0% 0% 55714ms 99.92% __libc_start_call_main 0 0% 0% 55714ms 99.92% __libc_start_main_impl 0 0% 0% 55714ms 99.92% _start 0 0% 0% 55700ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 55700ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 55700ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 55700ms 99.90% main 0 0% 0% 55654ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55654ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 55653ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55432ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 47094ms 84.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47061ms 84.40% MeshBasedCellPopulation::Update 0 0% 0% 27058ms 48.53% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 27057ms 48.53% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 169ms 0.3% 0.3% 23452ms 42.06% VertexMesh::VertexMesh 0 0% 0.3% 16383ms 29.38% MutableMesh::ReMesh 1ms 0.0018% 0.3% 12523ms 22.46% tetgen::tetrahedralize 3ms 0.0054% 0.31% 12396ms 22.23% tetgen::tetgenmesh::delaunizevertices 9ms 0.016% 0.33% 12390ms 22.22% tetgen::tetgenmesh::incrflipdelaunay 469ms 0.84% 1.17% 11199ms 20.09% TetrahedralMesh::EdgeIterator::operator++ 404ms 0.72% 1.89% 11078ms 19.87% tetgen::tetgenmesh::lawson 22ms 0.039% 1.93% 9063ms 16.25% std::set::insert (inline) 167ms 0.3% 2.23% 8680ms 15.57% std::_Rb_tree::_M_insert_unique 395ms 0.71% 2.94% 8322ms 14.93% VertexElement::AddFace 2473ms 4.44% 7.37% 8201ms 14.71% std::_Rb_tree::_M_lower_bound (inline) 203ms 0.36% 7.74% 7616ms 13.66% std::_Rb_tree::find (inline) 0 0% 7.74% 7185ms 12.89% std::set::count (inline) 106ms 0.19% 7.93% 5462ms 9.80% std::less::operator() (inline) 5407ms 9.70% 17.63% 5407ms 9.70% std::operator< (inline) 5402ms 9.69% 27.31% 5402ms 9.69% std::_Rb_tree_increment 261ms 0.47% 27.78% 5130ms 9.20% std::_Rb_tree::_M_insert_ (inline) 145ms 0.26% 28.04% 4877ms 8.75% operator new 0 0% 28.04% 4814ms 8.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 924ms 1.66% 29.70% 4681ms 8.40% __GI___libc_malloc 0 0% 29.70% 4673ms 8.38% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0072% 29.71% 4653ms 8.35% AbstractNumericalMethod::ComputeForcesIncludingDamping 37ms 0.066% 29.77% 4082ms 7.32% std::__new_allocator::allocate (inline) 0 0% 29.77% 4065ms 7.29% std::allocator_traits::allocate (inline) 2ms 0.0036% 29.78% 4046ms 7.26% std::set_intersection (inline) 230ms 0.41% 30.19% 4044ms 7.25% std::__set_intersection 5ms 0.009% 30.20% 4028ms 7.22% std::_Rb_tree::~_Rb_tree (inline) 1571ms 2.82% 33.02% 4018ms 7.21% std::_Rb_tree::_M_erase 0 0% 33.02% 3971ms 7.12% std::set::~set (inline) 0 0% 33.02% 3910ms 7.01% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0054% 33.02% 3908ms 7.01% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1083ms 1.94% 34.96% 3780ms 6.78% __GI___libc_free 16ms 0.029% 34.99% 3776ms 6.77% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 34.99% 3627ms 6.51% VertexMesh::~VertexMesh 1083ms 1.94% 36.94% 3622ms 6.50% std::_Rb_tree::_M_get_insert_unique_pos 37ms 0.066% 37.00% 3459ms 6.20% Node::AddElement 2494ms 4.47% 41.47% 3425ms 6.14% _int_malloc 0 0% 41.47% 3400ms 6.10% AbstractCellPopulation::WriteResultsToFiles 125ms 0.22% 41.70% 3394ms 6.09% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 41.70% 3347ms 6.00% std::_Rb_tree::_M_create_node (inline) 0 0% 41.70% 3318ms 5.95% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.70% 3316ms 5.95% std::_Rb_tree::_M_get_node (inline) 3256ms 5.84% 47.54% 3256ms 5.84% std::_Rb_tree::_S_right (inline) 115ms 0.21% 47.74% 3252ms 5.83% std::__new_allocator::deallocate (inline) 0 0% 47.74% 3236ms 5.80% std::allocator_traits::deallocate (inline) 3ms 0.0054% 47.75% 3145ms 5.64% TetrahedralMesh::ImportFromMesher 80ms 0.14% 47.89% 2889ms 5.18% tetgen::tetgenmesh::insphere_sos 2584ms 4.63% 52.53% 2795ms 5.01% tetgen::insphere 81ms 0.15% 52.67% 2750ms 4.93% tetgen::tetgenmesh::flip23 1161ms 2.08% 54.76% 2696ms 4.84% _int_free 233ms 0.42% 55.17% 2601ms 4.66% Node::~Node 70ms 0.13% 55.30% 2588ms 4.64% MutableElement::AddNode 165ms 0.3% 55.59% 2391ms 4.29% VertexMesh::Clear 143ms 0.26% 55.85% 2373ms 4.26% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 55.85% 2340ms 4.20% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 55.85% 2239ms 4.02% std::_Rb_tree_iterator::operator++ (inline) 126ms 0.23% 56.08% 2085ms 3.74% tetgen::tetgenmesh::flip32 0 0% 56.08% 1778ms 3.19% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.08% 1772ms 3.18% std::_Rb_tree::_M_put_node (inline) 1669ms 2.99% 59.07% 1669ms 2.99% Node::GetIndex 1622ms 2.91% 61.98% 1622ms 2.91% std::_Rb_tree_insert_and_rebalance 166ms 0.3% 62.28% 1588ms 2.85% tetgen::tetgenmesh::enqueueflipface 1034ms 1.85% 64.13% 1520ms 2.73% malloc_consolidate 5ms 0.009% 64.14% 1518ms 2.72% Element::Element 26ms 0.047% 64.19% 1490ms 2.67% std::_Vector_base::_M_deallocate (inline) 0 0% 64.19% 1422ms 2.55% std::vector::~vector (inline) 0 0% 64.19% 1354ms 2.43% std::_Vector_base::~_Vector_base (inline) 4ms 0.0072% 64.19% 1311ms 2.35% _int_free_maybe_consolidate 88ms 0.16% 64.35% 1305ms 2.34% TetrahedralMesh::Clear 3ms 0.0054% 64.36% 1254ms 2.25% Element::RegisterWithNodes (inline) 1180ms 2.12% 66.47% 1245ms 2.23% tetgen::orient3d 1126ms 2.02% 68.49% 1126ms 2.02% unlink_chunk 27ms 0.048% 68.54% 1062ms 1.90% tetgen::tetgenmesh::locate 53ms 0.095% 68.64% 1060ms 1.90% std::map::operator[] 831ms 1.49% 70.13% 1010ms 1.81% AbstractElement::GetNodeGlobalIndex 82ms 0.15% 70.27% 992ms 1.78% tetgen::tetgenmesh::preciselocate 49ms 0.088% 70.36% 958ms 1.72% std::vector::_M_realloc_insert 0 0% 70.36% 943ms 1.69% std::_Rb_tree::lower_bound (inline) 0 0% 70.36% 943ms 1.69% std::map::lower_bound (inline) 3ms 0.0054% 70.37% 922ms 1.65% VertexMesh::GenerateVerticesFromElementCircumcentres 872ms 1.56% 71.93% 872ms 1.56% tetgen::tetgenmesh::triface::triface 0 0% 71.93% 843ms 1.51% VoronoiDataWriter::Visit 839ms 1.50% 73.44% 839ms 1.50% tetgen::tetgenmesh::oppo 114ms 0.2% 73.64% 823ms 1.48% std::vector::push_back (inline) 5ms 0.009% 73.65% 754ms 1.35% std::_Vector_base::_M_allocate (inline) 222ms 0.4% 74.05% 700ms 1.26% tetgen::tetgenmesh::sym 0 0% 74.05% 692ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 625ms 1.12% 75.17% 625ms 1.12% [libchaste_mesh.so] 262ms 0.47% 75.64% 614ms 1.10% AbstractElement::GetNodeLocation 614ms 1.10% 76.74% 614ms 1.10% AbstractElement::IsDeleted 8ms 0.014% 76.75% 611ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 611ms 1.10% 77.85% 611ms 1.10% Node::rGetLocation 588ms 1.05% 78.90% 588ms 1.05% tetgen::tetgenmesh::triface::operator= 1ms 0.0018% 78.91% 576ms 1.03% AbstractTwoBodyInteractionForce::AddForceContribution 18ms 0.032% 78.94% 566ms 1.02% AbstractTetrahedralElement::CalculateJacobian 562ms 1.01% 79.95% 562ms 1.01% std::vector::size (inline) 7ms 0.013% 79.96% 541ms 0.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 27ms 0.048% 80.01% 524ms 0.94% tetgen::tetgenmesh::queue::push 506ms 0.91% 80.92% 506ms 0.91% tetgen::tetgenmesh::decode 314ms 0.56% 81.48% 497ms 0.89% tetgen::tetgenmesh::link::add 36ms 0.065% 81.54% 493ms 0.88% __atan2 7ms 0.013% 81.56% 490ms 0.88% boost::numeric::ublas::vector_assign (inline) 293ms 0.53% 82.08% 487ms 0.87% tetgen::tetgenmesh::fnextself 4ms 0.0072% 82.09% 471ms 0.84% boost::numeric::ublas::c_vector::c_vector (inline) 193ms 0.35% 82.43% 461ms 0.83% tetgen::tetgenmesh::bond 360ms 0.65% 83.08% 457ms 0.82% __ieee754_atan2_fma 17ms 0.03% 83.11% 442ms 0.79% Element::CalculateCircumsphere 39ms 0.07% 83.18% 442ms 0.79% tetgen::tetgenmesh::enext2fnext 48ms 0.086% 83.27% 434ms 0.78% tetgen::tetgenmesh::enextfnext 0 0% 83.27% 426ms 0.76% std::set::find (inline) 0 0% 83.27% 416ms 0.75% boost::numeric::ublas::inner_prod (inline) 28ms 0.05% 83.32% 414ms 0.74% AbstractTetrahedralElement::RefreshJacobian 37ms 0.066% 83.38% 414ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.38% 414ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 83.38% 402ms 0.72% std::insert_iterator::operator= (inline) 11ms 0.02% 83.40% 373ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.0072% 83.41% 363ms 0.65% VertexElement::~VertexElement 360ms 0.65% 84.06% 360ms 0.65% tetgen::tetgenmesh::org 0 0% 84.06% 358ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 166ms 0.3% 84.35% 339ms 0.61% AbstractTetrahedralMesh::GetElement 0 0% 84.35% 328ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 19ms 0.034% 84.39% 325ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 149ms 0.27% 84.65% 324ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.65% 319ms 0.57% VertexMeshWriter::WriteVtkUsingMesh 8ms 0.014% 84.67% 316ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 5ms 0.009% 84.68% 308ms 0.55% CellPropertyCollection::GetPropertiesType (inline) 79ms 0.14% 84.82% 304ms 0.55% boost::numeric::ublas::indexing_vector_assign 303ms 0.54% 85.36% 303ms 0.54% boost::numeric::ublas::c_vector::operator() 2ms 0.0036% 85.37% 297ms 0.53% VertexMesh::GetVolumeOfElement 85ms 0.15% 85.52% 294ms 0.53% __dynamic_cast 0 0% 85.52% 292ms 0.52% tcache_get (inline) 292ms 0.52% 86.04% 292ms 0.52% tcache_get_n (inline) 2ms 0.0036% 86.05% 289ms 0.52% Cell::GetCellId 289ms 0.52% 86.56% 289ms 0.52% std::_Rb_tree_decrement 2ms 0.0036% 86.57% 281ms 0.5% Element::~Element 0 0% 86.57% 279ms 0.5% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline)