File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 70783ms, 87.62% of 80780ms total Dropped 919 nodes (cum <= 403.90ms) flat flat% sum% cum cum% 0 0% 0% 80715ms 99.92% __libc_start_call_main 0 0% 0% 80715ms 99.92% __libc_start_main_impl 0 0% 0% 80715ms 99.92% _start 0 0% 0% 80696ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 80696ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 80696ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 80696ms 99.90% main 0 0% 0% 80656ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 80656ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 80656ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 80351ms 99.47% AbstractCellBasedSimulation::Solve 0 0% 0% 69046ms 85.47% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 68984ms 85.40% MeshBasedCellPopulation::Update 0 0% 0% 41892ms 51.86% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 41892ms 51.86% MeshBasedCellPopulation::TessellateIfNeeded 337ms 0.42% 0.42% 36313ms 44.95% VertexMesh::VertexMesh 0 0% 0.42% 22132ms 27.40% MutableMesh::ReMesh 0 0% 0.42% 16503ms 20.43% tetgen::tetrahedralize 4ms 0.005% 0.42% 16354ms 20.25% tetgen::tetgenmesh::delaunizevertices 16ms 0.02% 0.44% 16343ms 20.23% tetgen::tetgenmesh::incrflipdelaunay 616ms 0.76% 1.20% 15925ms 19.71% TetrahedralMesh::EdgeIterator::operator++ 510ms 0.63% 1.84% 14582ms 18.05% tetgen::tetgenmesh::lawson 36ms 0.045% 1.88% 13074ms 16.18% std::set::insert (inline) 229ms 0.28% 2.16% 12648ms 15.66% std::_Rb_tree::_M_insert_unique 531ms 0.66% 2.82% 11812ms 14.62% VertexElement::AddFace 3265ms 4.04% 6.86% 11609ms 14.37% std::_Rb_tree::_M_lower_bound (inline) 278ms 0.34% 7.21% 10755ms 13.31% std::_Rb_tree::find (inline) 0 0% 7.21% 10172ms 12.59% std::set::count (inline) 8915ms 11.04% 18.24% 8915ms 11.04% std::_Rb_tree_increment 117ms 0.14% 18.39% 7883ms 9.76% std::less::operator() (inline) 7837ms 9.70% 28.09% 7837ms 9.70% std::operator< (inline) 188ms 0.23% 28.32% 7571ms 9.37% operator new 1268ms 1.57% 29.89% 7305ms 9.04% __GI___libc_malloc 306ms 0.38% 30.27% 7260ms 8.99% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0012% 30.27% 7160ms 8.86% std::set_intersection (inline) 352ms 0.44% 30.71% 7159ms 8.86% std::__set_intersection 0 0% 30.71% 6629ms 8.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.71% 6453ms 7.99% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.012% 30.72% 6430ms 7.96% AbstractNumericalMethod::ComputeForcesIncludingDamping 213ms 0.26% 30.98% 6284ms 7.78% std::_Rb_tree_const_iterator::operator++ (inline) 38ms 0.047% 31.03% 5997ms 7.42% std::__new_allocator::allocate (inline) 0 0% 31.03% 5974ms 7.40% std::allocator_traits::allocate (inline) 48ms 0.059% 31.09% 5877ms 7.28% Node::AddElement 4174ms 5.17% 36.26% 5682ms 7.03% _int_malloc 0 0% 36.26% 5618ms 6.95% VertexMesh::~VertexMesh 1375ms 1.70% 37.96% 5512ms 6.82% __GI___libc_free 1414ms 1.75% 39.71% 5405ms 6.69% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.0025% 39.71% 5391ms 6.67% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.0074% 39.72% 5367ms 6.64% std::_Rb_tree::~_Rb_tree (inline) 2129ms 2.64% 42.36% 5357ms 6.63% std::_Rb_tree::_M_erase 4ms 0.005% 42.36% 5356ms 6.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 42.36% 5292ms 6.55% std::set::~set (inline) 17ms 0.021% 42.38% 5207ms 6.45% MeshBasedCellPopulation::SpringIterator::operator++ 5181ms 6.41% 48.80% 5181ms 6.41% std::_Rb_tree::_S_right (inline) 135ms 0.17% 48.96% 4868ms 6.03% std::__new_allocator::deallocate (inline) 0 0% 48.96% 4849ms 6.00% std::allocator_traits::deallocate (inline) 0 0% 48.96% 4751ms 5.88% std::_Rb_tree::_M_create_node (inline) 0 0% 48.96% 4714ms 5.84% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.96% 4702ms 5.82% std::_Rb_tree::_M_get_node (inline) 10ms 0.012% 48.97% 4487ms 5.55% TetrahedralMesh::ImportFromMesher 0 0% 48.97% 4460ms 5.52% AbstractCellPopulation::WriteResultsToFiles 127ms 0.16% 49.13% 4455ms 5.51% tetgen::tetgenmesh::insphere_sos 56ms 0.069% 49.20% 4348ms 5.38% MutableElement::AddNode 3992ms 4.94% 54.14% 4317ms 5.34% tetgen::insphere 1339ms 1.66% 55.80% 4132ms 5.12% _int_free 131ms 0.16% 55.96% 3466ms 4.29% tetgen::tetgenmesh::flip23 244ms 0.3% 56.27% 3451ms 4.27% Node::~Node 217ms 0.27% 56.53% 3234ms 4.00% VertexMesh::Clear 211ms 0.26% 56.79% 3184ms 3.94% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3168ms 3.92% 60.72% 3168ms 3.92% Node::GetIndex 4ms 0.005% 60.72% 3074ms 3.81% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 60.72% 3009ms 3.72% std::_Rb_tree_iterator::operator++ (inline) 1942ms 2.40% 63.13% 2870ms 3.55% malloc_consolidate 22ms 0.027% 63.15% 2688ms 3.33% std::_Vector_base::_M_deallocate (inline) 1ms 0.0012% 63.15% 2570ms 3.18% std::vector::~vector (inline) 123ms 0.15% 63.31% 2553ms 3.16% tetgen::tetgenmesh::flip32 8ms 0.0099% 63.32% 2526ms 3.13% _int_free_maybe_consolidate 3ms 0.0037% 63.32% 2520ms 3.12% std::_Vector_base::~_Vector_base (inline) 2ms 0.0025% 63.32% 2452ms 3.04% Element::Element 2361ms 2.92% 66.25% 2361ms 2.92% std::_Rb_tree_insert_and_rebalance 0 0% 66.25% 2194ms 2.72% std::_Rb_tree::_M_drop_node (inline) 0 0% 66.25% 2183ms 2.70% std::_Rb_tree::_M_put_node (inline) 12ms 0.015% 66.26% 2068ms 2.56% Element::RegisterWithNodes (inline) 1983ms 2.45% 68.72% 1983ms 2.45% unlink_chunk 235ms 0.29% 69.01% 1916ms 2.37% tetgen::tetgenmesh::enqueueflipface 5ms 0.0062% 69.01% 1779ms 2.20% VertexMesh::GenerateVerticesFromElementCircumcentres 1463ms 1.81% 70.82% 1547ms 1.92% tetgen::orient3d 1334ms 1.65% 72.47% 1535ms 1.90% AbstractElement::GetNodeGlobalIndex 82ms 0.1% 72.58% 1519ms 1.88% TetrahedralMesh::Clear 72ms 0.089% 72.67% 1505ms 1.86% std::map::operator[] 80ms 0.099% 72.76% 1474ms 1.82% std::vector::_M_realloc_insert 32ms 0.04% 72.80% 1408ms 1.74% tetgen::tetgenmesh::locate 0 0% 72.80% 1333ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 72.80% 1333ms 1.65% std::map::lower_bound (inline) 103ms 0.13% 72.93% 1324ms 1.64% tetgen::tetgenmesh::preciselocate 4ms 0.005% 72.94% 1276ms 1.58% std::_Vector_base::_M_allocate (inline) 143ms 0.18% 73.11% 1224ms 1.52% std::vector::push_back (inline) 1182ms 1.46% 74.58% 1182ms 1.46% AbstractElement::IsDeleted 534ms 0.66% 75.24% 1142ms 1.41% AbstractElement::GetNodeLocation 0 0% 75.24% 1116ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0012% 75.24% 1116ms 1.38% VoronoiDataWriter::Visit 1113ms 1.38% 76.62% 1113ms 1.38% tetgen::tetgenmesh::oppo 1107ms 1.37% 77.99% 1107ms 1.37% Node::rGetLocation 1040ms 1.29% 79.27% 1040ms 1.29% tetgen::tetgenmesh::triface::triface 8ms 0.0099% 79.28% 876ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.022% 79.31% 835ms 1.03% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0012% 79.31% 818ms 1.01% AbstractTwoBodyInteractionForce::AddForceContribution 792ms 0.98% 80.29% 792ms 0.98% [libchaste_mesh.so] 9ms 0.011% 80.30% 763ms 0.94% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 13ms 0.016% 80.32% 763ms 0.94% Element::CalculateCircumsphere 749ms 0.93% 81.24% 749ms 0.93% std::vector::size (inline) 307ms 0.38% 81.62% 735ms 0.91% tetgen::tetgenmesh::sym 681ms 0.84% 82.47% 681ms 0.84% tetgen::tetgenmesh::triface::operator= 36ms 0.045% 82.51% 664ms 0.82% AbstractTetrahedralElement::RefreshJacobian 415ms 0.51% 83.02% 660ms 0.82% tetgen::tetgenmesh::fnextself 10ms 0.012% 83.04% 640ms 0.79% boost::numeric::ublas::vector_assign (inline) 53ms 0.066% 83.10% 635ms 0.79% __atan2 10ms 0.012% 83.11% 634ms 0.78% boost::numeric::ublas::c_vector::c_vector (inline) 60ms 0.074% 83.19% 623ms 0.77% tetgen::tetgenmesh::enext2fnext 40ms 0.05% 83.24% 610ms 0.76% tetgen::tetgenmesh::queue::push 450ms 0.56% 83.80% 580ms 0.72% __ieee754_atan2_fma 50ms 0.062% 83.86% 578ms 0.72% tetgen::tetgenmesh::enextfnext 0 0% 83.86% 575ms 0.71% std::set::find (inline) 361ms 0.45% 84.30% 570ms 0.71% tetgen::tetgenmesh::link::add 224ms 0.28% 84.58% 529ms 0.65% tetgen::tetgenmesh::bond 0 0% 84.58% 511ms 0.63% boost::numeric::ublas::inner_prod (inline) 1ms 0.0012% 84.58% 511ms 0.63% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.04% 84.62% 510ms 0.63% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0012% 84.62% 486ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 127ms 0.16% 84.78% 475ms 0.59% __dynamic_cast 35ms 0.043% 84.82% 467ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.0037% 84.83% 462ms 0.57% Cell::GetCellId 18ms 0.022% 84.85% 462ms 0.57% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.85% 455ms 0.56% std::insert_iterator::operator= (inline) 0 0% 84.85% 453ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 453ms 0.56% 85.41% 453ms 0.56% tetgen::tetgenmesh::decode 442ms 0.55% 85.96% 442ms 0.55% tetgen::tetgenmesh::pointmark 440ms 0.54% 86.50% 440ms 0.54% tetgen::tetgenmesh::org 0 0% 86.50% 429ms 0.53% VertexMeshWriter::WriteVtkUsingMesh 16ms 0.02% 86.52% 418ms 0.52% std::vector::insert (inline) 173ms 0.21% 86.74% 416ms 0.51% AbstractTetrahedralMesh::GetElement 117ms 0.14% 86.88% 413ms 0.51% boost::numeric::ublas::indexing_vector_assign 408ms 0.51% 87.39% 408ms 0.51% std::_Rb_tree_decrement 192ms 0.24% 87.62% 407ms 0.5% boost::numeric::ublas::vector_inner_prod::apply (inline)