File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 57106ms, 85.93% of 66458ms total Dropped 872 nodes (cum <= 332.29ms) flat flat% sum% cum cum% 0 0% 0% 66406ms 99.92% __libc_start_call_main 0 0% 0% 66406ms 99.92% __libc_start_main_impl 0 0% 0% 66406ms 99.92% _start 0 0% 0% 66388ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66388ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66388ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66388ms 99.89% main 0 0% 0% 66341ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66341ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66341ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66061ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 55592ms 83.65% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55546ms 83.58% MeshBasedCellPopulation::Update 0 0% 0% 31085ms 46.77% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 31084ms 46.77% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 239ms 0.36% 0.36% 27539ms 41.44% VertexMesh::VertexMesh 0 0% 0.36% 19936ms 30.00% MutableMesh::ReMesh 1ms 0.0015% 0.36% 15759ms 23.71% tetgen::tetrahedralize 5ms 0.0075% 0.37% 15612ms 23.49% tetgen::tetgenmesh::delaunizevertices 12ms 0.018% 0.39% 15606ms 23.48% tetgen::tetgenmesh::incrflipdelaunay 514ms 0.77% 1.16% 13903ms 20.92% tetgen::tetgenmesh::lawson 591ms 0.89% 2.05% 13824ms 20.80% TetrahedralMesh::EdgeIterator::operator++ 3288ms 4.95% 7.00% 10554ms 15.88% std::_Rb_tree::_M_lower_bound (inline) 48ms 0.072% 7.07% 10506ms 15.81% std::set::insert (inline) 378ms 0.57% 7.64% 10156ms 15.28% VertexElement::AddFace 267ms 0.4% 8.04% 10030ms 15.09% std::_Rb_tree::_M_insert_unique 270ms 0.41% 8.45% 9862ms 14.84% std::_Rb_tree::find (inline) 0 0% 8.45% 9298ms 13.99% std::set::count (inline) 113ms 0.17% 8.62% 6928ms 10.42% std::less::operator() (inline) 6878ms 10.35% 18.97% 6878ms 10.35% std::operator< (inline) 6186ms 9.31% 28.27% 6186ms 9.31% std::_Rb_tree_increment 0 0% 28.27% 5999ms 9.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 291ms 0.44% 28.71% 5887ms 8.86% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0015% 28.71% 5839ms 8.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.0075% 28.72% 5816ms 8.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 158ms 0.24% 28.96% 5455ms 8.21% operator new 1246ms 1.87% 30.83% 5230ms 7.87% __GI___libc_malloc 1ms 0.0015% 30.83% 4884ms 7.35% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.018% 30.85% 4860ms 7.31% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.017% 30.87% 4727ms 7.11% MeshBasedCellPopulation::SpringIterator::operator++ 33ms 0.05% 30.92% 4653ms 7.00% std::__new_allocator::allocate (inline) 0 0% 30.92% 4631ms 6.97% std::allocator_traits::allocate (inline) 6ms 0.009% 30.93% 4493ms 6.76% std::_Rb_tree::~_Rb_tree (inline) 1664ms 2.50% 33.43% 4487ms 6.75% std::_Rb_tree::_M_erase 0 0% 33.43% 4437ms 6.68% std::set::~set (inline) 3ms 0.0045% 33.44% 4325ms 6.51% std::set_intersection (inline) 247ms 0.37% 33.81% 4322ms 6.50% std::__set_intersection 0 0% 33.81% 4313ms 6.49% AbstractCellPopulation::WriteResultsToFiles 1305ms 1.96% 35.77% 4143ms 6.23% std::_Rb_tree::_M_get_insert_unique_pos 1140ms 1.72% 37.49% 4082ms 6.14% __GI___libc_free 100ms 0.15% 37.64% 3830ms 5.76% tetgen::tetgenmesh::insphere_sos 44ms 0.066% 37.70% 3736ms 5.62% Node::AddElement 3399ms 5.11% 42.82% 3719ms 5.60% tetgen::insphere 0 0% 42.82% 3707ms 5.58% std::_Rb_tree::_M_create_node (inline) 0 0% 42.82% 3672ms 5.53% std::_Rb_tree::_M_get_node (inline) 0 0% 42.82% 3659ms 5.51% std::_Rb_tree::_Alloc_node::operator() (inline) 117ms 0.18% 42.99% 3611ms 5.43% std::__new_allocator::deallocate (inline) 189ms 0.28% 43.28% 3608ms 5.43% std::_Rb_tree_const_iterator::operator++ (inline) 3603ms 5.42% 48.70% 3603ms 5.42% std::_Rb_tree::_S_right (inline) 2573ms 3.87% 52.57% 3599ms 5.42% _int_malloc 0 0% 52.57% 3593ms 5.41% std::allocator_traits::deallocate (inline) 0 0% 52.57% 3571ms 5.37% VertexMesh::~VertexMesh 123ms 0.19% 52.76% 3505ms 5.27% tetgen::tetgenmesh::flip23 9ms 0.014% 52.77% 3359ms 5.05% TetrahedralMesh::ImportFromMesher 197ms 0.3% 53.07% 3087ms 4.65% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.003% 53.07% 3012ms 4.53% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1395ms 2.10% 55.17% 2942ms 4.43% _int_free 0 0% 55.17% 2905ms 4.37% std::_Rb_tree_iterator::operator++ (inline) 50ms 0.075% 55.24% 2891ms 4.35% MutableElement::AddNode 216ms 0.33% 55.57% 2571ms 3.87% Node::~Node 141ms 0.21% 55.78% 2521ms 3.79% tetgen::tetgenmesh::flip32 180ms 0.27% 56.05% 2353ms 3.54% VertexMesh::Clear 0 0% 56.05% 2106ms 3.17% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.05% 2095ms 3.15% std::_Rb_tree::_M_put_node (inline) 2011ms 3.03% 59.08% 2011ms 3.03% std::_Rb_tree_insert_and_rebalance 1960ms 2.95% 62.03% 1960ms 2.95% Node::GetIndex 252ms 0.38% 62.41% 1956ms 2.94% tetgen::tetgenmesh::enqueueflipface 6ms 0.009% 62.42% 1715ms 2.58% Element::Element 1588ms 2.39% 64.80% 1666ms 2.51% tetgen::orient3d 1021ms 1.54% 66.34% 1566ms 2.36% malloc_consolidate 36ms 0.054% 66.40% 1534ms 2.31% std::_Vector_base::_M_deallocate (inline) 0 0% 66.40% 1440ms 2.17% std::vector::~vector (inline) 27ms 0.041% 66.44% 1423ms 2.14% tetgen::tetgenmesh::locate 0 0% 66.44% 1360ms 2.05% std::_Vector_base::~_Vector_base (inline) 8ms 0.012% 66.45% 1345ms 2.02% Element::RegisterWithNodes (inline) 96ms 0.14% 66.59% 1343ms 2.02% TetrahedralMesh::Clear 87ms 0.13% 66.72% 1343ms 2.02% tetgen::tetgenmesh::preciselocate 10ms 0.015% 66.74% 1318ms 1.98% _int_free_maybe_consolidate 58ms 0.087% 66.83% 1314ms 1.98% std::map::operator[] 1177ms 1.77% 68.60% 1177ms 1.77% unlink_chunk 0 0% 68.60% 1163ms 1.75% std::_Rb_tree::lower_bound (inline) 0 0% 68.60% 1163ms 1.75% std::map::lower_bound (inline) 69ms 0.1% 68.70% 1149ms 1.73% std::vector::_M_realloc_insert 885ms 1.33% 70.03% 1068ms 1.61% AbstractElement::GetNodeGlobalIndex 1061ms 1.60% 71.63% 1061ms 1.60% tetgen::tetgenmesh::oppo 0 0% 71.63% 1043ms 1.57% VoronoiDataWriter::Visit 3ms 0.0045% 71.63% 1020ms 1.53% VertexMesh::GenerateVerticesFromElementCircumcentres 972ms 1.46% 73.10% 972ms 1.46% tetgen::tetgenmesh::triface::triface 2ms 0.003% 73.10% 961ms 1.45% std::_Vector_base::_M_allocate (inline) 123ms 0.19% 73.28% 916ms 1.38% std::vector::push_back (inline) 0 0% 73.28% 798ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 771ms 1.16% 74.44% 771ms 1.16% [libchaste_mesh.so] 1ms 0.0015% 74.45% 745ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.02% 74.47% 731ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 714ms 1.07% 75.54% 714ms 1.07% Node::rGetLocation 273ms 0.41% 75.95% 705ms 1.06% tetgen::tetgenmesh::sym 15ms 0.023% 75.97% 698ms 1.05% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 22ms 0.033% 76.01% 696ms 1.05% AbstractTetrahedralElement::CalculateJacobian 693ms 1.04% 77.05% 693ms 1.04% tetgen::tetgenmesh::triface::operator= 291ms 0.44% 77.49% 682ms 1.03% AbstractElement::GetNodeLocation 645ms 0.97% 78.46% 645ms 0.97% AbstractElement::IsDeleted 56ms 0.084% 78.54% 636ms 0.96% __atan2 387ms 0.58% 79.12% 634ms 0.95% tetgen::tetgenmesh::fnextself 11ms 0.017% 79.14% 633ms 0.95% boost::numeric::ublas::vector_assign (inline) 234ms 0.35% 79.49% 627ms 0.94% tetgen::tetgenmesh::bond 35ms 0.053% 79.54% 617ms 0.93% tetgen::tetgenmesh::queue::push 60ms 0.09% 79.64% 614ms 0.92% tetgen::tetgenmesh::enext2fnext 9ms 0.014% 79.65% 595ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 352ms 0.53% 80.18% 582ms 0.88% tetgen::tetgenmesh::link::add 435ms 0.65% 80.83% 576ms 0.87% __ieee754_atan2_fma 0 0% 80.83% 556ms 0.84% std::set::find (inline) 0 0% 80.83% 542ms 0.82% boost::numeric::ublas::inner_prod (inline) 2ms 0.003% 80.84% 536ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 46ms 0.069% 80.91% 536ms 0.81% tetgen::tetgenmesh::enextfnext 42ms 0.063% 80.97% 534ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 522ms 0.79% 81.75% 522ms 0.79% std::vector::size (inline) 44ms 0.066% 81.82% 506ms 0.76% AbstractTetrahedralElement::RefreshJacobian 10ms 0.015% 81.84% 482ms 0.73% Element::CalculateCircumsphere 0 0% 81.84% 481ms 0.72% std::insert_iterator::operator= (inline) 453ms 0.68% 82.52% 453ms 0.68% tetgen::tetgenmesh::decode 15ms 0.023% 82.54% 437ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 2ms 0.003% 82.54% 431ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 189ms 0.28% 82.83% 431ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.83% 425ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 16ms 0.024% 82.85% 421ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 419ms 0.63% 83.48% 419ms 0.63% tetgen::tetgenmesh::org 4ms 0.006% 83.49% 403ms 0.61% Cell::GetCellId 2ms 0.003% 83.49% 401ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 397ms 0.6% 84.09% 397ms 0.6% boost::numeric::ublas::c_vector::operator() 90ms 0.14% 84.22% 394ms 0.59% boost::numeric::ublas::indexing_vector_assign 0 0% 84.22% 391ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 21ms 0.032% 84.25% 387ms 0.58% std::vector::insert (inline) 383ms 0.58% 84.83% 383ms 0.58% tetgen::tetgenmesh::encode 382ms 0.57% 85.41% 382ms 0.57% std::_Rb_tree_decrement 84ms 0.13% 85.53% 371ms 0.56% __dynamic_cast 190ms 0.29% 85.82% 368ms 0.55% AbstractTetrahedralMesh::GetElement 5ms 0.0075% 85.83% 366ms 0.55% VertexElement::~VertexElement 6ms 0.009% 85.83% 365ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.83% 360ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 62ms 0.093% 85.93% 334ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)