File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53418ms, 87.53% of 61025ms total Dropped 870 nodes (cum <= 305.12ms) flat flat% sum% cum cum% 0 0% 0% 60957ms 99.89% __libc_start_call_main 0 0% 0% 60957ms 99.89% __libc_start_main_impl 0 0% 0% 60957ms 99.89% _start 0 0% 0% 60942ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60942ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60942ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60942ms 99.86% main 0 0% 0% 60907ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60907ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60907ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60649ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 50013ms 81.95% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 49974ms 81.89% MeshBasedCellPopulation::Update 0 0% 0% 28678ms 46.99% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 28678ms 46.99% MeshBasedCellPopulation::TessellateIfNeeded 231ms 0.38% 0.38% 25318ms 41.49% VertexMesh::VertexMesh 0 0% 0.38% 17150ms 28.10% MutableMesh::ReMesh 0 0% 0.38% 12812ms 20.99% tetgen::tetrahedralize 547ms 0.9% 1.27% 12739ms 20.88% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.0082% 1.28% 12682ms 20.78% tetgen::tetgenmesh::delaunizevertices 8ms 0.013% 1.30% 12674ms 20.77% tetgen::tetgenmesh::incrflipdelaunay 520ms 0.85% 2.15% 11264ms 18.46% tetgen::tetgenmesh::lawson 3082ms 5.05% 7.20% 10199ms 16.71% std::_Rb_tree::_M_lower_bound (inline) 45ms 0.074% 7.27% 9982ms 16.36% std::set::insert (inline) 208ms 0.34% 7.61% 9480ms 15.53% std::_Rb_tree::_M_insert_unique 237ms 0.39% 8.00% 9376ms 15.36% std::_Rb_tree::find (inline) 328ms 0.54% 8.54% 9234ms 15.13% VertexElement::AddFace 0 0% 8.54% 8821ms 14.45% std::set::count (inline) 125ms 0.2% 8.74% 6729ms 11.03% std::less::operator() (inline) 6667ms 10.93% 19.67% 6667ms 10.93% std::operator< (inline) 6232ms 10.21% 29.88% 6232ms 10.21% std::_Rb_tree_increment 0 0% 29.88% 5612ms 9.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 254ms 0.42% 30.30% 5610ms 9.19% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.30% 5464ms 8.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0049% 30.30% 5439ms 8.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 205ms 0.34% 30.64% 5105ms 8.37% operator new 0 0% 30.64% 4875ms 7.99% AbstractCellPopulation::WriteResultsToFiles 1093ms 1.79% 32.43% 4822ms 7.90% __GI___libc_malloc 7ms 0.011% 32.44% 4491ms 7.36% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0016% 32.44% 4484ms 7.35% MeshBasedCellPopulation::UpdateNodePairs 38ms 0.062% 32.50% 4376ms 7.17% std::__new_allocator::allocate (inline) 0 0% 32.50% 4363ms 7.15% std::allocator_traits::allocate (inline) 7ms 0.011% 32.52% 4344ms 7.12% MeshBasedCellPopulation::SpringIterator::operator++ 4ms 0.0066% 32.52% 4247ms 6.96% std::_Rb_tree::~_Rb_tree (inline) 1761ms 2.89% 35.41% 4240ms 6.95% std::_Rb_tree::_M_erase 0 0% 35.41% 4187ms 6.86% std::set::~set (inline) 1176ms 1.93% 37.34% 3964ms 6.50% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.0033% 37.34% 3784ms 6.20% std::set_intersection (inline) 252ms 0.41% 37.75% 3782ms 6.20% std::__set_intersection 26ms 0.043% 37.79% 3752ms 6.15% Node::AddElement 1084ms 1.78% 39.57% 3723ms 6.10% __GI___libc_free 239ms 0.39% 39.96% 3683ms 6.04% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3599ms 5.90% 45.86% 3599ms 5.90% std::_Rb_tree::_S_right (inline) 4ms 0.0066% 45.87% 3517ms 5.76% TetrahedralMesh::ImportFromMesher 109ms 0.18% 46.05% 3514ms 5.76% tetgen::tetgenmesh::insphere_sos 0 0% 46.05% 3506ms 5.75% std::_Rb_tree::_M_create_node (inline) 0 0% 46.05% 3472ms 5.69% std::_Rb_tree::_M_get_node (inline) 0 0% 46.05% 3471ms 5.69% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0016% 46.05% 3455ms 5.66% std::_Rb_tree_iterator::operator++ (inline) 3ms 0.0049% 46.05% 3441ms 5.64% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3095ms 5.07% 51.12% 3395ms 5.56% tetgen::insphere 0 0% 51.12% 3382ms 5.54% VertexMesh::~VertexMesh 2413ms 3.95% 55.08% 3351ms 5.49% _int_malloc 125ms 0.2% 55.28% 3256ms 5.34% std::__new_allocator::deallocate (inline) 0 0% 55.28% 3238ms 5.31% std::allocator_traits::deallocate (inline) 175ms 0.29% 55.57% 3082ms 5.05% std::_Rb_tree_const_iterator::operator++ (inline) 254ms 0.42% 55.99% 2763ms 4.53% tetgen::tetgenmesh::flip23 92ms 0.15% 56.14% 2745ms 4.50% MutableElement::AddNode 1126ms 1.85% 57.98% 2637ms 4.32% _int_free 152ms 0.25% 58.23% 2407ms 3.94% Node::~Node 171ms 0.28% 58.51% 2222ms 3.64% VertexMesh::Clear 1964ms 3.22% 61.73% 1964ms 3.22% std::_Rb_tree_insert_and_rebalance 5ms 0.0082% 61.74% 1825ms 2.99% Element::Element 149ms 0.24% 61.98% 1816ms 2.98% tetgen::tetgenmesh::flip32 0 0% 61.98% 1810ms 2.97% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.98% 1796ms 2.94% std::_Rb_tree::_M_put_node (inline) 1646ms 2.70% 64.68% 1646ms 2.70% Node::GetIndex 4ms 0.0066% 64.68% 1499ms 2.46% Element::RegisterWithNodes (inline) 882ms 1.45% 66.13% 1480ms 2.43% malloc_consolidate 13ms 0.021% 66.15% 1455ms 2.38% std::_Vector_base::_M_deallocate (inline) 1301ms 2.13% 68.28% 1366ms 2.24% tetgen::orient3d 67ms 0.11% 68.39% 1358ms 2.23% std::map::operator[] 0 0% 68.39% 1356ms 2.22% std::vector::~vector (inline) 176ms 0.29% 68.68% 1334ms 2.19% TetrahedralMesh::Clear 173ms 0.28% 68.97% 1308ms 2.14% tetgen::tetgenmesh::enqueueflipface 5ms 0.0082% 68.97% 1274ms 2.09% _int_free_maybe_consolidate 1ms 0.0016% 68.98% 1258ms 2.06% std::_Vector_base::~_Vector_base (inline) 0 0% 68.98% 1222ms 2.00% std::_Rb_tree::lower_bound (inline) 0 0% 68.98% 1222ms 2.00% std::map::lower_bound (inline) 1203ms 1.97% 70.95% 1203ms 1.97% unlink_chunk 45ms 0.074% 71.02% 1190ms 1.95% tetgen::tetgenmesh::locate 1ms 0.0016% 71.02% 1183ms 1.94% VoronoiDataWriter::Visit 84ms 0.14% 71.16% 1094ms 1.79% tetgen::tetgenmesh::preciselocate 53ms 0.087% 71.25% 1083ms 1.77% std::vector::_M_realloc_insert 7ms 0.011% 71.26% 1011ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 117ms 0.19% 71.45% 899ms 1.47% std::vector::push_back (inline) 6ms 0.0098% 71.46% 897ms 1.47% std::_Vector_base::_M_allocate (inline) 862ms 1.41% 72.87% 862ms 1.41% tetgen::tetgenmesh::triface::triface 734ms 1.20% 74.07% 859ms 1.41% AbstractElement::GetNodeGlobalIndex 0 0% 74.07% 800ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0016% 74.08% 755ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.018% 74.09% 725ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 704ms 1.15% 75.25% 704ms 1.15% [libchaste_mesh.so] 18ms 0.029% 75.28% 696ms 1.14% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 284ms 0.47% 75.74% 692ms 1.13% AbstractElement::GetNodeLocation 382ms 0.63% 76.37% 692ms 1.13% tetgen::tetgenmesh::fnextself 687ms 1.13% 77.49% 687ms 1.13% tetgen::tetgenmesh::oppo 19ms 0.031% 77.53% 666ms 1.09% AbstractTetrahedralElement::CalculateJacobian 53ms 0.087% 77.61% 638ms 1.05% __atan2 12ms 0.02% 77.63% 634ms 1.04% boost::numeric::ublas::vector_assign (inline) 634ms 1.04% 78.67% 634ms 1.04% tetgen::tetgenmesh::triface::operator= 609ms 1% 79.67% 609ms 1% Node::rGetLocation 8ms 0.013% 79.68% 608ms 1% boost::numeric::ublas::c_vector::c_vector (inline) 460ms 0.75% 80.44% 585ms 0.96% __ieee754_atan2_fma 0 0% 80.44% 550ms 0.9% std::set::find (inline) 13ms 0.021% 80.46% 532ms 0.87% Element::CalculateCircumsphere 40ms 0.066% 80.52% 504ms 0.83% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.52% 494ms 0.81% std::insert_iterator::operator= (inline) 46ms 0.075% 80.60% 483ms 0.79% tetgen::tetgenmesh::enext2fnext 0 0% 80.60% 471ms 0.77% boost::numeric::ublas::inner_prod (inline) 6ms 0.0098% 80.61% 469ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 467ms 0.77% 81.37% 467ms 0.77% std::vector::size (inline) 463ms 0.76% 82.13% 463ms 0.76% AbstractElement::IsDeleted 26ms 0.043% 82.17% 463ms 0.76% boost::numeric::ublas::vector_scalar_binary::evaluate 41ms 0.067% 82.24% 443ms 0.73% tetgen::tetgenmesh::enextfnext 277ms 0.45% 82.70% 438ms 0.72% tetgen::tetgenmesh::sym 0 0% 82.70% 433ms 0.71% std::_Rb_tree::_M_insert_unique_ (inline) 231ms 0.38% 83.07% 420ms 0.69% AbstractTetrahedralMesh::GetElement 113ms 0.19% 83.26% 419ms 0.69% boost::numeric::ublas::indexing_vector_assign 24ms 0.039% 83.30% 413ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 411ms 0.67% 83.97% 411ms 0.67% boost::numeric::ublas::c_vector::operator() 0 0% 83.97% 392ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 29ms 0.048% 84.02% 392ms 0.64% tetgen::tetgenmesh::queue::push 158ms 0.26% 84.28% 389ms 0.64% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.28% 374ms 0.61% Cell::GetCellId 9ms 0.015% 84.29% 372ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 366ms 0.6% 84.89% 366ms 0.6% tetgen::tetgenmesh::org 95ms 0.16% 85.05% 359ms 0.59% __dynamic_cast 265ms 0.43% 85.48% 357ms 0.59% tetgen::tetgenmesh::link::add 7ms 0.011% 85.49% 355ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 21ms 0.034% 85.53% 350ms 0.57% std::_Rb_tree_iterator::operator-- (inline) 260ms 0.43% 85.95% 349ms 0.57% tetgen::tetgenmesh::bond 20ms 0.033% 85.99% 340ms 0.56% std::vector::insert (inline) 9ms 0.015% 86.00% 338ms 0.55% VertexElement::~VertexElement 0 0% 86.00% 338ms 0.55% tcache_get (inline) 338ms 0.55% 86.56% 338ms 0.55% tcache_get_n (inline) 0 0% 86.56% 327ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 150ms 0.25% 86.80% 325ms 0.53% Inverse 4ms 0.0066% 86.81% 322ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 56ms 0.092% 86.90% 320ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 73ms 0.12% 87.02% 315ms 0.52% tetgen::tetgenmesh::queue::pop 314ms 0.51% 87.53% 314ms 0.51% std::_Rb_tree_decrement