File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 46561ms, 86.25% of 53986ms total Dropped 874 nodes (cum <= 269.93ms) flat flat% sum% cum cum% 0 0% 0% 53922ms 99.88% __libc_start_call_main 0 0% 0% 53922ms 99.88% __libc_start_main_impl 0 0% 0% 53922ms 99.88% _start 0 0% 0% 53908ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 53908ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 53908ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 53908ms 99.86% main 0 0% 0% 53871ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 53871ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 53871ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 53591ms 99.27% AbstractCellBasedSimulation::Solve 0 0% 0% 45231ms 83.78% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45183ms 83.69% MeshBasedCellPopulation::Update 0 0% 0% 24990ms 46.29% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24990ms 46.29% MeshBasedCellPopulation::TessellateIfNeeded 189ms 0.35% 0.35% 22343ms 41.39% VertexMesh::VertexMesh 0 0% 0.35% 16566ms 30.69% MutableMesh::ReMesh 0 0% 0.35% 12777ms 23.67% tetgen::tetrahedralize 1ms 0.0019% 0.35% 12645ms 23.42% tetgen::tetgenmesh::delaunizevertices 7ms 0.013% 0.36% 12641ms 23.42% tetgen::tetgenmesh::incrflipdelaunay 573ms 1.06% 1.43% 11185ms 20.72% tetgen::tetgenmesh::lawson 590ms 1.09% 2.52% 10929ms 20.24% TetrahedralMesh::EdgeIterator::operator++ 25ms 0.046% 2.57% 9175ms 17.00% std::set::insert (inline) 325ms 0.6% 3.17% 8744ms 16.20% VertexElement::AddFace 251ms 0.46% 3.63% 8696ms 16.11% std::_Rb_tree::_M_insert_unique 3006ms 5.57% 9.20% 8390ms 15.54% std::_Rb_tree::_M_lower_bound (inline) 233ms 0.43% 9.63% 7910ms 14.65% std::_Rb_tree::find (inline) 0 0% 9.63% 7374ms 13.66% std::set::count (inline) 100ms 0.19% 9.82% 5272ms 9.77% std::less::operator() (inline) 5229ms 9.69% 19.50% 5229ms 9.69% std::operator< (inline) 278ms 0.51% 20.02% 5222ms 9.67% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.02% 4914ms 9.10% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0019% 20.02% 4819ms 8.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0019% 20.02% 4783ms 8.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 210ms 0.39% 20.41% 4591ms 8.50% operator new 1049ms 1.94% 22.35% 4303ms 7.97% __GI___libc_malloc 4147ms 7.68% 30.04% 4147ms 7.68% std::_Rb_tree_increment 1ms 0.0019% 30.04% 3955ms 7.33% MeshBasedCellPopulation::UpdateNodePairs 44ms 0.082% 30.12% 3953ms 7.32% std::__new_allocator::allocate (inline) 6ms 0.011% 30.13% 3941ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 30.13% 3937ms 7.29% std::allocator_traits::allocate (inline) 11ms 0.02% 30.15% 3828ms 7.09% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.013% 30.16% 3764ms 6.97% std::_Rb_tree::~_Rb_tree (inline) 1332ms 2.47% 32.63% 3755ms 6.96% std::_Rb_tree::_M_erase 0 0% 32.63% 3714ms 6.88% std::set::~set (inline) 1258ms 2.33% 34.96% 3531ms 6.54% std::_Rb_tree::_M_get_insert_unique_pos 101ms 0.19% 35.15% 3483ms 6.45% tetgen::tetgenmesh::insphere_sos 994ms 1.84% 36.99% 3386ms 6.27% __GI___libc_free 3067ms 5.68% 42.67% 3369ms 6.24% tetgen::insphere 0 0% 42.67% 3306ms 6.12% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.67% 3232ms 5.99% std::_Rb_tree::_M_create_node (inline) 0 0% 42.67% 3208ms 5.94% std::_Rb_tree::_M_get_node (inline) 0 0% 42.67% 3198ms 5.92% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.0093% 42.68% 3092ms 5.73% std::set_intersection (inline) 210ms 0.39% 43.07% 3087ms 5.72% std::__set_intersection 7ms 0.013% 43.08% 3036ms 5.62% TetrahedralMesh::ImportFromMesher 149ms 0.28% 43.36% 3026ms 5.61% std::__new_allocator::deallocate (inline) 32ms 0.059% 43.42% 3014ms 5.58% Node::AddElement 0 0% 43.42% 3002ms 5.56% std::allocator_traits::deallocate (inline) 2201ms 4.08% 47.49% 2880ms 5.33% _int_malloc 207ms 0.38% 47.88% 2747ms 5.09% tetgen::tetgenmesh::flip23 0 0% 47.88% 2688ms 4.98% VertexMesh::~VertexMesh 2641ms 4.89% 52.77% 2641ms 4.89% std::_Rb_tree::_S_right (inline) 201ms 0.37% 53.14% 2460ms 4.56% std::_Rb_tree_const_iterator::operator++ (inline) 1193ms 2.21% 55.35% 2389ms 4.43% _int_free 85ms 0.16% 55.51% 2246ms 4.16% MutableElement::AddNode 6ms 0.011% 55.52% 2236ms 4.14% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 230ms 0.43% 55.95% 2206ms 4.09% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0019% 55.95% 1984ms 3.68% std::_Rb_tree_iterator::operator++ (inline) 129ms 0.24% 56.19% 1980ms 3.67% Node::~Node 0 0% 56.19% 1889ms 3.50% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.19% 1876ms 3.47% std::_Rb_tree::_M_put_node (inline) 157ms 0.29% 56.48% 1808ms 3.35% VertexMesh::Clear 1791ms 3.32% 59.80% 1791ms 3.32% std::_Rb_tree_insert_and_rebalance 156ms 0.29% 60.08% 1770ms 3.28% tetgen::tetgenmesh::flip32 9ms 0.017% 60.10% 1530ms 2.83% Element::Element 1317ms 2.44% 62.54% 1403ms 2.60% tetgen::orient3d 207ms 0.38% 62.92% 1289ms 2.39% tetgen::tetgenmesh::enqueueflipface 1272ms 2.36% 65.28% 1272ms 2.36% Node::GetIndex 37ms 0.069% 65.35% 1246ms 2.31% tetgen::tetgenmesh::locate 3ms 0.0056% 65.35% 1222ms 2.26% Element::RegisterWithNodes (inline) 148ms 0.27% 65.63% 1200ms 2.22% TetrahedralMesh::Clear 33ms 0.061% 65.69% 1159ms 2.15% std::_Vector_base::_M_deallocate (inline) 96ms 0.18% 65.87% 1150ms 2.13% tetgen::tetgenmesh::preciselocate 741ms 1.37% 67.24% 1149ms 2.13% malloc_consolidate 2ms 0.0037% 67.24% 1078ms 2.00% std::vector::~vector (inline) 69ms 0.13% 67.37% 1034ms 1.92% std::map::operator[] 1ms 0.0019% 67.37% 990ms 1.83% std::_Vector_base::~_Vector_base (inline) 8ms 0.015% 67.39% 975ms 1.81% _int_free_maybe_consolidate 65ms 0.12% 67.51% 959ms 1.78% std::vector::_M_realloc_insert 0 0% 67.51% 893ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 67.51% 893ms 1.65% std::map::lower_bound (inline) 0 0% 67.51% 851ms 1.58% VoronoiDataWriter::Visit 838ms 1.55% 69.06% 838ms 1.55% unlink_chunk 2ms 0.0037% 69.06% 801ms 1.48% VertexMesh::GenerateVerticesFromElementCircumcentres 106ms 0.2% 69.26% 792ms 1.47% std::vector::push_back (inline) 785ms 1.45% 70.71% 785ms 1.45% tetgen::tetgenmesh::triface::triface 454ms 0.84% 71.56% 742ms 1.37% tetgen::tetgenmesh::fnextself 10ms 0.019% 71.57% 739ms 1.37% std::_Vector_base::_M_allocate (inline) 1ms 0.0019% 71.58% 733ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 0 0% 71.58% 702ms 1.30% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.0056% 71.58% 688ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 674ms 1.25% 72.83% 674ms 1.25% tetgen::tetgenmesh::oppo 20ms 0.037% 72.87% 672ms 1.24% boost::numeric::ublas::vector_assign (inline) 13ms 0.024% 72.89% 659ms 1.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 518ms 0.96% 73.85% 652ms 1.21% AbstractElement::GetNodeGlobalIndex 14ms 0.026% 73.88% 651ms 1.21% boost::numeric::ublas::c_vector::c_vector (inline) 60ms 0.11% 73.99% 642ms 1.19% __atan2 638ms 1.18% 75.17% 638ms 1.18% [libchaste_mesh.so] 21ms 0.039% 75.21% 627ms 1.16% AbstractTetrahedralElement::CalculateJacobian 594ms 1.10% 76.31% 594ms 1.10% tetgen::tetgenmesh::triface::operator= 456ms 0.84% 77.15% 582ms 1.08% __ieee754_atan2_fma 253ms 0.47% 77.62% 579ms 1.07% AbstractElement::GetNodeLocation 0 0% 77.62% 534ms 0.99% std::set::find (inline) 46ms 0.085% 77.71% 494ms 0.92% tetgen::tetgenmesh::enextfnext 0 0% 77.71% 485ms 0.9% boost::numeric::ublas::inner_prod (inline) 0 0% 77.71% 483ms 0.89% std::insert_iterator::operator= (inline) 4ms 0.0074% 77.71% 480ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 33ms 0.061% 77.78% 476ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 37ms 0.069% 77.84% 473ms 0.88% AbstractTetrahedralElement::RefreshJacobian 33ms 0.061% 77.91% 463ms 0.86% tetgen::tetgenmesh::enext2fnext 131ms 0.24% 78.15% 458ms 0.85% boost::numeric::ublas::indexing_vector_assign 308ms 0.57% 78.72% 456ms 0.84% tetgen::tetgenmesh::sym 454ms 0.84% 79.56% 454ms 0.84% Node::rGetLocation 20ms 0.037% 79.60% 443ms 0.82% Element::CalculateCircumsphere 0 0% 79.60% 433ms 0.8% std::_Rb_tree::_M_insert_unique_ (inline) 5ms 0.0093% 79.61% 424ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 420ms 0.78% 80.38% 420ms 0.78% std::vector::size (inline) 24ms 0.044% 80.43% 405ms 0.75% std::_Rb_tree_iterator::operator-- (inline) 405ms 0.75% 81.18% 405ms 0.75% tetgen::tetgenmesh::org 229ms 0.42% 81.60% 396ms 0.73% AbstractTetrahedralMesh::GetElement 5ms 0.0093% 81.61% 387ms 0.72% CellPropertyCollection::GetPropertiesType (inline) 387ms 0.72% 82.33% 387ms 0.72% boost::numeric::ublas::c_vector::operator() 15ms 0.028% 82.36% 387ms 0.72% tetgen::tetgenmesh::queue::push 160ms 0.3% 82.65% 379ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 15ms 0.028% 82.68% 378ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.68% 378ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 84ms 0.16% 82.84% 378ms 0.7% __dynamic_cast 0 0% 82.84% 371ms 0.69% Cell::GetCellId 275ms 0.51% 83.35% 368ms 0.68% tetgen::tetgenmesh::link::add 366ms 0.68% 84.02% 366ms 0.68% std::_Rb_tree_decrement 251ms 0.46% 84.49% 359ms 0.66% tetgen::tetgenmesh::bond 0 0% 84.49% 333ms 0.62% tcache_get (inline) 333ms 0.62% 85.11% 333ms 0.62% tcache_get_n (inline) 313ms 0.58% 85.69% 313ms 0.58% AbstractElement::IsDeleted 3ms 0.0056% 85.69% 310ms 0.57% AbstractCellProperty::IsSubType (inline) 133ms 0.25% 85.94% 309ms 0.57% Inverse 16ms 0.03% 85.97% 302ms 0.56% std::vector::insert (inline) 33ms 0.061% 86.03% 302ms 0.56% tetgen::insphereadapt 55ms 0.1% 86.13% 299ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0019% 86.13% 298ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 56ms 0.1% 86.24% 293ms 0.54% tetgen::tetgenmesh::queue::pop 6ms 0.011% 86.25% 290ms 0.54% VertexElement::~VertexElement