File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 60606ms, 86.12% of 70370ms total Dropped 842 nodes (cum <= 351.85ms) flat flat% sum% cum cum% 0 0% 0% 70318ms 99.93% __libc_start_call_main 0 0% 0% 70318ms 99.93% __libc_start_main_impl 0 0% 0% 70318ms 99.93% _start 0 0% 0% 70298ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 70298ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 70298ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 70298ms 99.90% main 0 0% 0% 70263ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 70263ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 70263ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 70023ms 99.51% AbstractCellBasedSimulation::Solve 0 0% 0% 58063ms 82.51% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 57994ms 82.41% MeshBasedCellPopulation::Update 0 0% 0% 36844ms 52.36% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 36844ms 52.36% MeshBasedCellPopulation::TessellateIfNeeded 283ms 0.4% 0.4% 32917ms 46.78% VertexMesh::VertexMesh 1ms 0.0014% 0.4% 16292ms 23.15% MutableMesh::ReMesh 560ms 0.8% 1.20% 15164ms 21.55% TetrahedralMesh::EdgeIterator::operator++ 36ms 0.051% 1.25% 13830ms 19.65% std::set::insert (inline) 152ms 0.22% 1.47% 13242ms 18.82% std::_Rb_tree::_M_insert_unique 370ms 0.53% 1.99% 12084ms 17.17% VertexElement::AddFace 4099ms 5.82% 7.82% 11727ms 16.66% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.82% 11456ms 16.28% tetgen::tetrahedralize 1ms 0.0014% 7.82% 11337ms 16.11% tetgen::tetgenmesh::delaunizevertices 6ms 0.0085% 7.83% 11333ms 16.10% tetgen::tetgenmesh::incrflipdelaunay 208ms 0.3% 8.12% 11114ms 15.79% std::_Rb_tree::find (inline) 0 0% 8.12% 10498ms 14.92% std::set::count (inline) 490ms 0.7% 8.82% 10017ms 14.23% tetgen::tetgenmesh::lawson 245ms 0.35% 9.17% 8853ms 12.58% operator new 317ms 0.45% 9.62% 8768ms 12.46% std::_Rb_tree::_M_insert_ (inline) 2991ms 4.25% 13.87% 8540ms 12.14% __GI___libc_malloc 7532ms 10.70% 24.57% 7532ms 10.70% std::_Rb_tree_increment 88ms 0.13% 24.70% 7512ms 10.68% std::__new_allocator::allocate (inline) 0 0% 24.70% 7483ms 10.63% std::allocator_traits::allocate (inline) 6670ms 9.48% 34.18% 6670ms 9.48% std::operator< (inline) 80ms 0.11% 34.29% 6667ms 9.47% std::less::operator() (inline) 0 0% 34.29% 6595ms 9.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0028% 34.29% 6411ms 9.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0043% 34.30% 6394ms 9.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 34.30% 6037ms 8.58% std::_Rb_tree::_M_create_node (inline) 0 0% 34.30% 5989ms 8.51% std::_Rb_tree::_M_get_node (inline) 0 0% 34.30% 5986ms 8.51% std::_Rb_tree::_Alloc_node::operator() (inline) 314ms 0.45% 34.74% 5471ms 7.77% std::__set_intersection 0 0% 34.74% 5471ms 7.77% std::set_intersection (inline) 985ms 1.40% 36.14% 5347ms 7.60% __GI___libc_free 4ms 0.0057% 36.15% 5305ms 7.54% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 36.15% 5202ms 7.39% MeshBasedCellPopulation::UpdateNodePairs 0 0% 36.15% 5185ms 7.37% AbstractCellPopulation::WriteResultsToFiles 3949ms 5.61% 41.76% 5079ms 7.22% _int_malloc 26ms 0.037% 41.80% 5052ms 7.18% MeshBasedCellPopulation::SpringIterator::operator++ 71ms 0.1% 41.90% 4996ms 7.10% Node::AddElement 1515ms 2.15% 44.05% 4685ms 6.66% std::_Rb_tree::_M_get_insert_unique_pos 12ms 0.017% 44.07% 4685ms 6.66% std::_Rb_tree::~_Rb_tree (inline) 1370ms 1.95% 46.01% 4660ms 6.62% std::_Rb_tree::_M_erase 0 0% 46.01% 4640ms 6.59% std::set::~set (inline) 322ms 0.46% 46.47% 4533ms 6.44% std::_Rb_tree_const_iterator::operator++ (inline) 62ms 0.088% 46.56% 4501ms 6.40% std::__new_allocator::deallocate (inline) 0 0% 46.56% 4490ms 6.38% std::allocator_traits::deallocate (inline) 2138ms 3.04% 49.60% 4339ms 6.17% _int_free 4330ms 6.15% 55.75% 4330ms 6.15% std::_Rb_tree::_S_right (inline) 311ms 0.44% 56.19% 3964ms 5.63% std::_Rb_tree_iterator::operator++ (inline) 0 0% 56.19% 3957ms 5.62% VertexMesh::~VertexMesh 4ms 0.0057% 56.20% 3952ms 5.62% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 8ms 0.011% 56.21% 3838ms 5.45% TetrahedralMesh::ImportFromMesher 46ms 0.065% 56.28% 3750ms 5.33% MutableElement::AddNode 4ms 0.0057% 56.28% 3745ms 5.32% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 89ms 0.13% 56.41% 3038ms 4.32% tetgen::tetgenmesh::insphere_sos 2696ms 3.83% 60.24% 2919ms 4.15% tetgen::insphere 0 0% 60.24% 2682ms 3.81% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.24% 2642ms 3.75% std::_Rb_tree::_M_put_node (inline) 2564ms 3.64% 63.88% 2564ms 3.64% std::_Rb_tree_insert_and_rebalance 53ms 0.075% 63.96% 2492ms 3.54% Node::~Node 34ms 0.048% 64.01% 2481ms 3.53% VertexMesh::Clear 253ms 0.36% 64.37% 2350ms 3.34% tetgen::tetgenmesh::flip23 1ms 0.0014% 64.37% 2222ms 3.16% Element::Element 2129ms 3.03% 67.39% 2129ms 3.03% [libchaste_mesh.so] 1287ms 1.83% 69.22% 1962ms 2.79% malloc_consolidate 25ms 0.036% 69.26% 1873ms 2.66% std::_Vector_base::_M_deallocate (inline) 4ms 0.0057% 69.26% 1863ms 2.65% Element::RegisterWithNodes (inline) 1ms 0.0014% 69.26% 1680ms 2.39% std::vector::~vector (inline) 41ms 0.058% 69.32% 1672ms 2.38% std::vector::_M_realloc_insert 8ms 0.011% 69.33% 1657ms 2.35% _int_free_maybe_consolidate 1ms 0.0014% 69.33% 1649ms 2.34% std::_Vector_base::~_Vector_base (inline) 1567ms 2.23% 71.56% 1626ms 2.31% tetgen::orient3d 223ms 0.32% 71.88% 1624ms 2.31% tetgen::tetgenmesh::flip32 3ms 0.0043% 71.88% 1497ms 2.13% std::_Vector_base::_M_allocate (inline) 1496ms 2.13% 74.01% 1496ms 2.13% Node::GetIndex 62ms 0.088% 74.10% 1351ms 1.92% std::map::operator[] 1335ms 1.90% 75.99% 1335ms 1.90% unlink_chunk 72ms 0.1% 76.10% 1297ms 1.84% std::vector::push_back (inline) 2ms 0.0028% 76.10% 1279ms 1.82% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0014% 76.10% 1198ms 1.70% VoronoiDataWriter::Visit 0 0% 76.10% 1185ms 1.68% std::_Rb_tree::lower_bound (inline) 0 0% 76.10% 1185ms 1.68% std::map::lower_bound (inline) 14ms 0.02% 76.12% 1156ms 1.64% TetrahedralMesh::Clear 769ms 1.09% 77.21% 1152ms 1.64% AbstractElement::GetNodeGlobalIndex 32ms 0.045% 77.26% 1144ms 1.63% tetgen::tetgenmesh::locate 92ms 0.13% 77.39% 1081ms 1.54% tetgen::tetgenmesh::preciselocate 211ms 0.3% 77.69% 1025ms 1.46% tetgen::tetgenmesh::enqueueflipface 0 0% 77.69% 966ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 917ms 1.30% 78.99% 917ms 1.30% Node::rGetLocation 5ms 0.0071% 79.00% 841ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0014% 79.00% 805ms 1.14% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.0057% 79.01% 766ms 1.09% boost::numeric::ublas::vector_assign (inline) 17ms 0.024% 79.03% 765ms 1.09% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 9ms 0.013% 79.04% 751ms 1.07% boost::numeric::ublas::c_vector::c_vector (inline) 369ms 0.52% 79.57% 711ms 1.01% AbstractElement::GetNodeLocation 11ms 0.016% 79.58% 710ms 1.01% AbstractTetrahedralElement::CalculateJacobian 11ms 0.016% 79.60% 668ms 0.95% Element::CalculateCircumsphere 643ms 0.91% 80.51% 643ms 0.91% std::vector::size (inline) 386ms 0.55% 81.06% 642ms 0.91% tetgen::tetgenmesh::sym 0 0% 81.06% 611ms 0.87% std::set::find (inline) 0 0% 81.06% 577ms 0.82% std::insert_iterator::operator= (inline) 37ms 0.053% 81.11% 571ms 0.81% __atan2 110ms 0.16% 81.27% 567ms 0.81% std::_Rb_tree_iterator::operator-- (inline) 551ms 0.78% 82.05% 551ms 0.78% tetgen::tetgenmesh::oppo 45ms 0.064% 82.12% 545ms 0.77% AbstractTetrahedralElement::RefreshJacobian 475ms 0.68% 82.79% 528ms 0.75% __ieee754_atan2_fma 19ms 0.027% 82.82% 519ms 0.74% std::vector::insert (inline) 0 0% 82.82% 510ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 477ms 0.68% 83.50% 477ms 0.68% AbstractElement::IsDeleted 11ms 0.016% 83.51% 465ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 6ms 0.0085% 83.52% 450ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0014% 83.52% 444ms 0.63% Cell::GetCellId 430ms 0.61% 84.13% 430ms 0.61% boost::numeric::ublas::c_vector::operator() 426ms 0.61% 84.74% 426ms 0.61% std::_Rb_tree_decrement 184ms 0.26% 85.00% 422ms 0.6% Inverse 0 0% 85.00% 402ms 0.57% boost::numeric::ublas::inner_prod (inline) 20ms 0.028% 85.03% 401ms 0.57% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.03% 401ms 0.57% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 133ms 0.19% 85.22% 392ms 0.56% _int_free_merge_chunk 0 0% 85.22% 388ms 0.55% VertexMeshWriter::WriteVtkUsingMesh 0 0% 85.22% 378ms 0.54% tcache_get (inline) 378ms 0.54% 85.76% 378ms 0.54% tcache_get_n (inline) 99ms 0.14% 85.90% 366ms 0.52% __dynamic_cast 4ms 0.0057% 85.90% 364ms 0.52% VertexElement::~VertexElement 14ms 0.02% 85.92% 360ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline) 101ms 0.14% 86.07% 359ms 0.51% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0028% 86.07% 358ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.0057% 86.07% 354ms 0.5% VertexMesh::GetVolumeOfElement 5ms 0.0071% 86.08% 353ms 0.5% boost::numeric::ublas::c_vector::operator= (inline) 31ms 0.044% 86.12% 352ms 0.5% tetgen::tetgenmesh::enextfnext