File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 38132ms, 86.07% of 44303ms total Dropped 808 nodes (cum <= 221.51ms) flat flat% sum% cum cum% 0 0% 0% 44272ms 99.93% __libc_start_call_main 0 0% 0% 44272ms 99.93% __libc_start_main_impl 0 0% 0% 44272ms 99.93% _start 0 0% 0% 44259ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 44259ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 44259ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 44259ms 99.90% main 0 0% 0% 44226ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 44226ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 44226ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 44063ms 99.46% AbstractCellBasedSimulation::Solve 0 0% 0% 36937ms 83.37% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 36887ms 83.26% MeshBasedCellPopulation::Update 0 0% 0% 22935ms 51.77% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 22935ms 51.77% MeshBasedCellPopulation::TessellateIfNeeded 257ms 0.58% 0.58% 20665ms 46.64% VertexMesh::VertexMesh 0 0% 0.58% 10861ms 24.52% MutableMesh::ReMesh 431ms 0.97% 1.55% 9669ms 21.82% TetrahedralMesh::EdgeIterator::operator++ 25ms 0.056% 1.61% 8617ms 19.45% std::set::insert (inline) 108ms 0.24% 1.85% 8189ms 18.48% std::_Rb_tree::_M_insert_unique 0 0% 1.85% 7823ms 17.66% tetgen::tetrahedralize 203ms 0.46% 2.31% 7742ms 17.48% VertexElement::AddFace 1ms 0.0023% 2.31% 7732ms 17.45% tetgen::tetgenmesh::delaunizevertices 3ms 0.0068% 2.32% 7731ms 17.45% tetgen::tetgenmesh::incrflipdelaunay 2945ms 6.65% 8.97% 7312ms 16.50% std::_Rb_tree::_M_lower_bound (inline) 124ms 0.28% 9.25% 6939ms 15.66% std::_Rb_tree::find (inline) 346ms 0.78% 10.03% 6835ms 15.43% tetgen::tetgenmesh::lawson 0 0% 10.03% 6522ms 14.72% std::set::count (inline) 210ms 0.47% 10.50% 5389ms 12.16% std::_Rb_tree::_M_insert_ (inline) 153ms 0.35% 10.85% 5288ms 11.94% operator new 1591ms 3.59% 14.44% 5085ms 11.48% __GI___libc_malloc 61ms 0.14% 14.58% 4581ms 10.34% std::__new_allocator::allocate (inline) 0 0% 14.58% 4561ms 10.30% std::allocator_traits::allocate (inline) 0 0% 14.58% 4276ms 9.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 14.58% 4164ms 9.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0045% 14.58% 4150ms 9.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 4146ms 9.36% 23.94% 4146ms 9.36% std::_Rb_tree_increment 50ms 0.11% 24.05% 3863ms 8.72% std::less::operator() (inline) 3858ms 8.71% 32.76% 3858ms 8.71% std::operator< (inline) 0 0% 32.76% 3753ms 8.47% std::_Rb_tree::_M_create_node (inline) 0 0% 32.76% 3729ms 8.42% std::_Rb_tree::_M_get_node (inline) 0 0% 32.76% 3725ms 8.41% std::_Rb_tree::_Alloc_node::operator() (inline) 688ms 1.55% 34.31% 3467ms 7.83% __GI___libc_free 2ms 0.0045% 34.32% 3445ms 7.78% std::set_intersection (inline) 224ms 0.51% 34.82% 3443ms 7.77% std::__set_intersection 0 0% 34.82% 3339ms 7.54% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0023% 34.83% 3317ms 7.49% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2606ms 5.88% 40.71% 3211ms 7.25% _int_malloc 15ms 0.034% 40.74% 3206ms 7.24% MeshBasedCellPopulation::SpringIterator::operator++ 62ms 0.14% 40.88% 3087ms 6.97% std::__new_allocator::deallocate (inline) 0 0% 40.88% 3074ms 6.94% std::allocator_traits::deallocate (inline) 10ms 0.023% 40.90% 3006ms 6.79% std::_Rb_tree::~_Rb_tree (inline) 812ms 1.83% 42.74% 2992ms 6.75% std::_Rb_tree::_M_erase 0 0% 42.74% 2984ms 6.74% std::set::~set (inline) 64ms 0.14% 42.88% 2981ms 6.73% Node::AddElement 997ms 2.25% 45.13% 2945ms 6.65% std::_Rb_tree::_M_get_insert_unique_pos 187ms 0.42% 45.55% 2766ms 6.24% std::_Rb_tree_const_iterator::operator++ (inline) 1356ms 3.06% 48.62% 2758ms 6.23% _int_free 0 0% 48.62% 2718ms 6.14% AbstractCellPopulation::WriteResultsToFiles 2557ms 5.77% 54.39% 2557ms 5.77% std::_Rb_tree::_S_right (inline) 1ms 0.0023% 54.39% 2429ms 5.48% TetrahedralMesh::ImportFromMesher 0 0% 54.39% 2288ms 5.16% VertexMesh::~VertexMesh 37ms 0.084% 54.47% 2156ms 4.87% tetgen::tetgenmesh::insphere_sos 1935ms 4.37% 58.84% 2099ms 4.74% tetgen::insphere 37ms 0.084% 58.92% 2089ms 4.72% MutableElement::AddNode 189ms 0.43% 59.35% 1981ms 4.47% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0045% 59.35% 1969ms 4.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0045% 59.36% 1920ms 4.33% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 59.36% 1821ms 4.11% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.36% 1796ms 4.05% std::_Rb_tree::_M_put_node (inline) 1595ms 3.60% 62.96% 1595ms 3.60% [libchaste_mesh.so] 162ms 0.37% 63.33% 1532ms 3.46% tetgen::tetgenmesh::flip23 1529ms 3.45% 66.78% 1529ms 3.45% std::_Rb_tree_insert_and_rebalance 2ms 0.0045% 66.78% 1455ms 3.28% Element::Element 18ms 0.041% 66.82% 1383ms 3.12% Node::~Node 789ms 1.78% 68.60% 1355ms 3.06% malloc_consolidate 11ms 0.025% 68.63% 1289ms 2.91% std::_Vector_base::_M_deallocate (inline) 5ms 0.011% 68.64% 1225ms 2.77% VertexMesh::Clear 3ms 0.0068% 68.65% 1224ms 2.76% Element::RegisterWithNodes (inline) 4ms 0.009% 68.65% 1179ms 2.66% _int_free_maybe_consolidate 0 0% 68.65% 1173ms 2.65% std::vector::~vector (inline) 0 0% 68.65% 1149ms 2.59% std::_Vector_base::~_Vector_base (inline) 144ms 0.33% 68.98% 1102ms 2.49% tetgen::tetgenmesh::flip32 1009ms 2.28% 71.26% 1060ms 2.39% tetgen::orient3d 1047ms 2.36% 73.62% 1047ms 2.36% Node::GetIndex 36ms 0.081% 73.70% 938ms 2.12% std::vector::_M_realloc_insert 937ms 2.11% 75.82% 937ms 2.11% unlink_chunk 51ms 0.12% 75.93% 856ms 1.93% std::map::operator[] 1ms 0.0023% 75.93% 833ms 1.88% std::_Vector_base::_M_allocate (inline) 5ms 0.011% 75.95% 779ms 1.76% VertexMesh::GenerateVerticesFromElementCircumcentres 22ms 0.05% 75.99% 739ms 1.67% tetgen::tetgenmesh::locate 32ms 0.072% 76.07% 734ms 1.66% std::vector::push_back (inline) 0 0% 76.07% 730ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 76.07% 730ms 1.65% std::map::lower_bound (inline) 4ms 0.009% 76.08% 701ms 1.58% TetrahedralMesh::Clear 52ms 0.12% 76.19% 692ms 1.56% tetgen::tetgenmesh::preciselocate 471ms 1.06% 77.26% 689ms 1.56% AbstractElement::GetNodeGlobalIndex 110ms 0.25% 77.50% 687ms 1.55% tetgen::tetgenmesh::enqueueflipface 0 0% 77.50% 642ms 1.45% VoronoiDataWriter::Visit 2ms 0.0045% 77.51% 613ms 1.38% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 77.51% 593ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.023% 77.53% 571ms 1.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 561ms 1.27% 78.80% 561ms 1.27% Node::rGetLocation 253ms 0.57% 79.37% 521ms 1.18% AbstractElement::GetNodeLocation 2ms 0.0045% 79.37% 515ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.025% 79.40% 498ms 1.12% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0023% 79.40% 441ms 1% boost::numeric::ublas::vector_assign (inline) 273ms 0.62% 80.02% 439ms 0.99% tetgen::tetgenmesh::sym 5ms 0.011% 80.03% 437ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.03% 433ms 0.98% std::insert_iterator::operator= (inline) 421ms 0.95% 80.98% 421ms 0.95% tetgen::tetgenmesh::oppo 26ms 0.059% 81.04% 413ms 0.93% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.04% 413ms 0.93% std::set::find (inline) 17ms 0.038% 81.08% 391ms 0.88% __atan2 0 0% 81.08% 376ms 0.85% std::_Rb_tree::_M_insert_unique_ (inline) 374ms 0.84% 81.92% 374ms 0.84% std::vector::size (inline) 336ms 0.76% 82.68% 371ms 0.84% __ieee754_atan2_fma 11ms 0.025% 82.70% 369ms 0.83% Element::CalculateCircumsphere 13ms 0.029% 82.73% 331ms 0.75% CellPropertyCollection::GetPropertiesType (inline) 35ms 0.079% 82.81% 320ms 0.72% std::_Rb_tree_iterator::operator-- (inline) 0 0% 82.81% 302ms 0.68% Cell::GetCellId 211ms 0.48% 83.29% 280ms 0.63% AbstractTetrahedralMesh::GetElement 0 0% 83.29% 271ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 0 0% 83.29% 271ms 0.61% boost::numeric::ublas::inner_prod (inline) 10ms 0.023% 83.31% 271ms 0.61% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.31% 271ms 0.61% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.027% 83.34% 265ms 0.6% std::vector::insert (inline) 0 0% 83.34% 260ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 25ms 0.056% 83.39% 259ms 0.58% tetgen::tetgenmesh::enext2fnext 70ms 0.16% 83.55% 254ms 0.57% __dynamic_cast 75ms 0.17% 83.72% 253ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 253ms 0.57% 84.29% 253ms 0.57% std::_Rb_tree_decrement 195ms 0.44% 84.73% 240ms 0.54% tetgen::tetgenmesh::fnextself 239ms 0.54% 85.27% 239ms 0.54% AbstractElement::IsDeleted 17ms 0.038% 85.31% 233ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.31% 230ms 0.52% tcache_get (inline) 230ms 0.52% 85.83% 230ms 0.52% tcache_get_n (inline) 49ms 0.11% 85.94% 229ms 0.52% boost::numeric::ublas::indexing_vector_assign 4ms 0.009% 85.95% 228ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.02% 85.97% 228ms 0.51% VertexMesh::CalculateUnitNormalToFaceWithArea 3ms 0.0068% 85.98% 227ms 0.51% boost::numeric::ublas::c_vector::operator= (inline) 42ms 0.095% 86.07% 223ms 0.5% tetgen::tetgenmesh::queue::pop