File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 61479ms, 86.85% of 70786ms total Dropped 903 nodes (cum <= 353.93ms) flat flat% sum% cum cum% 0 0% 0% 70720ms 99.91% __libc_start_call_main 0 0% 0% 70720ms 99.91% __libc_start_main_impl 0 0% 0% 70720ms 99.91% _start 0 0% 0% 70702ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 70702ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 70702ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 70702ms 99.88% main 0 0% 0% 70664ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 70664ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 70664ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 70360ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 60892ms 86.02% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 60838ms 85.95% MeshBasedCellPopulation::Update 0 0% 0% 35909ms 50.73% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 35906ms 50.72% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 284ms 0.4% 0.4% 31004ms 43.80% VertexMesh::VertexMesh 0 0% 0.4% 20646ms 29.17% MutableMesh::ReMesh 0 0% 0.4% 15920ms 22.49% tetgen::tetrahedralize 1ms 0.0014% 0.4% 15765ms 22.27% tetgen::tetgenmesh::delaunizevertices 13ms 0.018% 0.42% 15759ms 22.26% tetgen::tetgenmesh::incrflipdelaunay 528ms 0.75% 1.17% 14028ms 19.82% tetgen::tetgenmesh::lawson 623ms 0.88% 2.05% 13323ms 18.82% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.041% 2.09% 11937ms 16.86% std::set::insert (inline) 250ms 0.35% 2.44% 11473ms 16.21% std::_Rb_tree::_M_insert_unique 465ms 0.66% 3.10% 10732ms 15.16% VertexElement::AddFace 3292ms 4.65% 7.75% 9346ms 13.20% std::_Rb_tree::_M_lower_bound (inline) 267ms 0.38% 8.13% 8796ms 12.43% std::_Rb_tree::find (inline) 0 0% 8.13% 8181ms 11.56% std::set::count (inline) 350ms 0.49% 8.62% 6841ms 9.66% std::_Rb_tree::_M_insert_ (inline) 6607ms 9.33% 17.95% 6607ms 9.33% std::_Rb_tree_increment 184ms 0.26% 18.21% 6558ms 9.26% operator new 1327ms 1.87% 20.09% 6284ms 8.88% __GI___libc_malloc 126ms 0.18% 20.27% 5839ms 8.25% std::less::operator() (inline) 5764ms 8.14% 28.41% 5764ms 8.14% std::operator< (inline) 1ms 0.0014% 28.41% 5753ms 8.13% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0014% 28.41% 5616ms 7.93% std::set_intersection (inline) 309ms 0.44% 28.85% 5615ms 7.93% std::__set_intersection 0 0% 28.85% 5594ms 7.90% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0014% 28.85% 5571ms 7.87% AbstractNumericalMethod::ComputeForcesIncludingDamping 29ms 0.041% 28.89% 5384ms 7.61% std::__new_allocator::allocate (inline) 0 0% 28.89% 5363ms 7.58% std::allocator_traits::allocate (inline) 1540ms 2.18% 31.07% 5091ms 7.19% __GI___libc_free 13ms 0.018% 31.09% 5083ms 7.18% std::_Rb_tree::~_Rb_tree (inline) 1908ms 2.70% 33.78% 5067ms 7.16% std::_Rb_tree::_M_erase 0 0% 33.78% 5024ms 7.10% std::set::~set (inline) 0 0% 33.78% 4941ms 6.98% VertexMesh::~VertexMesh 50ms 0.071% 33.85% 4878ms 6.89% Node::AddElement 209ms 0.3% 34.15% 4775ms 6.75% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0014% 34.15% 4691ms 6.63% MeshBasedCellPopulation::UpdateNodePairs 1385ms 1.96% 36.10% 4672ms 6.60% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.0099% 36.11% 4620ms 6.53% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 3347ms 4.73% 40.84% 4607ms 6.51% _int_malloc 137ms 0.19% 41.04% 4525ms 6.39% std::__new_allocator::deallocate (inline) 17ms 0.024% 41.06% 4515ms 6.38% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 41.06% 4514ms 6.38% std::allocator_traits::deallocate (inline) 0 0% 41.06% 4401ms 6.22% std::_Rb_tree::_M_create_node (inline) 0 0% 41.06% 4370ms 6.17% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.06% 4368ms 6.17% std::_Rb_tree::_M_get_node (inline) 4053ms 5.73% 46.79% 4053ms 5.73% std::_Rb_tree::_S_right (inline) 119ms 0.17% 46.95% 3911ms 5.53% tetgen::tetgenmesh::insphere_sos 75ms 0.11% 47.06% 3848ms 5.44% MutableElement::AddNode 3494ms 4.94% 52.00% 3779ms 5.34% tetgen::insphere 3ms 0.0042% 52.00% 3748ms 5.29% TetrahedralMesh::ImportFromMesher 1296ms 1.83% 53.83% 3548ms 5.01% _int_free 0 0% 53.83% 3537ms 5.00% AbstractCellPopulation::WriteResultsToFiles 138ms 0.19% 54.03% 3406ms 4.81% tetgen::tetgenmesh::flip23 259ms 0.37% 54.39% 3277ms 4.63% Node::~Node 198ms 0.28% 54.67% 3072ms 4.34% VertexMesh::Clear 132ms 0.19% 54.86% 2557ms 3.61% tetgen::tetgenmesh::flip32 5ms 0.0071% 54.87% 2349ms 3.32% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 189ms 0.27% 55.13% 2332ms 3.29% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 55.13% 2327ms 3.29% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.13% 2319ms 3.28% std::_Rb_tree::_M_put_node (inline) 1660ms 2.35% 57.48% 2255ms 3.19% malloc_consolidate 38ms 0.054% 57.53% 2233ms 3.15% std::_Vector_base::_M_deallocate (inline) 2178ms 3.08% 60.61% 2178ms 3.08% std::_Rb_tree_insert_and_rebalance 1ms 0.0014% 60.61% 2164ms 3.06% std::_Rb_tree_iterator::operator++ (inline) 0 0% 60.61% 2106ms 2.98% std::vector::~vector (inline) 2070ms 2.92% 63.53% 2070ms 2.92% Node::GetIndex 1ms 0.0014% 63.54% 2040ms 2.88% std::_Vector_base::~_Vector_base (inline) 223ms 0.32% 63.85% 1984ms 2.80% tetgen::tetgenmesh::enqueueflipface 6ms 0.0085% 63.86% 1976ms 2.79% _int_free_maybe_consolidate 6ms 0.0085% 63.87% 1890ms 2.67% Element::Element 1588ms 2.24% 66.11% 1668ms 2.36% tetgen::orient3d 7ms 0.0099% 66.12% 1546ms 2.18% Element::RegisterWithNodes (inline) 1520ms 2.15% 68.27% 1520ms 2.15% unlink_chunk 86ms 0.12% 68.39% 1480ms 2.09% TetrahedralMesh::Clear 6ms 0.0085% 68.40% 1420ms 2.01% VertexMesh::GenerateVerticesFromElementCircumcentres 39ms 0.055% 68.45% 1387ms 1.96% tetgen::tetgenmesh::locate 1124ms 1.59% 70.04% 1365ms 1.93% AbstractElement::GetNodeGlobalIndex 79ms 0.11% 70.15% 1300ms 1.84% tetgen::tetgenmesh::preciselocate 42ms 0.059% 70.21% 1237ms 1.75% std::vector::_M_realloc_insert 64ms 0.09% 70.30% 1149ms 1.62% std::map::operator[] 0 0% 70.30% 1013ms 1.43% std::_Rb_tree::lower_bound (inline) 0 0% 70.30% 1013ms 1.43% std::map::lower_bound (inline) 1007ms 1.42% 71.72% 1007ms 1.42% tetgen::tetgenmesh::oppo 125ms 0.18% 71.90% 1005ms 1.42% std::vector::push_back (inline) 6ms 0.0085% 71.91% 1001ms 1.41% std::_Vector_base::_M_allocate (inline) 975ms 1.38% 73.29% 975ms 1.38% tetgen::tetgenmesh::triface::triface 957ms 1.35% 74.64% 957ms 1.35% AbstractElement::IsDeleted 0 0% 74.64% 950ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 943ms 1.33% 75.97% 943ms 1.33% Node::rGetLocation 456ms 0.64% 76.62% 938ms 1.33% AbstractElement::GetNodeLocation 0 0% 76.62% 938ms 1.33% VoronoiDataWriter::Visit 805ms 1.14% 77.75% 805ms 1.14% [libchaste_mesh.so] 282ms 0.4% 78.15% 789ms 1.11% tetgen::tetgenmesh::sym 7ms 0.0099% 78.16% 786ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 752ms 1.06% 79.22% 752ms 1.06% std::vector::size (inline) 1ms 0.0014% 79.22% 751ms 1.06% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.017% 79.24% 746ms 1.05% AbstractTetrahedralElement::CalculateJacobian 12ms 0.017% 79.26% 707ms 1% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 23ms 0.032% 79.29% 674ms 0.95% Element::CalculateCircumsphere 44ms 0.062% 79.35% 673ms 0.95% tetgen::tetgenmesh::queue::push 60ms 0.085% 79.44% 651ms 0.92% __atan2 358ms 0.51% 79.94% 629ms 0.89% tetgen::tetgenmesh::link::add 208ms 0.29% 80.24% 619ms 0.87% tetgen::tetgenmesh::bond 614ms 0.87% 81.11% 614ms 0.87% tetgen::tetgenmesh::triface::operator= 0 0% 81.11% 610ms 0.86% std::set::find (inline) 349ms 0.49% 81.60% 606ms 0.86% tetgen::tetgenmesh::fnextself 11ms 0.016% 81.61% 592ms 0.84% boost::numeric::ublas::c_vector::c_vector (inline) 18ms 0.025% 81.64% 591ms 0.83% boost::numeric::ublas::vector_assign (inline) 469ms 0.66% 82.30% 587ms 0.83% __ieee754_atan2_fma 45ms 0.064% 82.37% 585ms 0.83% AbstractTetrahedralElement::RefreshJacobian 54ms 0.076% 82.44% 565ms 0.8% tetgen::tetgenmesh::enextfnext 66ms 0.093% 82.53% 550ms 0.78% tetgen::tetgenmesh::enext2fnext 0 0% 82.53% 528ms 0.75% boost::numeric::ublas::inner_prod (inline) 6ms 0.0085% 82.54% 526ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 48ms 0.068% 82.61% 520ms 0.73% boost::numeric::ublas::vector_scalar_binary::evaluate 512ms 0.72% 83.33% 512ms 0.72% tetgen::tetgenmesh::decode 0 0% 83.33% 501ms 0.71% std::insert_iterator::operator= (inline) 5ms 0.0071% 83.34% 444ms 0.63% VertexElement::~VertexElement 6ms 0.0085% 83.35% 440ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.024% 83.37% 440ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.37% 431ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 201ms 0.28% 83.66% 419ms 0.59% AbstractTetrahedralMesh::GetElement 27ms 0.038% 83.70% 419ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 83ms 0.12% 83.81% 412ms 0.58% __dynamic_cast 187ms 0.26% 84.08% 409ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0028% 84.08% 407ms 0.57% Cell::GetCellId 402ms 0.57% 84.65% 402ms 0.57% tetgen::tetgenmesh::pointmark 401ms 0.57% 85.21% 401ms 0.57% tetgen::tetgenmesh::encode 0 0% 85.21% 396ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 396ms 0.56% 85.77% 396ms 0.56% tetgen::tetgenmesh::org 387ms 0.55% 86.32% 387ms 0.55% boost::numeric::ublas::c_vector::operator() 0 0% 86.32% 380ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 10ms 0.014% 86.33% 373ms 0.53% std::vector::insert (inline) 365ms 0.52% 86.85% 365ms 0.52% std::_Rb_tree_decrement 1ms 0.0014% 86.85% 359ms 0.51% boost::numeric::ublas::c_vector::operator= (inline)