File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 61077ms, 87.14% of 70091ms total Dropped 923 nodes (cum <= 350.45ms) flat flat% sum% cum cum% 0 0% 0% 70038ms 99.92% __libc_start_call_main 0 0% 0% 70038ms 99.92% __libc_start_main_impl 0 0% 0% 70038ms 99.92% _start 0 0% 0% 70018ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 70018ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 70018ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 70018ms 99.90% main 0 0% 0% 69972ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 69972ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 69972ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0014% 0.0014% 69681ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0.0014% 59034ms 84.22% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0014% 58983ms 84.15% MeshBasedCellPopulation::Update 0 0% 0.0014% 33180ms 47.34% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0014% 33179ms 47.34% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 209ms 0.3% 0.3% 29208ms 41.67% VertexMesh::VertexMesh 0 0% 0.3% 21164ms 30.20% MutableMesh::ReMesh 1ms 0.0014% 0.3% 16510ms 23.56% tetgen::tetrahedralize 4ms 0.0057% 0.31% 16361ms 23.34% tetgen::tetgenmesh::delaunizevertices 11ms 0.016% 0.32% 16352ms 23.33% tetgen::tetgenmesh::incrflipdelaunay 528ms 0.75% 1.08% 14660ms 20.92% tetgen::tetgenmesh::lawson 594ms 0.85% 1.92% 14227ms 20.30% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.041% 1.96% 11337ms 16.17% std::set::insert (inline) 237ms 0.34% 2.30% 10881ms 15.52% std::_Rb_tree::_M_insert_unique 3136ms 4.47% 6.78% 10630ms 15.17% std::_Rb_tree::_M_lower_bound (inline) 422ms 0.6% 7.38% 10483ms 14.96% VertexElement::AddFace 262ms 0.37% 7.75% 9898ms 14.12% std::_Rb_tree::find (inline) 0 0% 7.75% 9352ms 13.34% std::set::count (inline) 106ms 0.15% 7.90% 7150ms 10.20% std::less::operator() (inline) 7105ms 10.14% 18.04% 7105ms 10.14% std::operator< (inline) 6783ms 9.68% 27.72% 6783ms 9.68% std::_Rb_tree_increment 309ms 0.44% 28.16% 6357ms 9.07% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.16% 6150ms 8.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 163ms 0.23% 28.39% 5978ms 8.53% operator new 1ms 0.0014% 28.39% 5974ms 8.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0043% 28.40% 5959ms 8.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 1183ms 1.69% 30.09% 5728ms 8.17% __GI___libc_malloc 28ms 0.04% 30.13% 5055ms 7.21% std::__new_allocator::allocate (inline) 0 0% 30.13% 5034ms 7.18% std::allocator_traits::allocate (inline) 0 0% 30.13% 5007ms 7.14% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.0029% 30.13% 4997ms 7.13% std::set_intersection (inline) 283ms 0.4% 30.53% 4995ms 7.13% std::__set_intersection 7ms 0.01% 30.54% 4973ms 7.10% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.017% 30.56% 4832ms 6.89% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.019% 30.58% 4682ms 6.68% std::_Rb_tree::~_Rb_tree (inline) 1683ms 2.40% 32.98% 4666ms 6.66% std::_Rb_tree::_M_erase 0 0% 32.98% 4624ms 6.60% std::set::~set (inline) 1347ms 1.92% 34.90% 4574ms 6.53% std::_Rb_tree::_M_get_insert_unique_pos 1272ms 1.81% 36.72% 4557ms 6.50% __GI___libc_free 56ms 0.08% 36.80% 4344ms 6.20% Node::AddElement 0 0% 36.80% 4338ms 6.19% AbstractCellPopulation::WriteResultsToFiles 223ms 0.32% 37.11% 4203ms 6.00% std::_Rb_tree_const_iterator::operator++ (inline) 3017ms 4.30% 41.42% 4153ms 5.93% _int_malloc 0 0% 41.42% 4118ms 5.88% std::_Rb_tree::_M_create_node (inline) 0 0% 41.42% 4088ms 5.83% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.42% 4079ms 5.82% std::_Rb_tree::_M_get_node (inline) 149ms 0.21% 41.63% 4018ms 5.73% std::__new_allocator::deallocate (inline) 0 0% 41.63% 4005ms 5.71% std::allocator_traits::deallocate (inline) 0 0% 41.63% 3998ms 5.70% VertexMesh::~VertexMesh 3997ms 5.70% 47.33% 3997ms 5.70% std::_Rb_tree::_S_right (inline) 141ms 0.2% 47.53% 3984ms 5.68% tetgen::tetgenmesh::insphere_sos 3537ms 5.05% 52.58% 3818ms 5.45% tetgen::insphere 8ms 0.011% 52.59% 3749ms 5.35% TetrahedralMesh::ImportFromMesher 141ms 0.2% 52.79% 3539ms 5.05% tetgen::tetgenmesh::flip23 1404ms 2.00% 54.80% 3285ms 4.69% _int_free 55ms 0.078% 54.87% 3180ms 4.54% MutableElement::AddNode 185ms 0.26% 55.14% 3102ms 4.43% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0043% 55.14% 3016ms 4.30% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0029% 55.15% 2937ms 4.19% std::_Rb_tree_iterator::operator++ (inline) 170ms 0.24% 55.39% 2675ms 3.82% Node::~Node 133ms 0.19% 55.58% 2528ms 3.61% tetgen::tetgenmesh::flip32 176ms 0.25% 55.83% 2474ms 3.53% VertexMesh::Clear 2271ms 3.24% 59.07% 2271ms 3.24% Node::GetIndex 0 0% 59.07% 2243ms 3.20% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.07% 2226ms 3.18% std::_Rb_tree::_M_put_node (inline) 2046ms 2.92% 61.99% 2046ms 2.92% std::_Rb_tree_insert_and_rebalance 5ms 0.0071% 62.00% 1988ms 2.84% Element::Element 1234ms 1.76% 63.76% 1902ms 2.71% malloc_consolidate 25ms 0.036% 63.79% 1804ms 2.57% std::_Vector_base::_M_deallocate (inline) 228ms 0.33% 64.12% 1773ms 2.53% tetgen::tetgenmesh::enqueueflipface 0 0% 64.12% 1735ms 2.48% std::vector::~vector (inline) 6ms 0.0086% 64.13% 1652ms 2.36% _int_free_maybe_consolidate 2ms 0.0029% 64.13% 1651ms 2.36% std::_Vector_base::~_Vector_base (inline) 7ms 0.01% 64.14% 1631ms 2.33% Element::RegisterWithNodes (inline) 1496ms 2.13% 66.27% 1594ms 2.27% tetgen::orient3d 1426ms 2.03% 68.31% 1426ms 2.03% unlink_chunk 45ms 0.064% 68.37% 1403ms 2.00% tetgen::tetgenmesh::locate 90ms 0.13% 68.50% 1384ms 1.97% TetrahedralMesh::Clear 80ms 0.11% 68.61% 1360ms 1.94% std::map::operator[] 89ms 0.13% 68.74% 1317ms 1.88% tetgen::tetgenmesh::preciselocate 0 0% 68.74% 1191ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 68.74% 1191ms 1.70% std::map::lower_bound (inline) 88ms 0.13% 68.87% 1173ms 1.67% std::vector::_M_realloc_insert 944ms 1.35% 70.21% 1142ms 1.63% AbstractElement::GetNodeGlobalIndex 7ms 0.01% 70.22% 1119ms 1.60% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 70.22% 1061ms 1.51% VoronoiDataWriter::Visit 142ms 0.2% 70.43% 1002ms 1.43% std::vector::push_back (inline) 978ms 1.40% 71.82% 978ms 1.40% tetgen::tetgenmesh::triface::triface 1ms 0.0014% 71.82% 956ms 1.36% std::_Vector_base::_M_allocate (inline) 905ms 1.29% 73.11% 905ms 1.29% tetgen::tetgenmesh::oppo 0 0% 73.11% 878ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 856ms 1.22% 74.33% 856ms 1.22% tetgen::tetgenmesh::triface::operator= 809ms 1.15% 75.49% 809ms 1.15% [libchaste_mesh.so] 312ms 0.45% 75.93% 796ms 1.14% tetgen::tetgenmesh::sym 305ms 0.44% 76.37% 775ms 1.11% AbstractElement::GetNodeLocation 11ms 0.016% 76.38% 768ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 761ms 1.09% 77.47% 761ms 1.09% Node::rGetLocation 0 0% 77.47% 757ms 1.08% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.014% 77.48% 720ms 1.03% AbstractTetrahedralElement::CalculateJacobian 14ms 0.02% 77.50% 702ms 1.00% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 700ms 1% 78.50% 700ms 1% AbstractElement::IsDeleted 73ms 0.1% 78.61% 661ms 0.94% tetgen::tetgenmesh::enext2fnext 229ms 0.33% 78.93% 660ms 0.94% tetgen::tetgenmesh::bond 402ms 0.57% 79.51% 660ms 0.94% tetgen::tetgenmesh::fnextself 22ms 0.031% 79.54% 631ms 0.9% boost::numeric::ublas::vector_assign (inline) 51ms 0.073% 79.61% 628ms 0.9% __atan2 44ms 0.063% 79.67% 614ms 0.88% tetgen::tetgenmesh::queue::push 50ms 0.071% 79.75% 600ms 0.86% tetgen::tetgenmesh::enextfnext 600ms 0.86% 80.60% 600ms 0.86% tetgen::tetgenmesh::pointmark 12ms 0.017% 80.62% 594ms 0.85% boost::numeric::ublas::c_vector::c_vector (inline) 586ms 0.84% 81.46% 586ms 0.84% std::vector::size (inline) 380ms 0.54% 82.00% 570ms 0.81% tetgen::tetgenmesh::link::add 459ms 0.65% 82.65% 569ms 0.81% __ieee754_atan2_fma 14ms 0.02% 82.67% 566ms 0.81% Element::CalculateCircumsphere 0 0% 82.67% 541ms 0.77% std::set::find (inline) 39ms 0.056% 82.73% 532ms 0.76% AbstractTetrahedralElement::RefreshJacobian 511ms 0.73% 83.46% 511ms 0.73% tetgen::tetgenmesh::decode 0 0% 83.46% 504ms 0.72% boost::numeric::ublas::inner_prod (inline) 1ms 0.0014% 83.46% 498ms 0.71% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 44ms 0.063% 83.52% 497ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 484ms 0.69% 84.21% 484ms 0.69% tetgen::tetgenmesh::org 0 0% 84.21% 477ms 0.68% std::insert_iterator::operator= (inline) 19ms 0.027% 84.24% 464ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 79ms 0.11% 84.35% 447ms 0.64% tetgen::tetgenmesh::queue::pop 32ms 0.046% 84.40% 440ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 2ms 0.0029% 84.40% 424ms 0.6% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0029% 84.40% 420ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 418ms 0.6% 85.00% 418ms 0.6% tetgen::tetgenmesh::encode 2ms 0.0029% 85.00% 416ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 101ms 0.14% 85.15% 402ms 0.57% __dynamic_cast 178ms 0.25% 85.40% 400ms 0.57% AbstractTetrahedralMesh::GetElement 149ms 0.21% 85.61% 395ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 102ms 0.15% 85.76% 391ms 0.56% boost::numeric::ublas::indexing_vector_assign 0 0% 85.76% 390ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 389ms 0.55% 86.31% 389ms 0.55% boost::numeric::ublas::c_vector::operator() 5ms 0.0071% 86.32% 387ms 0.55% Cell::GetCellId 0 0% 86.32% 383ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 380ms 0.54% 86.86% 380ms 0.54% std::_Rb_tree_decrement 6ms 0.0086% 86.87% 362ms 0.52% VertexElement::~VertexElement 182ms 0.26% 87.13% 361ms 0.52% tetgen::tetgenmesh::link::deletenode 6ms 0.0086% 87.14% 353ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement