File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 37332ms, 86.75% of 43035ms total Dropped 785 nodes (cum <= 215.18ms) flat flat% sum% cum cum% 0 0% 0% 42984ms 99.88% __libc_start_call_main 0 0% 0% 42984ms 99.88% __libc_start_main_impl 0 0% 0% 42984ms 99.88% _start 0 0% 0% 42970ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 42970ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 42970ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 42970ms 99.85% main 0 0% 0% 42940ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 42940ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 42940ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 42742ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 35741ms 83.05% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 35703ms 82.96% MeshBasedCellPopulation::Update 0 0% 0% 21128ms 49.09% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 21128ms 49.09% MeshBasedCellPopulation::TessellateIfNeeded 126ms 0.29% 0.29% 18359ms 42.66% VertexMesh::VertexMesh 0 0% 0.29% 11433ms 26.57% MutableMesh::ReMesh 503ms 1.17% 1.46% 9574ms 22.25% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.46% 8669ms 20.14% tetgen::tetrahedralize 1ms 0.0023% 1.46% 8589ms 19.96% tetgen::tetgenmesh::delaunizevertices 4ms 0.0093% 1.47% 8586ms 19.95% tetgen::tetgenmesh::incrflipdelaunay 305ms 0.71% 2.18% 7582ms 17.62% tetgen::tetgenmesh::lawson 40ms 0.093% 2.27% 7263ms 16.88% std::set::insert (inline) 2664ms 6.19% 8.47% 7216ms 16.77% std::_Rb_tree::_M_lower_bound (inline) 182ms 0.42% 8.89% 6894ms 16.02% std::_Rb_tree::_M_insert_unique 220ms 0.51% 9.40% 6819ms 15.85% std::_Rb_tree::find (inline) 250ms 0.58% 9.98% 6795ms 15.79% VertexElement::AddFace 0 0% 9.98% 6379ms 14.82% std::set::count (inline) 97ms 0.23% 10.21% 4402ms 10.23% std::less::operator() (inline) 4352ms 10.11% 20.32% 4352ms 10.11% std::operator< (inline) 142ms 0.33% 20.65% 4316ms 10.03% operator new 205ms 0.48% 21.12% 4250ms 9.88% std::_Rb_tree::_M_insert_ (inline) 1395ms 3.24% 24.37% 4137ms 9.61% __GI___libc_malloc 0 0% 24.37% 4065ms 9.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 4015ms 9.33% 33.70% 4015ms 9.33% std::_Rb_tree_increment 1ms 0.0023% 33.70% 3972ms 9.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0023% 33.70% 3955ms 9.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 37ms 0.086% 33.79% 3634ms 8.44% std::__new_allocator::allocate (inline) 0 0% 33.79% 3623ms 8.42% std::allocator_traits::allocate (inline) 0 0% 33.79% 3383ms 7.86% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0023% 33.79% 3351ms 7.79% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.04% 33.83% 3344ms 7.77% std::_Rb_tree::~_Rb_tree (inline) 1157ms 2.69% 36.52% 3324ms 7.72% std::_Rb_tree::_M_erase 0 0% 36.52% 3310ms 7.69% std::set::~set (inline) 12ms 0.028% 36.54% 3284ms 7.63% MeshBasedCellPopulation::SpringIterator::operator++ 714ms 1.66% 38.20% 3194ms 7.42% __GI___libc_free 0 0% 38.20% 2939ms 6.83% std::_Rb_tree::_M_create_node (inline) 4ms 0.0093% 38.21% 2929ms 6.81% std::set_intersection (inline) 210ms 0.49% 38.70% 2925ms 6.80% std::__set_intersection 0 0% 38.70% 2919ms 6.78% std::_Rb_tree::_M_get_node (inline) 0 0% 38.70% 2908ms 6.76% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 38.70% 2844ms 6.61% AbstractCellPopulation::WriteResultsToFiles 0 0% 38.70% 2790ms 6.48% VertexMesh::~VertexMesh 68ms 0.16% 38.86% 2767ms 6.43% std::__new_allocator::deallocate (inline) 0 0% 38.86% 2756ms 6.40% std::allocator_traits::deallocate (inline) 920ms 2.14% 41.00% 2675ms 6.22% std::_Rb_tree::_M_get_insert_unique_pos 1875ms 4.36% 45.35% 2505ms 5.82% _int_malloc 1327ms 3.08% 48.44% 2477ms 5.76% _int_free 154ms 0.36% 48.80% 2385ms 5.54% std::_Rb_tree_const_iterator::operator++ (inline) 33ms 0.077% 48.87% 2377ms 5.52% Node::AddElement 87ms 0.2% 49.07% 2350ms 5.46% tetgen::tetgenmesh::insphere_sos 1ms 0.0023% 49.08% 2280ms 5.30% TetrahedralMesh::ImportFromMesher 2076ms 4.82% 53.90% 2250ms 5.23% tetgen::insphere 143ms 0.33% 54.23% 2082ms 4.84% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2078ms 4.83% 59.06% 2078ms 4.83% std::_Rb_tree::_S_right (inline) 3ms 0.007% 59.07% 2024ms 4.70% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 100ms 0.23% 59.30% 2011ms 4.67% Node::~Node 0 0% 59.30% 1949ms 4.53% std::_Rb_tree_iterator::operator++ (inline) 77ms 0.18% 59.48% 1889ms 4.39% VertexMesh::Clear 48ms 0.11% 59.59% 1833ms 4.26% MutableElement::AddNode 76ms 0.18% 59.77% 1720ms 4.00% tetgen::tetgenmesh::flip23 0 0% 59.77% 1706ms 3.96% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.77% 1680ms 3.90% std::_Rb_tree::_M_put_node (inline) 63ms 0.15% 59.91% 1231ms 2.86% tetgen::tetgenmesh::flip32 1190ms 2.77% 62.68% 1190ms 2.77% std::_Rb_tree_insert_and_rebalance 785ms 1.82% 64.50% 1128ms 2.62% malloc_consolidate 15ms 0.035% 64.54% 1091ms 2.54% std::_Vector_base::_M_deallocate (inline) 0 0% 64.54% 1068ms 2.48% std::vector::~vector (inline) 1ms 0.0023% 64.54% 1062ms 2.47% Element::Element 957ms 2.22% 66.76% 1013ms 2.35% tetgen::orient3d 53ms 0.12% 66.89% 989ms 2.30% TetrahedralMesh::Clear 0 0% 66.89% 968ms 2.25% std::_Vector_base::~_Vector_base (inline) 5ms 0.012% 66.90% 962ms 2.24% _int_free_maybe_consolidate 86ms 0.2% 67.10% 923ms 2.14% tetgen::tetgenmesh::enqueueflipface 22ms 0.051% 67.15% 867ms 2.01% tetgen::tetgenmesh::locate 2ms 0.0046% 67.15% 845ms 1.96% Element::RegisterWithNodes (inline) 623ms 1.45% 68.60% 840ms 1.95% AbstractElement::GetNodeGlobalIndex 70ms 0.16% 68.76% 833ms 1.94% std::map::operator[] 74ms 0.17% 68.94% 831ms 1.93% tetgen::tetgenmesh::preciselocate 41ms 0.095% 69.03% 800ms 1.86% std::vector::_M_realloc_insert 784ms 1.82% 70.85% 784ms 1.82% Node::GetIndex 749ms 1.74% 72.59% 749ms 1.74% unlink_chunk 739ms 1.72% 74.31% 739ms 1.72% [libchaste_mesh.so] 2ms 0.0046% 74.32% 706ms 1.64% std::_Vector_base::_M_allocate (inline) 0 0% 74.32% 703ms 1.63% std::_Rb_tree::lower_bound (inline) 0 0% 74.32% 703ms 1.63% std::map::lower_bound (inline) 5ms 0.012% 74.33% 685ms 1.59% VertexMesh::GenerateVerticesFromElementCircumcentres 68ms 0.16% 74.49% 678ms 1.58% std::vector::push_back (inline) 0 0% 74.49% 652ms 1.52% VoronoiDataWriter::Visit 576ms 1.34% 75.82% 576ms 1.34% tetgen::tetgenmesh::oppo 337ms 0.78% 76.61% 567ms 1.32% tetgen::tetgenmesh::sym 1ms 0.0023% 76.61% 475ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 76.61% 474ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 464ms 1.08% 77.69% 464ms 1.08% std::vector::size (inline) 215ms 0.5% 78.19% 452ms 1.05% AbstractElement::GetNodeLocation 11ms 0.026% 78.21% 451ms 1.05% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 78.21% 440ms 1.02% std::set::find (inline) 6ms 0.014% 78.23% 439ms 1.02% AbstractTetrahedralElement::CalculateJacobian 8ms 0.019% 78.25% 433ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 27ms 0.063% 78.31% 400ms 0.93% __atan2 291ms 0.68% 78.98% 373ms 0.87% __ieee754_atan2_fma 365ms 0.85% 79.83% 365ms 0.85% AbstractElement::IsDeleted 0 0% 79.83% 365ms 0.85% std::insert_iterator::operator= (inline) 361ms 0.84% 80.67% 361ms 0.84% Node::rGetLocation 3ms 0.007% 80.68% 359ms 0.83% boost::numeric::ublas::vector_assign (inline) 6ms 0.014% 80.69% 357ms 0.83% boost::numeric::ublas::c_vector::c_vector (inline) 245ms 0.57% 81.26% 339ms 0.79% tetgen::tetgenmesh::fnextself 2ms 0.0046% 81.27% 329ms 0.76% std::_Rb_tree::_M_insert_unique_ (inline) 37ms 0.086% 81.35% 327ms 0.76% AbstractTetrahedralElement::RefreshJacobian 320ms 0.74% 82.10% 320ms 0.74% boost::numeric::ublas::c_vector::operator() 10ms 0.023% 82.12% 316ms 0.73% Element::CalculateCircumsphere 24ms 0.056% 82.17% 314ms 0.73% std::_Rb_tree_iterator::operator-- (inline) 11ms 0.026% 82.20% 311ms 0.72% VertexElement::~VertexElement 150ms 0.35% 82.55% 307ms 0.71% AbstractTetrahedralMesh::GetElement 306ms 0.71% 83.26% 306ms 0.71% tetgen::tetgenmesh::triface::triface 303ms 0.7% 83.96% 303ms 0.7% tetgen::tetgenmesh::triface::operator= 0 0% 83.96% 289ms 0.67% boost::numeric::ublas::inner_prod (inline) 288ms 0.67% 84.63% 288ms 0.67% std::_Rb_tree_decrement 24ms 0.056% 84.69% 288ms 0.67% tetgen::tetgenmesh::enext2fnext 2ms 0.0046% 84.69% 286ms 0.66% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.058% 84.75% 284ms 0.66% boost::numeric::ublas::vector_scalar_binary::evaluate 276ms 0.64% 85.39% 276ms 0.64% tetgen::tetgenmesh::org 0 0% 85.39% 262ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 0 0% 85.39% 254ms 0.59% Cell::GetCellId 12ms 0.028% 85.42% 251ms 0.58% boost::numeric::ublas::vector_reference::operator() (inline) 47ms 0.11% 85.53% 245ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 9ms 0.021% 85.55% 243ms 0.56% VertexMesh::CalculateUnitNormalToFaceWithArea 24ms 0.056% 85.61% 243ms 0.56% tetgen::tetgenmesh::enextfnext 2ms 0.0046% 85.61% 237ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 15ms 0.035% 85.65% 236ms 0.55% tetgen::tetgenmesh::queue::push 2ms 0.0046% 85.65% 235ms 0.55% CellPropertyCollection::GetPropertiesType (inline) 129ms 0.3% 85.95% 232ms 0.54% tetgen::tetgenmesh::bond 56ms 0.13% 86.08% 230ms 0.53% tetgen::tetgenmesh::queue::pop 58ms 0.13% 86.22% 229ms 0.53% boost::numeric::ublas::indexing_vector_assign 0 0% 86.22% 226ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 224ms 0.52% 86.74% 224ms 0.52% tetgen::tetgenmesh::decode 5ms 0.012% 86.75% 216ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement