File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 65922ms, 87.81% of 75076ms total Dropped 886 nodes (cum <= 375.38ms) flat flat% sum% cum cum% 0 0% 0% 75012ms 99.91% __libc_start_call_main 0 0% 0% 75012ms 99.91% __libc_start_main_impl 0 0% 0% 75012ms 99.91% _start 0 0% 0% 74995ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 74995ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 74995ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 74995ms 99.89% main 0 0% 0% 74955ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74955ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74955ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 74649ms 99.43% AbstractCellBasedSimulation::Solve 0 0% 0% 63269ms 84.27% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 63220ms 84.21% MeshBasedCellPopulation::Update 0 0% 0% 40035ms 53.33% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 40035ms 53.33% MeshBasedCellPopulation::TessellateIfNeeded 397ms 0.53% 0.53% 34481ms 45.93% VertexMesh::VertexMesh 0 0% 0.53% 18422ms 24.54% MutableMesh::ReMesh 557ms 0.74% 1.27% 14908ms 19.86% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.27% 12809ms 17.06% tetgen::tetrahedralize 0 0% 1.27% 12672ms 16.88% tetgen::tetgenmesh::delaunizevertices 8ms 0.011% 1.28% 12669ms 16.87% tetgen::tetgenmesh::incrflipdelaunay 33ms 0.044% 1.33% 12632ms 16.83% std::set::insert (inline) 182ms 0.24% 1.57% 12115ms 16.14% std::_Rb_tree::_M_insert_unique 3045ms 4.06% 5.62% 11263ms 15.00% std::_Rb_tree::_M_lower_bound (inline) 569ms 0.76% 6.38% 11182ms 14.89% tetgen::tetgenmesh::lawson 479ms 0.64% 7.02% 11132ms 14.83% VertexElement::AddFace 248ms 0.33% 7.35% 10277ms 13.69% std::_Rb_tree::find (inline) 0 0% 7.35% 9716ms 12.94% std::set::count (inline) 8815ms 11.74% 19.09% 8815ms 11.74% std::_Rb_tree_increment 116ms 0.15% 19.25% 7596ms 10.12% std::less::operator() (inline) 7536ms 10.04% 29.28% 7536ms 10.04% std::operator< (inline) 202ms 0.27% 29.55% 6958ms 9.27% operator new 271ms 0.36% 29.91% 6936ms 9.24% std::_Rb_tree::_M_insert_ (inline) 1055ms 1.41% 31.32% 6700ms 8.92% __GI___libc_malloc 3ms 0.004% 31.32% 6549ms 8.72% std::set_intersection (inline) 341ms 0.45% 31.78% 6546ms 8.72% std::__set_intersection 0 0% 31.78% 6310ms 8.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0013% 31.78% 6124ms 8.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.004% 31.78% 6103ms 8.13% AbstractNumericalMethod::ComputeForcesIncludingDamping 33ms 0.044% 31.83% 5845ms 7.79% Node::AddElement 173ms 0.23% 32.06% 5695ms 7.59% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 32.06% 5606ms 7.47% VertexMesh::~VertexMesh 15ms 0.02% 32.08% 5590ms 7.45% std::_Rb_tree::~_Rb_tree (inline) 2487ms 3.31% 35.39% 5575ms 7.43% std::_Rb_tree::_M_erase 59ms 0.079% 35.47% 5533ms 7.37% std::__new_allocator::allocate (inline) 0 0% 35.47% 5513ms 7.34% std::set::~set (inline) 0 0% 35.47% 5509ms 7.34% std::allocator_traits::allocate (inline) 5418ms 7.22% 42.68% 5418ms 7.22% std::_Rb_tree::_S_right (inline) 1296ms 1.73% 44.41% 5322ms 7.09% std::_Rb_tree::_M_get_insert_unique_pos 3891ms 5.18% 49.59% 5289ms 7.04% _int_malloc 1362ms 1.81% 51.41% 5210ms 6.94% __GI___libc_free 6ms 0.008% 51.42% 5120ms 6.82% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0013% 51.42% 5119ms 6.82% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.016% 51.43% 4908ms 6.54% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 51.43% 4899ms 6.53% AbstractCellPopulation::WriteResultsToFiles 7ms 0.0093% 51.44% 4537ms 6.04% TetrahedralMesh::ImportFromMesher 125ms 0.17% 51.61% 4529ms 6.03% std::__new_allocator::deallocate (inline) 0 0% 51.61% 4515ms 6.01% std::allocator_traits::deallocate (inline) 0 0% 51.61% 4416ms 5.88% std::_Rb_tree::_M_create_node (inline) 0 0% 51.61% 4375ms 5.83% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 51.61% 4366ms 5.82% std::_Rb_tree::_M_get_node (inline) 84ms 0.11% 51.72% 4297ms 5.72% MutableElement::AddNode 1181ms 1.57% 53.29% 3844ms 5.12% _int_free 256ms 0.34% 53.63% 3608ms 4.81% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 214ms 0.29% 53.92% 3567ms 4.75% Node::~Node 132ms 0.18% 54.10% 3523ms 4.69% tetgen::tetgenmesh::insphere_sos 4ms 0.0053% 54.10% 3411ms 4.54% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0027% 54.10% 3385ms 4.51% std::_Rb_tree_iterator::operator++ (inline) 3087ms 4.11% 58.22% 3375ms 4.50% tetgen::insphere 285ms 0.38% 58.60% 3361ms 4.48% VertexMesh::Clear 3028ms 4.03% 62.63% 3028ms 4.03% Node::GetIndex 1842ms 2.45% 65.08% 2746ms 3.66% malloc_consolidate 194ms 0.26% 65.34% 2694ms 3.59% tetgen::tetgenmesh::flip23 18ms 0.024% 65.36% 2528ms 3.37% std::_Vector_base::_M_deallocate (inline) 5ms 0.0067% 65.37% 2429ms 3.24% _int_free_maybe_consolidate 2421ms 3.22% 68.60% 2421ms 3.22% std::_Rb_tree_insert_and_rebalance 6ms 0.008% 68.60% 2414ms 3.22% Element::Element 0 0% 68.60% 2395ms 3.19% std::vector::~vector (inline) 0 0% 68.60% 2357ms 3.14% std::_Vector_base::~_Vector_base (inline) 6ms 0.008% 68.61% 2074ms 2.76% Element::RegisterWithNodes (inline) 0 0% 68.61% 2018ms 2.69% std::_Rb_tree::_M_drop_node (inline) 0 0% 68.61% 2005ms 2.67% std::_Rb_tree::_M_put_node (inline) 1888ms 2.51% 71.13% 1888ms 2.51% unlink_chunk 193ms 0.26% 71.38% 1773ms 2.36% tetgen::tetgenmesh::flip32 4ms 0.0053% 71.39% 1760ms 2.34% VertexMesh::GenerateVerticesFromElementCircumcentres 243ms 0.32% 71.71% 1681ms 2.24% TetrahedralMesh::Clear 65ms 0.087% 71.80% 1553ms 2.07% std::map::operator[] 1360ms 1.81% 73.61% 1443ms 1.92% tetgen::orient3d 0 0% 73.61% 1397ms 1.86% std::_Rb_tree::lower_bound (inline) 0 0% 73.61% 1397ms 1.86% std::map::lower_bound (inline) 69ms 0.092% 73.70% 1327ms 1.77% std::vector::_M_realloc_insert 1155ms 1.54% 75.24% 1307ms 1.74% AbstractElement::GetNodeGlobalIndex 165ms 0.22% 75.46% 1261ms 1.68% tetgen::tetgenmesh::enqueueflipface 48ms 0.064% 75.52% 1238ms 1.65% tetgen::tetgenmesh::locate 3ms 0.004% 75.53% 1229ms 1.64% VoronoiDataWriter::Visit 6ms 0.008% 75.54% 1149ms 1.53% std::_Vector_base::_M_allocate (inline) 93ms 0.12% 75.66% 1137ms 1.51% tetgen::tetgenmesh::preciselocate 144ms 0.19% 75.85% 1116ms 1.49% std::vector::push_back (inline) 503ms 0.67% 76.52% 1097ms 1.46% AbstractElement::GetNodeLocation 1090ms 1.45% 77.97% 1090ms 1.45% Node::rGetLocation 0 0% 77.97% 1056ms 1.41% TetrahedralMesh::RefreshJacobianCachedData 943ms 1.26% 79.23% 943ms 1.26% tetgen::tetgenmesh::triface::triface 931ms 1.24% 80.47% 931ms 1.24% AbstractElement::IsDeleted 4ms 0.0053% 80.48% 861ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.021% 80.50% 840ms 1.12% AbstractTetrahedralElement::CalculateJacobian 20ms 0.027% 80.52% 779ms 1.04% Element::CalculateCircumsphere 376ms 0.5% 81.02% 756ms 1.01% tetgen::tetgenmesh::fnextself 0 0% 81.02% 735ms 0.98% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.017% 81.04% 715ms 0.95% boost::numeric::ublas::vector_assign (inline) 61ms 0.081% 81.12% 694ms 0.92% __atan2 41ms 0.055% 81.18% 678ms 0.9% AbstractTetrahedralElement::RefreshJacobian 9ms 0.012% 81.19% 677ms 0.9% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 9ms 0.012% 81.20% 651ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 638ms 0.85% 82.05% 638ms 0.85% tetgen::tetgenmesh::oppo 521ms 0.69% 82.75% 633ms 0.84% __ieee754_atan2_fma 627ms 0.84% 83.58% 627ms 0.84% [libchaste_mesh.so] 603ms 0.8% 84.38% 603ms 0.8% std::vector::size (inline) 594ms 0.79% 85.18% 594ms 0.79% tetgen::tetgenmesh::triface::operator= 0 0% 85.18% 559ms 0.74% std::set::find (inline) 0 0% 85.18% 510ms 0.68% std::insert_iterator::operator= (inline) 0 0% 85.18% 509ms 0.68% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 38ms 0.051% 85.23% 491ms 0.65% tetgen::tetgenmesh::enext2fnext 0 0% 85.23% 488ms 0.65% boost::numeric::ublas::inner_prod (inline) 3ms 0.004% 85.23% 485ms 0.65% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 30ms 0.04% 85.27% 482ms 0.64% boost::numeric::ublas::vector_scalar_binary::evaluate 47ms 0.063% 85.33% 476ms 0.63% tetgen::tetgenmesh::enextfnext 124ms 0.17% 85.50% 474ms 0.63% boost::numeric::ublas::indexing_vector_assign 20ms 0.027% 85.52% 473ms 0.63% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 85.52% 456ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 303ms 0.4% 85.93% 446ms 0.59% tetgen::tetgenmesh::sym 260ms 0.35% 86.27% 437ms 0.58% AbstractTetrahedralMesh::GetElement 437ms 0.58% 86.86% 437ms 0.58% boost::numeric::ublas::c_vector::operator() 16ms 0.021% 86.88% 425ms 0.57% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.004% 86.88% 420ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 0 0% 86.88% 405ms 0.54% VertexMeshWriter::WriteVtkUsingMesh 161ms 0.21% 87.10% 405ms 0.54% boost::numeric::ublas::vector_inner_prod::apply (inline) 28ms 0.037% 87.13% 401ms 0.53% tetgen::tetgenmesh::queue::push 114ms 0.15% 87.28% 400ms 0.53% __dynamic_cast 1ms 0.0013% 87.29% 394ms 0.52% Cell::GetCellId 391ms 0.52% 87.81% 391ms 0.52% std::_Rb_tree_decrement