File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48255ms, 88.10% of 54770ms total Dropped 832 nodes (cum <= 273.85ms) flat flat% sum% cum cum% 0 0% 0% 54722ms 99.91% __libc_start_call_main 0 0% 0% 54722ms 99.91% __libc_start_main_impl 0 0% 0% 54722ms 99.91% _start 0 0% 0% 54709ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54709ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54709ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54709ms 99.89% main 0 0% 0% 54674ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54674ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54674ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54480ms 99.47% AbstractCellBasedSimulation::Solve 0 0% 0% 46892ms 85.62% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46854ms 85.55% MeshBasedCellPopulation::Update 0 0% 0% 30299ms 55.32% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 30299ms 55.32% MeshBasedCellPopulation::TessellateIfNeeded 169ms 0.31% 0.31% 25724ms 46.97% VertexMesh::VertexMesh 0 0% 0.31% 12983ms 23.70% MutableMesh::ReMesh 475ms 0.87% 1.18% 10895ms 19.89% TetrahedralMesh::EdgeIterator::operator++ 28ms 0.051% 1.23% 9875ms 18.03% std::set::insert (inline) 145ms 0.26% 1.49% 9505ms 17.35% std::_Rb_tree::_M_insert_unique 0 0% 1.49% 8738ms 15.95% tetgen::tetrahedralize 1ms 0.0018% 1.49% 8659ms 15.81% tetgen::tetgenmesh::delaunizevertices 3ms 0.0055% 1.50% 8657ms 15.81% tetgen::tetgenmesh::incrflipdelaunay 383ms 0.7% 2.20% 8010ms 14.62% VertexElement::AddFace 295ms 0.54% 2.74% 7606ms 13.89% tetgen::tetgenmesh::lawson 2460ms 4.49% 7.23% 7329ms 13.38% std::_Rb_tree::_M_lower_bound (inline) 209ms 0.38% 7.61% 6833ms 12.48% std::_Rb_tree::find (inline) 6597ms 12.04% 19.65% 6597ms 12.04% std::_Rb_tree_increment 0 0% 19.65% 6428ms 11.74% std::set::count (inline) 151ms 0.28% 19.93% 6352ms 11.60% operator new 1548ms 2.83% 22.76% 6164ms 11.25% __GI___libc_malloc 194ms 0.35% 23.11% 5750ms 10.50% std::_Rb_tree::_M_insert_ (inline) 4ms 0.0073% 23.12% 5688ms 10.39% std::set_intersection (inline) 320ms 0.58% 23.70% 5684ms 10.38% std::__set_intersection 33ms 0.06% 23.76% 5050ms 9.22% std::__new_allocator::allocate (inline) 0 0% 23.76% 5028ms 9.18% std::allocator_traits::allocate (inline) 163ms 0.3% 24.06% 4921ms 8.98% std::_Rb_tree_const_iterator::operator++ (inline) 1065ms 1.94% 26.01% 4650ms 8.49% __GI___libc_free 85ms 0.16% 26.16% 4623ms 8.44% std::less::operator() (inline) 0 0% 26.16% 4612ms 8.42% VertexMesh::~VertexMesh 4575ms 8.35% 34.51% 4575ms 8.35% std::operator< (inline) 25ms 0.046% 34.56% 4563ms 8.33% Node::AddElement 0 0% 34.56% 4490ms 8.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.02% 34.58% 4450ms 8.12% std::_Rb_tree::~_Rb_tree (inline) 1706ms 3.11% 37.69% 4434ms 8.10% std::_Rb_tree::_M_erase 0 0% 37.69% 4384ms 8.00% std::set::~set (inline) 3191ms 5.83% 43.52% 4368ms 7.98% _int_malloc 0 0% 43.52% 4363ms 7.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0018% 43.52% 4347ms 7.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 43.52% 4062ms 7.42% std::_Rb_tree::_M_create_node (inline) 0 0% 43.52% 4027ms 7.35% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.52% 4017ms 7.33% std::_Rb_tree::_M_get_node (inline) 65ms 0.12% 43.64% 3944ms 7.20% std::__new_allocator::deallocate (inline) 0 0% 43.64% 3940ms 7.19% std::allocator_traits::deallocate (inline) 1017ms 1.86% 45.50% 3851ms 7.03% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 45.50% 3819ms 6.97% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.016% 45.51% 3695ms 6.75% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.011% 45.52% 3693ms 6.74% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1374ms 2.51% 48.03% 3582ms 6.54% _int_free 3574ms 6.53% 54.56% 3574ms 6.53% std::_Rb_tree::_S_right (inline) 9ms 0.016% 54.58% 3479ms 6.35% TetrahedralMesh::ImportFromMesher 55ms 0.1% 54.68% 3464ms 6.32% MutableElement::AddNode 147ms 0.27% 54.94% 3009ms 5.49% Node::~Node 0 0% 54.94% 2966ms 5.42% AbstractCellPopulation::WriteResultsToFiles 128ms 0.23% 55.18% 2762ms 5.04% VertexMesh::Clear 84ms 0.15% 55.33% 2356ms 4.30% tetgen::tetgenmesh::insphere_sos 2107ms 3.85% 59.18% 2261ms 4.13% tetgen::insphere 1638ms 2.99% 62.17% 2246ms 4.10% malloc_consolidate 106ms 0.19% 62.36% 2062ms 3.76% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 18ms 0.033% 62.40% 2058ms 3.76% std::_Vector_base::_M_deallocate (inline) 3ms 0.0055% 62.40% 2025ms 3.70% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0018% 62.40% 1982ms 3.62% std::_Rb_tree_iterator::operator++ (inline) 0 0% 62.40% 1978ms 3.61% std::vector::~vector (inline) 6ms 0.011% 62.41% 1950ms 3.56% _int_free_maybe_consolidate 0 0% 62.41% 1937ms 3.54% std::_Vector_base::~_Vector_base (inline) 0 0% 62.41% 1926ms 3.52% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.41% 1900ms 3.47% std::_Rb_tree::_M_put_node (inline) 85ms 0.16% 62.57% 1703ms 3.11% tetgen::tetgenmesh::flip23 2ms 0.0037% 62.57% 1700ms 3.10% Element::Element 1621ms 2.96% 65.53% 1621ms 2.96% std::_Rb_tree_insert_and_rebalance 1516ms 2.77% 68.30% 1516ms 2.77% Node::GetIndex 1ms 0.0018% 68.30% 1481ms 2.70% Element::RegisterWithNodes (inline) 1440ms 2.63% 70.93% 1440ms 2.63% unlink_chunk 102ms 0.19% 71.12% 1416ms 2.59% TetrahedralMesh::Clear 1126ms 2.06% 73.17% 1346ms 2.46% AbstractElement::GetNodeGlobalIndex 3ms 0.0055% 73.18% 1298ms 2.37% VertexMesh::GenerateVerticesFromElementCircumcentres 70ms 0.13% 73.31% 1207ms 2.20% tetgen::tetgenmesh::flip32 1036ms 1.89% 75.20% 1036ms 1.89% AbstractElement::IsDeleted 35ms 0.064% 75.26% 1026ms 1.87% std::vector::_M_realloc_insert 2ms 0.0037% 75.27% 1013ms 1.85% std::_Vector_base::_M_allocate (inline) 923ms 1.69% 76.95% 977ms 1.78% tetgen::orient3d 44ms 0.08% 77.03% 895ms 1.63% std::map::operator[] 31ms 0.057% 77.09% 880ms 1.61% tetgen::tetgenmesh::locate 81ms 0.15% 77.24% 877ms 1.60% tetgen::tetgenmesh::enqueueflipface 74ms 0.14% 77.37% 831ms 1.52% std::vector::push_back (inline) 73ms 0.13% 77.50% 820ms 1.50% tetgen::tetgenmesh::preciselocate 430ms 0.79% 78.29% 809ms 1.48% AbstractElement::GetNodeLocation 0 0% 78.29% 779ms 1.42% std::_Rb_tree::lower_bound (inline) 0 0% 78.29% 779ms 1.42% std::map::lower_bound (inline) 753ms 1.37% 79.66% 753ms 1.37% Node::rGetLocation 1ms 0.0018% 79.67% 751ms 1.37% VoronoiDataWriter::Visit 0 0% 79.67% 730ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 673ms 1.23% 80.89% 673ms 1.23% [libchaste_mesh.so] 651ms 1.19% 82.08% 651ms 1.19% std::vector::size (inline) 637ms 1.16% 83.25% 637ms 1.16% tetgen::tetgenmesh::oppo 11ms 0.02% 83.27% 563ms 1.03% AbstractTetrahedralElement::CalculateJacobian 9ms 0.016% 83.28% 554ms 1.01% Element::CalculateCircumsphere 3ms 0.0055% 83.29% 552ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 314ms 0.57% 83.86% 535ms 0.98% tetgen::tetgenmesh::sym 0 0% 83.86% 497ms 0.91% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.0073% 83.87% 478ms 0.87% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 29ms 0.053% 83.92% 452ms 0.83% AbstractTetrahedralElement::RefreshJacobian 0 0% 83.92% 400ms 0.73% std::set::find (inline) 7ms 0.013% 83.93% 385ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.0055% 83.94% 376ms 0.69% VertexElement::~VertexElement 249ms 0.45% 84.39% 375ms 0.68% tetgen::tetgenmesh::fnextself 0 0% 84.39% 374ms 0.68% std::insert_iterator::operator= (inline) 27ms 0.049% 84.44% 372ms 0.68% __atan2 4ms 0.0073% 84.45% 345ms 0.63% boost::numeric::ublas::vector_assign (inline) 344ms 0.63% 85.08% 344ms 0.63% tetgen::tetgenmesh::org 265ms 0.48% 85.56% 343ms 0.63% __ieee754_atan2_fma 0 0% 85.56% 342ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 7ms 0.013% 85.58% 330ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 28ms 0.051% 85.63% 330ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 0 0% 85.63% 318ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 311ms 0.57% 86.19% 311ms 0.57% tetgen::tetgenmesh::triface::triface 304ms 0.56% 86.75% 304ms 0.56% boost::numeric::ublas::c_vector::operator() 295ms 0.54% 87.29% 295ms 0.54% tetgen::tetgenmesh::triface::operator= 13ms 0.024% 87.31% 293ms 0.53% std::vector::insert (inline) 26ms 0.047% 87.36% 293ms 0.53% tetgen::tetgenmesh::enextfnext 286ms 0.52% 87.88% 286ms 0.52% std::_Rb_tree_decrement 122ms 0.22% 88.10% 276ms 0.5% AbstractTetrahedralMesh::GetElement 0 0% 88.10% 276ms 0.5% VertexMeshWriter::WriteVtkUsingMesh