File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56285ms, 85.80% of 65604ms total Dropped 885 nodes (cum <= 328.02ms) flat flat% sum% cum cum% 0 0% 0% 65542ms 99.91% __libc_start_call_main 0 0% 0% 65542ms 99.91% __libc_start_main_impl 0 0% 0% 65542ms 99.91% _start 0 0% 0% 65524ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65524ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65524ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65524ms 99.88% main 0 0% 0% 65478ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65478ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65478ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65180ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 55812ms 85.07% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55766ms 85.00% MeshBasedCellPopulation::Update 0 0% 0% 31401ms 47.86% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 31401ms 47.86% MeshBasedCellPopulation::TessellateIfNeeded 209ms 0.32% 0.32% 27625ms 42.11% VertexMesh::VertexMesh 0 0% 0.32% 20240ms 30.85% MutableMesh::ReMesh 0 0% 0.32% 15978ms 24.36% tetgen::tetrahedralize 4ms 0.0061% 0.32% 15817ms 24.11% tetgen::tetgenmesh::delaunizevertices 8ms 0.012% 0.34% 15810ms 24.10% tetgen::tetgenmesh::incrflipdelaunay 533ms 0.81% 1.15% 14086ms 21.47% tetgen::tetgenmesh::lawson 656ms 1% 2.15% 12795ms 19.50% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.044% 2.19% 10817ms 16.49% std::set::insert (inline) 242ms 0.37% 2.56% 10411ms 15.87% std::_Rb_tree::_M_insert_unique 416ms 0.63% 3.20% 10207ms 15.56% VertexElement::AddFace 3194ms 4.87% 8.07% 9173ms 13.98% std::_Rb_tree::_M_lower_bound (inline) 275ms 0.42% 8.48% 8653ms 13.19% std::_Rb_tree::find (partial-inline) 0 0% 8.48% 8079ms 12.31% std::set::count (inline) 290ms 0.44% 8.93% 6210ms 9.47% std::_Rb_tree::_M_insert_ (inline) 113ms 0.17% 9.10% 5836ms 8.90% std::less::operator() (inline) 148ms 0.23% 9.32% 5824ms 8.88% operator new 5784ms 8.82% 18.14% 5785ms 8.82% std::operator< (inline) 5635ms 8.59% 26.73% 5635ms 8.59% std::_Rb_tree_increment 0 0% 26.73% 5632ms 8.58% OffLatticeSimulation::UpdateCellLocationsAndTopology 1444ms 2.20% 28.93% 5584ms 8.51% __GI___libc_malloc 1ms 0.0015% 28.93% 5490ms 8.37% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0015% 28.93% 5468ms 8.33% AbstractNumericalMethod::ComputeForcesIncludingDamping 43ms 0.066% 29.00% 5005ms 7.63% std::__new_allocator::allocate (inline) 0 0% 29.00% 4985ms 7.60% std::allocator_traits::allocate (inline) 1ms 0.0015% 29.00% 4568ms 6.96% std::set_intersection (inline) 293ms 0.45% 29.45% 4567ms 6.96% std::__set_intersection 10ms 0.015% 29.46% 4565ms 6.96% std::_Rb_tree::~_Rb_tree (inline) 1702ms 2.59% 32.06% 4555ms 6.94% std::_Rb_tree::_M_erase 11ms 0.017% 32.07% 4554ms 6.94% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0015% 32.08% 4515ms 6.88% MeshBasedCellPopulation::UpdateNodePairs 0 0% 32.08% 4500ms 6.86% std::set::~set (inline) 16ms 0.024% 32.10% 4366ms 6.66% MeshBasedCellPopulation::SpringIterator::operator++ 1304ms 1.99% 34.09% 4236ms 6.46% __GI___libc_free 1345ms 2.05% 36.14% 4194ms 6.39% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 36.14% 4083ms 6.22% std::_Rb_tree::_M_create_node (inline) 0 0% 36.14% 4051ms 6.17% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.14% 4035ms 6.15% std::_Rb_tree::_M_get_node (inline) 46ms 0.07% 36.21% 3946ms 6.01% Node::AddElement 112ms 0.17% 36.38% 3869ms 5.90% tetgen::tetgenmesh::insphere_sos 218ms 0.33% 36.71% 3849ms 5.87% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 36.71% 3808ms 5.80% VertexMesh::~VertexMesh 164ms 0.25% 36.96% 3747ms 5.71% std::__new_allocator::deallocate (inline) 3461ms 5.28% 42.24% 3744ms 5.71% tetgen::insphere 2679ms 4.08% 46.32% 3742ms 5.70% _int_malloc 0 0% 46.32% 3730ms 5.69% std::allocator_traits::deallocate (inline) 0 0% 46.32% 3567ms 5.44% AbstractCellPopulation::WriteResultsToFiles 3437ms 5.24% 51.56% 3437ms 5.24% std::_Rb_tree::_S_right (inline) 6ms 0.0091% 51.57% 3421ms 5.21% TetrahedralMesh::ImportFromMesher 136ms 0.21% 51.78% 3417ms 5.21% tetgen::tetgenmesh::flip23 80ms 0.12% 51.90% 3202ms 4.88% MutableElement::AddNode 1245ms 1.90% 53.80% 2926ms 4.46% _int_free 216ms 0.33% 54.12% 2691ms 4.10% Node::~Node 152ms 0.23% 54.36% 2483ms 3.78% tetgen::tetgenmesh::flip32 176ms 0.27% 54.62% 2478ms 3.78% VertexMesh::Clear 3ms 0.0046% 54.63% 2381ms 3.63% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 206ms 0.31% 54.94% 2339ms 3.57% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 54.94% 2153ms 3.28% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.94% 2147ms 3.27% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.94% 2134ms 3.25% std::_Rb_tree::_M_put_node (inline) 1946ms 2.97% 57.91% 1946ms 2.97% std::_Rb_tree_insert_and_rebalance 232ms 0.35% 58.26% 1903ms 2.90% tetgen::tetgenmesh::enqueueflipface 1707ms 2.60% 60.87% 1707ms 2.60% Node::GetIndex 3ms 0.0046% 60.87% 1636ms 2.49% Element::Element 25ms 0.038% 60.91% 1621ms 2.47% std::_Vector_base::_M_deallocate (inline) 1122ms 1.71% 62.62% 1617ms 2.46% malloc_consolidate 1514ms 2.31% 64.93% 1586ms 2.42% tetgen::orient3d 0 0% 64.93% 1558ms 2.37% std::vector::~vector (inline) 4ms 0.0061% 64.93% 1454ms 2.22% std::_Vector_base::~_Vector_base (inline) 99ms 0.15% 65.08% 1428ms 2.18% TetrahedralMesh::Clear 30ms 0.046% 65.13% 1404ms 2.14% tetgen::tetgenmesh::locate 12ms 0.018% 65.15% 1401ms 2.14% _int_free_maybe_consolidate 89ms 0.14% 65.28% 1317ms 2.01% tetgen::tetgenmesh::preciselocate 5ms 0.0076% 65.29% 1283ms 1.96% Element::RegisterWithNodes (inline) 1268ms 1.93% 67.22% 1268ms 1.93% unlink_chunk 64ms 0.098% 67.32% 1171ms 1.78% std::vector::_M_realloc_insert 82ms 0.12% 67.45% 1164ms 1.77% std::map::operator[] 937ms 1.43% 68.87% 1156ms 1.76% AbstractElement::GetNodeGlobalIndex 1138ms 1.73% 70.61% 1138ms 1.73% tetgen::tetgenmesh::oppo 0 0% 70.61% 1004ms 1.53% std::_Rb_tree::lower_bound (inline) 0 0% 70.61% 1004ms 1.53% std::map::lower_bound (inline) 1003ms 1.53% 72.14% 1003ms 1.53% tetgen::tetgenmesh::triface::triface 8ms 0.012% 72.15% 1001ms 1.53% VertexMesh::GenerateVerticesFromElementCircumcentres 4ms 0.0061% 72.16% 954ms 1.45% std::_Vector_base::_M_allocate (inline) 0 0% 72.16% 937ms 1.43% VoronoiDataWriter::Visit 119ms 0.18% 72.34% 932ms 1.42% std::vector::push_back (inline) 830ms 1.27% 73.60% 830ms 1.27% [libchaste_mesh.so] 0 0% 73.60% 818ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 775ms 1.18% 74.78% 775ms 1.18% tetgen::tetgenmesh::triface::operator= 0 0% 74.78% 733ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.017% 74.80% 726ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 697ms 1.06% 75.86% 697ms 1.06% AbstractElement::IsDeleted 14ms 0.021% 75.88% 692ms 1.05% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 262ms 0.4% 76.28% 687ms 1.05% tetgen::tetgenmesh::sym 670ms 1.02% 77.30% 670ms 1.02% Node::rGetLocation 12ms 0.018% 77.32% 666ms 1.02% AbstractTetrahedralElement::CalculateJacobian 281ms 0.43% 77.75% 660ms 1.01% AbstractElement::GetNodeLocation 655ms 1% 78.75% 655ms 1% std::vector::size (inline) 17ms 0.026% 78.78% 647ms 0.99% boost::numeric::ublas::vector_assign (inline) 10ms 0.015% 78.79% 616ms 0.94% boost::numeric::ublas::c_vector::c_vector (inline) 45ms 0.069% 78.86% 608ms 0.93% __atan2 355ms 0.54% 79.40% 597ms 0.91% tetgen::tetgenmesh::fnextself 34ms 0.052% 79.45% 597ms 0.91% tetgen::tetgenmesh::queue::push 252ms 0.38% 79.84% 591ms 0.9% tetgen::tetgenmesh::bond 71ms 0.11% 79.94% 591ms 0.9% tetgen::tetgenmesh::enext2fnext 0 0% 79.94% 572ms 0.87% std::set::find (inline) 362ms 0.55% 80.50% 563ms 0.86% tetgen::tetgenmesh::link::add 449ms 0.68% 81.18% 560ms 0.85% __ieee754_atan2_fma 54ms 0.082% 81.26% 549ms 0.84% tetgen::tetgenmesh::enextfnext 0 0% 81.26% 539ms 0.82% boost::numeric::ublas::inner_prod (inline) 1ms 0.0015% 81.26% 534ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 46ms 0.07% 81.33% 533ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 25ms 0.038% 81.37% 512ms 0.78% Element::CalculateCircumsphere 40ms 0.061% 81.43% 478ms 0.73% AbstractTetrahedralElement::RefreshJacobian 453ms 0.69% 82.12% 453ms 0.69% tetgen::tetgenmesh::org 11ms 0.017% 82.14% 452ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 231ms 0.35% 82.49% 445ms 0.68% AbstractTetrahedralMesh::GetElement 0 0% 82.49% 442ms 0.67% std::insert_iterator::operator= (inline) 440ms 0.67% 83.16% 440ms 0.67% tetgen::tetgenmesh::decode 432ms 0.66% 83.82% 432ms 0.66% boost::numeric::ublas::c_vector::operator() 5ms 0.0076% 83.83% 427ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 103ms 0.16% 83.99% 423ms 0.64% boost::numeric::ublas::indexing_vector_assign 7ms 0.011% 84.00% 422ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 174ms 0.27% 84.26% 418ms 0.64% boost::numeric::ublas::vector_inner_prod::apply (inline) 9ms 0.014% 84.28% 403ms 0.61% VertexElement::~VertexElement 25ms 0.038% 84.31% 403ms 0.61% std::vector::insert (inline) 4ms 0.0061% 84.32% 400ms 0.61% Cell::GetCellId 27ms 0.041% 84.36% 400ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.36% 393ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 111ms 0.17% 84.53% 381ms 0.58% __dynamic_cast 1ms 0.0015% 84.53% 375ms 0.57% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.003% 84.54% 353ms 0.54% tcache_get (inline) 0 0% 84.54% 351ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 351ms 0.54% 85.07% 351ms 0.54% tcache_get_n (inline) 10ms 0.015% 85.09% 350ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 343ms 0.52% 85.61% 343ms 0.52% std::_Rb_tree_decrement 122ms 0.19% 85.80% 336ms 0.51% Inverse