File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53274ms, 86.73% of 61425ms total Dropped 909 nodes (cum <= 307.12ms) flat flat% sum% cum cum% 0 0% 0% 61363ms 99.90% __libc_start_call_main 0 0% 0% 61363ms 99.90% __libc_start_main_impl 0 0% 0% 61363ms 99.90% _start 0 0% 0% 61345ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61345ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61345ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61345ms 99.87% main 0 0% 0% 61301ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61301ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61301ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61029ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 51882ms 84.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51842ms 84.40% MeshBasedCellPopulation::Update 0 0% 0% 28018ms 45.61% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 28017ms 45.61% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 199ms 0.32% 0.32% 25238ms 41.09% VertexMesh::VertexMesh 0 0% 0.32% 19771ms 32.19% MutableMesh::ReMesh 0 0% 0.32% 15984ms 26.02% tetgen::tetrahedralize 0 0% 0.32% 15826ms 25.76% tetgen::tetgenmesh::delaunizevertices 11ms 0.018% 0.34% 15818ms 25.75% tetgen::tetgenmesh::incrflipdelaunay 559ms 0.91% 1.25% 14131ms 23.01% tetgen::tetgenmesh::lawson 589ms 0.96% 2.21% 12332ms 20.08% TetrahedralMesh::EdgeIterator::operator++ 38ms 0.062% 2.27% 9934ms 16.17% std::set::insert (inline) 356ms 0.58% 2.85% 9678ms 15.76% VertexElement::AddFace 242ms 0.39% 3.25% 9455ms 15.39% std::_Rb_tree::_M_insert_unique 3190ms 5.19% 8.44% 9133ms 14.87% std::_Rb_tree::_M_lower_bound (inline) 273ms 0.44% 8.88% 8584ms 13.97% std::_Rb_tree::find (inline) 0 0% 8.88% 7968ms 12.97% std::set::count (inline) 121ms 0.2% 9.08% 5780ms 9.41% std::less::operator() (inline) 5713ms 9.30% 18.38% 5713ms 9.30% std::operator< (inline) 306ms 0.5% 18.88% 5660ms 9.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 18.88% 5443ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.88% 5313ms 8.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0016% 18.88% 5291ms 8.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 5078ms 8.27% 27.15% 5078ms 8.27% std::_Rb_tree_increment 167ms 0.27% 27.42% 4990ms 8.12% operator new 1206ms 1.96% 29.38% 4748ms 7.73% __GI___libc_malloc 1ms 0.0016% 29.39% 4426ms 7.21% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 29.40% 4385ms 7.14% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 36ms 0.059% 29.46% 4344ms 7.07% std::__new_allocator::allocate (inline) 0 0% 29.46% 4334ms 7.06% std::allocator_traits::allocate (inline) 14ms 0.023% 29.48% 4269ms 6.95% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.011% 29.49% 3939ms 6.41% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.0049% 29.49% 3939ms 6.41% std::set_intersection (inline) 285ms 0.46% 29.96% 3936ms 6.41% std::__set_intersection 1300ms 2.12% 32.07% 3931ms 6.40% std::_Rb_tree::_M_erase 0 0% 32.07% 3895ms 6.34% std::set::~set (inline) 119ms 0.19% 32.27% 3866ms 6.29% tetgen::tetgenmesh::insphere_sos 1306ms 2.13% 34.39% 3848ms 6.26% std::_Rb_tree::_M_get_insert_unique_pos 1123ms 1.83% 36.22% 3738ms 6.09% __GI___libc_free 3434ms 5.59% 41.81% 3736ms 6.08% tetgen::insphere 0 0% 41.81% 3545ms 5.77% AbstractCellPopulation::WriteResultsToFiles 0 0% 41.81% 3543ms 5.77% std::_Rb_tree::_M_create_node (inline) 0 0% 41.81% 3510ms 5.71% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.81% 3509ms 5.71% std::_Rb_tree::_M_get_node (inline) 105ms 0.17% 41.98% 3503ms 5.70% tetgen::tetgenmesh::flip23 153ms 0.25% 42.23% 3347ms 5.45% std::__new_allocator::deallocate (inline) 0 0% 42.23% 3326ms 5.41% std::allocator_traits::deallocate (inline) 49ms 0.08% 42.31% 3184ms 5.18% Node::AddElement 2259ms 3.68% 45.99% 3170ms 5.16% _int_malloc 184ms 0.3% 46.29% 3166ms 5.15% std::_Rb_tree_const_iterator::operator++ (inline) 9ms 0.015% 46.31% 3034ms 4.94% TetrahedralMesh::ImportFromMesher 2924ms 4.76% 51.07% 2924ms 4.76% std::_Rb_tree::_S_right (inline) 0 0% 51.07% 2796ms 4.55% VertexMesh::~VertexMesh 1361ms 2.22% 53.28% 2610ms 4.25% _int_free 73ms 0.12% 53.40% 2571ms 4.19% MutableElement::AddNode 138ms 0.22% 53.62% 2529ms 4.12% tetgen::tetgenmesh::flip32 193ms 0.31% 53.94% 2412ms 3.93% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0033% 53.94% 2406ms 3.92% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 53.94% 2236ms 3.64% std::_Rb_tree_iterator::operator++ (inline) 0 0% 53.94% 2129ms 3.47% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.94% 2117ms 3.45% std::_Rb_tree::_M_put_node (inline) 163ms 0.27% 54.21% 2101ms 3.42% Node::~Node 1904ms 3.10% 57.31% 1904ms 3.10% std::_Rb_tree_insert_and_rebalance 212ms 0.35% 57.65% 1871ms 3.05% tetgen::tetgenmesh::enqueueflipface 158ms 0.26% 57.91% 1866ms 3.04% VertexMesh::Clear 1558ms 2.54% 60.45% 1646ms 2.68% tetgen::orient3d 1559ms 2.54% 62.98% 1559ms 2.54% Node::GetIndex 6ms 0.0098% 62.99% 1407ms 2.29% Element::Element 37ms 0.06% 63.05% 1377ms 2.24% tetgen::tetgenmesh::locate 92ms 0.15% 63.20% 1335ms 2.17% TetrahedralMesh::Clear 91ms 0.15% 63.35% 1289ms 2.10% tetgen::tetgenmesh::preciselocate 29ms 0.047% 63.40% 1238ms 2.02% std::_Vector_base::_M_deallocate (inline) 773ms 1.26% 64.66% 1210ms 1.97% malloc_consolidate 73ms 0.12% 64.78% 1185ms 1.93% std::map::operator[] 0 0% 64.78% 1171ms 1.91% std::vector::~vector (inline) 57ms 0.093% 64.87% 1104ms 1.80% std::vector::_M_realloc_insert 3ms 0.0049% 64.87% 1072ms 1.75% Element::RegisterWithNodes (inline) 1068ms 1.74% 66.61% 1068ms 1.74% unlink_chunk 1ms 0.0016% 66.61% 1067ms 1.74% std::_Vector_base::~_Vector_base (inline) 1050ms 1.71% 68.32% 1050ms 1.71% tetgen::tetgenmesh::triface::triface 1030ms 1.68% 70.00% 1030ms 1.68% tetgen::tetgenmesh::oppo 0 0% 70.00% 1023ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 70.00% 1023ms 1.67% std::map::lower_bound (inline) 8ms 0.013% 70.01% 1019ms 1.66% _int_free_maybe_consolidate 787ms 1.28% 71.30% 986ms 1.61% AbstractElement::GetNodeGlobalIndex 102ms 0.17% 71.46% 914ms 1.49% std::vector::push_back (inline) 1ms 0.0016% 71.46% 896ms 1.46% VoronoiDataWriter::Visit 5ms 0.0081% 71.47% 830ms 1.35% std::_Vector_base::_M_allocate (inline) 799ms 1.30% 72.77% 799ms 1.30% [libchaste_mesh.so] 298ms 0.49% 73.26% 798ms 1.30% tetgen::tetgenmesh::sym 4ms 0.0065% 73.26% 793ms 1.29% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 73.26% 731ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 0 0% 73.26% 724ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 700ms 1.14% 74.40% 700ms 1.14% tetgen::tetgenmesh::triface::operator= 15ms 0.024% 74.43% 687ms 1.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 10ms 0.016% 74.44% 674ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 369ms 0.6% 75.04% 665ms 1.08% tetgen::tetgenmesh::fnextself 34ms 0.055% 75.10% 658ms 1.07% tetgen::tetgenmesh::queue::push 13ms 0.021% 75.12% 634ms 1.03% boost::numeric::ublas::vector_assign (inline) 18ms 0.029% 75.15% 625ms 1.02% AbstractTetrahedralElement::CalculateJacobian 389ms 0.63% 75.78% 623ms 1.01% tetgen::tetgenmesh::link::add 62ms 0.1% 75.88% 622ms 1.01% __atan2 0 0% 75.88% 613ms 1% std::set::find (inline) 238ms 0.39% 76.27% 612ms 1% tetgen::tetgenmesh::bond 45ms 0.073% 76.35% 608ms 0.99% tetgen::tetgenmesh::enextfnext 14ms 0.023% 76.37% 604ms 0.98% boost::numeric::ublas::c_vector::c_vector (inline) 67ms 0.11% 76.48% 574ms 0.93% tetgen::tetgenmesh::enext2fnext 421ms 0.69% 77.16% 553ms 0.9% __ieee754_atan2_fma 233ms 0.38% 77.54% 536ms 0.87% AbstractElement::GetNodeLocation 533ms 0.87% 78.41% 533ms 0.87% Node::rGetLocation 532ms 0.87% 79.28% 532ms 0.87% tetgen::tetgenmesh::decode 531ms 0.86% 80.14% 531ms 0.86% AbstractElement::IsDeleted 0 0% 80.14% 510ms 0.83% std::insert_iterator::operator= (inline) 0 0% 80.14% 506ms 0.82% boost::numeric::ublas::inner_prod (inline) 1ms 0.0016% 80.14% 500ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 52ms 0.085% 80.23% 499ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 483ms 0.79% 81.01% 483ms 0.79% tetgen::tetgenmesh::org 482ms 0.78% 81.80% 482ms 0.78% std::vector::size (inline) 0 0% 81.80% 440ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 13ms 0.021% 81.82% 427ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 210ms 0.34% 82.16% 426ms 0.69% AbstractTetrahedralMesh::GetElement 426ms 0.69% 82.85% 426ms 0.69% boost::numeric::ublas::c_vector::operator() 33ms 0.054% 82.91% 416ms 0.68% AbstractTetrahedralElement::RefreshJacobian 11ms 0.018% 82.93% 416ms 0.68% Element::CalculateCircumsphere 3ms 0.0049% 82.93% 402ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 18ms 0.029% 82.96% 399ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 97ms 0.16% 83.12% 391ms 0.64% boost::numeric::ublas::indexing_vector_assign 173ms 0.28% 83.40% 389ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.40% 381ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 379ms 0.62% 84.02% 379ms 0.62% std::_Rb_tree_decrement 9ms 0.015% 84.03% 374ms 0.61% Cell::GetCellId 98ms 0.16% 84.19% 368ms 0.6% __dynamic_cast 4ms 0.0065% 84.20% 367ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 362ms 0.59% 84.79% 362ms 0.59% tetgen::tetgenmesh::encode 350ms 0.57% 85.36% 350ms 0.57% tetgen::tetgenmesh::pointmark 8ms 0.013% 85.37% 347ms 0.56% VertexElement::~VertexElement 0 0% 85.37% 345ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 344ms 0.56% 85.93% 344ms 0.56% tetgen::tetgenmesh::face::face 9ms 0.015% 85.94% 329ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.026% 85.97% 322ms 0.52% std::vector::insert (inline) 1ms 0.0016% 85.97% 319ms 0.52% tcache_get (inline) 318ms 0.52% 86.49% 318ms 0.52% tcache_get_n (inline) 39ms 0.063% 86.55% 312ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline) 109ms 0.18% 86.73% 309ms 0.5% Inverse