File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 66336ms, 87.55% of 75769ms total Dropped 916 nodes (cum <= 378.85ms) flat flat% sum% cum cum% 0 0% 0% 75709ms 99.92% __libc_start_call_main 0 0% 0% 75709ms 99.92% __libc_start_main_impl 0 0% 0% 75709ms 99.92% _start 0 0% 0% 75690ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 75690ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 75690ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 75690ms 99.90% main 0 0% 0% 75650ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 75650ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 75650ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 75344ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 65201ms 86.05% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 65144ms 85.98% MeshBasedCellPopulation::Update 0 0% 0% 39301ms 51.87% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 39300ms 51.87% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 308ms 0.41% 0.41% 34344ms 45.33% VertexMesh::VertexMesh 0 0% 0.41% 21301ms 28.11% MutableMesh::ReMesh 0 0% 0.41% 16135ms 21.29% tetgen::tetrahedralize 4ms 0.0053% 0.41% 15979ms 21.09% tetgen::tetgenmesh::delaunizevertices 8ms 0.011% 0.42% 15970ms 21.08% tetgen::tetgenmesh::incrflipdelaunay 624ms 0.82% 1.25% 14534ms 19.18% TetrahedralMesh::EdgeIterator::operator++ 532ms 0.7% 1.95% 14242ms 18.80% tetgen::tetgenmesh::lawson 16ms 0.021% 1.97% 12762ms 16.84% std::set::insert (inline) 214ms 0.28% 2.25% 12303ms 16.24% std::_Rb_tree::_M_insert_unique 495ms 0.65% 2.90% 11548ms 15.24% VertexElement::AddFace 3275ms 4.32% 7.23% 10293ms 13.58% std::_Rb_tree::_M_lower_bound (inline) 281ms 0.37% 7.60% 9622ms 12.70% std::_Rb_tree::find (inline) 0 0% 7.60% 9033ms 11.92% std::set::count (inline) 7778ms 10.27% 17.86% 7778ms 10.27% std::_Rb_tree_increment 279ms 0.37% 18.23% 7078ms 9.34% std::_Rb_tree::_M_insert_ (inline) 184ms 0.24% 18.47% 7066ms 9.33% operator new 1223ms 1.61% 20.09% 6804ms 8.98% __GI___libc_malloc 128ms 0.17% 20.26% 6749ms 8.91% std::less::operator() (inline) 6683ms 8.82% 29.08% 6683ms 8.82% std::operator< (inline) 2ms 0.0026% 29.08% 6663ms 8.79% std::set_intersection (inline) 360ms 0.48% 29.56% 6661ms 8.79% std::__set_intersection 0 0% 29.56% 6145ms 8.11% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.56% 5976ms 7.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0079% 29.56% 5947ms 7.85% AbstractNumericalMethod::ComputeForcesIncludingDamping 41ms 0.054% 29.62% 5760ms 7.60% std::__new_allocator::allocate (inline) 0 0% 29.62% 5740ms 7.58% std::allocator_traits::allocate (inline) 189ms 0.25% 29.87% 5720ms 7.55% std::_Rb_tree_const_iterator::operator++ (inline) 59ms 0.078% 29.94% 5559ms 7.34% Node::AddElement 1384ms 1.83% 31.77% 5296ms 6.99% std::_Rb_tree::_M_get_insert_unique_pos 3790ms 5.00% 36.77% 5219ms 6.89% _int_malloc 1360ms 1.79% 38.57% 5198ms 6.86% __GI___libc_free 14ms 0.018% 38.59% 5161ms 6.81% std::_Rb_tree::~_Rb_tree (inline) 1923ms 2.54% 41.12% 5146ms 6.79% std::_Rb_tree::_M_erase 0 0% 41.12% 5095ms 6.72% std::set::~set (inline) 0 0% 41.12% 4997ms 6.60% VertexMesh::~VertexMesh 5ms 0.0066% 41.13% 4990ms 6.59% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0013% 41.13% 4946ms 6.53% MeshBasedCellPopulation::UpdateNodePairs 4787ms 6.32% 47.45% 4787ms 6.32% std::_Rb_tree::_S_right (inline) 15ms 0.02% 47.47% 4768ms 6.29% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 47.47% 4625ms 6.10% std::_Rb_tree::_M_create_node (inline) 138ms 0.18% 47.65% 4594ms 6.06% std::__new_allocator::deallocate (inline) 0 0% 47.65% 4584ms 6.05% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 47.65% 4583ms 6.05% std::_Rb_tree::_M_get_node (inline) 0 0% 47.65% 4581ms 6.05% std::allocator_traits::deallocate (inline) 71ms 0.094% 47.75% 4329ms 5.71% MutableElement::AddNode 8ms 0.011% 47.76% 4093ms 5.40% TetrahedralMesh::ImportFromMesher 131ms 0.17% 47.93% 3896ms 5.14% tetgen::tetgenmesh::insphere_sos 1390ms 1.83% 49.76% 3832ms 5.06% _int_free 0 0% 49.76% 3811ms 5.03% AbstractCellPopulation::WriteResultsToFiles 3462ms 4.57% 54.33% 3752ms 4.95% tetgen::insphere 125ms 0.16% 54.50% 3379ms 4.46% tetgen::tetgenmesh::flip23 238ms 0.31% 54.81% 3205ms 4.23% Node::~Node 190ms 0.25% 55.06% 2979ms 3.93% VertexMesh::Clear 2876ms 3.80% 58.86% 2876ms 3.80% Node::GetIndex 3ms 0.004% 58.86% 2553ms 3.37% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 204ms 0.27% 59.13% 2549ms 3.36% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1766ms 2.33% 61.46% 2488ms 3.28% malloc_consolidate 134ms 0.18% 61.64% 2424ms 3.20% tetgen::tetgenmesh::flip32 1ms 0.0013% 61.64% 2370ms 3.13% std::_Rb_tree_iterator::operator++ (inline) 20ms 0.026% 61.67% 2334ms 3.08% std::_Vector_base::_M_deallocate (inline) 2308ms 3.05% 64.71% 2308ms 3.05% std::_Rb_tree_insert_and_rebalance 0 0% 64.71% 2282ms 3.01% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.71% 2267ms 2.99% std::_Rb_tree::_M_put_node (inline) 0 0% 64.71% 2205ms 2.91% std::vector::~vector (inline) 9ms 0.012% 64.73% 2165ms 2.86% _int_free_maybe_consolidate 1ms 0.0013% 64.73% 2161ms 2.85% std::_Vector_base::~_Vector_base (inline) 9ms 0.012% 64.74% 2144ms 2.83% Element::Element 255ms 0.34% 65.08% 1785ms 2.36% tetgen::tetgenmesh::enqueueflipface 4ms 0.0053% 65.08% 1767ms 2.33% Element::RegisterWithNodes (inline) 1760ms 2.32% 67.40% 1760ms 2.32% unlink_chunk 1520ms 2.01% 69.41% 1602ms 2.11% tetgen::orient3d 5ms 0.0066% 69.42% 1475ms 1.95% VertexMesh::GenerateVerticesFromElementCircumcentres 83ms 0.11% 69.53% 1452ms 1.92% TetrahedralMesh::Clear 46ms 0.061% 69.59% 1437ms 1.90% tetgen::tetgenmesh::locate 1234ms 1.63% 71.22% 1431ms 1.89% AbstractElement::GetNodeGlobalIndex 68ms 0.09% 71.30% 1360ms 1.79% std::vector::_M_realloc_insert 96ms 0.13% 71.43% 1346ms 1.78% tetgen::tetgenmesh::preciselocate 67ms 0.088% 71.52% 1293ms 1.71% std::map::operator[] 6ms 0.0079% 71.53% 1163ms 1.53% std::_Vector_base::_M_allocate (inline) 0 0% 71.53% 1132ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 71.53% 1132ms 1.49% std::map::lower_bound (inline) 116ms 0.15% 71.68% 1101ms 1.45% std::vector::push_back (inline) 1058ms 1.40% 73.08% 1058ms 1.40% Node::rGetLocation 1048ms 1.38% 74.46% 1048ms 1.38% AbstractElement::IsDeleted 0 0% 74.46% 1041ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 1037ms 1.37% 75.83% 1037ms 1.37% tetgen::tetgenmesh::oppo 1ms 0.0013% 75.83% 1008ms 1.33% VoronoiDataWriter::Visit 488ms 0.64% 76.47% 989ms 1.31% AbstractElement::GetNodeLocation 6ms 0.0079% 76.48% 847ms 1.12% AbstractTetrahedralElement::CalculateInverseJacobian 819ms 1.08% 77.56% 819ms 1.08% tetgen::tetgenmesh::triface::triface 14ms 0.018% 77.58% 808ms 1.07% AbstractTetrahedralElement::CalculateJacobian 305ms 0.4% 77.98% 805ms 1.06% tetgen::tetgenmesh::sym 790ms 1.04% 79.03% 790ms 1.04% [libchaste_mesh.so] 1ms 0.0013% 79.03% 751ms 0.99% AbstractTwoBodyInteractionForce::AddForceContribution 723ms 0.95% 79.98% 723ms 0.95% tetgen::tetgenmesh::triface::operator= 710ms 0.94% 80.92% 710ms 0.94% std::vector::size (inline) 9ms 0.012% 80.93% 698ms 0.92% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 248ms 0.33% 81.26% 676ms 0.89% tetgen::tetgenmesh::bond 16ms 0.021% 81.28% 666ms 0.88% Element::CalculateCircumsphere 46ms 0.061% 81.34% 625ms 0.82% __atan2 49ms 0.065% 81.41% 622ms 0.82% AbstractTetrahedralElement::RefreshJacobian 46ms 0.061% 81.47% 605ms 0.8% tetgen::tetgenmesh::enext2fnext 406ms 0.54% 82.00% 604ms 0.8% tetgen::tetgenmesh::fnextself 20ms 0.026% 82.03% 597ms 0.79% boost::numeric::ublas::vector_assign (inline) 10ms 0.013% 82.04% 586ms 0.77% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.04% 583ms 0.77% std::set::find (inline) 453ms 0.6% 82.64% 574ms 0.76% __ieee754_atan2_fma 36ms 0.048% 82.69% 558ms 0.74% tetgen::tetgenmesh::queue::push 0 0% 82.69% 550ms 0.73% boost::numeric::ublas::inner_prod (inline) 2ms 0.0026% 82.69% 549ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 47ms 0.062% 82.75% 547ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 51ms 0.067% 82.82% 535ms 0.71% tetgen::tetgenmesh::enextfnext 327ms 0.43% 83.25% 522ms 0.69% tetgen::tetgenmesh::link::add 511ms 0.67% 83.92% 511ms 0.67% tetgen::tetgenmesh::decode 0 0% 83.92% 494ms 0.65% std::insert_iterator::operator= (inline) 485ms 0.64% 84.56% 485ms 0.64% tetgen::tetgenmesh::org 483ms 0.64% 85.20% 483ms 0.64% tetgen::tetgenmesh::pointmark 12ms 0.016% 85.22% 471ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 85.22% 439ms 0.58% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.03% 85.25% 434ms 0.57% std::_Rb_tree_iterator::operator-- (inline) 0 0% 85.25% 430ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.004% 85.25% 419ms 0.55% Cell::GetCellId 199ms 0.26% 85.52% 419ms 0.55% boost::numeric::ublas::vector_inner_prod::apply (inline) 219ms 0.29% 85.80% 416ms 0.55% AbstractTetrahedralMesh::GetElement 5ms 0.0066% 85.81% 411ms 0.54% CellPropertyCollection::GetPropertiesType (inline) 411ms 0.54% 86.35% 411ms 0.54% tetgen::tetgenmesh::encode 17ms 0.022% 86.38% 405ms 0.53% std::vector::insert (inline) 10ms 0.013% 86.39% 398ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 103ms 0.14% 86.52% 397ms 0.52% __dynamic_cast 0 0% 86.52% 391ms 0.52% VertexMeshWriter::WriteVtkUsingMesh 387ms 0.51% 87.04% 387ms 0.51% std::_Rb_tree_decrement 384ms 0.51% 87.54% 384ms 0.51% boost::numeric::ublas::c_vector::operator() 6ms 0.0079% 87.55% 379ms 0.5% VertexElement::~VertexElement