File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45577ms, 86.42% of 52736ms total Dropped 830 nodes (cum <= 263.68ms) flat flat% sum% cum cum% 0 0% 0% 52689ms 99.91% __libc_start_call_main 0 0% 0% 52689ms 99.91% __libc_start_main_impl 0 0% 0% 52689ms 99.91% _start 0 0% 0% 52675ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52675ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52675ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52675ms 99.88% main 0 0% 0% 52639ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52639ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52639ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52399ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 44935ms 85.21% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 44896ms 85.13% MeshBasedCellPopulation::Update 0 0% 0% 25564ms 48.48% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25564ms 48.48% MeshBasedCellPopulation::TessellateIfNeeded 179ms 0.34% 0.34% 22214ms 42.12% VertexMesh::VertexMesh 0 0% 0.34% 16023ms 30.38% MutableMesh::ReMesh 0 0% 0.34% 12382ms 23.48% tetgen::tetrahedralize 3ms 0.0057% 0.35% 12266ms 23.26% tetgen::tetgenmesh::delaunizevertices 2ms 0.0038% 0.35% 12259ms 23.25% tetgen::tetgenmesh::incrflipdelaunay 435ms 0.82% 1.17% 11046ms 20.95% tetgen::tetgenmesh::lawson 480ms 0.91% 2.08% 10333ms 19.59% TetrahedralMesh::EdgeIterator::operator++ 32ms 0.061% 2.14% 8693ms 16.48% std::set::insert (inline) 170ms 0.32% 2.47% 8339ms 15.81% std::_Rb_tree::_M_insert_unique 319ms 0.6% 3.07% 7874ms 14.93% VertexElement::AddFace 2458ms 4.66% 7.73% 7379ms 13.99% std::_Rb_tree::_M_lower_bound (inline) 201ms 0.38% 8.11% 6948ms 13.18% std::_Rb_tree::find (inline) 0 0% 8.11% 6517ms 12.36% std::set::count (inline) 249ms 0.47% 8.59% 4888ms 9.27% std::_Rb_tree::_M_insert_ (inline) 102ms 0.19% 8.78% 4764ms 9.03% std::less::operator() (inline) 4711ms 8.93% 17.71% 4711ms 8.93% std::_Rb_tree_increment 4705ms 8.92% 26.63% 4705ms 8.92% std::operator< (inline) 106ms 0.2% 26.84% 4539ms 8.61% operator new 1ms 0.0019% 26.84% 4456ms 8.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 943ms 1.79% 28.63% 4374ms 8.29% __GI___libc_malloc 0 0% 28.63% 4342ms 8.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0038% 28.63% 4323ms 8.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 4ms 0.0076% 28.64% 3886ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 1480ms 2.81% 31.44% 3881ms 7.36% std::_Rb_tree::_M_erase 37ms 0.07% 31.51% 3852ms 7.30% std::__new_allocator::allocate (inline) 0 0% 31.51% 3844ms 7.29% std::set::~set (inline) 0 0% 31.51% 3834ms 7.27% std::allocator_traits::allocate (inline) 4ms 0.0076% 31.52% 3824ms 7.25% std::set_intersection (inline) 240ms 0.46% 31.98% 3820ms 7.24% std::__set_intersection 1111ms 2.11% 34.08% 3628ms 6.88% __GI___libc_free 7ms 0.013% 34.10% 3601ms 6.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 34.10% 3599ms 6.82% MeshBasedCellPopulation::UpdateNodePairs 1080ms 2.05% 36.14% 3489ms 6.62% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.021% 36.17% 3469ms 6.58% MeshBasedCellPopulation::SpringIterator::operator++ 40ms 0.076% 36.24% 3388ms 6.42% Node::AddElement 0 0% 36.24% 3386ms 6.42% VertexMesh::~VertexMesh 182ms 0.35% 36.59% 3218ms 6.10% std::_Rb_tree_const_iterator::operator++ (inline) 94ms 0.18% 36.76% 3162ms 6.00% std::__new_allocator::deallocate (inline) 0 0% 36.76% 3146ms 5.97% std::allocator_traits::deallocate (inline) 2255ms 4.28% 41.04% 3139ms 5.95% _int_malloc 0 0% 41.04% 3111ms 5.90% std::_Rb_tree::_M_create_node (inline) 0 0% 41.04% 3076ms 5.83% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.04% 3071ms 5.82% std::_Rb_tree::_M_get_node (inline) 5ms 0.0095% 41.05% 2968ms 5.63% TetrahedralMesh::ImportFromMesher 2952ms 5.60% 46.65% 2952ms 5.60% std::_Rb_tree::_S_right (inline) 89ms 0.17% 46.82% 2948ms 5.59% tetgen::tetgenmesh::insphere_sos 0 0% 46.82% 2885ms 5.47% AbstractCellPopulation::WriteResultsToFiles 2653ms 5.03% 51.85% 2851ms 5.41% tetgen::insphere 104ms 0.2% 52.04% 2681ms 5.08% tetgen::tetgenmesh::flip23 52ms 0.099% 52.14% 2602ms 4.93% MutableElement::AddNode 1061ms 2.01% 54.15% 2511ms 4.76% _int_free 166ms 0.31% 54.47% 2431ms 4.61% Node::~Node 148ms 0.28% 54.75% 2217ms 4.20% VertexMesh::Clear 115ms 0.22% 54.97% 1972ms 3.74% tetgen::tetgenmesh::flip32 4ms 0.0076% 54.98% 1936ms 3.67% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 146ms 0.28% 55.25% 1920ms 3.64% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 55.25% 1791ms 3.40% std::_Rb_tree_iterator::operator++ (inline) 0 0% 55.25% 1748ms 3.31% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.25% 1735ms 3.29% std::_Rb_tree::_M_put_node (inline) 1630ms 3.09% 58.34% 1630ms 3.09% std::_Rb_tree_insert_and_rebalance 182ms 0.35% 58.69% 1447ms 2.74% tetgen::tetgenmesh::enqueueflipface 979ms 1.86% 60.54% 1446ms 2.74% malloc_consolidate 32ms 0.061% 60.61% 1443ms 2.74% std::_Vector_base::_M_deallocate (inline) 6ms 0.011% 60.62% 1442ms 2.73% Element::Element 1426ms 2.70% 63.32% 1426ms 2.70% Node::GetIndex 0 0% 63.32% 1373ms 2.60% std::vector::~vector (inline) 1ms 0.0019% 63.32% 1292ms 2.45% std::_Vector_base::~_Vector_base (inline) 1186ms 2.25% 65.57% 1255ms 2.38% tetgen::orient3d 68ms 0.13% 65.70% 1248ms 2.37% TetrahedralMesh::Clear 6ms 0.011% 65.71% 1241ms 2.35% _int_free_maybe_consolidate 5ms 0.0095% 65.72% 1203ms 2.28% Element::RegisterWithNodes (inline) 1109ms 2.10% 67.82% 1109ms 2.10% unlink_chunk 34ms 0.064% 67.89% 995ms 1.89% tetgen::tetgenmesh::locate 52ms 0.099% 67.99% 977ms 1.85% std::vector::_M_realloc_insert 67ms 0.13% 68.11% 931ms 1.77% tetgen::tetgenmesh::preciselocate 764ms 1.45% 69.56% 929ms 1.76% AbstractElement::GetNodeGlobalIndex 57ms 0.11% 69.67% 914ms 1.73% std::map::operator[] 4ms 0.0076% 69.68% 841ms 1.59% VertexMesh::GenerateVerticesFromElementCircumcentres 107ms 0.2% 69.88% 798ms 1.51% std::vector::push_back (inline) 0 0% 69.88% 788ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 69.88% 788ms 1.49% std::map::lower_bound (inline) 767ms 1.45% 71.34% 767ms 1.45% tetgen::tetgenmesh::triface::triface 1ms 0.0019% 71.34% 764ms 1.45% std::_Vector_base::_M_allocate (inline) 0 0% 71.34% 749ms 1.42% VoronoiDataWriter::Visit 729ms 1.38% 72.72% 729ms 1.38% tetgen::tetgenmesh::oppo 231ms 0.44% 73.16% 686ms 1.30% tetgen::tetgenmesh::sym 671ms 1.27% 74.43% 671ms 1.27% [libchaste_mesh.so] 0 0% 74.43% 658ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 607ms 1.15% 75.58% 607ms 1.15% tetgen::tetgenmesh::triface::operator= 588ms 1.11% 76.70% 588ms 1.11% AbstractElement::IsDeleted 6ms 0.011% 76.71% 583ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 76.71% 578ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 247ms 0.47% 77.18% 555ms 1.05% AbstractElement::GetNodeLocation 7ms 0.013% 77.19% 542ms 1.03% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 535ms 1.01% 78.20% 535ms 1.01% Node::rGetLocation 526ms 1% 79.20% 526ms 1% std::vector::size (inline) 27ms 0.051% 79.25% 505ms 0.96% tetgen::tetgenmesh::queue::push 48ms 0.091% 79.34% 494ms 0.94% tetgen::tetgenmesh::enext2fnext 289ms 0.55% 79.89% 492ms 0.93% tetgen::tetgenmesh::fnextself 12ms 0.023% 79.92% 490ms 0.93% AbstractTetrahedralElement::CalculateJacobian 46ms 0.087% 80.00% 489ms 0.93% __atan2 166ms 0.31% 80.32% 481ms 0.91% tetgen::tetgenmesh::bond 9ms 0.017% 80.33% 479ms 0.91% boost::numeric::ublas::vector_assign (inline) 293ms 0.56% 80.89% 478ms 0.91% tetgen::tetgenmesh::link::add 10ms 0.019% 80.91% 476ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 457ms 0.87% 81.78% 457ms 0.87% tetgen::tetgenmesh::decode 352ms 0.67% 82.44% 438ms 0.83% __ieee754_atan2_fma 0 0% 82.44% 426ms 0.81% std::set::find (inline) 20ms 0.038% 82.48% 419ms 0.79% Element::CalculateCircumsphere 31ms 0.059% 82.54% 408ms 0.77% tetgen::tetgenmesh::enextfnext 0 0% 82.54% 401ms 0.76% boost::numeric::ublas::inner_prod (inline) 38ms 0.072% 82.61% 398ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.61% 398ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 24ms 0.046% 82.66% 364ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 39ms 0.074% 82.73% 363ms 0.69% AbstractTetrahedralElement::RefreshJacobian 10ms 0.019% 82.75% 361ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 195ms 0.37% 83.12% 358ms 0.68% AbstractTetrahedralMesh::GetElement 0 0% 83.12% 357ms 0.68% std::insert_iterator::operator= (inline) 356ms 0.68% 83.79% 356ms 0.68% tetgen::tetgenmesh::org 8ms 0.015% 83.81% 344ms 0.65% VertexElement::~VertexElement 5ms 0.0095% 83.82% 335ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.0057% 83.83% 329ms 0.62% Cell::GetCellId 2ms 0.0038% 83.83% 329ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 325ms 0.62% 84.45% 325ms 0.62% std::_Rb_tree_decrement 138ms 0.26% 84.71% 318ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 316ms 0.6% 85.31% 316ms 0.6% boost::numeric::ublas::c_vector::operator() 1ms 0.0019% 85.31% 316ms 0.6% std::_Rb_tree::_M_insert_unique_ (inline) 77ms 0.15% 85.45% 309ms 0.59% __dynamic_cast 308ms 0.58% 86.04% 308ms 0.58% tetgen::tetgenmesh::encode 0 0% 86.04% 306ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 10ms 0.019% 86.06% 304ms 0.58% std::vector::insert (inline) 77ms 0.15% 86.20% 303ms 0.57% boost::numeric::ublas::indexing_vector_assign 0 0% 86.20% 289ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.0038% 86.21% 279ms 0.53% Element::~Element 111ms 0.21% 86.42% 278ms 0.53% Inverse 2ms 0.0038% 86.42% 277ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 2ms 0.0038% 86.42% 265ms 0.5% VertexMesh::GetVolumeOfElement