File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 63912ms, 87.86% of 72746ms total Dropped 867 nodes (cum <= 363.73ms) flat flat% sum% cum cum% 0 0% 0% 72688ms 99.92% __libc_start_call_main 0 0% 0% 72688ms 99.92% __libc_start_main_impl 0 0% 0% 72688ms 99.92% _start 0 0% 0% 72671ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 72671ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 72671ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 72671ms 99.90% main 0 0% 0% 72632ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 72632ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 72632ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 72345ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0% 60852ms 83.65% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0014% 0.0014% 60802ms 83.58% MeshBasedCellPopulation::Update 0 0% 0.0014% 37784ms 51.94% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0014% 37784ms 51.94% MeshBasedCellPopulation::TessellateIfNeeded 337ms 0.46% 0.46% 32653ms 44.89% VertexMesh::VertexMesh 0 0% 0.46% 18359ms 25.24% MutableMesh::ReMesh 573ms 0.79% 1.25% 14516ms 19.95% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.0027% 1.26% 12974ms 17.83% tetgen::tetrahedralize 2ms 0.0027% 1.26% 12833ms 17.64% tetgen::tetgenmesh::delaunizevertices 6ms 0.0082% 1.27% 12825ms 17.63% tetgen::tetgenmesh::incrflipdelaunay 28ms 0.038% 1.30% 12218ms 16.80% std::set::insert (inline) 203ms 0.28% 1.58% 11698ms 16.08% std::_Rb_tree::_M_insert_unique 586ms 0.81% 2.39% 11343ms 15.59% tetgen::tetgenmesh::lawson 3045ms 4.19% 6.57% 10930ms 15.02% std::_Rb_tree::_M_lower_bound (inline) 452ms 0.62% 7.20% 10743ms 14.77% VertexElement::AddFace 223ms 0.31% 7.50% 9952ms 13.68% std::_Rb_tree::find (inline) 0 0% 7.50% 9423ms 12.95% std::set::count (inline) 8340ms 11.46% 18.97% 8340ms 11.46% std::_Rb_tree_increment 124ms 0.17% 19.14% 7349ms 10.10% std::less::operator() (inline) 7294ms 10.03% 29.16% 7294ms 10.03% std::operator< (inline) 239ms 0.33% 29.49% 6788ms 9.33% std::_Rb_tree::_M_insert_ (inline) 191ms 0.26% 29.76% 6605ms 9.08% operator new 1131ms 1.55% 31.31% 6354ms 8.73% __GI___libc_malloc 0 0% 31.31% 6304ms 8.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.31% 6118ms 8.41% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.0096% 31.32% 6084ms 8.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0027% 31.32% 5989ms 8.23% std::set_intersection (inline) 280ms 0.38% 31.71% 5987ms 8.23% std::__set_intersection 36ms 0.049% 31.76% 5397ms 7.42% Node::AddElement 8ms 0.011% 31.77% 5323ms 7.32% std::_Rb_tree::~_Rb_tree (inline) 2367ms 3.25% 35.02% 5314ms 7.30% std::_Rb_tree::_M_erase 51ms 0.07% 35.09% 5308ms 7.30% std::__new_allocator::allocate (inline) 0 0% 35.09% 5282ms 7.26% std::allocator_traits::allocate (inline) 0 0% 35.09% 5242ms 7.21% std::set::~set (inline) 194ms 0.27% 35.36% 5206ms 7.16% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 35.36% 5171ms 7.11% VertexMesh::~VertexMesh 4ms 0.0055% 35.36% 5078ms 6.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0014% 35.37% 5033ms 6.92% MeshBasedCellPopulation::UpdateNodePairs 1181ms 1.62% 36.99% 5030ms 6.91% std::_Rb_tree::_M_get_insert_unique_pos 5019ms 6.90% 43.89% 5019ms 6.90% std::_Rb_tree::_S_right (inline) 0 0% 43.89% 5009ms 6.89% AbstractCellPopulation::WriteResultsToFiles 1352ms 1.86% 45.75% 4925ms 6.77% __GI___libc_free 3531ms 4.85% 50.60% 4904ms 6.74% _int_malloc 9ms 0.012% 50.61% 4835ms 6.65% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.015% 50.63% 4316ms 5.93% TetrahedralMesh::ImportFromMesher 136ms 0.19% 50.82% 4280ms 5.88% std::__new_allocator::deallocate (inline) 0 0% 50.82% 4251ms 5.84% std::allocator_traits::deallocate (inline) 0 0% 50.82% 4241ms 5.83% std::_Rb_tree::_M_create_node (inline) 0 0% 50.82% 4204ms 5.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.82% 4189ms 5.76% std::_Rb_tree::_M_get_node (inline) 67ms 0.092% 50.91% 4078ms 5.61% MutableElement::AddNode 225ms 0.31% 51.22% 3631ms 4.99% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1173ms 1.61% 52.83% 3570ms 4.91% _int_free 113ms 0.16% 52.98% 3564ms 4.90% tetgen::tetgenmesh::insphere_sos 4ms 0.0055% 52.99% 3454ms 4.75% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3167ms 4.35% 57.34% 3438ms 4.73% tetgen::insphere 2ms 0.0027% 57.35% 3435ms 4.72% std::_Rb_tree_iterator::operator++ (inline) 233ms 0.32% 57.67% 3385ms 4.65% Node::~Node 261ms 0.36% 58.03% 3157ms 4.34% VertexMesh::Clear 199ms 0.27% 58.30% 2837ms 3.90% tetgen::tetgenmesh::flip23 2690ms 3.70% 62.00% 2690ms 3.70% Node::GetIndex 2458ms 3.38% 65.38% 2458ms 3.38% std::_Rb_tree_insert_and_rebalance 1586ms 2.18% 67.56% 2441ms 3.36% malloc_consolidate 23ms 0.032% 67.59% 2291ms 3.15% std::_Vector_base::_M_deallocate (inline) 2ms 0.0027% 67.59% 2201ms 3.03% Element::Element 0 0% 67.59% 2164ms 2.97% std::vector::~vector (inline) 6ms 0.0082% 67.60% 2133ms 2.93% _int_free_maybe_consolidate 0 0% 67.60% 2128ms 2.93% std::_Vector_base::~_Vector_base (inline) 0 0% 67.60% 1992ms 2.74% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.60% 1983ms 2.73% std::_Rb_tree::_M_put_node (inline) 1838ms 2.53% 70.12% 1838ms 2.53% unlink_chunk 6ms 0.0082% 70.13% 1800ms 2.47% Element::RegisterWithNodes (inline) 159ms 0.22% 70.35% 1755ms 2.41% tetgen::tetgenmesh::flip32 237ms 0.33% 70.68% 1660ms 2.28% TetrahedralMesh::Clear 69ms 0.095% 70.77% 1527ms 2.10% std::map::operator[] 1ms 0.0014% 70.77% 1522ms 2.09% VertexMesh::GenerateVerticesFromElementCircumcentres 1335ms 1.84% 72.61% 1420ms 1.95% tetgen::orient3d 0 0% 72.61% 1368ms 1.88% std::_Rb_tree::lower_bound (inline) 0 0% 72.61% 1368ms 1.88% std::map::lower_bound (inline) 1ms 0.0014% 72.61% 1280ms 1.76% VoronoiDataWriter::Visit 66ms 0.091% 72.70% 1272ms 1.75% std::vector::_M_realloc_insert 1123ms 1.54% 74.24% 1259ms 1.73% AbstractElement::GetNodeGlobalIndex 169ms 0.23% 74.48% 1246ms 1.71% tetgen::tetgenmesh::enqueueflipface 37ms 0.051% 74.53% 1226ms 1.69% tetgen::tetgenmesh::locate 91ms 0.13% 74.65% 1131ms 1.55% tetgen::tetgenmesh::preciselocate 4ms 0.0055% 74.66% 1097ms 1.51% std::_Vector_base::_M_allocate (inline) 144ms 0.2% 74.86% 1080ms 1.48% std::vector::push_back (inline) 1058ms 1.45% 76.31% 1058ms 1.45% Node::rGetLocation 468ms 0.64% 76.95% 1047ms 1.44% AbstractElement::GetNodeLocation 1ms 0.0014% 76.96% 1041ms 1.43% TetrahedralMesh::RefreshJacobianCachedData 956ms 1.31% 78.27% 956ms 1.31% AbstractElement::IsDeleted 13ms 0.018% 78.29% 881ms 1.21% AbstractTetrahedralElement::CalculateJacobian 9ms 0.012% 78.30% 880ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 858ms 1.18% 79.48% 858ms 1.18% tetgen::tetgenmesh::triface::triface 483ms 0.66% 80.14% 853ms 1.17% tetgen::tetgenmesh::fnextself 0 0% 80.14% 765ms 1.05% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.022% 80.17% 763ms 1.05% boost::numeric::ublas::vector_assign (inline) 23ms 0.032% 80.20% 727ms 1% Element::CalculateCircumsphere 18ms 0.025% 80.22% 723ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 16ms 0.022% 80.24% 702ms 0.97% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 43ms 0.059% 80.30% 694ms 0.95% AbstractTetrahedralElement::RefreshJacobian 685ms 0.94% 81.24% 685ms 0.94% [libchaste_mesh.so] 656ms 0.9% 82.15% 656ms 0.9% tetgen::tetgenmesh::triface::operator= 639ms 0.88% 83.02% 639ms 0.88% tetgen::tetgenmesh::oppo 41ms 0.056% 83.08% 638ms 0.88% __atan2 476ms 0.65% 83.74% 597ms 0.82% __ieee754_atan2_fma 566ms 0.78% 84.51% 566ms 0.78% std::vector::size (inline) 40ms 0.055% 84.57% 547ms 0.75% tetgen::tetgenmesh::enextfnext 11ms 0.015% 84.58% 530ms 0.73% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.58% 524ms 0.72% std::set::find (inline) 45ms 0.062% 84.65% 522ms 0.72% tetgen::tetgenmesh::enext2fnext 0 0% 84.65% 513ms 0.71% boost::numeric::ublas::inner_prod (inline) 6ms 0.0082% 84.65% 506ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 84.65% 506ms 0.7% std::insert_iterator::operator= (inline) 35ms 0.048% 84.70% 500ms 0.69% boost::numeric::ublas::vector_scalar_binary::evaluate 328ms 0.45% 85.15% 485ms 0.67% tetgen::tetgenmesh::sym 0 0% 85.15% 480ms 0.66% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 153ms 0.21% 85.36% 479ms 0.66% boost::numeric::ublas::indexing_vector_assign 0 0% 85.36% 463ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 448ms 0.62% 85.98% 448ms 0.62% boost::numeric::ublas::c_vector::operator() 6ms 0.0082% 85.99% 437ms 0.6% boost::numeric::ublas::c_vector::operator= (inline) 21ms 0.029% 86.02% 435ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 7ms 0.0096% 86.03% 425ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 417ms 0.57% 86.60% 417ms 0.57% tetgen::tetgenmesh::org 0 0% 86.60% 407ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 177ms 0.24% 86.84% 406ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 7ms 0.0096% 86.85% 399ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 106ms 0.15% 87.00% 395ms 0.54% __dynamic_cast 0 0% 87.00% 392ms 0.54% Cell::GetCellId 392ms 0.54% 87.54% 392ms 0.54% std::_Rb_tree_decrement 25ms 0.034% 87.57% 388ms 0.53% tetgen::tetgenmesh::queue::push 208ms 0.29% 87.86% 383ms 0.53% AbstractTetrahedralMesh::GetElement