File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 65289ms, 88.30% of 73939ms total Dropped 872 nodes (cum <= 369.69ms) flat flat% sum% cum cum% 0 0% 0% 73882ms 99.92% __libc_start_call_main 0 0% 0% 73882ms 99.92% __libc_start_main_impl 0 0% 0% 73882ms 99.92% _start 0 0% 0% 73867ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 73867ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 73867ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 73867ms 99.90% main 0 0% 0% 73828ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 73828ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 73828ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 73544ms 99.47% AbstractCellBasedSimulation::Solve 0 0% 0% 62270ms 84.22% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 62216ms 84.15% MeshBasedCellPopulation::Update 0 0% 0% 38756ms 52.42% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 38754ms 52.41% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 315ms 0.43% 0.43% 33277ms 45.01% VertexMesh::VertexMesh 0 0% 0.43% 18889ms 25.55% MutableMesh::ReMesh 540ms 0.73% 1.16% 14359ms 19.42% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0014% 1.16% 13327ms 18.02% tetgen::tetrahedralize 4ms 0.0054% 1.16% 13193ms 17.84% tetgen::tetgenmesh::delaunizevertices 10ms 0.014% 1.18% 13183ms 17.83% tetgen::tetgenmesh::incrflipdelaunay 36ms 0.049% 1.23% 12491ms 16.89% std::set::insert (inline) 211ms 0.29% 1.51% 12040ms 16.28% std::_Rb_tree::_M_insert_unique 565ms 0.76% 2.27% 11713ms 15.84% tetgen::tetgenmesh::lawson 3010ms 4.07% 6.35% 10910ms 14.76% std::_Rb_tree::_M_lower_bound (inline) 507ms 0.69% 7.03% 10876ms 14.71% VertexElement::AddFace 219ms 0.3% 7.33% 9859ms 13.33% std::_Rb_tree::find (inline) 0 0% 7.33% 9334ms 12.62% std::set::count (inline) 8582ms 11.61% 18.93% 8582ms 11.61% std::_Rb_tree_increment 106ms 0.14% 19.08% 7341ms 9.93% std::less::operator() (inline) 7301ms 9.87% 28.95% 7301ms 9.87% std::operator< (inline) 264ms 0.36% 29.31% 6987ms 9.45% std::_Rb_tree::_M_insert_ (inline) 206ms 0.28% 29.59% 6985ms 9.45% operator new 1147ms 1.55% 31.14% 6718ms 9.09% __GI___libc_malloc 4ms 0.0054% 31.14% 6160ms 8.33% std::set_intersection (inline) 334ms 0.45% 31.60% 6156ms 8.33% std::__set_intersection 0 0% 31.60% 6082ms 8.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.60% 5906ms 7.99% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0041% 31.60% 5882ms 7.96% AbstractNumericalMethod::ComputeForcesIncludingDamping 43ms 0.058% 31.66% 5581ms 7.55% std::__new_allocator::allocate (inline) 40ms 0.054% 31.71% 5575ms 7.54% Node::AddElement 0 0% 31.71% 5561ms 7.52% std::allocator_traits::allocate (inline) 0 0% 31.71% 5517ms 7.46% VertexMesh::~VertexMesh 10ms 0.014% 31.73% 5503ms 7.44% std::_Rb_tree::~_Rb_tree (inline) 2472ms 3.34% 35.07% 5491ms 7.43% std::_Rb_tree::_M_erase 0 0% 35.07% 5417ms 7.33% std::set::~set (inline) 196ms 0.27% 35.33% 5369ms 7.26% std::_Rb_tree_const_iterator::operator++ (inline) 3691ms 4.99% 40.33% 5206ms 7.04% _int_malloc 1254ms 1.70% 42.02% 5130ms 6.94% std::_Rb_tree::_M_get_insert_unique_pos 5075ms 6.86% 48.89% 5075ms 6.86% std::_Rb_tree::_S_right (inline) 1369ms 1.85% 50.74% 5074ms 6.86% __GI___libc_free 0 0% 50.74% 5018ms 6.79% AbstractCellPopulation::WriteResultsToFiles 0 0% 50.74% 4941ms 6.68% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0068% 50.74% 4905ms 6.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.016% 50.76% 4750ms 6.42% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 50.76% 4523ms 6.12% std::_Rb_tree::_M_create_node (inline) 0 0% 50.76% 4482ms 6.06% std::_Rb_tree::_Alloc_node::operator() (inline) 23ms 0.031% 50.79% 4478ms 6.06% TetrahedralMesh::ImportFromMesher 0 0% 50.79% 4474ms 6.05% std::_Rb_tree::_M_get_node (inline) 132ms 0.18% 50.97% 4428ms 5.99% std::__new_allocator::deallocate (inline) 0 0% 50.97% 4410ms 5.96% std::allocator_traits::deallocate (inline) 66ms 0.089% 51.06% 4191ms 5.67% MutableElement::AddNode 230ms 0.31% 51.37% 3720ms 5.03% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1204ms 1.63% 53.00% 3702ms 5.01% _int_free 256ms 0.35% 53.35% 3618ms 4.89% Node::~Node 0 0% 53.35% 3525ms 4.77% std::_Rb_tree_iterator::operator++ (inline) 7ms 0.0095% 53.35% 3485ms 4.71% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 111ms 0.15% 53.50% 3468ms 4.69% tetgen::tetgenmesh::insphere_sos 310ms 0.42% 53.92% 3393ms 4.59% VertexMesh::Clear 3048ms 4.12% 58.05% 3340ms 4.52% tetgen::insphere 219ms 0.3% 58.34% 2740ms 3.71% tetgen::tetgenmesh::flip23 2639ms 3.57% 61.91% 2639ms 3.57% Node::GetIndex 1744ms 2.36% 64.27% 2563ms 3.47% malloc_consolidate 21ms 0.028% 64.30% 2425ms 3.28% std::_Vector_base::_M_deallocate (inline) 2380ms 3.22% 67.52% 2380ms 3.22% std::_Rb_tree_insert_and_rebalance 0 0% 67.52% 2274ms 3.08% std::vector::~vector (inline) 3ms 0.0041% 67.52% 2261ms 3.06% Element::Element 8ms 0.011% 67.53% 2245ms 3.04% _int_free_maybe_consolidate 2ms 0.0027% 67.54% 2241ms 3.03% std::_Vector_base::~_Vector_base (inline) 164ms 0.22% 67.76% 2050ms 2.77% tetgen::tetgenmesh::flip32 0 0% 67.76% 2016ms 2.73% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.76% 2006ms 2.71% std::_Rb_tree::_M_put_node (inline) 3ms 0.0041% 67.76% 1913ms 2.59% Element::RegisterWithNodes (inline) 1897ms 2.57% 70.33% 1897ms 2.57% unlink_chunk 275ms 0.37% 70.70% 1740ms 2.35% TetrahedralMesh::Clear 1ms 0.0014% 70.70% 1634ms 2.21% VertexMesh::GenerateVerticesFromElementCircumcentres 67ms 0.091% 70.79% 1566ms 2.12% std::map::operator[] 1350ms 1.83% 72.62% 1427ms 1.93% tetgen::orient3d 0 0% 72.62% 1395ms 1.89% std::_Rb_tree::lower_bound (inline) 0 0% 72.62% 1395ms 1.89% std::map::lower_bound (inline) 77ms 0.1% 72.72% 1332ms 1.80% std::vector::_M_realloc_insert 192ms 0.26% 72.98% 1330ms 1.80% tetgen::tetgenmesh::enqueueflipface 0 0% 72.98% 1267ms 1.71% VoronoiDataWriter::Visit 1089ms 1.47% 74.45% 1242ms 1.68% AbstractElement::GetNodeGlobalIndex 34ms 0.046% 74.50% 1231ms 1.66% tetgen::tetgenmesh::locate 121ms 0.16% 74.66% 1155ms 1.56% tetgen::tetgenmesh::preciselocate 2ms 0.0027% 74.67% 1089ms 1.47% std::_Vector_base::_M_allocate (inline) 132ms 0.18% 74.84% 1086ms 1.47% std::vector::push_back (inline) 1064ms 1.44% 76.28% 1064ms 1.44% Node::rGetLocation 1ms 0.0014% 76.28% 1054ms 1.43% TetrahedralMesh::RefreshJacobianCachedData 1033ms 1.40% 77.68% 1033ms 1.40% tetgen::tetgenmesh::triface::triface 446ms 0.6% 78.28% 1008ms 1.36% AbstractElement::GetNodeLocation 985ms 1.33% 79.62% 985ms 1.33% AbstractElement::IsDeleted 440ms 0.6% 80.21% 941ms 1.27% tetgen::tetgenmesh::fnextself 845ms 1.14% 81.35% 845ms 1.14% tetgen::tetgenmesh::triface::operator= 10ms 0.014% 81.37% 822ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.019% 81.39% 797ms 1.08% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0014% 81.39% 754ms 1.02% AbstractTwoBodyInteractionForce::AddForceContribution 22ms 0.03% 81.42% 720ms 0.97% Element::CalculateCircumsphere 21ms 0.028% 81.45% 715ms 0.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 14ms 0.019% 81.47% 669ms 0.9% boost::numeric::ublas::vector_assign (inline) 640ms 0.87% 82.33% 640ms 0.87% [libchaste_mesh.so] 41ms 0.055% 82.39% 635ms 0.86% AbstractTetrahedralElement::RefreshJacobian 633ms 0.86% 83.24% 633ms 0.86% std::vector::size (inline) 51ms 0.069% 83.31% 616ms 0.83% __atan2 11ms 0.015% 83.33% 609ms 0.82% boost::numeric::ublas::c_vector::c_vector (inline) 51ms 0.069% 83.40% 596ms 0.81% tetgen::tetgenmesh::enextfnext 50ms 0.068% 83.46% 577ms 0.78% tetgen::tetgenmesh::enext2fnext 569ms 0.77% 84.23% 569ms 0.77% tetgen::tetgenmesh::oppo 467ms 0.63% 84.86% 564ms 0.76% __ieee754_atan2_fma 0 0% 84.86% 515ms 0.7% std::set::find (inline) 0 0% 84.86% 483ms 0.65% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.86% 470ms 0.64% boost::numeric::ublas::inner_prod (inline) 7ms 0.0095% 84.87% 467ms 0.63% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.02% 84.89% 463ms 0.63% VertexMesh::CalculateUnitNormalToFaceWithArea 29ms 0.039% 84.93% 460ms 0.62% boost::numeric::ublas::vector_scalar_binary::evaluate 31ms 0.042% 84.98% 441ms 0.6% tetgen::tetgenmesh::queue::push 131ms 0.18% 85.15% 439ms 0.59% boost::numeric::ublas::indexing_vector_assign 0 0% 85.15% 435ms 0.59% std::insert_iterator::operator= (inline) 282ms 0.38% 85.53% 427ms 0.58% tetgen::tetgenmesh::sym 21ms 0.028% 85.56% 426ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 8ms 0.011% 85.57% 416ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 99ms 0.13% 85.71% 412ms 0.56% __dynamic_cast 245ms 0.33% 86.04% 409ms 0.55% AbstractTetrahedralMesh::GetElement 317ms 0.43% 86.47% 407ms 0.55% tetgen::tetgenmesh::link::add 0 0% 86.47% 406ms 0.55% VertexMeshWriter::WriteVtkUsingMesh 9ms 0.012% 86.48% 401ms 0.54% std::vector::insert (inline) 394ms 0.53% 87.01% 394ms 0.53% boost::numeric::ublas::c_vector::operator() 0 0% 87.01% 392ms 0.53% std::_Rb_tree::_M_insert_unique_ (inline) 181ms 0.24% 87.26% 389ms 0.53% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0027% 87.26% 386ms 0.52% Cell::GetCellId 386ms 0.52% 87.78% 386ms 0.52% tetgen::tetgenmesh::org 382ms 0.52% 88.30% 382ms 0.52% std::_Rb_tree_decrement 2ms 0.0027% 88.30% 381ms 0.52% boost::numeric::ublas::c_vector::operator= (inline)