File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 68917ms, 86.53% of 79647ms total Dropped 909 nodes (cum <= 398.24ms) flat flat% sum% cum cum% 0 0% 0% 79583ms 99.92% __libc_start_call_main 0 0% 0% 79583ms 99.92% __libc_start_main_impl 0 0% 0% 79583ms 99.92% _start 0 0% 0% 79564ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 79564ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 79564ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 79564ms 99.90% main 0 0% 0% 79521ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 79521ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 79521ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 79212ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0% 68118ms 85.52% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 68057ms 85.45% MeshBasedCellPopulation::Update 0 0% 0% 41500ms 52.10% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 41499ms 52.10% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 303ms 0.38% 0.38% 35771ms 44.91% VertexMesh::VertexMesh 0 0% 0.38% 21586ms 27.10% MutableMesh::ReMesh 0 0% 0.38% 15957ms 20.03% tetgen::tetrahedralize 3ms 0.0038% 0.38% 15808ms 19.85% tetgen::tetgenmesh::delaunizevertices 15ms 0.019% 0.4% 15800ms 19.84% tetgen::tetgenmesh::incrflipdelaunay 600ms 0.75% 1.16% 15514ms 19.48% TetrahedralMesh::EdgeIterator::operator++ 526ms 0.66% 1.82% 14176ms 17.80% tetgen::tetgenmesh::lawson 34ms 0.043% 1.86% 13344ms 16.75% std::set::insert (inline) 229ms 0.29% 2.15% 12897ms 16.19% std::_Rb_tree::_M_insert_unique 537ms 0.67% 2.82% 11614ms 14.58% VertexElement::AddFace 3358ms 4.22% 7.04% 11115ms 13.96% std::_Rb_tree::_M_lower_bound (inline) 248ms 0.31% 7.35% 10271ms 12.90% std::_Rb_tree::find (inline) 0 0% 7.35% 9673ms 12.14% std::set::count (inline) 8737ms 10.97% 18.32% 8737ms 10.97% std::_Rb_tree_increment 193ms 0.24% 18.56% 7726ms 9.70% operator new 322ms 0.4% 18.96% 7536ms 9.46% std::_Rb_tree::_M_insert_ (inline) 1303ms 1.64% 20.60% 7452ms 9.36% __GI___libc_malloc 126ms 0.16% 20.76% 7301ms 9.17% std::less::operator() (inline) 7245ms 9.10% 29.86% 7245ms 9.10% std::operator< (inline) 1ms 0.0013% 29.86% 7030ms 8.83% std::set_intersection (inline) 337ms 0.42% 30.28% 7029ms 8.83% std::__set_intersection 0 0% 30.28% 6454ms 8.10% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.28% 6268ms 7.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0038% 30.28% 6245ms 7.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 35ms 0.044% 30.33% 6178ms 7.76% std::__new_allocator::allocate (inline) 178ms 0.22% 30.55% 6168ms 7.74% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 30.55% 6160ms 7.73% std::allocator_traits::allocate (inline) 71ms 0.089% 30.64% 5990ms 7.52% Node::AddElement 0 0% 30.64% 5774ms 7.25% VertexMesh::~VertexMesh 4187ms 5.26% 35.90% 5740ms 7.21% _int_malloc 1508ms 1.89% 37.79% 5656ms 7.10% __GI___libc_free 5ms 0.0063% 37.80% 5537ms 6.95% std::_Rb_tree::~_Rb_tree (inline) 2179ms 2.74% 40.53% 5530ms 6.94% std::_Rb_tree::_M_erase 0 0% 40.53% 5468ms 6.87% std::set::~set (inline) 1378ms 1.73% 42.26% 5410ms 6.79% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 42.26% 5364ms 6.73% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.01% 42.27% 5237ms 6.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.018% 42.29% 5188ms 6.51% MeshBasedCellPopulation::SpringIterator::operator++ 5185ms 6.51% 48.80% 5185ms 6.51% std::_Rb_tree::_S_right (inline) 0 0% 48.80% 4951ms 6.22% std::_Rb_tree::_M_create_node (inline) 132ms 0.17% 48.97% 4940ms 6.20% std::__new_allocator::deallocate (inline) 0 0% 48.97% 4930ms 6.19% std::allocator_traits::deallocate (inline) 0 0% 48.97% 4912ms 6.17% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.97% 4897ms 6.15% std::_Rb_tree::_M_get_node (inline) 86ms 0.11% 49.07% 4570ms 5.74% MutableElement::AddNode 0 0% 49.07% 4461ms 5.60% AbstractCellPopulation::WriteResultsToFiles 41ms 0.051% 49.13% 4461ms 5.60% TetrahedralMesh::ImportFromMesher 1392ms 1.75% 50.87% 4144ms 5.20% _int_free 115ms 0.14% 51.02% 3863ms 4.85% tetgen::tetgenmesh::insphere_sos 3440ms 4.32% 55.34% 3735ms 4.69% tetgen::insphere 272ms 0.34% 55.68% 3655ms 4.59% Node::~Node 140ms 0.18% 55.85% 3481ms 4.37% tetgen::tetgenmesh::flip23 254ms 0.32% 56.17% 3458ms 4.34% VertexMesh::Clear 205ms 0.26% 56.43% 3095ms 3.89% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 7ms 0.0088% 56.44% 3044ms 3.82% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0013% 56.44% 2914ms 3.66% std::_Rb_tree_iterator::operator++ (inline) 1972ms 2.48% 58.92% 2810ms 3.53% malloc_consolidate 2775ms 3.48% 62.40% 2775ms 3.48% Node::GetIndex 33ms 0.041% 62.44% 2650ms 3.33% std::_Vector_base::_M_deallocate (inline) 0 0% 62.44% 2531ms 3.18% std::vector::~vector (inline) 115ms 0.14% 62.59% 2522ms 3.17% tetgen::tetgenmesh::flip32 1ms 0.0013% 62.59% 2482ms 3.12% std::_Vector_base::~_Vector_base (inline) 3ms 0.0038% 62.59% 2449ms 3.07% _int_free_maybe_consolidate 2410ms 3.03% 65.62% 2410ms 3.03% std::_Rb_tree_insert_and_rebalance 4ms 0.005% 65.62% 2335ms 2.93% Element::Element 0 0% 65.62% 2320ms 2.91% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.62% 2313ms 2.90% std::_Rb_tree::_M_put_node (inline) 4ms 0.005% 65.63% 1967ms 2.47% Element::RegisterWithNodes (inline) 1927ms 2.42% 68.05% 1927ms 2.42% unlink_chunk 219ms 0.27% 68.32% 1894ms 2.38% tetgen::tetgenmesh::enqueueflipface 4ms 0.005% 68.33% 1789ms 2.25% VertexMesh::GenerateVerticesFromElementCircumcentres 79ms 0.099% 68.43% 1608ms 2.02% TetrahedralMesh::Clear 1517ms 1.90% 70.33% 1599ms 2.01% tetgen::orient3d 1321ms 1.66% 71.99% 1539ms 1.93% AbstractElement::GetNodeGlobalIndex 73ms 0.092% 72.08% 1455ms 1.83% std::map::operator[] 67ms 0.084% 72.16% 1435ms 1.80% std::vector::_M_realloc_insert 38ms 0.048% 72.21% 1302ms 1.63% tetgen::tetgenmesh::locate 0 0% 72.21% 1289ms 1.62% std::_Rb_tree::lower_bound (inline) 0 0% 72.21% 1289ms 1.62% std::map::lower_bound (inline) 6ms 0.0075% 72.22% 1269ms 1.59% std::_Vector_base::_M_allocate (inline) 155ms 0.19% 72.41% 1222ms 1.53% std::vector::push_back (inline) 83ms 0.1% 72.52% 1221ms 1.53% tetgen::tetgenmesh::preciselocate 1212ms 1.52% 74.04% 1212ms 1.52% Node::rGetLocation 1179ms 1.48% 75.52% 1179ms 1.48% AbstractElement::IsDeleted 511ms 0.64% 76.16% 1150ms 1.44% AbstractElement::GetNodeLocation 0 0% 76.16% 1136ms 1.43% VoronoiDataWriter::Visit 0 0% 76.16% 1128ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 1072ms 1.35% 77.51% 1072ms 1.35% tetgen::tetgenmesh::oppo 1056ms 1.33% 78.83% 1056ms 1.33% tetgen::tetgenmesh::triface::triface 10ms 0.013% 78.85% 897ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.02% 78.87% 869ms 1.09% AbstractTetrahedralElement::CalculateJacobian 846ms 1.06% 79.93% 846ms 1.06% [libchaste_mesh.so] 777ms 0.98% 80.90% 777ms 0.98% std::vector::size (inline) 13ms 0.016% 80.92% 771ms 0.97% Element::CalculateCircumsphere 1ms 0.0013% 80.92% 770ms 0.97% AbstractTwoBodyInteractionForce::AddForceContribution 291ms 0.37% 81.29% 733ms 0.92% tetgen::tetgenmesh::sym 16ms 0.02% 81.31% 714ms 0.9% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 692ms 0.87% 82.18% 692ms 0.87% tetgen::tetgenmesh::triface::operator= 50ms 0.063% 82.24% 682ms 0.86% AbstractTetrahedralElement::RefreshJacobian 375ms 0.47% 82.71% 668ms 0.84% tetgen::tetgenmesh::fnextself 58ms 0.073% 82.78% 656ms 0.82% __atan2 48ms 0.06% 82.84% 626ms 0.79% tetgen::tetgenmesh::enext2fnext 37ms 0.046% 82.89% 604ms 0.76% tetgen::tetgenmesh::queue::push 15ms 0.019% 82.91% 595ms 0.75% boost::numeric::ublas::vector_assign (inline) 473ms 0.59% 83.50% 592ms 0.74% __ieee754_atan2_fma 0 0% 83.50% 590ms 0.74% std::set::find (inline) 11ms 0.014% 83.52% 581ms 0.73% boost::numeric::ublas::c_vector::c_vector (inline) 47ms 0.059% 83.58% 578ms 0.73% tetgen::tetgenmesh::enextfnext 346ms 0.43% 84.01% 567ms 0.71% tetgen::tetgenmesh::link::add 220ms 0.28% 84.29% 525ms 0.66% tetgen::tetgenmesh::bond 15ms 0.019% 84.30% 521ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.30% 483ms 0.61% boost::numeric::ublas::inner_prod (inline) 2ms 0.0025% 84.31% 482ms 0.61% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 48ms 0.06% 84.37% 480ms 0.6% boost::numeric::ublas::vector_scalar_binary::evaluate 38ms 0.048% 84.41% 476ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.41% 476ms 0.6% std::insert_iterator::operator= (inline) 2ms 0.0025% 84.42% 467ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 459ms 0.58% 84.99% 459ms 0.58% tetgen::tetgenmesh::decode 233ms 0.29% 85.29% 447ms 0.56% AbstractTetrahedralMesh::GetElement 0 0% 85.29% 438ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 7ms 0.0088% 85.30% 431ms 0.54% VertexElement::~VertexElement 126ms 0.16% 85.45% 430ms 0.54% __dynamic_cast 424ms 0.53% 85.99% 424ms 0.53% tetgen::tetgenmesh::org 415ms 0.52% 86.51% 415ms 0.52% std::_Rb_tree_decrement 5ms 0.0063% 86.51% 411ms 0.52% Cell::GetCellId 0 0% 86.51% 410ms 0.51% std::_Rb_tree::_M_insert_unique_ (inline) 5ms 0.0063% 86.52% 408ms 0.51% VertexMesh::GetVolumeOfElement 7ms 0.0088% 86.53% 407ms 0.51% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 86.53% 406ms 0.51% VertexMeshWriter::WriteVtkUsingMesh