File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 38591ms, 86.82% of 44451ms total Dropped 775 nodes (cum <= 222.25ms) flat flat% sum% cum cum% 0 0% 0% 44400ms 99.89% __libc_start_call_main 0 0% 0% 44400ms 99.89% __libc_start_main_impl 0 0% 0% 44400ms 99.89% _start 0 0% 0% 44388ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 44388ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 44388ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 44388ms 99.86% main 0 0% 0% 44355ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 44355ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 44355ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 44197ms 99.43% AbstractCellBasedSimulation::Solve 0 0% 0% 37921ms 85.31% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 37891ms 85.24% MeshBasedCellPopulation::Update 0 0% 0% 23260ms 52.33% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 23259ms 52.33% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 137ms 0.31% 0.31% 20041ms 45.09% VertexMesh::VertexMesh 0 0% 0.31% 11593ms 26.08% MutableMesh::ReMesh 458ms 1.03% 1.34% 9271ms 20.86% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.34% 8472ms 19.06% tetgen::tetrahedralize 0 0% 1.34% 8395ms 18.89% tetgen::tetgenmesh::delaunizevertices 1ms 0.0022% 1.34% 8394ms 18.88% tetgen::tetgenmesh::incrflipdelaunay 42ms 0.094% 1.44% 7925ms 17.83% std::set::insert (inline) 140ms 0.31% 1.75% 7564ms 17.02% std::_Rb_tree::_M_insert_unique 345ms 0.78% 2.53% 7427ms 16.71% tetgen::tetgenmesh::lawson 290ms 0.65% 3.18% 7042ms 15.84% VertexElement::AddFace 2594ms 5.84% 9.01% 6539ms 14.71% std::_Rb_tree::_M_lower_bound (inline) 222ms 0.5% 9.51% 6174ms 13.89% std::_Rb_tree::find (inline) 0 0% 9.51% 5761ms 12.96% std::set::count (inline) 136ms 0.31% 9.82% 4672ms 10.51% operator new 182ms 0.41% 10.23% 4535ms 10.20% std::_Rb_tree::_M_insert_ (inline) 1411ms 3.17% 13.40% 4496ms 10.11% __GI___libc_malloc 4319ms 9.72% 23.12% 4319ms 9.72% std::_Rb_tree_increment 116ms 0.26% 23.38% 3884ms 8.74% std::less::operator() (inline) 0 0% 23.38% 3850ms 8.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 29ms 0.065% 23.45% 3834ms 8.63% std::__new_allocator::allocate (inline) 3826ms 8.61% 32.05% 3826ms 8.61% std::operator< (inline) 0 0% 32.05% 3824ms 8.60% std::allocator_traits::allocate (inline) 4ms 0.009% 32.06% 3796ms 8.54% std::set_intersection (inline) 233ms 0.52% 32.59% 3792ms 8.53% std::__set_intersection 0 0% 32.59% 3752ms 8.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0045% 32.59% 3741ms 8.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 12ms 0.027% 32.62% 3549ms 7.98% std::_Rb_tree::~_Rb_tree (inline) 1278ms 2.88% 35.49% 3534ms 7.95% std::_Rb_tree::_M_erase 841ms 1.89% 37.38% 3513ms 7.90% __GI___libc_free 0 0% 37.38% 3505ms 7.89% std::set::~set (inline) 1ms 0.0022% 37.39% 3287ms 7.39% MeshBasedCellPopulation::UpdateNodePairs 0 0% 37.39% 3227ms 7.26% VertexMesh::~VertexMesh 3ms 0.0067% 37.39% 3184ms 7.16% MeshBasedCellPopulation::SpringIterator::operator++ 144ms 0.32% 37.72% 3182ms 7.16% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0022% 37.72% 3165ms 7.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 37.72% 3143ms 7.07% std::_Rb_tree::_M_create_node (inline) 0 0% 37.72% 3123ms 7.03% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.72% 3108ms 6.99% std::_Rb_tree::_M_get_node (inline) 915ms 2.06% 39.78% 3084ms 6.94% std::_Rb_tree::_M_get_insert_unique_pos 32ms 0.072% 39.85% 3056ms 6.87% Node::AddElement 70ms 0.16% 40.01% 3016ms 6.78% std::__new_allocator::deallocate (inline) 0 0% 40.01% 3013ms 6.78% std::allocator_traits::deallocate (inline) 2151ms 4.84% 44.85% 2878ms 6.47% _int_malloc 1276ms 2.87% 47.72% 2670ms 6.01% _int_free 3ms 0.0067% 47.72% 2558ms 5.75% TetrahedralMesh::ImportFromMesher 2448ms 5.51% 53.23% 2448ms 5.51% std::_Rb_tree::_S_right (inline) 54ms 0.12% 53.35% 2427ms 5.46% MutableElement::AddNode 83ms 0.19% 53.54% 2349ms 5.28% tetgen::tetgenmesh::insphere_sos 0 0% 53.54% 2298ms 5.17% AbstractCellPopulation::WriteResultsToFiles 83ms 0.19% 53.73% 2257ms 5.08% Node::~Node 2078ms 4.67% 58.40% 2255ms 5.07% tetgen::insphere 99ms 0.22% 58.62% 2116ms 4.76% VertexMesh::Clear 0 0% 58.62% 1733ms 3.90% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.62% 1712ms 3.85% std::_Rb_tree::_M_put_node (inline) 116ms 0.26% 58.89% 1631ms 3.67% tetgen::tetgenmesh::flip23 3ms 0.0067% 58.89% 1565ms 3.52% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 120ms 0.27% 59.16% 1528ms 3.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 59.16% 1422ms 3.20% std::_Rb_tree_iterator::operator++ (inline) 1003ms 2.26% 61.42% 1368ms 3.08% malloc_consolidate 24ms 0.054% 61.47% 1325ms 2.98% std::_Vector_base::_M_deallocate (inline) 1285ms 2.89% 64.36% 1285ms 2.89% std::_Rb_tree_insert_and_rebalance 0 0% 64.36% 1269ms 2.85% std::vector::~vector (inline) 0 0% 64.36% 1199ms 2.70% std::_Vector_base::~_Vector_base (inline) 67ms 0.15% 64.51% 1192ms 2.68% tetgen::tetgenmesh::flip32 5ms 0.011% 64.52% 1180ms 2.65% _int_free_maybe_consolidate 4ms 0.009% 64.53% 1171ms 2.63% Element::Element 67ms 0.15% 64.68% 1100ms 2.47% TetrahedralMesh::Clear 829ms 1.86% 66.55% 1048ms 2.36% AbstractElement::GetNodeGlobalIndex 4ms 0.009% 66.56% 989ms 2.22% Element::RegisterWithNodes (inline) 971ms 2.18% 68.74% 971ms 2.18% Node::GetIndex 894ms 2.01% 70.75% 939ms 2.11% tetgen::orient3d 84ms 0.19% 70.94% 897ms 2.02% tetgen::tetgenmesh::enqueueflipface 873ms 1.96% 72.91% 873ms 1.96% unlink_chunk 42ms 0.094% 73.00% 844ms 1.90% std::vector::_M_realloc_insert 24ms 0.054% 73.06% 806ms 1.81% tetgen::tetgenmesh::locate 4ms 0.009% 73.06% 779ms 1.75% VertexMesh::GenerateVerticesFromElementCircumcentres 71ms 0.16% 73.22% 756ms 1.70% tetgen::tetgenmesh::preciselocate 46ms 0.1% 73.33% 749ms 1.69% std::map::operator[] 1ms 0.0022% 73.33% 717ms 1.61% std::_Vector_base::_M_allocate (inline) 691ms 1.55% 74.88% 691ms 1.55% [libchaste_mesh.so] 0 0% 74.88% 662ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 74.88% 662ms 1.49% std::map::lower_bound (inline) 55ms 0.12% 75.01% 638ms 1.44% std::vector::push_back (inline) 611ms 1.37% 76.38% 611ms 1.37% tetgen::tetgenmesh::oppo 582ms 1.31% 77.69% 582ms 1.31% AbstractElement::IsDeleted 1ms 0.0022% 77.69% 576ms 1.30% VoronoiDataWriter::Visit 1ms 0.0022% 77.70% 546ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 309ms 0.7% 78.39% 529ms 1.19% tetgen::tetgenmesh::sym 524ms 1.18% 79.57% 524ms 1.18% std::vector::size (inline) 286ms 0.64% 80.21% 515ms 1.16% AbstractElement::GetNodeLocation 0 0% 80.21% 464ms 1.04% AbstractTwoBodyInteractionForce::AddForceContribution 20ms 0.045% 80.26% 458ms 1.03% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0022% 80.26% 456ms 1.03% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.02% 80.28% 451ms 1.01% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 442ms 0.99% 81.28% 442ms 0.99% Node::rGetLocation 0 0% 81.28% 412ms 0.93% std::set::find (inline) 13ms 0.029% 81.31% 362ms 0.81% Element::CalculateCircumsphere 32ms 0.072% 81.38% 359ms 0.81% __atan2 6ms 0.013% 81.39% 358ms 0.81% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.39% 356ms 0.8% std::insert_iterator::operator= (inline) 6ms 0.013% 81.40% 350ms 0.79% boost::numeric::ublas::vector_assign (inline) 228ms 0.51% 81.92% 349ms 0.79% tetgen::tetgenmesh::fnextself 28ms 0.063% 81.98% 341ms 0.77% AbstractTetrahedralElement::RefreshJacobian 251ms 0.56% 82.54% 322ms 0.72% __ieee754_atan2_fma 0 0% 82.54% 319ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 314ms 0.71% 83.25% 314ms 0.71% tetgen::tetgenmesh::triface::triface 3ms 0.0067% 83.26% 305ms 0.69% VertexElement::~VertexElement 24ms 0.054% 83.31% 295ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 134ms 0.3% 83.61% 289ms 0.65% AbstractTetrahedralMesh::GetElement 286ms 0.64% 84.26% 286ms 0.64% tetgen::tetgenmesh::org 285ms 0.64% 84.90% 285ms 0.64% boost::numeric::ublas::c_vector::operator() 28ms 0.063% 84.96% 274ms 0.62% tetgen::tetgenmesh::enext2fnext 6ms 0.013% 84.97% 269ms 0.61% std::vector::insert (inline) 0 0% 84.97% 267ms 0.6% boost::numeric::ublas::inner_prod (inline) 20ms 0.045% 85.02% 267ms 0.6% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.02% 267ms 0.6% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 263ms 0.59% 85.61% 263ms 0.59% std::_Rb_tree_decrement 21ms 0.047% 85.66% 261ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 85.66% 256ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 10ms 0.022% 85.68% 254ms 0.57% tetgen::tetgenmesh::queue::push 2ms 0.0045% 85.69% 247ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.067% 85.75% 241ms 0.54% tetgen::tetgenmesh::enextfnext 166ms 0.37% 86.13% 240ms 0.54% tetgen::tetgenmesh::link::add 0 0% 86.13% 237ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.013% 86.14% 236ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.0022% 86.14% 235ms 0.53% Cell::GetCellId 232ms 0.52% 86.66% 232ms 0.52% tetgen::tetgenmesh::triface::operator= 51ms 0.11% 86.78% 228ms 0.51% boost::numeric::ublas::vector_inner_prod::apply (inline) 17ms 0.038% 86.82% 225ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)