File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45474ms, 86.12% of 52806ms total Dropped 816 nodes (cum <= 264.03ms) flat flat% sum% cum cum% 0 0% 0% 52756ms 99.91% __libc_start_call_main 0 0% 0% 52756ms 99.91% __libc_start_main_impl 0 0% 0% 52756ms 99.91% _start 0 0% 0% 52742ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52742ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52742ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52742ms 99.88% main 0 0% 0% 52705ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52705ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52705ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52475ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 45016ms 85.25% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 44981ms 85.18% MeshBasedCellPopulation::Update 0 0% 0% 25514ms 48.32% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25514ms 48.32% MeshBasedCellPopulation::TessellateIfNeeded 174ms 0.33% 0.33% 22102ms 41.86% VertexMesh::VertexMesh 0 0% 0.33% 16156ms 30.60% MutableMesh::ReMesh 0 0% 0.33% 12475ms 23.62% tetgen::tetrahedralize 0 0% 0.33% 12352ms 23.39% tetgen::tetgenmesh::delaunizevertices 10ms 0.019% 0.35% 12350ms 23.39% tetgen::tetgenmesh::incrflipdelaunay 394ms 0.75% 1.09% 11033ms 20.89% tetgen::tetgenmesh::lawson 461ms 0.87% 1.97% 10322ms 19.55% TetrahedralMesh::EdgeIterator::operator++ 27ms 0.051% 2.02% 8677ms 16.43% std::set::insert (inline) 160ms 0.3% 2.32% 8342ms 15.80% std::_Rb_tree::_M_insert_unique 338ms 0.64% 2.96% 8002ms 15.15% VertexElement::AddFace 2478ms 4.69% 7.65% 7380ms 13.98% std::_Rb_tree::_M_lower_bound (inline) 177ms 0.34% 7.99% 6935ms 13.13% std::_Rb_tree::find (inline) 0 0% 7.99% 6494ms 12.30% std::set::count (inline) 253ms 0.48% 8.47% 5018ms 9.50% std::_Rb_tree::_M_insert_ (inline) 93ms 0.18% 8.64% 4815ms 9.12% std::less::operator() (inline) 112ms 0.21% 8.86% 4803ms 9.10% operator new 4772ms 9.04% 17.89% 4772ms 9.04% std::operator< (inline) 1052ms 1.99% 19.89% 4622ms 8.75% __GI___libc_malloc 4606ms 8.72% 28.61% 4606ms 8.72% std::_Rb_tree_increment 0 0% 28.61% 4449ms 8.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.61% 4336ms 8.21% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0076% 28.62% 4314ms 8.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 21ms 0.04% 28.66% 4010ms 7.59% std::__new_allocator::allocate (inline) 0 0% 28.66% 3995ms 7.57% std::allocator_traits::allocate (inline) 2ms 0.0038% 28.66% 3794ms 7.18% std::_Rb_tree::~_Rb_tree (inline) 1443ms 2.73% 31.39% 3791ms 7.18% std::_Rb_tree::_M_erase 0 0% 31.39% 3751ms 7.10% std::set::~set (inline) 3ms 0.0057% 31.40% 3678ms 6.97% std::set_intersection (inline) 205ms 0.39% 31.79% 3675ms 6.96% std::__set_intersection 1063ms 2.01% 33.80% 3638ms 6.89% __GI___libc_free 1ms 0.0019% 33.80% 3611ms 6.84% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0095% 33.81% 3581ms 6.78% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.019% 33.83% 3494ms 6.62% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.0019% 33.83% 3441ms 6.52% VertexMesh::~VertexMesh 1057ms 2.00% 35.83% 3363ms 6.37% std::_Rb_tree::_M_get_insert_unique_pos 2411ms 4.57% 40.40% 3306ms 6.26% _int_malloc 0 0% 40.40% 3268ms 6.19% std::_Rb_tree::_M_create_node (inline) 0 0% 40.40% 3248ms 6.15% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.40% 3238ms 6.13% std::_Rb_tree::_M_get_node (inline) 47ms 0.089% 40.49% 3186ms 6.03% Node::AddElement 94ms 0.18% 40.67% 3131ms 5.93% std::__new_allocator::deallocate (inline) 0 0% 40.67% 3123ms 5.91% std::allocator_traits::deallocate (inline) 163ms 0.31% 40.97% 3106ms 5.88% std::_Rb_tree_const_iterator::operator++ (inline) 107ms 0.2% 41.18% 3002ms 5.68% tetgen::tetgenmesh::insphere_sos 5ms 0.0095% 41.19% 2992ms 5.67% TetrahedralMesh::ImportFromMesher 2674ms 5.06% 46.25% 2888ms 5.47% tetgen::insphere 0 0% 46.25% 2878ms 5.45% AbstractCellPopulation::WriteResultsToFiles 2795ms 5.29% 51.54% 2795ms 5.29% std::_Rb_tree::_S_right (inline) 93ms 0.18% 51.72% 2678ms 5.07% tetgen::tetgenmesh::flip23 1046ms 1.98% 53.70% 2571ms 4.87% _int_free 55ms 0.1% 53.80% 2454ms 4.65% MutableElement::AddNode 177ms 0.34% 54.14% 2448ms 4.64% Node::~Node 160ms 0.3% 54.44% 2247ms 4.26% VertexMesh::Clear 2ms 0.0038% 54.45% 1934ms 3.66% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 144ms 0.27% 54.72% 1891ms 3.58% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 101ms 0.19% 54.91% 1873ms 3.55% tetgen::tetgenmesh::flip32 2ms 0.0038% 54.91% 1763ms 3.34% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.91% 1719ms 3.26% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.91% 1715ms 3.25% std::_Rb_tree::_M_put_node (inline) 1566ms 2.97% 57.88% 1566ms 2.97% std::_Rb_tree_insert_and_rebalance 1032ms 1.95% 59.83% 1475ms 2.79% malloc_consolidate 1466ms 2.78% 62.61% 1466ms 2.78% Node::GetIndex 36ms 0.068% 62.68% 1444ms 2.73% std::_Vector_base::_M_deallocate (inline) 169ms 0.32% 63.00% 1440ms 2.73% tetgen::tetgenmesh::enqueueflipface 0 0% 63.00% 1419ms 2.69% std::vector::~vector (inline) 1ms 0.0019% 63.00% 1375ms 2.60% Element::Element 104ms 0.2% 63.20% 1323ms 2.51% TetrahedralMesh::Clear 1ms 0.0019% 63.20% 1322ms 2.50% std::_Vector_base::~_Vector_base (inline) 8ms 0.015% 63.21% 1287ms 2.44% _int_free_maybe_consolidate 1214ms 2.30% 65.51% 1264ms 2.39% tetgen::orient3d 6ms 0.011% 65.52% 1120ms 2.12% Element::RegisterWithNodes (inline) 32ms 0.061% 65.59% 1086ms 2.06% tetgen::tetgenmesh::locate 1084ms 2.05% 67.64% 1084ms 2.05% unlink_chunk 69ms 0.13% 67.77% 1006ms 1.91% tetgen::tetgenmesh::preciselocate 808ms 1.53% 69.30% 999ms 1.89% AbstractElement::GetNodeGlobalIndex 47ms 0.089% 69.39% 932ms 1.76% std::vector::_M_realloc_insert 8ms 0.015% 69.40% 898ms 1.70% VertexMesh::GenerateVerticesFromElementCircumcentres 66ms 0.12% 69.53% 887ms 1.68% std::map::operator[] 842ms 1.59% 71.12% 842ms 1.59% tetgen::tetgenmesh::oppo 0 0% 71.12% 774ms 1.47% std::_Rb_tree::lower_bound (inline) 0 0% 71.12% 774ms 1.47% std::map::lower_bound (inline) 95ms 0.18% 71.30% 767ms 1.45% std::vector::push_back (inline) 2ms 0.0038% 71.31% 759ms 1.44% std::_Vector_base::_M_allocate (inline) 0 0% 71.31% 744ms 1.41% VoronoiDataWriter::Visit 742ms 1.41% 72.71% 742ms 1.41% tetgen::tetgenmesh::triface::triface 235ms 0.45% 73.16% 715ms 1.35% tetgen::tetgenmesh::sym 0 0% 73.16% 663ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 637ms 1.21% 74.36% 637ms 1.21% tetgen::tetgenmesh::triface::operator= 625ms 1.18% 75.55% 625ms 1.18% [libchaste_mesh.so] 13ms 0.025% 75.57% 587ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0019% 75.57% 582ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 275ms 0.52% 76.09% 575ms 1.09% AbstractElement::GetNodeLocation 558ms 1.06% 77.15% 558ms 1.06% AbstractElement::IsDeleted 19ms 0.036% 77.19% 553ms 1.05% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 543ms 1.03% 78.21% 543ms 1.03% std::vector::size (inline) 531ms 1.01% 79.22% 531ms 1.01% Node::rGetLocation 12ms 0.023% 79.24% 510ms 0.97% AbstractTetrahedralElement::CalculateJacobian 24ms 0.045% 79.29% 491ms 0.93% tetgen::tetgenmesh::queue::push 11ms 0.021% 79.31% 485ms 0.92% boost::numeric::ublas::vector_assign (inline) 479ms 0.91% 80.22% 479ms 0.91% tetgen::tetgenmesh::decode 32ms 0.061% 80.28% 477ms 0.9% __atan2 8ms 0.015% 80.29% 469ms 0.89% boost::numeric::ublas::c_vector::c_vector (inline) 272ms 0.52% 80.81% 468ms 0.89% tetgen::tetgenmesh::fnextself 296ms 0.56% 81.37% 467ms 0.88% tetgen::tetgenmesh::link::add 42ms 0.08% 81.45% 455ms 0.86% tetgen::tetgenmesh::enext2fnext 345ms 0.65% 82.10% 445ms 0.84% __ieee754_atan2_fma 17ms 0.032% 82.13% 438ms 0.83% Element::CalculateCircumsphere 0 0% 82.13% 436ms 0.83% std::set::find (inline) 177ms 0.34% 82.47% 431ms 0.82% tetgen::tetgenmesh::bond 51ms 0.097% 82.56% 423ms 0.8% tetgen::tetgenmesh::enextfnext 26ms 0.049% 82.61% 387ms 0.73% AbstractTetrahedralElement::RefreshJacobian 7ms 0.013% 82.63% 384ms 0.73% VertexElement::~VertexElement 0 0% 82.63% 380ms 0.72% boost::numeric::ublas::inner_prod (inline) 28ms 0.053% 82.68% 379ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.68% 379ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.027% 82.71% 361ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.71% 355ms 0.67% std::insert_iterator::operator= (inline) 5ms 0.0095% 82.72% 340ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 166ms 0.31% 83.03% 329ms 0.62% AbstractTetrahedralMesh::GetElement 25ms 0.047% 83.08% 327ms 0.62% std::_Rb_tree_iterator::operator-- (inline) 323ms 0.61% 83.69% 323ms 0.61% tetgen::tetgenmesh::org 5ms 0.0095% 83.70% 319ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.70% 316ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 80ms 0.15% 83.85% 313ms 0.59% __dynamic_cast 310ms 0.59% 84.44% 310ms 0.59% boost::numeric::ublas::c_vector::operator() 145ms 0.27% 84.71% 308ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.71% 305ms 0.58% std::_Rb_tree::_M_insert_unique_ (inline) 1ms 0.0019% 84.71% 292ms 0.55% Cell::GetCellId 70ms 0.13% 84.85% 289ms 0.55% boost::numeric::ublas::indexing_vector_assign 15ms 0.028% 84.87% 281ms 0.53% std::vector::insert (inline) 277ms 0.52% 85.40% 277ms 0.52% std::_Rb_tree_decrement 0 0% 85.40% 276ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.0095% 85.41% 274ms 0.52% VertexMesh::GetVolumeOfElement 269ms 0.51% 85.92% 269ms 0.51% tetgen::tetgenmesh::pointmark 104ms 0.2% 86.12% 268ms 0.51% Inverse