File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54402ms, 87.19% of 62392ms total Dropped 882 nodes (cum <= 311.96ms) flat flat% sum% cum cum% 0 0% 0% 62331ms 99.90% __libc_start_call_main 0 0% 0% 62331ms 99.90% __libc_start_main_impl 0 0% 0% 62331ms 99.90% _start 0 0% 0% 62315ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62315ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62315ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62315ms 99.88% main 0 0% 0% 62277ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62277ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62277ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 62005ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 53063ms 85.05% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0016% 0.0016% 53024ms 84.99% MeshBasedCellPopulation::Update 0 0% 0.0016% 31749ms 50.89% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0016% 31747ms 50.88% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 202ms 0.32% 0.33% 27685ms 44.37% VertexMesh::VertexMesh 0 0% 0.33% 17311ms 27.75% MutableMesh::ReMesh 0 0% 0.33% 12845ms 20.59% tetgen::tetrahedralize 4ms 0.0064% 0.33% 12706ms 20.36% tetgen::tetgenmesh::delaunizevertices 6ms 0.0096% 0.34% 12695ms 20.35% tetgen::tetgenmesh::incrflipdelaunay 573ms 0.92% 1.26% 12189ms 19.54% TetrahedralMesh::EdgeIterator::operator++ 606ms 0.97% 2.23% 11206ms 17.96% tetgen::tetgenmesh::lawson 30ms 0.048% 2.28% 10830ms 17.36% std::set::insert (inline) 203ms 0.33% 2.60% 10333ms 16.56% std::_Rb_tree::_M_insert_unique 450ms 0.72% 3.33% 9667ms 15.49% VertexElement::AddFace 3026ms 4.85% 8.18% 8920ms 14.30% std::_Rb_tree::_M_lower_bound (inline) 226ms 0.36% 8.54% 8341ms 13.37% std::_Rb_tree::find (inline) 0 0% 8.54% 7792ms 12.49% std::set::count (inline) 289ms 0.46% 9.00% 6117ms 9.80% std::_Rb_tree::_M_insert_ (inline) 5855ms 9.38% 18.39% 5855ms 9.38% std::_Rb_tree_increment 116ms 0.19% 18.57% 5720ms 9.17% std::less::operator() (inline) 5660ms 9.07% 27.64% 5660ms 9.07% std::operator< (inline) 179ms 0.29% 27.93% 5640ms 9.04% operator new 1055ms 1.69% 29.62% 5385ms 8.63% __GI___libc_malloc 0 0% 29.62% 5339ms 8.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0032% 29.62% 5197ms 8.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0032% 29.63% 5174ms 8.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0016% 29.63% 4843ms 7.76% std::set_intersection (inline) 298ms 0.48% 30.11% 4842ms 7.76% std::__set_intersection 41ms 0.066% 30.17% 4659ms 7.47% std::__new_allocator::allocate (inline) 0 0% 30.17% 4640ms 7.44% std::allocator_traits::allocate (inline) 8ms 0.013% 30.18% 4566ms 7.32% std::_Rb_tree::~_Rb_tree (inline) 1869ms 3.00% 33.18% 4556ms 7.30% std::_Rb_tree::_M_erase 0 0% 33.18% 4489ms 7.19% std::set::~set (inline) 1221ms 1.96% 35.14% 4338ms 6.95% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 35.14% 4323ms 6.93% MeshBasedCellPopulation::UpdateNodePairs 23ms 0.037% 35.17% 4311ms 6.91% Node::AddElement 6ms 0.0096% 35.18% 4288ms 6.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1237ms 1.98% 37.17% 4278ms 6.86% __GI___libc_free 14ms 0.022% 37.19% 4166ms 6.68% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 37.19% 4091ms 6.56% VertexMesh::~VertexMesh 183ms 0.29% 37.48% 4067ms 6.52% std::_Rb_tree_const_iterator::operator++ (inline) 2927ms 4.69% 42.17% 3995ms 6.40% _int_malloc 117ms 0.19% 42.36% 3845ms 6.16% std::__new_allocator::deallocate (inline) 0 0% 42.36% 3822ms 6.13% std::allocator_traits::deallocate (inline) 0 0% 42.36% 3784ms 6.06% std::_Rb_tree::_M_create_node (inline) 0 0% 42.36% 3748ms 6.01% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.36% 3728ms 5.98% std::_Rb_tree::_M_get_node (inline) 3720ms 5.96% 48.32% 3720ms 5.96% std::_Rb_tree::_S_right (inline) 9ms 0.014% 48.34% 3551ms 5.69% TetrahedralMesh::ImportFromMesher 99ms 0.16% 48.50% 3496ms 5.60% tetgen::tetgenmesh::insphere_sos 73ms 0.12% 48.61% 3455ms 5.54% MutableElement::AddNode 0 0% 48.61% 3437ms 5.51% AbstractCellPopulation::WriteResultsToFiles 3068ms 4.92% 53.53% 3380ms 5.42% tetgen::insphere 1209ms 1.94% 55.47% 3036ms 4.87% _int_free 207ms 0.33% 55.80% 2747ms 4.40% Node::~Node 194ms 0.31% 56.11% 2691ms 4.31% tetgen::tetgenmesh::flip23 231ms 0.37% 56.48% 2543ms 4.08% VertexMesh::Clear 1ms 0.0016% 56.48% 2276ms 3.65% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 191ms 0.31% 56.79% 2244ms 3.60% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2173ms 3.48% 60.27% 2173ms 3.48% std::_Rb_tree_insert_and_rebalance 2ms 0.0032% 60.28% 2076ms 3.33% std::_Rb_tree_iterator::operator++ (inline) 0 0% 60.28% 1960ms 3.14% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.28% 1950ms 3.13% std::_Rb_tree::_M_put_node (inline) 16ms 0.026% 60.30% 1888ms 3.03% std::_Vector_base::_M_deallocate (inline) 1280ms 2.05% 62.35% 1864ms 2.99% malloc_consolidate 140ms 0.22% 62.58% 1817ms 2.91% tetgen::tetgenmesh::flip32 1794ms 2.88% 65.45% 1794ms 2.88% Node::GetIndex 3ms 0.0048% 65.46% 1719ms 2.76% Element::Element 0 0% 65.46% 1712ms 2.74% std::vector::~vector (inline) 3ms 0.0048% 65.46% 1668ms 2.67% std::_Vector_base::~_Vector_base (inline) 4ms 0.0064% 65.47% 1610ms 2.58% _int_free_maybe_consolidate 239ms 0.38% 65.85% 1431ms 2.29% TetrahedralMesh::Clear 1310ms 2.10% 67.95% 1393ms 2.23% tetgen::orient3d 5ms 0.008% 67.96% 1380ms 2.21% Element::RegisterWithNodes (inline) 1344ms 2.15% 70.11% 1344ms 2.15% unlink_chunk 198ms 0.32% 70.43% 1337ms 2.14% tetgen::tetgenmesh::enqueueflipface 37ms 0.059% 70.49% 1252ms 2.01% tetgen::tetgenmesh::locate 3ms 0.0048% 70.49% 1211ms 1.94% VertexMesh::GenerateVerticesFromElementCircumcentres 57ms 0.091% 70.59% 1197ms 1.92% std::vector::_M_realloc_insert 146ms 0.23% 70.82% 1157ms 1.85% tetgen::tetgenmesh::preciselocate 71ms 0.11% 70.93% 1144ms 1.83% std::map::operator[] 894ms 1.43% 72.37% 1017ms 1.63% AbstractElement::GetNodeGlobalIndex 0 0% 72.37% 993ms 1.59% std::_Rb_tree::lower_bound (inline) 0 0% 72.37% 993ms 1.59% std::map::lower_bound (inline) 115ms 0.18% 72.55% 963ms 1.54% std::vector::push_back (inline) 1ms 0.0016% 72.55% 920ms 1.47% VoronoiDataWriter::Visit 8ms 0.013% 72.57% 920ms 1.47% std::_Vector_base::_M_allocate (inline) 0 0% 72.57% 894ms 1.43% TetrahedralMesh::RefreshJacobianCachedData 851ms 1.36% 73.93% 851ms 1.36% tetgen::tetgenmesh::triface::triface 358ms 0.57% 74.50% 776ms 1.24% AbstractElement::GetNodeLocation 10ms 0.016% 74.52% 771ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.022% 74.54% 734ms 1.18% AbstractTetrahedralElement::CalculateJacobian 21ms 0.034% 74.58% 720ms 1.15% boost::numeric::ublas::vector_assign (inline) 0 0% 74.58% 709ms 1.14% AbstractTwoBodyInteractionForce::AddForceContribution 708ms 1.13% 75.71% 708ms 1.13% AbstractElement::IsDeleted 707ms 1.13% 76.84% 707ms 1.13% Node::rGetLocation 13ms 0.021% 76.86% 705ms 1.13% boost::numeric::ublas::c_vector::c_vector (inline) 705ms 1.13% 77.99% 705ms 1.13% tetgen::tetgenmesh::oppo 695ms 1.11% 79.11% 695ms 1.11% [libchaste_mesh.so] 11ms 0.018% 79.13% 664ms 1.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 355ms 0.57% 79.69% 659ms 1.06% tetgen::tetgenmesh::fnextself 65ms 0.1% 79.80% 624ms 1.00% __atan2 610ms 0.98% 80.78% 610ms 0.98% tetgen::tetgenmesh::triface::operator= 14ms 0.022% 80.80% 604ms 0.97% Element::CalculateCircumsphere 442ms 0.71% 81.51% 559ms 0.9% __ieee754_atan2_fma 41ms 0.066% 81.57% 558ms 0.89% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.57% 544ms 0.87% std::set::find (inline) 543ms 0.87% 82.44% 543ms 0.87% std::vector::size (inline) 0 0% 82.44% 516ms 0.83% boost::numeric::ublas::inner_prod (inline) 4ms 0.0064% 82.45% 515ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 24ms 0.038% 82.49% 511ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.49% 489ms 0.78% std::insert_iterator::operator= (inline) 332ms 0.53% 83.02% 487ms 0.78% tetgen::tetgenmesh::sym 122ms 0.2% 83.22% 458ms 0.73% boost::numeric::ublas::indexing_vector_assign 53ms 0.085% 83.30% 455ms 0.73% tetgen::tetgenmesh::enext2fnext 1ms 0.0016% 83.30% 448ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.037% 83.34% 446ms 0.71% std::_Rb_tree_iterator::operator-- (inline) 443ms 0.71% 84.05% 443ms 0.71% boost::numeric::ublas::c_vector::operator() 58ms 0.093% 84.14% 443ms 0.71% tetgen::tetgenmesh::enextfnext 14ms 0.022% 84.16% 432ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 198ms 0.32% 84.48% 427ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 220ms 0.35% 84.83% 424ms 0.68% AbstractTetrahedralMesh::GetElement 5ms 0.008% 84.84% 400ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.84% 400ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.0064% 84.85% 399ms 0.64% Cell::GetCellId 398ms 0.64% 85.49% 398ms 0.64% std::_Rb_tree_decrement 1ms 0.0016% 85.49% 376ms 0.6% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.49% 374ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 94ms 0.15% 85.64% 372ms 0.6% __dynamic_cast 14ms 0.022% 85.66% 370ms 0.59% std::vector::insert (inline) 364ms 0.58% 86.25% 364ms 0.58% tetgen::tetgenmesh::org 29ms 0.046% 86.29% 357ms 0.57% tetgen::tetgenmesh::queue::push 263ms 0.42% 86.71% 346ms 0.55% tetgen::tetgenmesh::bond 2ms 0.0032% 86.72% 334ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 48ms 0.077% 86.79% 334ms 0.54% boost::numeric::ublas::vector_reference::operator() (inline) 213ms 0.34% 87.13% 327ms 0.52% tetgen::tetgenmesh::link::add 5ms 0.008% 87.14% 325ms 0.52% VertexElement::~VertexElement 5ms 0.008% 87.15% 318ms 0.51% AbstractCellProperty::IsSubType (inline) 27ms 0.043% 87.19% 312ms 0.5% tetgen::insphereadapt