File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 71174ms, 87.22% of 81600ms total Dropped 898 nodes (cum <= 408ms) flat flat% sum% cum cum% 0 0% 0% 81538ms 99.92% __libc_start_call_main 0 0% 0% 81538ms 99.92% __libc_start_main_impl 0 0% 0% 81538ms 99.92% _start 0 0% 0% 81518ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 81518ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 81518ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 81518ms 99.90% main 0 0% 0% 81474ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 81474ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 81474ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 81163ms 99.46% AbstractCellBasedSimulation::Solve 0 0% 0% 69715ms 85.44% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 69656ms 85.36% MeshBasedCellPopulation::Update 0 0% 0% 42526ms 52.12% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 42525ms 52.11% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 325ms 0.4% 0.4% 36882ms 45.20% VertexMesh::VertexMesh 0 0% 0.4% 22104ms 27.09% MutableMesh::ReMesh 0 0% 0.4% 16490ms 20.21% tetgen::tetrahedralize 1ms 0.0012% 0.4% 16327ms 20.01% tetgen::tetgenmesh::delaunizevertices 7ms 0.0086% 0.41% 16318ms 20.00% tetgen::tetgenmesh::incrflipdelaunay 579ms 0.71% 1.12% 16105ms 19.74% TetrahedralMesh::EdgeIterator::operator++ 490ms 0.6% 1.72% 14592ms 17.88% tetgen::tetgenmesh::lawson 35ms 0.043% 1.76% 13135ms 16.10% std::set::insert (inline) 217ms 0.27% 2.03% 12657ms 15.51% std::_Rb_tree::_M_insert_unique 585ms 0.72% 2.74% 11961ms 14.66% VertexElement::AddFace 3292ms 4.03% 6.78% 11881ms 14.56% std::_Rb_tree::_M_lower_bound (inline) 229ms 0.28% 7.06% 10875ms 13.33% std::_Rb_tree::find (inline) 0 0% 7.06% 10320ms 12.65% std::set::count (inline) 8918ms 10.93% 17.99% 8918ms 10.93% std::_Rb_tree_increment 109ms 0.13% 18.12% 7981ms 9.78% std::less::operator() (inline) 7940ms 9.73% 27.85% 7940ms 9.73% std::operator< (inline) 197ms 0.24% 28.09% 7709ms 9.45% operator new 293ms 0.36% 28.45% 7431ms 9.11% std::_Rb_tree::_M_insert_ (inline) 1310ms 1.61% 30.06% 7421ms 9.09% __GI___libc_malloc 4ms 0.0049% 30.06% 7302ms 8.95% std::set_intersection (inline) 399ms 0.49% 30.55% 7298ms 8.94% std::__set_intersection 1ms 0.0012% 30.55% 6795ms 8.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.55% 6594ms 8.08% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0025% 30.56% 6564ms 8.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 193ms 0.24% 30.79% 6329ms 7.76% std::_Rb_tree_const_iterator::operator++ (inline) 50ms 0.061% 30.85% 6232ms 7.64% std::__new_allocator::allocate (inline) 0 0% 30.85% 6209ms 7.61% std::allocator_traits::allocate (inline) 51ms 0.062% 30.92% 5881ms 7.21% Node::AddElement 4155ms 5.09% 36.01% 5763ms 7.06% _int_malloc 1ms 0.0012% 36.01% 5686ms 6.97% VertexMesh::~VertexMesh 1447ms 1.77% 37.78% 5593ms 6.85% __GI___libc_free 10ms 0.012% 37.79% 5501ms 6.74% std::_Rb_tree::~_Rb_tree (inline) 2198ms 2.69% 40.49% 5491ms 6.73% std::_Rb_tree::_M_erase 5ms 0.0061% 40.49% 5479ms 6.71% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 40.49% 5413ms 6.63% MeshBasedCellPopulation::UpdateNodePairs 0 0% 40.49% 5413ms 6.63% std::set::~set (inline) 5354ms 6.56% 47.06% 5354ms 6.56% std::_Rb_tree::_S_right (inline) 1289ms 1.58% 48.63% 5292ms 6.49% std::_Rb_tree::_M_get_insert_unique_pos 12ms 0.015% 48.65% 5217ms 6.39% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 48.65% 4927ms 6.04% std::_Rb_tree::_M_create_node (inline) 0 0% 48.65% 4880ms 5.98% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.65% 4879ms 5.98% std::_Rb_tree::_M_get_node (inline) 121ms 0.15% 48.80% 4850ms 5.94% std::__new_allocator::deallocate (inline) 0 0% 48.80% 4833ms 5.92% std::allocator_traits::deallocate (inline) 0 0% 48.80% 4474ms 5.48% AbstractCellPopulation::WriteResultsToFiles 83ms 0.1% 48.90% 4469ms 5.48% MutableElement::AddNode 9ms 0.011% 48.91% 4460ms 5.47% TetrahedralMesh::ImportFromMesher 1379ms 1.69% 50.60% 4142ms 5.08% _int_free 130ms 0.16% 50.76% 3809ms 4.67% tetgen::tetgenmesh::insphere_sos 3382ms 4.14% 54.90% 3663ms 4.49% tetgen::insphere 282ms 0.35% 55.25% 3584ms 4.39% Node::~Node 137ms 0.17% 55.42% 3546ms 4.35% tetgen::tetgenmesh::flip23 194ms 0.24% 55.66% 3372ms 4.13% VertexMesh::Clear 3143ms 3.85% 59.51% 3143ms 3.85% Node::GetIndex 217ms 0.27% 59.77% 3096ms 3.79% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0012% 59.77% 3041ms 3.73% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0025% 59.78% 2920ms 3.58% std::_Rb_tree_iterator::operator++ (inline) 1942ms 2.38% 62.16% 2826ms 3.46% malloc_consolidate 131ms 0.16% 62.32% 2650ms 3.25% tetgen::tetgenmesh::flip32 40ms 0.049% 62.37% 2636ms 3.23% std::_Vector_base::_M_deallocate (inline) 0 0% 62.37% 2547ms 3.12% std::vector::~vector (inline) 1ms 0.0012% 62.37% 2468ms 3.02% std::_Vector_base::~_Vector_base (inline) 9ms 0.011% 62.38% 2461ms 3.02% _int_free_maybe_consolidate 2372ms 2.91% 65.29% 2372ms 2.91% std::_Rb_tree_insert_and_rebalance 8ms 0.0098% 65.30% 2343ms 2.87% Element::Element 0 0% 65.30% 2252ms 2.76% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.30% 2237ms 2.74% std::_Rb_tree::_M_put_node (inline) 2039ms 2.50% 67.79% 2039ms 2.50% unlink_chunk 7ms 0.0086% 67.80% 1971ms 2.42% Element::RegisterWithNodes (inline) 243ms 0.3% 68.10% 1962ms 2.40% tetgen::tetgenmesh::enqueueflipface 4ms 0.0049% 68.11% 1708ms 2.09% VertexMesh::GenerateVerticesFromElementCircumcentres 1397ms 1.71% 69.82% 1658ms 2.03% AbstractElement::GetNodeGlobalIndex 1556ms 1.91% 71.72% 1653ms 2.03% tetgen::orient3d 71ms 0.087% 71.81% 1613ms 1.98% std::map::operator[] 85ms 0.1% 71.92% 1608ms 1.97% TetrahedralMesh::Clear 69ms 0.085% 72.00% 1491ms 1.83% std::vector::_M_realloc_insert 0 0% 72.00% 1430ms 1.75% std::_Rb_tree::lower_bound (inline) 0 0% 72.00% 1430ms 1.75% std::map::lower_bound (inline) 39ms 0.048% 72.05% 1399ms 1.71% tetgen::tetgenmesh::locate 5ms 0.0061% 72.05% 1335ms 1.64% std::_Vector_base::_M_allocate (inline) 80ms 0.098% 72.15% 1296ms 1.59% tetgen::tetgenmesh::preciselocate 132ms 0.16% 72.31% 1237ms 1.52% std::vector::push_back (inline) 1189ms 1.46% 73.77% 1189ms 1.46% AbstractElement::IsDeleted 0 0% 73.77% 1159ms 1.42% VoronoiDataWriter::Visit 535ms 0.66% 74.43% 1129ms 1.38% AbstractElement::GetNodeLocation 0 0% 74.43% 1112ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 1098ms 1.35% 75.77% 1098ms 1.35% Node::rGetLocation 1071ms 1.31% 77.08% 1071ms 1.31% tetgen::tetgenmesh::oppo 1002ms 1.23% 78.31% 1002ms 1.23% tetgen::tetgenmesh::triface::triface 13ms 0.016% 78.33% 885ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.018% 78.35% 848ms 1.04% AbstractTetrahedralElement::CalculateJacobian 316ms 0.39% 78.73% 842ms 1.03% tetgen::tetgenmesh::sym 833ms 1.02% 79.75% 833ms 1.02% [libchaste_mesh.so] 819ms 1.00% 80.76% 819ms 1.00% tetgen::tetgenmesh::triface::operator= 0 0% 80.76% 815ms 1% AbstractTwoBodyInteractionForce::AddForceContribution 815ms 1% 81.76% 815ms 1% std::vector::size (inline) 15ms 0.018% 81.78% 781ms 0.96% Element::CalculateCircumsphere 12ms 0.015% 81.79% 762ms 0.93% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 56ms 0.069% 81.86% 667ms 0.82% AbstractTetrahedralElement::RefreshJacobian 63ms 0.077% 81.94% 665ms 0.81% tetgen::tetgenmesh::enext2fnext 409ms 0.5% 82.44% 662ms 0.81% tetgen::tetgenmesh::fnextself 17ms 0.021% 82.46% 654ms 0.8% boost::numeric::ublas::vector_assign (inline) 9ms 0.011% 82.47% 652ms 0.8% boost::numeric::ublas::c_vector::c_vector (inline) 261ms 0.32% 82.79% 645ms 0.79% tetgen::tetgenmesh::bond 48ms 0.059% 82.85% 631ms 0.77% tetgen::tetgenmesh::queue::push 48ms 0.059% 82.91% 610ms 0.75% __atan2 373ms 0.46% 83.36% 583ms 0.71% tetgen::tetgenmesh::link::add 0 0% 83.36% 556ms 0.68% boost::numeric::ublas::inner_prod (inline) 48ms 0.059% 83.42% 555ms 0.68% tetgen::tetgenmesh::enextfnext 436ms 0.53% 83.96% 553ms 0.68% __ieee754_atan2_fma 3ms 0.0037% 83.96% 553ms 0.68% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 21ms 0.026% 83.99% 551ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 48ms 0.059% 84.05% 550ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.05% 550ms 0.67% std::set::find (inline) 527ms 0.65% 84.69% 527ms 0.65% tetgen::tetgenmesh::org 520ms 0.64% 85.33% 520ms 0.64% tetgen::tetgenmesh::decode 0 0% 85.33% 503ms 0.62% std::insert_iterator::operator= (inline) 0 0% 85.33% 480ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 8ms 0.0098% 85.34% 465ms 0.57% VertexElement::~VertexElement 3ms 0.0037% 85.34% 458ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 23ms 0.028% 85.37% 453ms 0.56% std::_Rb_tree_iterator::operator-- (inline) 441ms 0.54% 85.91% 441ms 0.54% boost::numeric::ublas::c_vector::operator() 0 0% 85.91% 441ms 0.54% std::_Rb_tree::_M_insert_unique_ (inline) 180ms 0.22% 86.13% 437ms 0.54% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.0061% 86.14% 430ms 0.53% Cell::GetCellId 226ms 0.28% 86.41% 427ms 0.52% AbstractTetrahedralMesh::GetElement 114ms 0.14% 86.55% 417ms 0.51% __dynamic_cast 19ms 0.023% 86.58% 417ms 0.51% std::vector::insert (inline) 111ms 0.14% 86.71% 415ms 0.51% boost::numeric::ublas::indexing_vector_assign 4ms 0.0049% 86.72% 412ms 0.5% VertexMesh::GetVolumeOfElement 412ms 0.5% 87.22% 412ms 0.5% std::_Rb_tree_decrement