File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58332ms, 87.44% of 66710ms total Dropped 859 nodes (cum <= 333.55ms) flat flat% sum% cum cum% 0 0% 0% 66649ms 99.91% __libc_start_call_main 0 0% 0% 66649ms 99.91% __libc_start_main_impl 0 0% 0% 66649ms 99.91% _start 0 0% 0% 66633ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66633ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66633ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66633ms 99.88% main 0 0% 0% 66597ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66597ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66597ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66311ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 55217ms 82.77% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55160ms 82.69% MeshBasedCellPopulation::Update 0 0% 0% 32756ms 49.10% MeshBasedCellPopulation::TessellateIfNeeded 2ms 0.003% 0.003% 32755ms 49.10% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 245ms 0.37% 0.37% 28637ms 42.93% VertexMesh::VertexMesh 0 0% 0.37% 17973ms 26.94% MutableMesh::ReMesh 600ms 0.9% 1.27% 13543ms 20.30% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0015% 1.27% 13057ms 19.57% tetgen::tetrahedralize 2ms 0.003% 1.27% 12919ms 19.37% tetgen::tetgenmesh::delaunizevertices 11ms 0.016% 1.29% 12910ms 19.35% tetgen::tetgenmesh::incrflipdelaunay 594ms 0.89% 2.18% 11502ms 17.24% tetgen::tetgenmesh::lawson 35ms 0.052% 2.23% 10961ms 16.43% std::set::insert (inline) 3033ms 4.55% 6.78% 10553ms 15.82% std::_Rb_tree::_M_lower_bound (inline) 199ms 0.3% 7.08% 10461ms 15.68% std::_Rb_tree::_M_insert_unique 403ms 0.6% 7.68% 9792ms 14.68% VertexElement::AddFace 257ms 0.39% 8.07% 9687ms 14.52% std::_Rb_tree::find (inline) 0 0% 8.07% 9150ms 13.72% std::set::count (inline) 7358ms 11.03% 19.10% 7358ms 11.03% std::_Rb_tree_increment 140ms 0.21% 19.31% 7055ms 10.58% std::less::operator() (inline) 6965ms 10.44% 29.75% 6965ms 10.44% std::operator< (inline) 274ms 0.41% 30.16% 6088ms 9.13% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.16% 5927ms 8.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 234ms 0.35% 30.51% 5831ms 8.74% operator new 0 0% 30.51% 5765ms 8.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.003% 30.51% 5732ms 8.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 1067ms 1.60% 32.11% 5530ms 8.29% __GI___libc_malloc 0 0% 32.11% 5015ms 7.52% AbstractCellPopulation::WriteResultsToFiles 36ms 0.054% 32.17% 4827ms 7.24% std::__new_allocator::allocate (inline) 1ms 0.0015% 32.17% 4811ms 7.21% std::set_intersection (inline) 284ms 0.43% 32.59% 4810ms 7.21% std::__set_intersection 0 0% 32.59% 4795ms 7.19% std::allocator_traits::allocate (inline) 10ms 0.015% 32.61% 4780ms 7.17% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0015% 32.61% 4775ms 7.16% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.013% 32.62% 4772ms 7.15% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2030ms 3.04% 35.67% 4769ms 7.15% std::_Rb_tree::_M_erase 0 0% 35.67% 4716ms 7.07% std::set::~set (inline) 23ms 0.034% 35.70% 4598ms 6.89% Node::AddElement 12ms 0.018% 35.72% 4585ms 6.87% MeshBasedCellPopulation::SpringIterator::operator++ 1187ms 1.78% 37.50% 4498ms 6.74% std::_Rb_tree::_M_get_insert_unique_pos 4277ms 6.41% 43.91% 4277ms 6.41% std::_Rb_tree::_S_right (inline) 1148ms 1.72% 45.63% 4268ms 6.40% __GI___libc_free 0 0% 45.63% 4161ms 6.24% VertexMesh::~VertexMesh 3068ms 4.60% 50.23% 4131ms 6.19% _int_malloc 187ms 0.28% 50.51% 4068ms 6.10% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.01% 50.52% 4010ms 6.01% TetrahedralMesh::ImportFromMesher 0 0% 50.52% 3810ms 5.71% std::_Rb_tree::_M_create_node (inline) 237ms 0.36% 50.88% 3800ms 5.70% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 50.88% 3775ms 5.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.88% 3769ms 5.65% std::_Rb_tree::_M_get_node (inline) 149ms 0.22% 51.10% 3755ms 5.63% std::__new_allocator::deallocate (inline) 0 0% 51.10% 3739ms 5.60% std::allocator_traits::deallocate (inline) 102ms 0.15% 51.25% 3619ms 5.42% tetgen::tetgenmesh::insphere_sos 0 0% 51.25% 3581ms 5.37% std::_Rb_tree_iterator::operator++ (inline) 5ms 0.0075% 51.26% 3547ms 5.32% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3193ms 4.79% 56.05% 3499ms 5.25% tetgen::insphere 97ms 0.15% 56.19% 3308ms 4.96% MutableElement::AddNode 1216ms 1.82% 58.01% 3118ms 4.67% _int_free 173ms 0.26% 58.27% 2833ms 4.25% Node::~Node 203ms 0.3% 58.58% 2731ms 4.09% tetgen::tetgenmesh::flip23 223ms 0.33% 58.91% 2638ms 3.95% VertexMesh::Clear 2146ms 3.22% 62.13% 2146ms 3.22% Node::GetIndex 2144ms 3.21% 65.34% 2144ms 3.21% std::_Rb_tree_insert_and_rebalance 7ms 0.01% 65.35% 2140ms 3.21% Element::Element 0 0% 65.35% 1940ms 2.91% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.35% 1922ms 2.88% std::_Rb_tree::_M_put_node (inline) 1221ms 1.83% 67.18% 1912ms 2.87% malloc_consolidate 157ms 0.24% 67.42% 1876ms 2.81% tetgen::tetgenmesh::flip32 16ms 0.024% 67.44% 1833ms 2.75% std::_Vector_base::_M_deallocate (inline) 7ms 0.01% 67.45% 1795ms 2.69% Element::RegisterWithNodes (inline) 0 0% 67.45% 1726ms 2.59% std::vector::~vector (inline) 8ms 0.012% 67.47% 1667ms 2.50% _int_free_maybe_consolidate 1ms 0.0015% 67.47% 1644ms 2.46% std::_Vector_base::~_Vector_base (inline) 205ms 0.31% 67.77% 1478ms 2.22% TetrahedralMesh::Clear 1391ms 2.09% 69.86% 1476ms 2.21% tetgen::orient3d 82ms 0.12% 69.98% 1438ms 2.16% std::map::operator[] 1389ms 2.08% 72.06% 1389ms 2.08% unlink_chunk 191ms 0.29% 72.35% 1332ms 2.00% tetgen::tetgenmesh::enqueueflipface 0 0% 72.35% 1287ms 1.93% std::_Rb_tree::lower_bound (inline) 0 0% 72.35% 1287ms 1.93% std::map::lower_bound (inline) 50ms 0.075% 72.43% 1225ms 1.84% std::vector::_M_realloc_insert 6ms 0.009% 72.43% 1212ms 1.82% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 72.43% 1202ms 1.80% VoronoiDataWriter::Visit 33ms 0.049% 72.48% 1180ms 1.77% tetgen::tetgenmesh::locate 82ms 0.12% 72.61% 1100ms 1.65% tetgen::tetgenmesh::preciselocate 123ms 0.18% 72.79% 1031ms 1.55% std::vector::push_back (inline) 3ms 0.0045% 72.80% 1029ms 1.54% std::_Vector_base::_M_allocate (inline) 1024ms 1.54% 74.33% 1024ms 1.54% tetgen::tetgenmesh::triface::triface 846ms 1.27% 75.60% 971ms 1.46% AbstractElement::GetNodeGlobalIndex 1ms 0.0015% 75.60% 880ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 342ms 0.51% 76.11% 825ms 1.24% AbstractElement::GetNodeLocation 341ms 0.51% 76.62% 802ms 1.20% tetgen::tetgenmesh::fnextself 789ms 1.18% 77.81% 789ms 1.18% Node::rGetLocation 9ms 0.013% 77.82% 760ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0015% 77.82% 754ms 1.13% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.022% 77.84% 724ms 1.09% AbstractTetrahedralElement::CalculateJacobian 716ms 1.07% 78.92% 716ms 1.07% tetgen::tetgenmesh::triface::operator= 13ms 0.019% 78.94% 689ms 1.03% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 681ms 1.02% 79.96% 681ms 1.02% [libchaste_mesh.so] 681ms 1.02% 80.98% 681ms 1.02% tetgen::tetgenmesh::oppo 16ms 0.024% 81.00% 668ms 1.00% boost::numeric::ublas::vector_assign (inline) 12ms 0.018% 81.02% 665ms 1% boost::numeric::ublas::c_vector::c_vector (inline) 664ms 1% 82.02% 664ms 1% AbstractElement::IsDeleted 46ms 0.069% 82.09% 628ms 0.94% __atan2 6ms 0.009% 82.09% 586ms 0.88% Element::CalculateCircumsphere 468ms 0.7% 82.80% 582ms 0.87% __ieee754_atan2_fma 37ms 0.055% 82.85% 550ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.85% 534ms 0.8% std::set::find (inline) 48ms 0.072% 82.92% 517ms 0.77% tetgen::tetgenmesh::enextfnext 513ms 0.77% 83.69% 513ms 0.77% std::vector::size (inline) 50ms 0.075% 83.77% 512ms 0.77% tetgen::tetgenmesh::enext2fnext 0 0% 83.77% 494ms 0.74% std::insert_iterator::operator= (inline) 340ms 0.51% 84.28% 486ms 0.73% tetgen::tetgenmesh::sym 0 0% 84.28% 479ms 0.72% boost::numeric::ublas::inner_prod (inline) 3ms 0.0045% 84.28% 477ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 38ms 0.057% 84.34% 474ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.34% 440ms 0.66% std::_Rb_tree::_M_insert_unique_ (inline) 113ms 0.17% 84.51% 430ms 0.64% boost::numeric::ublas::indexing_vector_assign 0 0% 84.51% 415ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 224ms 0.34% 84.84% 412ms 0.62% AbstractTetrahedralMesh::GetElement 4ms 0.006% 84.85% 411ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 11ms 0.016% 84.87% 407ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 401ms 0.6% 85.47% 401ms 0.6% boost::numeric::ublas::c_vector::operator() 5ms 0.0075% 85.47% 397ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 0 0% 85.47% 393ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.027% 85.50% 388ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 181ms 0.27% 85.77% 385ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.003% 85.78% 374ms 0.56% Cell::GetCellId 372ms 0.56% 86.33% 372ms 0.56% tetgen::tetgenmesh::org 93ms 0.14% 86.47% 360ms 0.54% __dynamic_cast 356ms 0.53% 87.01% 356ms 0.53% std::_Rb_tree_decrement 232ms 0.35% 87.35% 346ms 0.52% tetgen::tetgenmesh::bond 18ms 0.027% 87.38% 345ms 0.52% std::vector::insert (inline) 8ms 0.012% 87.39% 339ms 0.51% VertexElement::~VertexElement 28ms 0.042% 87.44% 338ms 0.51% tetgen::tetgenmesh::queue::push 4ms 0.006% 87.44% 334ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement