File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45061ms, 85.40% of 52765ms total Dropped 931 nodes (cum <= 263.82ms) flat flat% sum% cum cum% 0 0% 0% 52695ms 99.87% __libc_start_call_main 0 0% 0% 52695ms 99.87% __libc_start_main_impl 0 0% 0% 52695ms 99.87% _start 0 0% 0% 52681ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52681ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52681ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52681ms 99.84% main 0 0% 0% 52643ms 99.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52643ms 99.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52643ms 99.77% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52396ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 46087ms 87.34% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46041ms 87.26% MeshBasedCellPopulation::Update 0 0% 0% 27937ms 52.95% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 27936ms 52.94% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 250ms 0.47% 0.47% 24757ms 46.92% VertexMesh::VertexMesh 0 0% 0.47% 16564ms 31.39% MutableMesh::ReMesh 1ms 0.0019% 0.48% 13089ms 24.81% tetgen::tetrahedralize 2ms 0.0038% 0.48% 12951ms 24.54% tetgen::tetgenmesh::delaunizevertices 10ms 0.019% 0.5% 12942ms 24.53% tetgen::tetgenmesh::incrflipdelaunay 500ms 0.95% 1.45% 11474ms 21.75% tetgen::tetgenmesh::lawson 459ms 0.87% 2.32% 9313ms 17.65% VertexElement::AddFace 4ms 0.0076% 2.32% 8601ms 16.30% std::set::insert (inline) 87ms 0.16% 2.49% 8130ms 15.41% std::_Rb_tree::_M_insert_unique 5831ms 11.05% 13.54% 5831ms 11.05% std::_Rb_tree_increment 155ms 0.29% 13.83% 4836ms 9.17% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.0038% 13.84% 4821ms 9.14% std::set_intersection (inline) 300ms 0.57% 14.41% 4819ms 9.13% std::__set_intersection 293ms 0.56% 14.96% 4537ms 8.60% std::_Rb_tree::_M_insert_ (inline) 27ms 0.051% 15.01% 4154ms 7.87% Node::AddElement 186ms 0.35% 15.36% 4032ms 7.64% std::_Rb_tree_const_iterator::operator++ (inline) 1169ms 2.22% 17.58% 3879ms 7.35% __GI___libc_free 1023ms 1.94% 19.52% 3829ms 7.26% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3789ms 7.18% 26.70% 3789ms 7.18% std::_Rb_tree::_S_right (inline) 6ms 0.011% 26.71% 3741ms 7.09% std::_Rb_tree::~_Rb_tree (inline) 1332ms 2.52% 29.24% 3734ms 7.08% std::_Rb_tree::_M_erase 0 0% 29.24% 3685ms 6.98% std::set::~set (inline) 62ms 0.12% 29.35% 3684ms 6.98% MutableElement::AddNode 212ms 0.4% 29.75% 3674ms 6.96% operator new 229ms 0.43% 30.19% 3574ms 6.77% std::__new_allocator::deallocate (inline) 0 0% 30.19% 3558ms 6.74% std::allocator_traits::deallocate (inline) 0 0% 30.19% 3484ms 6.60% AbstractCellPopulation::WriteResultsToFiles 100ms 0.19% 30.38% 3484ms 6.60% tetgen::tetgenmesh::insphere_sos 965ms 1.83% 32.21% 3389ms 6.42% __GI___libc_malloc 48ms 0.091% 32.30% 3383ms 6.41% std::__new_allocator::allocate (inline) 3055ms 5.79% 38.09% 3371ms 6.39% tetgen::insphere 0 0% 38.09% 3354ms 6.36% std::allocator_traits::allocate (inline) 0 0% 38.09% 3214ms 6.09% VertexMesh::~VertexMesh 11ms 0.021% 38.11% 2706ms 5.13% TetrahedralMesh::ImportFromMesher 1219ms 2.31% 40.42% 2706ms 5.13% _int_free 172ms 0.33% 40.74% 2690ms 5.10% tetgen::tetgenmesh::flip23 0 0% 40.74% 2672ms 5.06% std::_Hashtable::count (inline) 8ms 0.015% 40.76% 2672ms 5.06% std::_Hashtable::find (inline) 0 0% 40.76% 2672ms 5.06% std::unordered_set::count (inline) 0 0% 40.76% 2666ms 5.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0038% 40.76% 2604ms 4.94% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 40.76% 2569ms 4.87% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 40.76% 2354ms 4.46% std::_Rb_tree::_M_create_node (inline) 0 0% 40.76% 2334ms 4.42% std::_Rb_tree::_M_get_node (inline) 0 0% 40.76% 2321ms 4.40% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.0038% 40.77% 2272ms 4.31% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 194ms 0.37% 41.14% 2252ms 4.27% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 176ms 0.33% 41.47% 2161ms 4.10% VertexMesh::Clear 84ms 0.16% 41.63% 2160ms 4.09% Node::~Node 1777ms 3.37% 45.00% 2082ms 3.95% _int_malloc 0 0% 45.00% 2082ms 3.95% std::_Rb_tree_iterator::operator++ (inline) 173ms 0.33% 45.32% 2049ms 3.88% tetgen::tetgenmesh::flip32 181ms 0.34% 45.67% 1998ms 3.79% std::_Hashtable::_M_find_before_node (inline) 0 0% 45.67% 1998ms 3.79% std::_Hashtable::_M_find_node (inline) 1953ms 3.70% 49.37% 1953ms 3.70% std::_Rb_tree_insert_and_rebalance 0 0% 49.37% 1857ms 3.52% MeshBasedCellPopulation::UpdateNodePairs 1853ms 3.51% 52.88% 1853ms 3.51% Node::GetIndex 0 0% 52.88% 1767ms 3.35% std::_Rb_tree::_M_drop_node (inline) 0 0% 52.88% 1757ms 3.33% std::_Rb_tree::_M_put_node (inline) 19ms 0.036% 52.92% 1756ms 3.33% std::__detail::_Hashtable_base::_M_equals (inline) 9ms 0.017% 52.93% 1739ms 3.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.023% 52.96% 1629ms 3.09% MeshBasedCellPopulation::SpringIterator::operator++ 1558ms 2.95% 55.91% 1558ms 2.95% std::__detail::_Hashtable_base::_S_equals (inline) 647ms 1.23% 57.13% 1490ms 2.82% std::_Rb_tree::_M_lower_bound (inline) 1387ms 2.63% 59.76% 1479ms 2.80% tetgen::orient3d 14ms 0.027% 59.79% 1345ms 2.55% std::_Vector_base::_M_deallocate (inline) 196ms 0.37% 60.16% 1339ms 2.54% tetgen::tetgenmesh::enqueueflipface 3ms 0.0057% 60.17% 1312ms 2.49% Element::Element 886ms 1.68% 61.85% 1281ms 2.43% malloc_consolidate 6ms 0.011% 61.86% 1252ms 2.37% _int_free_maybe_consolidate 32ms 0.061% 61.92% 1214ms 2.30% tetgen::tetgenmesh::locate 0 0% 61.92% 1192ms 2.26% std::vector::~vector (inline) 1ms 0.0019% 61.92% 1157ms 2.19% std::_Vector_base::~_Vector_base (inline) 74ms 0.14% 62.06% 1157ms 2.19% std::map::operator[] 93ms 0.18% 62.24% 1136ms 2.15% tetgen::tetgenmesh::preciselocate 189ms 0.36% 62.59% 1094ms 2.07% TetrahedralMesh::Clear 0 0% 62.59% 1015ms 1.92% std::_Rb_tree::lower_bound (inline) 0 0% 62.59% 1015ms 1.92% std::map::lower_bound (inline) 5ms 0.0095% 62.60% 998ms 1.89% Element::RegisterWithNodes (inline) 976ms 1.85% 64.45% 976ms 1.85% tetgen::tetgenmesh::triface::triface 0 0% 64.45% 966ms 1.83% VoronoiDataWriter::Visit 729ms 1.38% 65.84% 896ms 1.70% AbstractElement::GetNodeGlobalIndex 50ms 0.095% 65.93% 872ms 1.65% std::vector::_M_realloc_insert 5ms 0.0095% 65.94% 861ms 1.63% VertexMesh::GenerateVerticesFromElementCircumcentres 336ms 0.64% 66.58% 814ms 1.54% AbstractElement::GetNodeLocation 388ms 0.74% 67.31% 801ms 1.52% tetgen::tetgenmesh::fnextself 779ms 1.48% 68.79% 779ms 1.48% tetgen::tetgenmesh::triface::operator= 768ms 1.46% 70.24% 768ms 1.46% Node::rGetLocation 1ms 0.0019% 70.25% 740ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 0 0% 70.25% 727ms 1.38% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.0095% 70.25% 719ms 1.36% std::_Hashtable::_M_bucket_index (inline) 0 0% 70.25% 714ms 1.35% std::__detail::_Hash_code_base::_M_bucket_index (inline) 714ms 1.35% 71.61% 714ms 1.35% std::__detail::_Mod_range_hashing::operator() (inline) 12ms 0.023% 71.63% 702ms 1.33% Element::CalculateCircumsphere 12ms 0.023% 71.65% 692ms 1.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 28ms 0.053% 71.71% 676ms 1.28% boost::numeric::ublas::vector_assign (inline) 675ms 1.28% 72.99% 675ms 1.28% [libchaste_mesh.so] 10ms 0.019% 73.00% 673ms 1.28% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.013% 73.02% 671ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 6ms 0.011% 73.03% 644ms 1.22% std::_Vector_base::_M_allocate (inline) 634ms 1.20% 74.23% 634ms 1.20% unlink_chunk 103ms 0.2% 74.43% 622ms 1.18% std::vector::push_back (inline) 14ms 0.027% 74.45% 621ms 1.18% AbstractTetrahedralElement::CalculateJacobian 608ms 1.15% 75.61% 608ms 1.15% std::vector::size (inline) 36ms 0.068% 75.67% 569ms 1.08% __atan2 568ms 1.08% 76.75% 568ms 1.08% tetgen::tetgenmesh::oppo 0 0% 76.75% 557ms 1.06% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 76.75% 557ms 1.06% std::_Hashtable::~_Hashtable (inline) 0 0% 76.75% 557ms 1.06% std::unordered_set::~unordered_set (inline) 68ms 0.13% 76.88% 547ms 1.04% std::_Rb_tree::find (inline) 0 0% 76.88% 544ms 1.03% std::set::find (inline) 539ms 1.02% 77.90% 539ms 1.02% AbstractElement::IsDeleted 431ms 0.82% 78.72% 533ms 1.01% __ieee754_atan2_fma 44ms 0.083% 78.80% 521ms 0.99% tetgen::tetgenmesh::enext2fnext 49ms 0.093% 78.89% 516ms 0.98% tetgen::tetgenmesh::enextfnext 0 0% 78.89% 490ms 0.93% std::_Hashtable::_M_insert (inline) 17ms 0.032% 78.93% 490ms 0.93% std::_Hashtable::_M_insert_unique_aux (inline) 0 0% 78.93% 490ms 0.93% std::__detail::_Insert_base::insert (inline) 0 0% 78.93% 490ms 0.93% std::unordered_set::insert (inline) 0 0% 78.93% 486ms 0.92% std::insert_iterator::operator= (inline) 26ms 0.049% 78.97% 474ms 0.9% VertexMesh::CalculateUnitNormalToFaceWithArea 12ms 0.023% 79.00% 473ms 0.9% std::_Hashtable::_M_insert_unique 312ms 0.59% 79.59% 473ms 0.9% tetgen::tetgenmesh::sym 0 0% 79.59% 463ms 0.88% boost::numeric::ublas::inner_prod (inline) 6ms 0.011% 79.60% 459ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 36ms 0.068% 79.67% 458ms 0.87% AbstractTetrahedralElement::RefreshJacobian 21ms 0.04% 79.71% 453ms 0.86% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.71% 440ms 0.83% std::_Rb_tree::_M_insert_unique_ (inline) 28ms 0.053% 79.76% 435ms 0.82% tetgen::tetgenmesh::queue::push 95ms 0.18% 79.94% 410ms 0.78% boost::numeric::ublas::indexing_vector_assign 11ms 0.021% 79.96% 409ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 347ms 0.66% 80.62% 405ms 0.77% tetgen::tetgenmesh::link::add 395ms 0.75% 81.37% 395ms 0.75% boost::numeric::ublas::c_vector::operator() 4ms 0.0076% 81.38% 393ms 0.74% CellPropertyCollection::GetPropertiesType (inline) 0 0% 81.38% 389ms 0.74% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.047% 81.42% 385ms 0.73% std::vector::insert (inline) 3ms 0.0057% 81.43% 382ms 0.72% Cell::GetCellId 76ms 0.14% 81.57% 379ms 0.72% __dynamic_cast 13ms 0.025% 81.60% 378ms 0.72% std::_Hashtable::clear (inline) 285ms 0.54% 82.14% 376ms 0.71% tetgen::tetgenmesh::bond 0 0% 82.14% 374ms 0.71% std::__detail::_AllocNode::operator() (inline) 0 0% 82.14% 374ms 0.71% std::__detail::_Hashtable_alloc::_M_allocate_node (inline) 0 0% 82.14% 374ms 0.71% std::__detail::_NodeBuilder::_S_build (inline) 161ms 0.31% 82.44% 369ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 359ms 0.68% 83.12% 359ms 0.68% tetgen::tetgenmesh::org 5ms 0.0095% 83.13% 336ms 0.64% VertexMesh::GetVolumeOfElement 10ms 0.019% 83.15% 317ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 37ms 0.07% 83.22% 316ms 0.6% tetgen::insphereadapt 1ms 0.0019% 83.22% 313ms 0.59% AbstractCellProperty::IsSubType (inline) 3ms 0.0057% 83.23% 313ms 0.59% AbstractTetrahedralElement::AbstractTetrahedralElement 311ms 0.59% 83.82% 311ms 0.59% tetgen::tetgenmesh::pointmark 123ms 0.23% 84.05% 309ms 0.59% Inverse 4ms 0.0076% 84.06% 300ms 0.57% std::__detail::_Hashtable_alloc::_M_deallocate_nodes (inline) 0 0% 84.06% 297ms 0.56% tcache_get (inline) 297ms 0.56% 84.62% 297ms 0.56% tcache_get_n (inline) 40ms 0.076% 84.70% 296ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.70% 296ms 0.56% std::__detail::_Hashtable_alloc::_M_deallocate_node (inline) 0 0% 84.70% 296ms 0.56% std::__detail::_Hashtable_alloc::_M_deallocate_node_ptr (inline) 292ms 0.55% 85.25% 292ms 0.55% std::_Rb_tree_decrement 72ms 0.14% 85.39% 281ms 0.53% tetgen::tetgenmesh::queue::pop 4ms 0.0076% 85.40% 266ms 0.5% VertexMeshWriter::MakeVtkMesh 2ms 0.0038% 85.40% 265ms 0.5% VertexElement::~VertexElement