File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58195ms, 87.89% of 66211ms total Dropped 896 nodes (cum <= 331.06ms) flat flat% sum% cum cum% 0 0% 0% 66140ms 99.89% __libc_start_call_main 0 0% 0% 66140ms 99.89% __libc_start_main_impl 0 0% 0% 66140ms 99.89% _start 0 0% 0% 66119ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66119ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66119ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66119ms 99.86% main 0 0% 0% 66080ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66080ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66080ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65811ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 54893ms 82.91% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 54844ms 82.83% MeshBasedCellPopulation::Update 0 0% 0% 32332ms 48.83% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 32332ms 48.83% MeshBasedCellPopulation::TessellateIfNeeded 232ms 0.35% 0.35% 28149ms 42.51% VertexMesh::VertexMesh 0 0% 0.35% 18180ms 27.46% MutableMesh::ReMesh 524ms 0.79% 1.14% 13423ms 20.27% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.14% 13230ms 19.98% tetgen::tetrahedralize 3ms 0.0045% 1.15% 13095ms 19.78% tetgen::tetgenmesh::delaunizevertices 5ms 0.0076% 1.15% 13088ms 19.77% tetgen::tetgenmesh::incrflipdelaunay 522ms 0.79% 1.94% 11693ms 17.66% tetgen::tetgenmesh::lawson 28ms 0.042% 1.98% 11032ms 16.66% std::set::insert (inline) 192ms 0.29% 2.27% 10541ms 15.92% std::_Rb_tree::_M_insert_unique 3030ms 4.58% 6.85% 10245ms 15.47% std::_Rb_tree::_M_lower_bound (inline) 475ms 0.72% 7.57% 9754ms 14.73% VertexElement::AddFace 244ms 0.37% 7.94% 9548ms 14.42% std::_Rb_tree::find (inline) 0 0% 7.94% 8991ms 13.58% std::set::count (inline) 7077ms 10.69% 18.63% 7077ms 10.69% std::_Rb_tree_increment 124ms 0.19% 18.81% 6917ms 10.45% std::less::operator() (inline) 6842ms 10.33% 29.15% 6842ms 10.33% std::operator< (inline) 284ms 0.43% 29.58% 6113ms 9.23% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0015% 29.58% 5824ms 8.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 214ms 0.32% 29.90% 5780ms 8.73% operator new 0 0% 29.90% 5666ms 8.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0091% 29.91% 5627ms 8.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 1085ms 1.64% 31.55% 5502ms 8.31% __GI___libc_malloc 0 0% 31.55% 4936ms 7.45% AbstractCellPopulation::WriteResultsToFiles 8ms 0.012% 31.56% 4875ms 7.36% std::_Rb_tree::~_Rb_tree (inline) 2069ms 3.12% 34.68% 4864ms 7.35% std::_Rb_tree::_M_erase 48ms 0.072% 34.76% 4820ms 7.28% std::__new_allocator::allocate (inline) 0 0% 34.76% 4805ms 7.26% std::set::~set (inline) 0 0% 34.76% 4797ms 7.25% std::allocator_traits::allocate (inline) 3ms 0.0045% 34.76% 4673ms 7.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0015% 34.76% 4671ms 7.05% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.003% 34.77% 4615ms 6.97% std::set_intersection (inline) 282ms 0.43% 35.19% 4613ms 6.97% std::__set_intersection 35ms 0.053% 35.24% 4599ms 6.95% Node::AddElement 1261ms 1.90% 37.15% 4571ms 6.90% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.012% 37.16% 4517ms 6.82% MeshBasedCellPopulation::SpringIterator::operator++ 1258ms 1.90% 39.06% 4288ms 6.48% __GI___libc_free 0 0% 39.06% 4216ms 6.37% VertexMesh::~VertexMesh 4177ms 6.31% 45.37% 4177ms 6.31% std::_Rb_tree::_S_right (inline) 2921ms 4.41% 49.78% 4067ms 6.14% _int_malloc 14ms 0.021% 49.80% 4025ms 6.08% TetrahedralMesh::ImportFromMesher 171ms 0.26% 50.06% 3857ms 5.83% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 50.06% 3840ms 5.80% std::_Rb_tree::_M_create_node (inline) 0 0% 50.06% 3807ms 5.75% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.06% 3794ms 5.73% std::_Rb_tree::_M_get_node (inline) 147ms 0.22% 50.28% 3719ms 5.62% std::__new_allocator::deallocate (inline) 0 0% 50.28% 3705ms 5.60% std::allocator_traits::deallocate (inline) 221ms 0.33% 50.62% 3687ms 5.57% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 117ms 0.18% 50.79% 3503ms 5.29% tetgen::tetgenmesh::insphere_sos 1ms 0.0015% 50.80% 3484ms 5.26% std::_Rb_tree_iterator::operator++ (inline) 77ms 0.12% 50.91% 3458ms 5.22% MutableElement::AddNode 4ms 0.006% 50.92% 3449ms 5.21% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3086ms 4.66% 55.58% 3376ms 5.10% tetgen::insphere 210ms 0.32% 55.90% 3031ms 4.58% tetgen::tetgenmesh::flip23 1199ms 1.81% 57.71% 3029ms 4.57% _int_free 222ms 0.34% 58.04% 3004ms 4.54% Node::~Node 244ms 0.37% 58.41% 2756ms 4.16% VertexMesh::Clear 2111ms 3.19% 61.60% 2111ms 3.19% std::_Rb_tree_insert_and_rebalance 180ms 0.27% 61.87% 2012ms 3.04% tetgen::tetgenmesh::flip32 6ms 0.0091% 61.88% 2006ms 3.03% Element::Element 0 0% 61.88% 1964ms 2.97% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.88% 1955ms 2.95% std::_Rb_tree::_M_put_node (inline) 1901ms 2.87% 64.75% 1901ms 2.87% Node::GetIndex 1269ms 1.92% 66.67% 1868ms 2.82% malloc_consolidate 22ms 0.033% 66.70% 1772ms 2.68% std::_Vector_base::_M_deallocate (inline) 0 0% 66.70% 1656ms 2.50% std::vector::~vector (inline) 6ms 0.0091% 66.71% 1655ms 2.50% Element::RegisterWithNodes (inline) 220ms 0.33% 67.04% 1615ms 2.44% TetrahedralMesh::Clear 0 0% 67.04% 1598ms 2.41% std::_Vector_base::~_Vector_base (inline) 8ms 0.012% 67.05% 1584ms 2.39% _int_free_maybe_consolidate 1331ms 2.01% 69.06% 1406ms 2.12% tetgen::orient3d 183ms 0.28% 69.34% 1400ms 2.11% tetgen::tetgenmesh::enqueueflipface 1344ms 2.03% 71.37% 1344ms 2.03% unlink_chunk 1311ms 1.98% 73.35% 1311ms 1.98% tetgen::tetgenmesh::triface::triface 61ms 0.092% 73.44% 1259ms 1.90% std::map::operator[] 1ms 0.0015% 73.44% 1220ms 1.84% VoronoiDataWriter::Visit 64ms 0.097% 73.54% 1192ms 1.80% std::vector::_M_realloc_insert 31ms 0.047% 73.59% 1179ms 1.78% tetgen::tetgenmesh::locate 6ms 0.0091% 73.60% 1165ms 1.76% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 73.60% 1128ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 73.60% 1128ms 1.70% std::map::lower_bound (inline) 87ms 0.13% 73.73% 1093ms 1.65% tetgen::tetgenmesh::preciselocate 934ms 1.41% 75.14% 1087ms 1.64% AbstractElement::GetNodeGlobalIndex 7ms 0.011% 75.15% 1010ms 1.53% std::_Vector_base::_M_allocate (inline) 122ms 0.18% 75.33% 969ms 1.46% std::vector::push_back (inline) 0 0% 75.33% 896ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 348ms 0.53% 75.86% 845ms 1.28% AbstractElement::GetNodeLocation 4ms 0.006% 75.87% 799ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.029% 75.89% 751ms 1.13% AbstractTetrahedralElement::CalculateJacobian 2ms 0.003% 75.90% 743ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 724ms 1.09% 76.99% 724ms 1.09% Node::rGetLocation 13ms 0.02% 77.01% 699ms 1.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 683ms 1.03% 78.04% 683ms 1.03% tetgen::tetgenmesh::oppo 362ms 0.55% 78.59% 680ms 1.03% tetgen::tetgenmesh::fnextself 53ms 0.08% 78.67% 676ms 1.02% __atan2 15ms 0.023% 78.69% 672ms 1.01% boost::numeric::ublas::vector_assign (inline) 643ms 0.97% 79.66% 643ms 0.97% [libchaste_mesh.so] 631ms 0.95% 80.62% 631ms 0.95% AbstractElement::IsDeleted 11ms 0.017% 80.63% 630ms 0.95% boost::numeric::ublas::c_vector::c_vector (inline) 523ms 0.79% 81.42% 623ms 0.94% __ieee754_atan2_fma 12ms 0.018% 81.44% 596ms 0.9% Element::CalculateCircumsphere 50ms 0.076% 81.52% 589ms 0.89% AbstractTetrahedralElement::RefreshJacobian 588ms 0.89% 82.40% 588ms 0.89% std::vector::size (inline) 583ms 0.88% 83.28% 583ms 0.88% tetgen::tetgenmesh::triface::operator= 0 0% 83.28% 552ms 0.83% std::set::find (inline) 350ms 0.53% 83.81% 496ms 0.75% tetgen::tetgenmesh::sym 0 0% 83.81% 483ms 0.73% std::insert_iterator::operator= (inline) 0 0% 83.81% 476ms 0.72% boost::numeric::ublas::inner_prod (inline) 5ms 0.0076% 83.82% 476ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.047% 83.87% 471ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 41ms 0.062% 83.93% 451ms 0.68% tetgen::tetgenmesh::enextfnext 18ms 0.027% 83.96% 449ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 45ms 0.068% 84.02% 438ms 0.66% tetgen::tetgenmesh::enext2fnext 0 0% 84.02% 437ms 0.66% std::_Rb_tree::_M_insert_unique_ (inline) 436ms 0.66% 84.68% 436ms 0.66% boost::numeric::ublas::c_vector::operator() 24ms 0.036% 84.72% 427ms 0.64% tetgen::tetgenmesh::queue::push 100ms 0.15% 84.87% 422ms 0.64% boost::numeric::ublas::indexing_vector_assign 246ms 0.37% 85.24% 417ms 0.63% AbstractTetrahedralMesh::GetElement 6ms 0.0091% 85.25% 404ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.029% 85.28% 401ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 302ms 0.46% 85.73% 400ms 0.6% tetgen::tetgenmesh::link::add 0 0% 85.73% 399ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 0 0% 85.73% 387ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 151ms 0.23% 85.96% 386ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 98ms 0.15% 86.11% 385ms 0.58% __dynamic_cast 5ms 0.0076% 86.12% 384ms 0.58% Cell::GetCellId 2ms 0.003% 86.12% 381ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 13ms 0.02% 86.14% 372ms 0.56% std::vector::insert (inline) 266ms 0.4% 86.54% 367ms 0.55% tetgen::tetgenmesh::bond 7ms 0.011% 86.55% 361ms 0.55% VertexElement::~VertexElement 140ms 0.21% 86.77% 349ms 0.53% Inverse 3ms 0.0045% 86.77% 345ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 63ms 0.095% 86.86% 343ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 343ms 0.52% 87.38% 343ms 0.52% std::_Rb_tree_decrement 338ms 0.51% 87.89% 338ms 0.51% tetgen::tetgenmesh::org