File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53609ms, 85.89% of 62415ms total Dropped 912 nodes (cum <= 312.07ms) flat flat% sum% cum cum% 0 0% 0% 62355ms 99.90% __libc_start_call_main 0 0% 0% 62355ms 99.90% __libc_start_main_impl 0 0% 0% 62355ms 99.90% _start 0 0% 0% 62337ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62337ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62337ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62337ms 99.88% main 0 0% 0% 62296ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62296ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62296ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 62023ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 52866ms 84.70% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0016% 0.0016% 52816ms 84.62% MeshBasedCellPopulation::Update 1ms 0.0016% 0.0032% 28633ms 45.88% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0032% 28631ms 45.87% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 202ms 0.32% 0.33% 25602ms 41.02% VertexMesh::VertexMesh 0 0% 0.33% 20156ms 32.29% MutableMesh::ReMesh 0 0% 0.33% 16277ms 26.08% tetgen::tetrahedralize 1ms 0.0016% 0.33% 16119ms 25.83% tetgen::tetgenmesh::delaunizevertices 7ms 0.011% 0.34% 16113ms 25.82% tetgen::tetgenmesh::incrflipdelaunay 576ms 0.92% 1.26% 14401ms 23.07% tetgen::tetgenmesh::lawson 613ms 0.98% 2.24% 12394ms 19.86% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.056% 2.30% 10097ms 16.18% std::set::insert (inline) 354ms 0.57% 2.87% 9837ms 15.76% VertexElement::AddFace 215ms 0.34% 3.21% 9626ms 15.42% std::_Rb_tree::_M_insert_unique 3219ms 5.16% 8.37% 9130ms 14.63% std::_Rb_tree::_M_lower_bound (inline) 254ms 0.41% 8.78% 8635ms 13.83% std::_Rb_tree::find (inline) 0 0% 8.78% 8035ms 12.87% std::set::count (inline) 118ms 0.19% 8.97% 5845ms 9.36% std::less::operator() (inline) 297ms 0.48% 9.44% 5793ms 9.28% std::_Rb_tree::_M_insert_ (inline) 5792ms 9.28% 18.72% 5792ms 9.28% std::operator< (inline) 0 0% 18.72% 5460ms 8.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.72% 5331ms 8.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 18.72% 5297ms 8.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 5085ms 8.15% 26.87% 5085ms 8.15% std::_Rb_tree_increment 162ms 0.26% 27.13% 5024ms 8.05% operator new 1213ms 1.94% 29.07% 4775ms 7.65% __GI___libc_malloc 6ms 0.0096% 29.08% 4408ms 7.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 29.08% 4404ms 7.06% MeshBasedCellPopulation::UpdateNodePairs 43ms 0.069% 29.15% 4387ms 7.03% std::__new_allocator::allocate (inline) 0 0% 29.15% 4359ms 6.98% std::allocator_traits::allocate (inline) 20ms 0.032% 29.18% 4261ms 6.83% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.016% 29.20% 4201ms 6.73% std::_Rb_tree::~_Rb_tree (inline) 1405ms 2.25% 31.45% 4189ms 6.71% std::_Rb_tree::_M_erase 0 0% 31.45% 4155ms 6.66% std::set::~set (inline) 121ms 0.19% 31.64% 3931ms 6.30% tetgen::tetgenmesh::insphere_sos 2ms 0.0032% 31.65% 3925ms 6.29% std::set_intersection (inline) 267ms 0.43% 32.07% 3923ms 6.29% std::__set_intersection 1143ms 1.83% 33.91% 3915ms 6.27% __GI___libc_free 1223ms 1.96% 35.86% 3896ms 6.24% std::_Rb_tree::_M_get_insert_unique_pos 3502ms 5.61% 41.48% 3795ms 6.08% tetgen::insphere 0 0% 41.48% 3616ms 5.79% std::_Rb_tree::_M_create_node (inline) 0 0% 41.48% 3591ms 5.75% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.48% 3579ms 5.73% std::_Rb_tree::_M_get_node (inline) 0 0% 41.48% 3532ms 5.66% AbstractCellPopulation::WriteResultsToFiles 139ms 0.22% 41.70% 3493ms 5.60% std::__new_allocator::deallocate (inline) 0 0% 41.70% 3484ms 5.58% std::allocator_traits::deallocate (inline) 115ms 0.18% 41.88% 3465ms 5.55% tetgen::tetgenmesh::flip23 46ms 0.074% 41.96% 3399ms 5.45% Node::AddElement 168ms 0.27% 42.23% 3198ms 5.12% std::_Rb_tree_const_iterator::operator++ (inline) 2365ms 3.79% 46.01% 3196ms 5.12% _int_malloc 10ms 0.016% 46.03% 3087ms 4.95% TetrahedralMesh::ImportFromMesher 0 0% 46.03% 3047ms 4.88% VertexMesh::~VertexMesh 3032ms 4.86% 50.89% 3032ms 4.86% std::_Rb_tree::_S_right (inline) 1408ms 2.26% 53.14% 2768ms 4.43% _int_free 80ms 0.13% 53.27% 2727ms 4.37% MutableElement::AddNode 157ms 0.25% 53.52% 2592ms 4.15% tetgen::tetgenmesh::flip32 4ms 0.0064% 53.53% 2402ms 3.85% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 182ms 0.29% 53.82% 2380ms 3.81% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0016% 53.82% 2213ms 3.55% std::_Rb_tree_iterator::operator++ (inline) 146ms 0.23% 54.06% 2212ms 3.54% Node::~Node 0 0% 54.06% 2174ms 3.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.06% 2161ms 3.46% std::_Rb_tree::_M_put_node (inline) 148ms 0.24% 54.29% 1990ms 3.19% VertexMesh::Clear 1969ms 3.15% 57.45% 1969ms 3.15% std::_Rb_tree_insert_and_rebalance 210ms 0.34% 57.79% 1916ms 3.07% tetgen::tetgenmesh::enqueueflipface 1665ms 2.67% 60.45% 1665ms 2.67% Node::GetIndex 1545ms 2.48% 62.93% 1635ms 2.62% tetgen::orient3d 4ms 0.0064% 62.94% 1548ms 2.48% Element::Element 42ms 0.067% 63.00% 1424ms 2.28% tetgen::tetgenmesh::locate 27ms 0.043% 63.05% 1350ms 2.16% std::_Vector_base::_M_deallocate (inline) 917ms 1.47% 64.51% 1345ms 2.15% malloc_consolidate 82ms 0.13% 64.65% 1331ms 2.13% tetgen::tetgenmesh::preciselocate 0 0% 64.65% 1271ms 2.04% std::vector::~vector (inline) 69ms 0.11% 64.76% 1256ms 2.01% TetrahedralMesh::Clear 4ms 0.0064% 64.76% 1186ms 1.90% Element::RegisterWithNodes (inline) 0 0% 64.76% 1185ms 1.90% std::_Vector_base::~_Vector_base (inline) 4ms 0.0064% 64.77% 1160ms 1.86% _int_free_maybe_consolidate 69ms 0.11% 64.88% 1065ms 1.71% std::map::operator[] 60ms 0.096% 64.98% 1062ms 1.70% std::vector::_M_realloc_insert 1062ms 1.70% 66.68% 1062ms 1.70% tetgen::tetgenmesh::triface::triface 1029ms 1.65% 68.33% 1029ms 1.65% tetgen::tetgenmesh::oppo 841ms 1.35% 69.67% 1026ms 1.64% AbstractElement::GetNodeGlobalIndex 993ms 1.59% 71.26% 993ms 1.59% unlink_chunk 0 0% 71.26% 926ms 1.48% std::_Rb_tree::lower_bound (inline) 0 0% 71.26% 926ms 1.48% std::map::lower_bound (inline) 1ms 0.0016% 71.27% 893ms 1.43% VoronoiDataWriter::Visit 303ms 0.49% 71.75% 888ms 1.42% tetgen::tetgenmesh::sym 880ms 1.41% 73.16% 880ms 1.41% [libchaste_mesh.so] 122ms 0.2% 73.36% 849ms 1.36% std::vector::push_back (inline) 5ms 0.008% 73.37% 847ms 1.36% VertexMesh::GenerateVerticesFromElementCircumcentres 806ms 1.29% 74.66% 806ms 1.29% tetgen::tetgenmesh::triface::operator= 6ms 0.0096% 74.67% 786ms 1.26% std::_Vector_base::_M_allocate (inline) 0 0% 74.67% 773ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 0 0% 74.67% 720ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.019% 74.69% 702ms 1.12% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.027% 74.71% 687ms 1.10% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 33ms 0.053% 74.77% 665ms 1.07% tetgen::tetgenmesh::queue::push 26ms 0.042% 74.81% 653ms 1.05% boost::numeric::ublas::vector_assign (inline) 17ms 0.027% 74.83% 650ms 1.04% AbstractTetrahedralElement::CalculateJacobian 391ms 0.63% 75.46% 645ms 1.03% tetgen::tetgenmesh::fnextself 55ms 0.088% 75.55% 642ms 1.03% __atan2 352ms 0.56% 76.11% 632ms 1.01% tetgen::tetgenmesh::link::add 242ms 0.39% 76.50% 628ms 1.01% tetgen::tetgenmesh::bond 9ms 0.014% 76.52% 617ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 79ms 0.13% 76.64% 611ms 0.98% tetgen::tetgenmesh::enext2fnext 602ms 0.96% 77.61% 602ms 0.96% tetgen::tetgenmesh::decode 0 0% 77.61% 590ms 0.95% std::set::find (inline) 267ms 0.43% 78.03% 583ms 0.93% AbstractElement::GetNodeLocation 459ms 0.74% 78.77% 582ms 0.93% __ieee754_atan2_fma 557ms 0.89% 79.66% 557ms 0.89% std::vector::size (inline) 48ms 0.077% 79.74% 556ms 0.89% tetgen::tetgenmesh::enextfnext 543ms 0.87% 80.61% 543ms 0.87% Node::rGetLocation 535ms 0.86% 81.47% 535ms 0.86% AbstractElement::IsDeleted 0 0% 81.47% 508ms 0.81% boost::numeric::ublas::inner_prod (inline) 2ms 0.0032% 81.47% 503ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 81.47% 503ms 0.81% std::insert_iterator::operator= (inline) 38ms 0.061% 81.53% 501ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 46ms 0.074% 81.60% 457ms 0.73% AbstractTetrahedralElement::RefreshJacobian 447ms 0.72% 82.32% 447ms 0.72% tetgen::tetgenmesh::org 15ms 0.024% 82.34% 441ms 0.71% Element::CalculateCircumsphere 1ms 0.0016% 82.35% 433ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 28ms 0.045% 82.39% 421ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 6ms 0.0096% 82.40% 418ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 190ms 0.3% 82.70% 403ms 0.65% AbstractTetrahedralMesh::GetElement 98ms 0.16% 82.86% 403ms 0.65% boost::numeric::ublas::indexing_vector_assign 176ms 0.28% 83.14% 403ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.019% 83.16% 401ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.008% 83.17% 388ms 0.62% Cell::GetCellId 0 0% 83.17% 384ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0048% 83.18% 375ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 371ms 0.59% 83.77% 371ms 0.59% tetgen::tetgenmesh::encode 368ms 0.59% 84.36% 368ms 0.59% boost::numeric::ublas::c_vector::operator() 368ms 0.59% 84.95% 368ms 0.59% std::_Rb_tree_decrement 19ms 0.03% 84.98% 362ms 0.58% std::vector::insert (inline) 3ms 0.0048% 84.98% 359ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 99ms 0.16% 85.14% 359ms 0.58% __dynamic_cast 133ms 0.21% 85.36% 345ms 0.55% Inverse 8ms 0.013% 85.37% 332ms 0.53% VertexElement::~VertexElement 0 0% 85.37% 327ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 326ms 0.52% 85.89% 326ms 0.52% tetgen::tetgenmesh::memorypool::alloc