File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 69084ms, 86.59% of 79784ms total Dropped 868 nodes (cum <= 398.92ms) flat flat% sum% cum cum% 0 0% 0% 79735ms 99.94% __libc_start_call_main 0 0% 0% 79735ms 99.94% __libc_start_main_impl 0 0% 0% 79735ms 99.94% _start 0 0% 0% 79719ms 99.92% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 79719ms 99.92% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 79719ms 99.92% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 79719ms 99.92% main 0 0% 0% 79687ms 99.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 79687ms 99.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 79687ms 99.88% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 79418ms 99.54% AbstractCellBasedSimulation::Solve 0 0% 0% 67533ms 84.64% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0013% 0.0013% 67459ms 84.55% MeshBasedCellPopulation::Update 0 0% 0.0013% 43690ms 54.76% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0013% 43689ms 54.76% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 509ms 0.64% 0.64% 38199ms 47.88% VertexMesh::VertexMesh 0 0% 0.64% 18749ms 23.50% MutableMesh::ReMesh 603ms 0.76% 1.40% 16135ms 20.22% TetrahedralMesh::EdgeIterator::operator++ 40ms 0.05% 1.45% 14688ms 18.41% std::set::insert (inline) 185ms 0.23% 1.68% 14137ms 17.72% std::_Rb_tree::_M_insert_unique 0 0% 1.68% 12983ms 16.27% tetgen::tetrahedralize 0 0% 1.68% 12817ms 16.06% tetgen::tetgenmesh::delaunizevertices 5ms 0.0063% 1.68% 12811ms 16.06% tetgen::tetgenmesh::incrflipdelaunay 412ms 0.52% 2.20% 12371ms 15.51% VertexElement::AddFace 2966ms 3.72% 5.92% 12059ms 15.11% std::_Rb_tree::_M_lower_bound (inline) 596ms 0.75% 6.66% 11382ms 14.27% tetgen::tetgenmesh::lawson 236ms 0.3% 6.96% 11176ms 14.01% std::_Rb_tree::find (inline) 0 0% 6.96% 10698ms 13.41% std::set::count (inline) 273ms 0.34% 7.30% 10248ms 12.84% operator new 3182ms 3.99% 11.29% 9870ms 12.37% __GI___libc_malloc 288ms 0.36% 11.65% 9070ms 11.37% std::_Rb_tree::_M_insert_ (inline) 8857ms 11.10% 22.75% 8857ms 11.10% std::_Rb_tree_increment 79ms 0.099% 22.85% 8277ms 10.37% std::__new_allocator::allocate (inline) 0 0% 22.85% 8242ms 10.33% std::allocator_traits::allocate (inline) 7725ms 9.68% 32.53% 7725ms 9.68% std::operator< (inline) 8ms 0.01% 32.54% 7666ms 9.61% std::less::operator() (inline) 4ms 0.005% 32.55% 7178ms 9.00% std::set_intersection (inline) 435ms 0.55% 33.09% 7174ms 8.99% std::__set_intersection 0 0% 33.09% 6960ms 8.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 33.09% 6755ms 8.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0075% 33.10% 6728ms 8.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 1159ms 1.45% 34.55% 6720ms 8.42% __GI___libc_free 0 0% 34.55% 6569ms 8.23% std::_Rb_tree::_M_create_node (inline) 0 0% 34.55% 6535ms 8.19% std::_Rb_tree::_M_get_node (inline) 0 0% 34.55% 6518ms 8.17% std::_Rb_tree::_Alloc_node::operator() (inline) 25ms 0.031% 34.59% 6300ms 7.90% Node::AddElement 4739ms 5.94% 40.53% 6231ms 7.81% _int_malloc 274ms 0.34% 40.87% 6126ms 7.68% std::_Rb_tree_const_iterator::operator++ (inline) 5776ms 7.24% 48.11% 5776ms 7.24% std::_Rb_tree::_S_right (inline) 76ms 0.095% 48.20% 5641ms 7.07% std::__new_allocator::deallocate (inline) 0 0% 48.20% 5628ms 7.05% std::allocator_traits::deallocate (inline) 0 0% 48.20% 5532ms 6.93% VertexMesh::~VertexMesh 6ms 0.0075% 48.21% 5527ms 6.93% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2181ms 2.73% 50.95% 5495ms 6.89% _int_free 2ms 0.0025% 50.95% 5369ms 6.73% MeshBasedCellPopulation::UpdateNodePairs 1221ms 1.53% 52.48% 5224ms 6.55% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.014% 52.49% 5182ms 6.50% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.011% 52.50% 5005ms 6.27% std::_Rb_tree::~_Rb_tree (inline) 1529ms 1.92% 54.42% 4983ms 6.25% std::_Rb_tree::_M_erase 0 0% 54.42% 4915ms 6.16% std::set::~set (inline) 0 0% 54.42% 4732ms 5.93% AbstractCellPopulation::WriteResultsToFiles 8ms 0.01% 54.43% 4669ms 5.85% TetrahedralMesh::ImportFromMesher 68ms 0.085% 54.51% 4623ms 5.79% MutableElement::AddNode 63ms 0.079% 54.59% 3501ms 4.39% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 232ms 0.29% 54.88% 3474ms 4.35% std::_Rb_tree_iterator::operator++ (inline) 3ms 0.0038% 54.89% 3367ms 4.22% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2216ms 2.78% 57.67% 3200ms 4.01% malloc_consolidate 20ms 0.025% 57.69% 3012ms 3.78% std::_Vector_base::_M_deallocate (inline) 268ms 0.34% 58.03% 3007ms 3.77% tetgen::tetgenmesh::flip23 119ms 0.15% 58.18% 2976ms 3.73% tetgen::tetgenmesh::insphere_sos 69ms 0.086% 58.26% 2880ms 3.61% VertexMesh::Clear 2853ms 3.58% 61.84% 2853ms 3.58% Node::GetIndex 2ms 0.0025% 61.84% 2843ms 3.56% Element::Element 2598ms 3.26% 65.10% 2837ms 3.56% tetgen::insphere 0 0% 65.10% 2822ms 3.54% std::vector::~vector (inline) 10ms 0.013% 65.11% 2821ms 3.54% _int_free_maybe_consolidate 4ms 0.005% 65.11% 2801ms 3.51% std::_Vector_base::~_Vector_base (inline) 51ms 0.064% 65.18% 2762ms 3.46% Node::~Node 0 0% 65.18% 2666ms 3.34% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.18% 2636ms 3.30% std::_Rb_tree::_M_put_node (inline) 6ms 0.0075% 65.19% 2402ms 3.01% Element::RegisterWithNodes (inline) 2375ms 2.98% 68.16% 2375ms 2.98% std::_Rb_tree_insert_and_rebalance 5ms 0.0063% 68.17% 2214ms 2.77% VertexMesh::GenerateVerticesFromElementCircumcentres 188ms 0.24% 68.40% 2102ms 2.63% tetgen::tetgenmesh::flip32 1971ms 2.47% 70.88% 1971ms 2.47% [libchaste_mesh.so] 1968ms 2.47% 73.34% 1968ms 2.47% unlink_chunk 54ms 0.068% 73.41% 1790ms 2.24% std::vector::_M_realloc_insert 1ms 0.0013% 73.41% 1708ms 2.14% std::_Vector_base::_M_allocate (inline) 82ms 0.1% 73.51% 1588ms 1.99% std::map::operator[] 169ms 0.21% 73.73% 1567ms 1.96% tetgen::tetgenmesh::enqueueflipface 1441ms 1.81% 75.53% 1494ms 1.87% tetgen::orient3d 99ms 0.12% 75.66% 1388ms 1.74% std::vector::push_back (inline) 0 0% 75.66% 1376ms 1.72% std::_Rb_tree::lower_bound (inline) 0 0% 75.66% 1376ms 1.72% std::map::lower_bound (inline) 1036ms 1.30% 76.95% 1235ms 1.55% AbstractElement::GetNodeGlobalIndex 49ms 0.061% 77.02% 1233ms 1.55% TetrahedralMesh::Clear 1225ms 1.54% 78.55% 1225ms 1.54% Node::rGetLocation 30ms 0.038% 78.59% 1173ms 1.47% tetgen::tetgenmesh::locate 619ms 0.78% 79.36% 1161ms 1.46% AbstractElement::GetNodeLocation 1ms 0.0013% 79.37% 1108ms 1.39% VoronoiDataWriter::Visit 80ms 0.1% 79.47% 1095ms 1.37% tetgen::tetgenmesh::preciselocate 15ms 0.019% 79.48% 1077ms 1.35% Element::CalculateCircumsphere 1ms 0.0013% 79.49% 1072ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 554ms 0.69% 80.18% 953ms 1.19% tetgen::tetgenmesh::sym 947ms 1.19% 81.37% 947ms 1.19% AbstractElement::IsDeleted 251ms 0.31% 81.68% 920ms 1.15% boost::numeric::ublas::vector_assign (inline) 5ms 0.0063% 81.69% 908ms 1.14% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.011% 81.70% 877ms 1.10% AbstractTetrahedralElement::CalculateJacobian 2ms 0.0025% 81.70% 877ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.0038% 81.71% 843ms 1.06% AbstractTetrahedralElement::CalculateInverseJacobian 20ms 0.025% 81.73% 806ms 1.01% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 53ms 0.066% 81.80% 714ms 0.89% AbstractTetrahedralElement::RefreshJacobian 621ms 0.78% 82.58% 621ms 0.78% tetgen::tetgenmesh::triface::triface 603ms 0.76% 83.33% 603ms 0.76% tetgen::tetgenmesh::oppo 42ms 0.053% 83.38% 595ms 0.75% __atan2 581ms 0.73% 84.11% 581ms 0.73% std::vector::size (inline) 39ms 0.049% 84.16% 576ms 0.72% std::vector::insert (inline) 0 0% 84.16% 555ms 0.7% std::insert_iterator::operator= (inline) 504ms 0.63% 84.79% 543ms 0.68% __ieee754_atan2_fma 42ms 0.053% 84.85% 529ms 0.66% tetgen::tetgenmesh::enext2fnext 79ms 0.099% 84.94% 516ms 0.65% tetgen::tetgenmesh::enextfnext 389ms 0.49% 85.43% 503ms 0.63% tetgen::tetgenmesh::fnextself 0 0% 85.43% 500ms 0.63% std::_Rb_tree::_M_insert_unique_ (inline) 110ms 0.14% 85.57% 495ms 0.62% std::_Rb_tree_iterator::operator-- (inline) 9ms 0.011% 85.58% 490ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 0 0% 85.58% 476ms 0.6% std::set::find (inline) 0 0% 85.58% 470ms 0.59% boost::numeric::ublas::inner_prod (inline) 0 0% 85.58% 467ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.0013% 85.58% 466ms 0.58% Cell::GetCellId 2ms 0.0025% 85.58% 463ms 0.58% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 10ms 0.013% 85.60% 461ms 0.58% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.005% 85.60% 440ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 22ms 0.028% 85.63% 435ms 0.55% tetgen::tetgenmesh::queue::push 164ms 0.21% 85.84% 430ms 0.54% boost::numeric::ublas::vector_inner_prod::apply (inline) 22ms 0.028% 85.86% 426ms 0.53% VertexMesh::CalculateUnitNormalToFaceWithArea 69ms 0.086% 85.95% 421ms 0.53% tetgen::tetgenmesh::queue::pop 0 0% 85.95% 411ms 0.52% VertexMeshWriter::WriteVtkUsingMesh 95ms 0.12% 86.07% 410ms 0.51% boost::numeric::ublas::indexing_vector_assign 125ms 0.16% 86.23% 409ms 0.51% __dynamic_cast 290ms 0.36% 86.59% 400ms 0.5% tetgen::tetgenmesh::link::add