File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 43807ms, 86.48% of 50653ms total Dropped 840 nodes (cum <= 253.26ms) flat flat% sum% cum cum% 0 0% 0% 50623ms 99.94% __libc_start_call_main 0 0% 0% 50623ms 99.94% __libc_start_main_impl 0 0% 0% 50623ms 99.94% _start 0 0% 0% 50608ms 99.91% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 50608ms 99.91% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 50608ms 99.91% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 50608ms 99.91% main 0 0% 0% 50573ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 50572ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 50572ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 50404ms 99.51% AbstractCellBasedSimulation::Solve 0 0% 0% 41593ms 82.11% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.002% 0.002% 41550ms 82.03% MeshBasedCellPopulation::Update 0 0% 0.002% 26297ms 51.92% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.002% 26296ms 51.91% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 302ms 0.6% 0.6% 23561ms 46.51% VertexMesh::VertexMesh 0 0% 0.6% 11704ms 23.11% MutableMesh::ReMesh 371ms 0.73% 1.33% 11058ms 21.83% TetrahedralMesh::EdgeIterator::operator++ 25ms 0.049% 1.38% 9793ms 19.33% std::set::insert (inline) 101ms 0.2% 1.58% 9352ms 18.46% std::_Rb_tree::_M_insert_unique 2902ms 5.73% 7.31% 8740ms 17.25% std::_Rb_tree::_M_lower_bound (inline) 216ms 0.43% 7.73% 8383ms 16.55% VertexElement::AddFace 110ms 0.22% 7.95% 8175ms 16.14% std::_Rb_tree::find (inline) 1ms 0.002% 7.95% 7908ms 15.61% tetgen::tetrahedralize 0 0% 7.95% 7807ms 15.41% tetgen::tetgenmesh::delaunizevertices 2ms 0.0039% 7.96% 7804ms 15.41% tetgen::tetgenmesh::incrflipdelaunay 0 0% 7.96% 7765ms 15.33% std::set::count (inline) 350ms 0.69% 8.65% 6856ms 13.54% tetgen::tetgenmesh::lawson 173ms 0.34% 8.99% 6325ms 12.49% operator new 1991ms 3.93% 12.92% 6100ms 12.04% __GI___libc_malloc 233ms 0.46% 13.38% 6094ms 12.03% std::_Rb_tree::_M_insert_ (inline) 5561ms 10.98% 24.36% 5561ms 10.98% std::_Rb_tree_increment 58ms 0.11% 24.47% 5395ms 10.65% std::__new_allocator::allocate (inline) 0 0% 24.47% 5378ms 10.62% std::allocator_traits::allocate (inline) 59ms 0.12% 24.59% 5157ms 10.18% std::less::operator() (inline) 5146ms 10.16% 34.75% 5146ms 10.16% std::operator< (inline) 0 0% 34.75% 4858ms 9.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 34.75% 4721ms 9.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0039% 34.75% 4701ms 9.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 34.75% 4332ms 8.55% std::_Rb_tree::_M_create_node (inline) 0 0% 34.75% 4306ms 8.50% std::_Rb_tree::_M_get_node (inline) 0 0% 34.75% 4294ms 8.48% std::_Rb_tree::_Alloc_node::operator() (inline) 265ms 0.52% 35.28% 4002ms 7.90% std::__set_intersection 0 0% 35.28% 4002ms 7.90% std::set_intersection (inline) 698ms 1.38% 36.66% 3839ms 7.58% __GI___libc_free 0 0% 36.66% 3824ms 7.55% AbstractCellPopulation::WriteResultsToFiles 6ms 0.012% 36.67% 3811ms 7.52% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.002% 36.67% 3787ms 7.48% MeshBasedCellPopulation::UpdateNodePairs 2999ms 5.92% 42.59% 3775ms 7.45% _int_malloc 45ms 0.089% 42.68% 3744ms 7.39% Node::AddElement 7ms 0.014% 42.69% 3658ms 7.22% MeshBasedCellPopulation::SpringIterator::operator++ 15ms 0.03% 42.72% 3485ms 6.88% std::_Rb_tree::~_Rb_tree (inline) 1107ms 2.19% 44.91% 3460ms 6.83% std::_Rb_tree::_M_erase 0 0% 44.91% 3446ms 6.80% std::set::~set (inline) 1069ms 2.11% 47.02% 3415ms 6.74% std::_Rb_tree::_M_get_insert_unique_pos 70ms 0.14% 47.16% 3357ms 6.63% std::__new_allocator::deallocate (inline) 0 0% 47.16% 3349ms 6.61% std::allocator_traits::deallocate (inline) 206ms 0.41% 47.56% 3293ms 6.50% std::_Rb_tree_const_iterator::operator++ (inline) 3248ms 6.41% 53.98% 3248ms 6.41% std::_Rb_tree::_S_right (inline) 2ms 0.0039% 53.98% 3137ms 6.19% TetrahedralMesh::ImportFromMesher 1448ms 2.86% 56.84% 3128ms 6.18% _int_free 255ms 0.5% 57.34% 2985ms 5.89% std::_Rb_tree_iterator::operator++ (inline) 4ms 0.0079% 57.35% 2969ms 5.86% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0059% 57.35% 2771ms 5.47% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 57.35% 2755ms 5.44% VertexMesh::~VertexMesh 53ms 0.1% 57.46% 2617ms 5.17% MutableElement::AddNode 58ms 0.11% 57.57% 2137ms 4.22% tetgen::tetgenmesh::insphere_sos 1926ms 3.80% 61.38% 2063ms 4.07% tetgen::insphere 0 0% 61.38% 1891ms 3.73% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.38% 1866ms 3.68% std::_Rb_tree::_M_put_node (inline) 4ms 0.0079% 61.38% 1811ms 3.58% Element::Element 29ms 0.057% 61.44% 1808ms 3.57% Node::~Node 1643ms 3.24% 64.69% 1643ms 3.24% std::_Rb_tree_insert_and_rebalance 948ms 1.87% 66.56% 1640ms 3.24% malloc_consolidate 1561ms 3.08% 69.64% 1561ms 3.08% [libchaste_mesh.so] 157ms 0.31% 69.95% 1553ms 3.07% tetgen::tetgenmesh::flip23 2ms 0.0039% 69.95% 1533ms 3.03% Element::RegisterWithNodes (inline) 10ms 0.02% 69.97% 1493ms 2.95% std::_Vector_base::_M_deallocate (inline) 12ms 0.024% 70.00% 1476ms 2.91% VertexMesh::Clear 6ms 0.012% 70.01% 1423ms 2.81% _int_free_maybe_consolidate 0 0% 70.01% 1392ms 2.75% std::vector::~vector (inline) 1ms 0.002% 70.01% 1370ms 2.70% std::_Vector_base::~_Vector_base (inline) 1272ms 2.51% 72.52% 1272ms 2.51% Node::GetIndex 1178ms 2.33% 74.85% 1178ms 2.33% unlink_chunk 46ms 0.091% 74.94% 1144ms 2.26% std::vector::_M_realloc_insert 1090ms 2.15% 77.09% 1129ms 2.23% tetgen::orient3d 132ms 0.26% 77.35% 1114ms 2.20% tetgen::tetgenmesh::flip32 2ms 0.0039% 77.35% 1074ms 2.12% std::_Vector_base::_M_allocate (inline) 68ms 0.13% 77.49% 1029ms 2.03% std::map::operator[] 6ms 0.012% 77.50% 998ms 1.97% TetrahedralMesh::Clear 71ms 0.14% 77.64% 957ms 1.89% std::vector::push_back (inline) 1ms 0.002% 77.64% 912ms 1.80% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 77.64% 897ms 1.77% std::_Rb_tree::lower_bound (inline) 0 0% 77.64% 897ms 1.77% std::map::lower_bound (inline) 1ms 0.002% 77.64% 864ms 1.71% VoronoiDataWriter::Visit 23ms 0.045% 77.69% 809ms 1.60% tetgen::tetgenmesh::locate 70ms 0.14% 77.83% 768ms 1.52% tetgen::tetgenmesh::preciselocate 537ms 1.06% 78.89% 744ms 1.47% AbstractElement::GetNodeGlobalIndex 111ms 0.22% 79.11% 729ms 1.44% tetgen::tetgenmesh::enqueueflipface 726ms 1.43% 80.54% 726ms 1.43% Node::rGetLocation 2ms 0.0039% 80.54% 643ms 1.27% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 80.54% 641ms 1.27% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.0099% 80.55% 599ms 1.18% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 263ms 0.52% 81.07% 591ms 1.17% AbstractElement::GetNodeLocation 7ms 0.014% 81.09% 567ms 1.12% AbstractTetrahedralElement::CalculateJacobian 4ms 0.0079% 81.09% 556ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 468ms 0.92% 82.02% 468ms 0.92% tetgen::tetgenmesh::oppo 40ms 0.079% 82.10% 467ms 0.92% AbstractTetrahedralElement::RefreshJacobian 3ms 0.0059% 82.10% 462ms 0.91% boost::numeric::ublas::vector_assign (inline) 8ms 0.016% 82.12% 436ms 0.86% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.12% 434ms 0.86% std::insert_iterator::operator= (inline) 0 0% 82.12% 408ms 0.81% std::set::find (inline) 7ms 0.014% 82.13% 407ms 0.8% Element::CalculateCircumsphere 26ms 0.051% 82.18% 403ms 0.8% __atan2 251ms 0.5% 82.68% 395ms 0.78% tetgen::tetgenmesh::sym 392ms 0.77% 83.45% 392ms 0.77% std::vector::size (inline) 0 0% 83.45% 385ms 0.76% std::_Rb_tree::_M_insert_unique_ (inline) 342ms 0.68% 84.13% 376ms 0.74% __ieee754_atan2_fma 7ms 0.014% 84.14% 355ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0059% 84.15% 343ms 0.68% Cell::GetCellId 37ms 0.073% 84.22% 321ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 14ms 0.028% 84.25% 307ms 0.61% std::vector::insert (inline) 294ms 0.58% 84.83% 294ms 0.58% AbstractElement::IsDeleted 0 0% 84.83% 287ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.83% 285ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 7ms 0.014% 84.84% 277ms 0.55% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.84% 277ms 0.55% tcache_get (inline) 277ms 0.55% 85.39% 277ms 0.55% tcache_get_n (inline) 80ms 0.16% 85.55% 276ms 0.54% __dynamic_cast 1ms 0.002% 85.55% 274ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.55% 264ms 0.52% boost::numeric::ublas::inner_prod (inline) 19ms 0.038% 85.59% 264ms 0.52% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.59% 264ms 0.52% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 261ms 0.52% 86.10% 261ms 0.52% std::_Rb_tree_decrement 6ms 0.012% 86.12% 259ms 0.51% boost::numeric::ublas::c_vector::operator= (inline) 187ms 0.37% 86.48% 256ms 0.51% AbstractTetrahedralMesh::GetElement