File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48891ms, 87.18% of 56082ms total Dropped 855 nodes (cum <= 280.41ms) flat flat% sum% cum cum% 0 0% 0% 56015ms 99.88% __libc_start_call_main 0 0% 0% 56015ms 99.88% __libc_start_main_impl 0 0% 0% 56015ms 99.88% _start 0 0% 0% 56001ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56001ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56001ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56001ms 99.86% main 0 0% 0% 55964ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55964ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 55964ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55715ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 47032ms 83.86% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0018% 0.0018% 46984ms 83.78% MeshBasedCellPopulation::Update 0 0% 0.0018% 26430ms 47.13% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0018% 26429ms 47.13% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 226ms 0.4% 0.4% 23326ms 41.59% VertexMesh::VertexMesh 0 0% 0.4% 16905ms 30.14% MutableMesh::ReMesh 0 0% 0.4% 13077ms 23.32% tetgen::tetrahedralize 1ms 0.0018% 0.41% 12934ms 23.06% tetgen::tetgenmesh::delaunizevertices 9ms 0.016% 0.42% 12933ms 23.06% tetgen::tetgenmesh::incrflipdelaunay 532ms 0.95% 1.37% 11512ms 20.53% tetgen::tetgenmesh::lawson 565ms 1.01% 2.38% 11180ms 19.94% TetrahedralMesh::EdgeIterator::operator++ 26ms 0.046% 2.43% 9555ms 17.04% std::set::insert (inline) 251ms 0.45% 2.87% 9064ms 16.16% std::_Rb_tree::_M_insert_unique 330ms 0.59% 3.46% 8991ms 16.03% VertexElement::AddFace 2977ms 5.31% 8.77% 8513ms 15.18% std::_Rb_tree::_M_lower_bound (inline) 194ms 0.35% 9.12% 7921ms 14.12% std::_Rb_tree::find (inline) 0 0% 9.12% 7389ms 13.18% std::set::count (inline) 261ms 0.47% 9.58% 5443ms 9.71% std::_Rb_tree::_M_insert_ (inline) 115ms 0.21% 9.79% 5402ms 9.63% std::less::operator() (inline) 5348ms 9.54% 19.32% 5348ms 9.54% std::operator< (inline) 1ms 0.0018% 19.32% 4975ms 8.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0036% 19.33% 4864ms 8.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0053% 19.33% 4836ms 8.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 214ms 0.38% 19.71% 4713ms 8.40% operator new 4578ms 8.16% 27.88% 4578ms 8.16% std::_Rb_tree_increment 1161ms 2.07% 29.95% 4435ms 7.91% __GI___libc_malloc 5ms 0.0089% 29.96% 4131ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 1568ms 2.80% 32.75% 4121ms 7.35% std::_Rb_tree::_M_erase 0 0% 32.75% 4086ms 7.29% std::set::~set (inline) 44ms 0.078% 32.83% 4070ms 7.26% std::__new_allocator::allocate (inline) 0 0% 32.83% 4059ms 7.24% std::allocator_traits::allocate (inline) 1ms 0.0018% 32.83% 3983ms 7.10% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0053% 32.84% 3974ms 7.09% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.03% 32.87% 3851ms 6.87% MeshBasedCellPopulation::SpringIterator::operator++ 1223ms 2.18% 35.05% 3694ms 6.59% std::_Rb_tree::_M_get_insert_unique_pos 99ms 0.18% 35.23% 3601ms 6.42% tetgen::tetgenmesh::insphere_sos 0 0% 35.23% 3569ms 6.36% AbstractCellPopulation::WriteResultsToFiles 1070ms 1.91% 37.13% 3550ms 6.33% __GI___libc_free 3212ms 5.73% 42.86% 3494ms 6.23% tetgen::insphere 4ms 0.0071% 42.87% 3374ms 6.02% std::set_intersection (inline) 246ms 0.44% 43.31% 3370ms 6.01% std::__set_intersection 0 0% 43.31% 3308ms 5.90% std::_Rb_tree::_M_create_node (inline) 0 0% 43.31% 3278ms 5.85% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.31% 3270ms 5.83% std::_Rb_tree::_M_get_node (inline) 127ms 0.23% 43.53% 3180ms 5.67% std::__new_allocator::deallocate (inline) 0 0% 43.53% 3158ms 5.63% std::allocator_traits::deallocate (inline) 18ms 0.032% 43.56% 3149ms 5.61% Node::AddElement 0 0% 43.56% 3119ms 5.56% VertexMesh::~VertexMesh 7ms 0.012% 43.58% 3088ms 5.51% TetrahedralMesh::ImportFromMesher 2944ms 5.25% 48.83% 2944ms 5.25% std::_Rb_tree::_S_right (inline) 2165ms 3.86% 52.69% 2923ms 5.21% _int_malloc 217ms 0.39% 53.07% 2663ms 4.75% tetgen::tetgenmesh::flip23 206ms 0.37% 53.44% 2644ms 4.71% std::_Rb_tree_const_iterator::operator++ (inline) 1221ms 2.18% 55.62% 2476ms 4.41% _int_free 93ms 0.17% 55.78% 2466ms 4.40% MutableElement::AddNode 211ms 0.38% 56.16% 2445ms 4.36% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0071% 56.17% 2405ms 4.29% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 169ms 0.3% 56.47% 2348ms 4.19% Node::~Node 2ms 0.0036% 56.47% 2241ms 4.00% std::_Rb_tree_iterator::operator++ (inline) 174ms 0.31% 56.78% 2140ms 3.82% VertexMesh::Clear 1964ms 3.50% 60.28% 1964ms 3.50% std::_Rb_tree_insert_and_rebalance 153ms 0.27% 60.56% 1948ms 3.47% tetgen::tetgenmesh::flip32 0 0% 60.56% 1909ms 3.40% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.56% 1900ms 3.39% std::_Rb_tree::_M_put_node (inline) 1ms 0.0018% 60.56% 1460ms 2.60% Element::Element 1346ms 2.40% 62.96% 1446ms 2.58% tetgen::orient3d 174ms 0.31% 63.27% 1315ms 2.34% TetrahedralMesh::Clear 193ms 0.34% 63.61% 1313ms 2.34% tetgen::tetgenmesh::enqueueflipface 22ms 0.039% 63.65% 1280ms 2.28% std::_Vector_base::_M_deallocate (inline) 1262ms 2.25% 65.90% 1262ms 2.25% Node::GetIndex 825ms 1.47% 67.37% 1237ms 2.21% malloc_consolidate 0 0% 67.37% 1188ms 2.12% std::vector::~vector (inline) 22ms 0.039% 67.41% 1173ms 2.09% tetgen::tetgenmesh::locate 5ms 0.0089% 67.42% 1155ms 2.06% Element::RegisterWithNodes (inline) 93ms 0.17% 67.59% 1112ms 1.98% tetgen::tetgenmesh::preciselocate 1ms 0.0018% 67.59% 1093ms 1.95% std::_Vector_base::~_Vector_base (inline) 56ms 0.1% 67.69% 1056ms 1.88% std::map::operator[] 6ms 0.011% 67.70% 1050ms 1.87% _int_free_maybe_consolidate 56ms 0.1% 67.80% 1047ms 1.87% std::vector::_M_realloc_insert 0 0% 67.80% 939ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 67.80% 939ms 1.67% std::map::lower_bound (inline) 934ms 1.67% 69.47% 934ms 1.67% tetgen::tetgenmesh::triface::triface 1ms 0.0018% 69.47% 930ms 1.66% VoronoiDataWriter::Visit 899ms 1.60% 71.07% 899ms 1.60% unlink_chunk 103ms 0.18% 71.25% 852ms 1.52% std::vector::push_back (inline) 6ms 0.011% 71.27% 842ms 1.50% VertexMesh::GenerateVerticesFromElementCircumcentres 655ms 1.17% 72.43% 830ms 1.48% AbstractElement::GetNodeGlobalIndex 6ms 0.011% 72.44% 795ms 1.42% std::_Vector_base::_M_allocate (inline) 727ms 1.30% 73.74% 727ms 1.30% tetgen::tetgenmesh::triface::operator= 0 0% 73.74% 721ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.0036% 73.74% 720ms 1.28% AbstractTwoBodyInteractionForce::AddForceContribution 316ms 0.56% 74.31% 704ms 1.26% tetgen::tetgenmesh::fnextself 13ms 0.023% 74.33% 677ms 1.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.027% 74.36% 665ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 612ms 1.09% 75.45% 612ms 1.09% [libchaste_mesh.so] 13ms 0.023% 75.47% 608ms 1.08% boost::numeric::ublas::vector_assign (inline) 21ms 0.037% 75.51% 600ms 1.07% AbstractTetrahedralElement::CalculateJacobian 54ms 0.096% 75.61% 595ms 1.06% __atan2 15ms 0.027% 75.63% 592ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 226ms 0.4% 76.04% 547ms 0.98% AbstractElement::GetNodeLocation 428ms 0.76% 76.80% 541ms 0.96% __ieee754_atan2_fma 529ms 0.94% 77.74% 529ms 0.94% Node::rGetLocation 0 0% 77.74% 528ms 0.94% std::set::find (inline) 526ms 0.94% 78.68% 526ms 0.94% tetgen::tetgenmesh::oppo 518ms 0.92% 79.60% 518ms 0.92% std::vector::size (inline) 0 0% 79.60% 501ms 0.89% std::insert_iterator::operator= (inline) 27ms 0.048% 79.65% 472ms 0.84% tetgen::tetgenmesh::queue::push 293ms 0.52% 80.17% 455ms 0.81% tetgen::tetgenmesh::sym 41ms 0.073% 80.25% 453ms 0.81% tetgen::tetgenmesh::enextfnext 0 0% 80.25% 451ms 0.8% std::_Rb_tree::_M_insert_unique_ (inline) 35ms 0.062% 80.31% 449ms 0.8% tetgen::tetgenmesh::enext2fnext 17ms 0.03% 80.34% 448ms 0.8% Element::CalculateCircumsphere 0 0% 80.34% 448ms 0.8% boost::numeric::ublas::inner_prod (inline) 5ms 0.0089% 80.35% 445ms 0.79% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 366ms 0.65% 81.00% 441ms 0.79% tetgen::tetgenmesh::link::add 28ms 0.05% 81.05% 440ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 44ms 0.078% 81.13% 426ms 0.76% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0036% 81.13% 422ms 0.75% CellPropertyCollection::GetPropertiesType (inline) 96ms 0.17% 81.30% 417ms 0.74% __dynamic_cast 221ms 0.39% 81.70% 414ms 0.74% AbstractTetrahedralMesh::GetElement 410ms 0.73% 82.43% 410ms 0.73% AbstractElement::IsDeleted 3ms 0.0053% 82.43% 401ms 0.72% Cell::GetCellId 23ms 0.041% 82.48% 386ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 13ms 0.023% 82.50% 385ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 385ms 0.69% 83.19% 385ms 0.69% tetgen::tetgenmesh::org 0 0% 83.19% 384ms 0.68% VertexMeshWriter::WriteVtkUsingMesh 383ms 0.68% 83.87% 383ms 0.68% boost::numeric::ublas::c_vector::operator() 101ms 0.18% 84.05% 375ms 0.67% boost::numeric::ublas::indexing_vector_assign 372ms 0.66% 84.71% 372ms 0.66% tetgen::tetgenmesh::pointmark 4ms 0.0071% 84.72% 363ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 155ms 0.28% 85.00% 355ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 352ms 0.63% 85.62% 352ms 0.63% std::_Rb_tree_decrement 3ms 0.0053% 85.63% 351ms 0.63% AbstractCellProperty::IsSubType (inline) 262ms 0.47% 86.10% 351ms 0.63% tetgen::tetgenmesh::bond 6ms 0.011% 86.11% 320ms 0.57% VertexElement::~VertexElement 65ms 0.12% 86.22% 319ms 0.57% tetgen::tetgenmesh::queue::pop 131ms 0.23% 86.46% 315ms 0.56% Inverse 8ms 0.014% 86.47% 314ms 0.56% std::vector::insert (inline) 7ms 0.012% 86.48% 306ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.48% 304ms 0.54% tcache_get (inline) 304ms 0.54% 87.02% 304ms 0.54% tcache_get_n (inline) 50ms 0.089% 87.11% 293ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 36ms 0.064% 87.18% 282ms 0.5% tetgen::insphereadapt