File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 30405ms, 86.87% of 35000ms total Dropped 762 nodes (cum <= 175ms) flat flat% sum% cum cum% 0 0% 0% 34954ms 99.87% __libc_start_call_main 0 0% 0% 34954ms 99.87% __libc_start_main_impl 0 0% 0% 34954ms 99.87% _start 0 0% 0% 34942ms 99.83% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34942ms 99.83% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34942ms 99.83% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34942ms 99.83% main 0 0% 0% 34913ms 99.75% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34913ms 99.75% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34913ms 99.75% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 34756ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 29155ms 83.30% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 29126ms 83.22% MeshBasedCellPopulation::Update 0 0% 0% 16304ms 46.58% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 16303ms 46.58% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 115ms 0.33% 0.33% 14409ms 41.17% VertexMesh::VertexMesh 0 0% 0.33% 10254ms 29.30% MutableMesh::ReMesh 1ms 0.0029% 0.33% 8065ms 23.04% tetgen::tetrahedralize 0 0% 0.33% 7999ms 22.85% tetgen::tetgenmesh::delaunizevertices 5ms 0.014% 0.35% 7996ms 22.85% tetgen::tetgenmesh::incrflipdelaunay 440ms 1.26% 1.60% 7633ms 21.81% TetrahedralMesh::EdgeIterator::operator++ 258ms 0.74% 2.34% 7079ms 20.23% tetgen::tetgenmesh::lawson 30ms 0.086% 2.43% 5911ms 16.89% std::set::insert (inline) 148ms 0.42% 2.85% 5878ms 16.79% VertexElement::AddFace 2346ms 6.70% 9.55% 5842ms 16.69% std::_Rb_tree::_M_lower_bound (inline) 117ms 0.33% 9.89% 5587ms 15.96% std::_Rb_tree::_M_insert_unique 258ms 0.74% 10.62% 5548ms 15.85% std::_Rb_tree::find (inline) 0 0% 10.62% 5152ms 14.72% std::set::count (inline) 194ms 0.55% 11.18% 3527ms 10.08% std::_Rb_tree::_M_insert_ (inline) 86ms 0.25% 11.42% 3428ms 9.79% std::less::operator() (inline) 138ms 0.39% 11.82% 3413ms 9.75% operator new 3386ms 9.67% 21.49% 3386ms 9.67% std::operator< (inline) 0 0% 21.49% 3347ms 9.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.49% 3269ms 9.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.011% 21.50% 3256ms 9.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 1245ms 3.56% 25.06% 3220ms 9.20% __GI___libc_malloc 27ms 0.077% 25.14% 2943ms 8.41% std::__new_allocator::allocate (inline) 0 0% 25.14% 2934ms 8.38% std::allocator_traits::allocate (inline) 0 0% 25.14% 2791ms 7.97% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.011% 25.15% 2775ms 7.93% std::_Rb_tree::~_Rb_tree (inline) 866ms 2.47% 27.62% 2764ms 7.90% std::_Rb_tree::_M_erase 0 0% 27.62% 2747ms 7.85% std::set::~set (inline) 15ms 0.043% 27.67% 2719ms 7.77% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.029% 27.69% 2709ms 7.74% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2677ms 7.65% 35.34% 2677ms 7.65% std::_Rb_tree_increment 576ms 1.65% 36.99% 2519ms 7.20% __GI___libc_free 0 0% 36.99% 2444ms 6.98% std::_Rb_tree::_M_create_node (inline) 0 0% 36.99% 2425ms 6.93% std::_Rb_tree::_M_get_node (inline) 0 0% 36.99% 2417ms 6.91% std::_Rb_tree::_Alloc_node::operator() (inline) 84ms 0.24% 37.23% 2226ms 6.36% tetgen::tetgenmesh::insphere_sos 78ms 0.22% 37.45% 2222ms 6.35% std::__new_allocator::deallocate (inline) 0 0% 37.45% 2217ms 6.33% std::allocator_traits::deallocate (inline) 0 0% 37.45% 2155ms 6.16% AbstractCellPopulation::WriteResultsToFiles 1940ms 5.54% 42.99% 2133ms 6.09% tetgen::insphere 784ms 2.24% 45.23% 2128ms 6.08% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.0086% 45.24% 1949ms 5.57% std::set_intersection (inline) 159ms 0.45% 45.70% 1946ms 5.56% std::__set_intersection 1219ms 3.48% 49.18% 1942ms 5.55% _int_free 0 0% 49.18% 1903ms 5.44% VertexMesh::~VertexMesh 2ms 0.0057% 49.19% 1770ms 5.06% TetrahedralMesh::ImportFromMesher 1371ms 3.92% 53.10% 1747ms 4.99% _int_malloc 24ms 0.069% 53.17% 1602ms 4.58% Node::AddElement 0 0% 53.17% 1592ms 4.55% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.17% 1562ms 4.46% std::_Rb_tree::_M_put_node (inline) 2ms 0.0057% 53.18% 1522ms 4.35% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 84ms 0.24% 53.42% 1516ms 4.33% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 83ms 0.24% 53.65% 1511ms 4.32% tetgen::tetgenmesh::flip23 105ms 0.3% 53.95% 1496ms 4.27% std::_Rb_tree_const_iterator::operator++ (inline) 48ms 0.14% 54.09% 1479ms 4.23% Node::~Node 1479ms 4.23% 58.32% 1479ms 4.23% std::_Rb_tree::_S_right (inline) 0 0% 58.32% 1437ms 4.11% std::_Rb_tree_iterator::operator++ (inline) 49ms 0.14% 58.46% 1408ms 4.02% VertexMesh::Clear 42ms 0.12% 58.58% 1248ms 3.57% MutableElement::AddNode 71ms 0.2% 58.78% 1126ms 3.22% tetgen::tetgenmesh::flip32 937ms 2.68% 61.46% 986ms 2.82% tetgen::orient3d 948ms 2.71% 64.17% 948ms 2.71% std::_Rb_tree_insert_and_rebalance 1ms 0.0029% 64.17% 822ms 2.35% Element::Element 82ms 0.23% 64.40% 785ms 2.24% tetgen::tetgenmesh::enqueueflipface 45ms 0.13% 64.53% 775ms 2.21% TetrahedralMesh::Clear 9ms 0.026% 64.56% 764ms 2.18% tetgen::tetgenmesh::locate 65ms 0.19% 64.74% 741ms 2.12% std::map::operator[] (partial-inline) 65ms 0.19% 64.93% 734ms 2.10% tetgen::tetgenmesh::preciselocate 16ms 0.046% 64.97% 671ms 1.92% std::_Vector_base::_M_deallocate (inline) 0 0% 64.97% 669ms 1.91% std::vector::~vector (inline) 439ms 1.25% 66.23% 666ms 1.90% malloc_consolidate 642ms 1.83% 68.06% 642ms 1.83% [libchaste_mesh.so] 46ms 0.13% 68.19% 631ms 1.80% std::vector::_M_realloc_insert 4ms 0.011% 68.21% 629ms 1.80% Element::RegisterWithNodes (inline) 0 0% 68.21% 626ms 1.79% std::_Rb_tree::lower_bound (inline) 0 0% 68.21% 626ms 1.79% std::map::lower_bound (inline) 0 0% 68.21% 576ms 1.65% std::_Vector_base::~_Vector_base (inline) 2ms 0.0057% 68.21% 565ms 1.61% _int_free_maybe_consolidate 385ms 1.10% 69.31% 556ms 1.59% AbstractElement::GetNodeGlobalIndex 555ms 1.59% 70.90% 555ms 1.59% tetgen::tetgenmesh::oppo 0 0% 70.90% 509ms 1.45% std::_Vector_base::_M_allocate (inline) 51ms 0.15% 71.04% 506ms 1.45% std::vector::push_back (inline) 0 0% 71.04% 501ms 1.43% VoronoiDataWriter::Visit 308ms 0.88% 71.92% 497ms 1.42% tetgen::tetgenmesh::sym 495ms 1.41% 73.34% 495ms 1.41% Node::GetIndex 1ms 0.0029% 73.34% 445ms 1.27% AbstractTwoBodyInteractionForce::AddForceContribution 442ms 1.26% 74.60% 442ms 1.26% unlink_chunk 4ms 0.011% 74.61% 440ms 1.26% VertexMesh::GenerateVerticesFromElementCircumcentres 7ms 0.02% 74.63% 431ms 1.23% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 74.63% 406ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 0 0% 74.63% 396ms 1.13% std::set::find (inline) 25ms 0.071% 74.71% 393ms 1.12% __atan2 5ms 0.014% 74.72% 391ms 1.12% boost::numeric::ublas::vector_assign (inline) 4ms 0.011% 74.73% 379ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.011% 74.74% 373ms 1.07% boost::numeric::ublas::c_vector::c_vector (inline) 369ms 1.05% 75.80% 369ms 1.05% std::vector::size (inline) 289ms 0.83% 76.62% 367ms 1.05% __ieee754_atan2_fma 229ms 0.65% 77.28% 363ms 1.04% tetgen::tetgenmesh::fnextself 9ms 0.026% 77.30% 339ms 0.97% AbstractTetrahedralElement::CalculateJacobian 0 0% 77.30% 330ms 0.94% std::insert_iterator::operator= (inline) 23ms 0.066% 77.37% 296ms 0.85% tetgen::tetgenmesh::enext2fnext 1ms 0.0029% 77.37% 294ms 0.84% std::_Rb_tree::_M_insert_unique_ (inline) 116ms 0.33% 77.70% 282ms 0.81% AbstractTetrahedralMesh::GetElement 281ms 0.8% 78.51% 281ms 0.8% boost::numeric::ublas::c_vector::operator() 4ms 0.011% 78.52% 280ms 0.8% VertexElement::~VertexElement 152ms 0.43% 78.95% 279ms 0.8% AbstractElement::GetNodeLocation 15ms 0.043% 78.99% 268ms 0.77% tetgen::tetgenmesh::queue::push 21ms 0.06% 79.05% 265ms 0.76% std::_Rb_tree_iterator::operator-- (inline) 54ms 0.15% 79.21% 262ms 0.75% boost::numeric::ublas::indexing_vector_assign 252ms 0.72% 79.93% 252ms 0.72% tetgen::tetgenmesh::org 0 0% 79.93% 246ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.086% 80.01% 244ms 0.7% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.01% 244ms 0.7% boost::numeric::ublas::inner_prod (inline) 2ms 0.0057% 80.02% 244ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.0029% 80.02% 243ms 0.69% Cell::GetCellId 243ms 0.69% 80.72% 243ms 0.69% tetgen::tetgenmesh::triface::triface 20ms 0.057% 80.77% 242ms 0.69% boost::numeric::ublas::vector_scalar_binary::evaluate 164ms 0.47% 81.24% 242ms 0.69% tetgen::tetgenmesh::link::add 27ms 0.077% 81.32% 241ms 0.69% tetgen::tetgenmesh::enextfnext 235ms 0.67% 81.99% 235ms 0.67% std::_Rb_tree_decrement 10ms 0.029% 82.02% 223ms 0.64% Element::CalculateCircumsphere 3ms 0.0086% 82.03% 222ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 217ms 0.62% 82.65% 217ms 0.62% tetgen::tetgenmesh::pointmark 113ms 0.32% 82.97% 214ms 0.61% tetgen::tetgenmesh::bond 3ms 0.0086% 82.98% 213ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.026% 83.01% 210ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 49ms 0.14% 83.15% 209ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.034% 83.18% 206ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 203ms 0.58% 83.76% 203ms 0.58% Node::rGetLocation 200ms 0.57% 84.33% 200ms 0.57% tetgen::tetgenmesh::triface::operator= 67ms 0.19% 84.52% 199ms 0.57% Inverse 1ms 0.0029% 84.53% 194ms 0.55% tcache_get (inline) 194ms 0.55% 85.08% 194ms 0.55% tetgen::tetgenmesh::decode 1ms 0.0029% 85.08% 193ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 193ms 0.55% 85.63% 193ms 0.55% tcache_get_n (inline) 18ms 0.051% 85.69% 193ms 0.55% tetgen::insphereadapt 62ms 0.18% 85.86% 192ms 0.55% tetgen::tetgenmesh::queue::pop 7ms 0.02% 85.88% 190ms 0.54% std::vector::insert (inline) 184ms 0.53% 86.41% 184ms 0.53% AbstractElement::IsDeleted 134ms 0.38% 86.79% 183ms 0.52% boost::numeric::ublas::c_matrix::operator() 28ms 0.08% 86.87% 180ms 0.51% __dynamic_cast