File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 55778ms, 87.51% of 63739ms total Dropped 881 nodes (cum <= 318.69ms) flat flat% sum% cum cum% 0 0% 0% 63682ms 99.91% __libc_start_call_main 0 0% 0% 63682ms 99.91% __libc_start_main_impl 0 0% 0% 63682ms 99.91% _start 0 0% 0% 63664ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63664ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63664ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63664ms 99.88% main 0 0% 0% 63618ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63618ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63618ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63325ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 54180ms 85.00% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 54126ms 84.92% MeshBasedCellPopulation::Update 0 0% 0% 29659ms 46.53% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 29655ms 46.53% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 202ms 0.32% 0.32% 26200ms 41.11% VertexMesh::VertexMesh 0 0% 0.32% 20371ms 31.96% MutableMesh::ReMesh 0 0% 0.32% 16142ms 25.33% tetgen::tetrahedralize 3ms 0.0047% 0.32% 15989ms 25.09% tetgen::tetgenmesh::delaunizevertices 10ms 0.016% 0.34% 15984ms 25.08% tetgen::tetgenmesh::incrflipdelaunay 486ms 0.76% 1.10% 14309ms 22.45% tetgen::tetgenmesh::lawson 615ms 0.96% 2.06% 12569ms 19.72% TetrahedralMesh::EdgeIterator::operator++ 25ms 0.039% 2.10% 10598ms 16.63% std::set::insert (inline) 221ms 0.35% 2.45% 10162ms 15.94% std::_Rb_tree::_M_insert_unique 382ms 0.6% 3.05% 9991ms 15.67% VertexElement::AddFace 3229ms 5.07% 8.12% 9033ms 14.17% std::_Rb_tree::_M_lower_bound (inline) 291ms 0.46% 8.57% 8545ms 13.41% std::_Rb_tree::find (inline) 0 0% 8.57% 7978ms 12.52% std::set::count (inline) 323ms 0.51% 9.08% 6059ms 9.51% std::_Rb_tree::_M_insert_ (inline) 120ms 0.19% 9.27% 5699ms 8.94% std::less::operator() (inline) 5641ms 8.85% 18.12% 5641ms 8.85% std::operator< (inline) 1ms 0.0016% 18.12% 5477ms 8.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 233ms 0.37% 18.48% 5406ms 8.48% operator new 1ms 0.0016% 18.49% 5338ms 8.37% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0047% 18.49% 5306ms 8.32% AbstractNumericalMethod::ComputeForcesIncludingDamping 5246ms 8.23% 26.72% 5246ms 8.23% std::_Rb_tree_increment 1169ms 1.83% 28.56% 5089ms 7.98% __GI___libc_malloc 37ms 0.058% 28.61% 4684ms 7.35% std::__new_allocator::allocate (inline) 0 0% 28.61% 4665ms 7.32% std::allocator_traits::allocate (inline) 0 0% 28.61% 4468ms 7.01% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.014% 28.63% 4416ms 6.93% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.011% 28.64% 4409ms 6.92% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1555ms 2.44% 31.08% 4404ms 6.91% std::_Rb_tree::_M_erase 0 0% 31.08% 4375ms 6.86% std::set::~set (inline) 14ms 0.022% 31.10% 4315ms 6.77% MeshBasedCellPopulation::SpringIterator::operator++ 1360ms 2.13% 33.23% 4142ms 6.50% std::_Rb_tree::_M_get_insert_unique_pos 1186ms 1.86% 35.09% 4124ms 6.47% __GI___libc_free 3ms 0.0047% 35.10% 4097ms 6.43% std::set_intersection (inline) 236ms 0.37% 35.47% 4094ms 6.42% std::__set_intersection 0 0% 35.47% 3853ms 6.04% std::_Rb_tree::_M_create_node (inline) 0 0% 35.47% 3821ms 5.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.47% 3820ms 5.99% std::_Rb_tree::_M_get_node (inline) 133ms 0.21% 35.68% 3807ms 5.97% tetgen::tetgenmesh::insphere_sos 40ms 0.063% 35.74% 3722ms 5.84% Node::AddElement 3370ms 5.29% 41.03% 3652ms 5.73% tetgen::insphere 145ms 0.23% 41.26% 3635ms 5.70% std::__new_allocator::deallocate (inline) 0 0% 41.26% 3620ms 5.68% std::allocator_traits::deallocate (inline) 141ms 0.22% 41.48% 3564ms 5.59% tetgen::tetgenmesh::flip23 2634ms 4.13% 45.61% 3552ms 5.57% _int_malloc 0 0% 45.61% 3508ms 5.50% AbstractCellPopulation::WriteResultsToFiles 0 0% 45.61% 3488ms 5.47% VertexMesh::~VertexMesh 217ms 0.34% 45.95% 3398ms 5.33% std::_Rb_tree_const_iterator::operator++ (inline) 13ms 0.02% 45.97% 3381ms 5.30% TetrahedralMesh::ImportFromMesher 3240ms 5.08% 51.05% 3240ms 5.08% std::_Rb_tree::_S_right (inline) 1451ms 2.28% 53.33% 2935ms 4.60% _int_free 60ms 0.094% 53.42% 2788ms 4.37% MutableElement::AddNode 141ms 0.22% 53.65% 2570ms 4.03% tetgen::tetgenmesh::flip32 225ms 0.35% 54.00% 2537ms 3.98% Node::~Node 5ms 0.0078% 54.01% 2375ms 3.73% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 167ms 0.26% 54.27% 2357ms 3.70% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 172ms 0.27% 54.54% 2334ms 3.66% VertexMesh::Clear 0 0% 54.54% 2218ms 3.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.54% 2207ms 3.46% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.54% 2206ms 3.46% std::_Rb_tree::_M_put_node (inline) 2002ms 3.14% 57.68% 2002ms 3.14% std::_Rb_tree_insert_and_rebalance 200ms 0.31% 57.99% 1958ms 3.07% tetgen::tetgenmesh::enqueueflipface 9ms 0.014% 58.01% 1723ms 2.70% Element::Element 1690ms 2.65% 60.66% 1690ms 2.65% Node::GetIndex 1528ms 2.40% 63.06% 1615ms 2.53% tetgen::orient3d 1034ms 1.62% 64.68% 1474ms 2.31% malloc_consolidate 23ms 0.036% 64.71% 1437ms 2.25% std::_Vector_base::_M_deallocate (inline) 13ms 0.02% 64.73% 1370ms 2.15% Element::RegisterWithNodes (inline) 39ms 0.061% 64.80% 1367ms 2.14% tetgen::tetgenmesh::locate 0 0% 64.80% 1362ms 2.14% std::vector::~vector (inline) 74ms 0.12% 64.91% 1295ms 2.03% TetrahedralMesh::Clear 88ms 0.14% 65.05% 1288ms 2.02% tetgen::tetgenmesh::preciselocate 1ms 0.0016% 65.05% 1279ms 2.01% std::_Vector_base::~_Vector_base (inline) 5ms 0.0078% 65.06% 1254ms 1.97% _int_free_maybe_consolidate 82ms 0.13% 65.19% 1128ms 1.77% std::map::operator[] 1101ms 1.73% 66.92% 1101ms 1.73% tetgen::tetgenmesh::oppo 71ms 0.11% 67.03% 1097ms 1.72% std::vector::_M_realloc_insert 1082ms 1.70% 68.72% 1082ms 1.70% tetgen::tetgenmesh::triface::triface 864ms 1.36% 70.08% 1073ms 1.68% AbstractElement::GetNodeGlobalIndex 1056ms 1.66% 71.74% 1056ms 1.66% unlink_chunk 0 0% 71.74% 963ms 1.51% std::_Rb_tree::lower_bound (inline) 0 0% 71.74% 963ms 1.51% std::map::lower_bound (inline) 127ms 0.2% 71.94% 939ms 1.47% std::vector::push_back (inline) 4ms 0.0063% 71.94% 896ms 1.41% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 71.94% 893ms 1.40% VoronoiDataWriter::Visit 6ms 0.0094% 71.95% 851ms 1.34% std::_Vector_base::_M_allocate (inline) 0 0% 71.95% 821ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 320ms 0.5% 72.45% 816ms 1.28% tetgen::tetgenmesh::sym 812ms 1.27% 73.73% 812ms 1.27% [libchaste_mesh.so] 13ms 0.02% 73.75% 757ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 753ms 1.18% 74.93% 753ms 1.18% tetgen::tetgenmesh::triface::operator= 3ms 0.0047% 74.93% 733ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 45ms 0.071% 75.00% 711ms 1.12% tetgen::tetgenmesh::queue::push 18ms 0.028% 75.03% 687ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 387ms 0.61% 75.64% 679ms 1.07% tetgen::tetgenmesh::fnextself 20ms 0.031% 75.67% 673ms 1.06% AbstractTetrahedralElement::CalculateJacobian 394ms 0.62% 76.29% 666ms 1.04% tetgen::tetgenmesh::link::add 64ms 0.1% 76.39% 644ms 1.01% tetgen::tetgenmesh::enextfnext 49ms 0.077% 76.47% 637ms 1% __atan2 208ms 0.33% 76.79% 635ms 1% tetgen::tetgenmesh::bond 298ms 0.47% 77.26% 632ms 0.99% AbstractElement::GetNodeLocation 612ms 0.96% 78.22% 612ms 0.96% AbstractElement::IsDeleted 18ms 0.028% 78.25% 595ms 0.93% boost::numeric::ublas::vector_assign (inline) 466ms 0.73% 78.98% 585ms 0.92% __ieee754_atan2_fma 11ms 0.017% 79.00% 572ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 79.00% 563ms 0.88% std::set::find (inline) 561ms 0.88% 79.88% 561ms 0.88% Node::rGetLocation 52ms 0.082% 79.96% 561ms 0.88% tetgen::tetgenmesh::enext2fnext 534ms 0.84% 80.80% 534ms 0.84% std::vector::size (inline) 520ms 0.82% 81.61% 520ms 0.82% tetgen::tetgenmesh::decode 0 0% 81.61% 514ms 0.81% boost::numeric::ublas::inner_prod (inline) 2ms 0.0031% 81.62% 511ms 0.8% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 48ms 0.075% 81.69% 509ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 50ms 0.078% 81.77% 492ms 0.77% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.77% 469ms 0.74% std::insert_iterator::operator= (inline) 16ms 0.025% 81.79% 454ms 0.71% Element::CalculateCircumsphere 210ms 0.33% 82.12% 428ms 0.67% AbstractTetrahedralMesh::GetElement 2ms 0.0031% 82.13% 419ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 110ms 0.17% 82.30% 419ms 0.66% __dynamic_cast 21ms 0.033% 82.33% 417ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 413ms 0.65% 82.98% 413ms 0.65% tetgen::tetgenmesh::org 0 0% 82.98% 406ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 10ms 0.016% 83.00% 405ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 405ms 0.64% 83.63% 405ms 0.64% tetgen::tetgenmesh::encode 2ms 0.0031% 83.63% 401ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.0047% 83.64% 389ms 0.61% Cell::GetCellId 0 0% 83.64% 385ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 166ms 0.26% 83.90% 385ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 95ms 0.15% 84.05% 372ms 0.58% boost::numeric::ublas::indexing_vector_assign 371ms 0.58% 84.63% 371ms 0.58% std::_Rb_tree_decrement 360ms 0.56% 85.20% 360ms 0.56% boost::numeric::ublas::c_vector::operator() 3ms 0.0047% 85.20% 357ms 0.56% VertexElement::~VertexElement 149ms 0.23% 85.43% 355ms 0.56% Inverse 354ms 0.56% 85.99% 354ms 0.56% tetgen::tetgenmesh::pointmark 1ms 0.0016% 85.99% 346ms 0.54% AbstractCellProperty::IsSubType (inline) 3ms 0.0047% 86.00% 344ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.00% 327ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 325ms 0.51% 86.51% 325ms 0.51% tetgen::tetgenmesh::memorypool::alloc 0 0% 86.51% 321ms 0.5% tcache_get (inline) 321ms 0.5% 87.01% 321ms 0.5% tcache_get_n (inline) 319ms 0.5% 87.51% 319ms 0.5% tetgen::tetgenmesh::face::face