File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54214ms, 87.31% of 62095ms total Dropped 852 nodes (cum <= 310.48ms) flat flat% sum% cum cum% 0 0% 0% 62022ms 99.88% __libc_start_call_main 0 0% 0% 62022ms 99.88% __libc_start_main_impl 0 0% 0% 62022ms 99.88% _start 0 0% 0% 62008ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62008ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62008ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62008ms 99.86% main 0 0% 0% 61970ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61970ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61970ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61711ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 52900ms 85.19% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52850ms 85.11% MeshBasedCellPopulation::Update 0 0% 0% 31459ms 50.66% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 31459ms 50.66% MeshBasedCellPopulation::TessellateIfNeeded 237ms 0.38% 0.38% 27359ms 44.06% VertexMesh::VertexMesh 0 0% 0.38% 17485ms 28.16% MutableMesh::ReMesh 0 0% 0.38% 12848ms 20.69% tetgen::tetrahedralize 4ms 0.0064% 0.39% 12710ms 20.47% tetgen::tetgenmesh::delaunizevertices 10ms 0.016% 0.4% 12702ms 20.46% tetgen::tetgenmesh::incrflipdelaunay 588ms 0.95% 1.35% 12127ms 19.53% TetrahedralMesh::EdgeIterator::operator++ 541ms 0.87% 2.22% 11284ms 18.17% tetgen::tetgenmesh::lawson 33ms 0.053% 2.28% 10845ms 17.47% std::set::insert (inline) 235ms 0.38% 2.65% 10336ms 16.65% std::_Rb_tree::_M_insert_unique 458ms 0.74% 3.39% 9786ms 15.76% VertexElement::AddFace 3007ms 4.84% 8.23% 8664ms 13.95% std::_Rb_tree::_M_lower_bound (inline) 248ms 0.4% 8.63% 8174ms 13.16% std::_Rb_tree::find (inline) 0 0% 8.63% 7644ms 12.31% std::set::count (inline) 284ms 0.46% 9.09% 6144ms 9.89% std::_Rb_tree::_M_insert_ (inline) 206ms 0.33% 9.42% 5750ms 9.26% operator new 119ms 0.19% 9.61% 5560ms 8.95% std::less::operator() (inline) 5532ms 8.91% 18.52% 5532ms 8.91% std::_Rb_tree_increment 5502ms 8.86% 27.38% 5502ms 8.86% std::operator< (inline) 1093ms 1.76% 29.14% 5459ms 8.79% __GI___libc_malloc 0 0% 29.14% 5314ms 8.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.14% 5181ms 8.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0048% 29.15% 5153ms 8.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 37ms 0.06% 29.21% 4743ms 7.64% std::__new_allocator::allocate (inline) 0 0% 29.21% 4720ms 7.60% std::allocator_traits::allocate (inline) 3ms 0.0048% 29.21% 4710ms 7.59% std::set_intersection (inline) 337ms 0.54% 29.76% 4707ms 7.58% std::__set_intersection 14ms 0.023% 29.78% 4686ms 7.55% std::_Rb_tree::~_Rb_tree (inline) 1849ms 2.98% 32.76% 4671ms 7.52% std::_Rb_tree::_M_erase 0 0% 32.76% 4624ms 7.45% std::set::~set (inline) 1266ms 2.04% 34.80% 4332ms 6.98% __GI___libc_free 1258ms 2.03% 36.82% 4287ms 6.90% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.013% 36.83% 4270ms 6.88% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.0032% 36.84% 4267ms 6.87% MeshBasedCellPopulation::UpdateNodePairs 28ms 0.045% 36.88% 4262ms 6.86% Node::AddElement 1ms 0.0016% 36.88% 4123ms 6.64% VertexMesh::~VertexMesh 19ms 0.031% 36.91% 4120ms 6.63% MeshBasedCellPopulation::SpringIterator::operator++ 3025ms 4.87% 41.79% 4040ms 6.51% _int_malloc 189ms 0.3% 42.09% 3867ms 6.23% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 42.09% 3862ms 6.22% std::_Rb_tree::_M_create_node (inline) 0 0% 42.09% 3830ms 6.17% std::_Rb_tree::_Alloc_node::operator() (inline) 127ms 0.2% 42.29% 3812ms 6.14% std::__new_allocator::deallocate (inline) 0 0% 42.29% 3809ms 6.13% std::_Rb_tree::_M_get_node (inline) 0 0% 42.29% 3787ms 6.10% std::allocator_traits::deallocate (inline) 8ms 0.013% 42.31% 3741ms 6.02% TetrahedralMesh::ImportFromMesher 3706ms 5.97% 48.28% 3706ms 5.97% std::_Rb_tree::_S_right (inline) 109ms 0.18% 48.45% 3483ms 5.61% tetgen::tetgenmesh::insphere_sos 3032ms 4.88% 53.33% 3367ms 5.42% tetgen::insphere 0 0% 53.33% 3336ms 5.37% AbstractCellPopulation::WriteResultsToFiles 85ms 0.14% 53.47% 3314ms 5.34% MutableElement::AddNode 1219ms 1.96% 55.43% 3062ms 4.93% _int_free 223ms 0.36% 55.79% 2846ms 4.58% Node::~Node 224ms 0.36% 56.15% 2753ms 4.43% tetgen::tetgenmesh::flip23 242ms 0.39% 56.54% 2608ms 4.20% VertexMesh::Clear 4ms 0.0064% 56.55% 2173ms 3.50% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 188ms 0.3% 56.85% 2138ms 3.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2130ms 3.43% 60.28% 2130ms 3.43% std::_Rb_tree_insert_and_rebalance 0 0% 60.28% 1992ms 3.21% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.28% 1985ms 3.20% std::_Rb_tree::_M_put_node (inline) 3ms 0.0048% 60.29% 1967ms 3.17% std::_Rb_tree_iterator::operator++ (inline) 159ms 0.26% 60.54% 1875ms 3.02% tetgen::tetgenmesh::flip32 1262ms 2.03% 62.58% 1850ms 2.98% malloc_consolidate 1815ms 2.92% 65.50% 1815ms 2.92% Node::GetIndex 13ms 0.021% 65.52% 1814ms 2.92% std::_Vector_base::_M_deallocate (inline) 4ms 0.0064% 65.53% 1759ms 2.83% Element::Element 0 0% 65.53% 1700ms 2.74% std::vector::~vector (inline) 2ms 0.0032% 65.53% 1643ms 2.65% std::_Vector_base::~_Vector_base (inline) 3ms 0.0048% 65.54% 1606ms 2.59% _int_free_maybe_consolidate 238ms 0.38% 65.92% 1551ms 2.50% TetrahedralMesh::Clear 4ms 0.0064% 65.92% 1429ms 2.30% Element::RegisterWithNodes (inline) 1284ms 2.07% 67.99% 1374ms 2.21% tetgen::orient3d 177ms 0.29% 68.28% 1329ms 2.14% tetgen::tetgenmesh::enqueueflipface 1320ms 2.13% 70.40% 1320ms 2.13% unlink_chunk 6ms 0.0097% 70.41% 1198ms 1.93% VertexMesh::GenerateVerticesFromElementCircumcentres 38ms 0.061% 70.47% 1180ms 1.90% tetgen::tetgenmesh::locate 63ms 0.1% 70.58% 1121ms 1.81% std::vector::_M_realloc_insert 91ms 0.15% 70.72% 1093ms 1.76% tetgen::tetgenmesh::preciselocate 925ms 1.49% 72.21% 1087ms 1.75% AbstractElement::GetNodeGlobalIndex 67ms 0.11% 72.32% 1062ms 1.71% std::map::operator[] 0 0% 72.32% 922ms 1.48% std::_Rb_tree::lower_bound (inline) 0 0% 72.32% 922ms 1.48% std::map::lower_bound (inline) 0 0% 72.32% 920ms 1.48% VoronoiDataWriter::Visit 9ms 0.014% 72.33% 920ms 1.48% std::_Vector_base::_M_allocate (inline) 95ms 0.15% 72.49% 920ms 1.48% std::vector::push_back (inline) 0 0% 72.49% 878ms 1.41% TetrahedralMesh::RefreshJacobianCachedData 835ms 1.34% 73.83% 835ms 1.34% tetgen::tetgenmesh::triface::triface 370ms 0.6% 74.43% 764ms 1.23% AbstractElement::GetNodeLocation 6ms 0.0097% 74.44% 745ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 444ms 0.72% 75.15% 742ms 1.19% tetgen::tetgenmesh::fnextself 729ms 1.17% 76.33% 729ms 1.17% AbstractElement::IsDeleted 0 0% 76.33% 715ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.021% 76.35% 696ms 1.12% AbstractTetrahedralElement::CalculateJacobian 695ms 1.12% 77.47% 695ms 1.12% tetgen::tetgenmesh::oppo 685ms 1.10% 78.57% 685ms 1.10% Node::rGetLocation 14ms 0.023% 78.59% 685ms 1.10% boost::numeric::ublas::vector_assign (inline) 21ms 0.034% 78.63% 671ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.013% 78.64% 669ms 1.08% boost::numeric::ublas::c_vector::c_vector (inline) 668ms 1.08% 79.71% 668ms 1.08% [libchaste_mesh.so] 20ms 0.032% 79.75% 590ms 0.95% Element::CalculateCircumsphere 586ms 0.94% 80.69% 586ms 0.94% tetgen::tetgenmesh::triface::operator= 43ms 0.069% 80.76% 565ms 0.91% __atan2 554ms 0.89% 81.65% 554ms 0.89% std::vector::size (inline) 52ms 0.084% 81.74% 535ms 0.86% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.74% 524ms 0.84% std::set::find (inline) 428ms 0.69% 82.43% 521ms 0.84% __ieee754_atan2_fma 0 0% 82.43% 515ms 0.83% std::insert_iterator::operator= (inline) 41ms 0.066% 82.49% 487ms 0.78% tetgen::tetgenmesh::enextfnext 0 0% 82.49% 483ms 0.78% boost::numeric::ublas::inner_prod (inline) 3ms 0.0048% 82.50% 480ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.04% 82.54% 477ms 0.77% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0016% 82.54% 452ms 0.73% std::_Rb_tree::_M_insert_unique_ (inline) 115ms 0.19% 82.72% 444ms 0.72% boost::numeric::ublas::indexing_vector_assign 40ms 0.064% 82.79% 443ms 0.71% tetgen::tetgenmesh::enext2fnext 25ms 0.04% 82.83% 441ms 0.71% tetgen::tetgenmesh::queue::push 279ms 0.45% 83.28% 430ms 0.69% tetgen::tetgenmesh::sym 17ms 0.027% 83.30% 415ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 297ms 0.48% 83.78% 414ms 0.67% tetgen::tetgenmesh::link::add 406ms 0.65% 84.44% 406ms 0.65% boost::numeric::ublas::c_vector::operator() 0 0% 84.44% 396ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 32ms 0.052% 84.49% 390ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 217ms 0.35% 84.84% 388ms 0.62% AbstractTetrahedralMesh::GetElement 152ms 0.24% 85.08% 388ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.0064% 85.09% 383ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 277ms 0.45% 85.54% 382ms 0.62% tetgen::tetgenmesh::bond 375ms 0.6% 86.14% 375ms 0.6% tetgen::tetgenmesh::org 3ms 0.0048% 86.14% 372ms 0.6% Cell::GetCellId 8ms 0.013% 86.16% 369ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 0 0% 86.16% 369ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 88ms 0.14% 86.30% 360ms 0.58% __dynamic_cast 11ms 0.018% 86.32% 339ms 0.55% VertexElement::~VertexElement 25ms 0.04% 86.36% 335ms 0.54% std::vector::insert (inline) 40ms 0.064% 86.42% 335ms 0.54% tetgen::insphereadapt 334ms 0.54% 86.96% 334ms 0.54% std::_Rb_tree_decrement 5ms 0.0081% 86.97% 327ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.011% 86.98% 315ms 0.51% VertexMesh::GetVolumeOfElement 145ms 0.23% 87.21% 312ms 0.5% Inverse 60ms 0.097% 87.31% 311ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)