File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 55787ms, 87.42% of 63815ms total Dropped 869 nodes (cum <= 319.07ms) flat flat% sum% cum cum% 0 0% 0% 63759ms 99.91% __libc_start_call_main 0 0% 0% 63759ms 99.91% __libc_start_main_impl 0 0% 0% 63759ms 99.91% _start 0 0% 0% 63742ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63742ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63742ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63742ms 99.89% main 0 0% 0% 63705ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63705ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63705ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63415ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 52504ms 82.28% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52454ms 82.20% MeshBasedCellPopulation::Update 0 0% 0% 30759ms 48.20% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30757ms 48.20% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 234ms 0.37% 0.37% 26852ms 42.08% VertexMesh::VertexMesh 0 0% 0.37% 17410ms 27.28% MutableMesh::ReMesh 548ms 0.86% 1.23% 13122ms 20.56% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.23% 12741ms 19.97% tetgen::tetrahedralize 3ms 0.0047% 1.23% 12598ms 19.74% tetgen::tetgenmesh::delaunizevertices 7ms 0.011% 1.24% 12594ms 19.74% tetgen::tetgenmesh::incrflipdelaunay 552ms 0.87% 2.11% 11152ms 17.48% tetgen::tetgenmesh::lawson 28ms 0.044% 2.15% 10516ms 16.48% std::set::insert (inline) 3057ms 4.79% 6.94% 10246ms 16.06% std::_Rb_tree::_M_lower_bound (inline) 202ms 0.32% 7.26% 10019ms 15.70% std::_Rb_tree::_M_insert_unique 267ms 0.42% 7.68% 9509ms 14.90% std::_Rb_tree::find (inline) 426ms 0.67% 8.34% 9480ms 14.86% VertexElement::AddFace 0 0% 8.34% 8954ms 14.03% std::set::count (inline) 134ms 0.21% 8.55% 6811ms 10.67% std::less::operator() (inline) 6739ms 10.56% 19.11% 6739ms 10.56% std::_Rb_tree_increment 6734ms 10.55% 29.67% 6734ms 10.55% std::operator< (inline) 279ms 0.44% 30.10% 5896ms 9.24% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.10% 5738ms 8.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.10% 5578ms 8.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0094% 30.11% 5557ms 8.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 216ms 0.34% 30.45% 5428ms 8.51% operator new 1011ms 1.58% 32.03% 5152ms 8.07% __GI___libc_malloc 0 0% 32.03% 5028ms 7.88% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0094% 32.04% 4704ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 1931ms 3.03% 35.07% 4692ms 7.35% std::_Rb_tree::_M_erase 0 0% 35.07% 4640ms 7.27% std::set::~set (inline) 0 0% 35.07% 4622ms 7.24% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0063% 35.08% 4614ms 7.23% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 42ms 0.066% 35.14% 4591ms 7.19% std::__new_allocator::allocate (inline) 0 0% 35.14% 4570ms 7.16% std::allocator_traits::allocate (inline) 18ms 0.028% 35.17% 4454ms 6.98% MeshBasedCellPopulation::SpringIterator::operator++ 1200ms 1.88% 37.05% 4237ms 6.64% std::_Rb_tree::_M_get_insert_unique_pos 30ms 0.047% 37.10% 4207ms 6.59% Node::AddElement 4ms 0.0063% 37.10% 4182ms 6.55% std::set_intersection (inline) 258ms 0.4% 37.51% 4178ms 6.55% std::__set_intersection 1213ms 1.90% 39.41% 4079ms 6.39% __GI___libc_free 3977ms 6.23% 45.64% 3977ms 6.23% std::_Rb_tree::_S_right (inline) 0 0% 45.64% 3952ms 6.19% VertexMesh::~VertexMesh 12ms 0.019% 45.66% 3805ms 5.96% TetrahedralMesh::ImportFromMesher 2765ms 4.33% 49.99% 3797ms 5.95% _int_malloc 235ms 0.37% 50.36% 3787ms 5.93% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 50.36% 3682ms 5.77% std::_Rb_tree::_M_create_node (inline) 0 0% 50.36% 3655ms 5.73% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.36% 3626ms 5.68% std::_Rb_tree::_M_get_node (inline) 0 0% 50.36% 3564ms 5.58% std::_Rb_tree_iterator::operator++ (inline) 117ms 0.18% 50.54% 3563ms 5.58% std::__new_allocator::deallocate (inline) 0 0% 50.54% 3550ms 5.56% std::allocator_traits::deallocate (inline) 1ms 0.0016% 50.55% 3517ms 5.51% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 153ms 0.24% 50.79% 3441ms 5.39% std::_Rb_tree_const_iterator::operator++ (inline) 109ms 0.17% 50.96% 3432ms 5.38% tetgen::tetgenmesh::insphere_sos 3031ms 4.75% 55.71% 3309ms 5.19% tetgen::insphere 71ms 0.11% 55.82% 3141ms 4.92% MutableElement::AddNode 1179ms 1.85% 57.67% 2862ms 4.48% _int_free 209ms 0.33% 57.99% 2847ms 4.46% Node::~Node 221ms 0.35% 58.34% 2722ms 4.27% tetgen::tetgenmesh::flip23 221ms 0.35% 58.69% 2600ms 4.07% VertexMesh::Clear 2059ms 3.23% 61.91% 2059ms 3.23% std::_Rb_tree_insert_and_rebalance 0 0% 61.91% 1936ms 3.03% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.91% 1924ms 3.01% std::_Rb_tree::_M_put_node (inline) 7ms 0.011% 61.92% 1918ms 3.01% Element::Element 133ms 0.21% 62.13% 1819ms 2.85% tetgen::tetgenmesh::flip32 1785ms 2.80% 64.93% 1785ms 2.80% Node::GetIndex 1126ms 1.76% 66.69% 1702ms 2.67% malloc_consolidate 18ms 0.028% 66.72% 1644ms 2.58% std::_Vector_base::_M_deallocate (inline) 3ms 0.0047% 66.73% 1568ms 2.46% Element::RegisterWithNodes (inline) 242ms 0.38% 67.10% 1553ms 2.43% TetrahedralMesh::Clear 0 0% 67.10% 1541ms 2.41% std::vector::~vector (inline) 1ms 0.0016% 67.11% 1467ms 2.30% std::_Vector_base::~_Vector_base (inline) 8ms 0.013% 67.12% 1461ms 2.29% _int_free_maybe_consolidate 1322ms 2.07% 69.19% 1413ms 2.21% tetgen::orient3d 59ms 0.092% 69.28% 1319ms 2.07% std::map::operator[] 2ms 0.0031% 69.29% 1247ms 1.95% VoronoiDataWriter::Visit 41ms 0.064% 69.35% 1247ms 1.95% tetgen::tetgenmesh::locate 161ms 0.25% 69.60% 1237ms 1.94% tetgen::tetgenmesh::enqueueflipface 1222ms 1.91% 71.52% 1222ms 1.91% unlink_chunk 0 0% 71.52% 1201ms 1.88% std::_Rb_tree::lower_bound (inline) 0 0% 71.52% 1201ms 1.88% std::map::lower_bound (inline) 56ms 0.088% 71.61% 1145ms 1.79% std::vector::_M_realloc_insert 93ms 0.15% 71.75% 1145ms 1.79% tetgen::tetgenmesh::preciselocate 4ms 0.0063% 71.76% 1092ms 1.71% VertexMesh::GenerateVerticesFromElementCircumcentres 807ms 1.26% 73.02% 954ms 1.49% AbstractElement::GetNodeGlobalIndex 5ms 0.0078% 73.03% 949ms 1.49% std::_Vector_base::_M_allocate (inline) 124ms 0.19% 73.22% 927ms 1.45% std::vector::push_back (inline) 862ms 1.35% 74.57% 862ms 1.35% tetgen::tetgenmesh::triface::triface 1ms 0.0016% 74.58% 847ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 426ms 0.67% 75.24% 765ms 1.20% tetgen::tetgenmesh::fnextself 6ms 0.0094% 75.25% 758ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 746ms 1.17% 76.42% 746ms 1.17% Node::rGetLocation 746ms 1.17% 77.59% 746ms 1.17% tetgen::tetgenmesh::oppo 295ms 0.46% 78.05% 744ms 1.17% AbstractElement::GetNodeLocation 0 0% 78.05% 737ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 18ms 0.028% 78.08% 718ms 1.13% AbstractTetrahedralElement::CalculateJacobian 713ms 1.12% 79.20% 713ms 1.12% [libchaste_mesh.so] 17ms 0.027% 79.23% 687ms 1.08% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 12ms 0.019% 79.24% 679ms 1.06% boost::numeric::ublas::vector_assign (inline) 6ms 0.0094% 79.25% 675ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 607ms 0.95% 80.21% 607ms 0.95% AbstractElement::IsDeleted 49ms 0.077% 80.28% 606ms 0.95% __atan2 24ms 0.038% 80.32% 588ms 0.92% Element::CalculateCircumsphere 560ms 0.88% 81.20% 560ms 0.88% tetgen::tetgenmesh::triface::operator= 452ms 0.71% 81.91% 556ms 0.87% __ieee754_atan2_fma 0 0% 81.91% 546ms 0.86% std::set::find (inline) 41ms 0.064% 81.97% 535ms 0.84% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.97% 530ms 0.83% boost::numeric::ublas::inner_prod (inline) 6ms 0.0094% 81.98% 528ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 524ms 0.82% 82.80% 524ms 0.82% std::vector::size (inline) 38ms 0.06% 82.86% 522ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 56ms 0.088% 82.95% 517ms 0.81% tetgen::tetgenmesh::enextfnext 0 0% 82.95% 494ms 0.77% std::insert_iterator::operator= (inline) 41ms 0.064% 83.01% 484ms 0.76% tetgen::tetgenmesh::enext2fnext 18ms 0.028% 83.04% 462ms 0.72% VertexMesh::CalculateUnitNormalToFaceWithArea 291ms 0.46% 83.50% 440ms 0.69% tetgen::tetgenmesh::sym 1ms 0.0016% 83.50% 436ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 123ms 0.19% 83.69% 427ms 0.67% boost::numeric::ublas::indexing_vector_assign 184ms 0.29% 83.98% 426ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 421ms 0.66% 84.64% 421ms 0.66% boost::numeric::ublas::c_vector::operator() 7ms 0.011% 84.65% 419ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.65% 395ms 0.62% Cell::GetCellId 0 0% 84.65% 392ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 7ms 0.011% 84.66% 389ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 101ms 0.16% 84.82% 388ms 0.61% __dynamic_cast 16ms 0.025% 84.84% 387ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 24ms 0.038% 84.88% 379ms 0.59% tetgen::tetgenmesh::queue::push 371ms 0.58% 85.46% 371ms 0.58% tetgen::tetgenmesh::org 17ms 0.027% 85.49% 368ms 0.58% std::vector::insert (inline) 254ms 0.4% 85.89% 366ms 0.57% tetgen::tetgenmesh::bond 0 0% 85.89% 359ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 10ms 0.016% 85.90% 357ms 0.56% VertexElement::~VertexElement 186ms 0.29% 86.19% 356ms 0.56% AbstractTetrahedralMesh::GetElement 246ms 0.39% 86.58% 352ms 0.55% tetgen::tetgenmesh::link::add 348ms 0.55% 87.13% 348ms 0.55% std::_Rb_tree_decrement 1ms 0.0016% 87.13% 346ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 52ms 0.081% 87.21% 339ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 6ms 0.0094% 87.22% 332ms 0.52% AbstractCellProperty::IsSubType (inline) 129ms 0.2% 87.42% 323ms 0.51% Inverse