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From: Roy Stogner <roy@st...>  20080731 13:09:12

On Thu, 31 Jul 2008, luyi wrote: > Some one had asked you about the multiphysical problems using libmesh, > and you tell us you are working the conjugate heat transfer problem. > > As the question "Associating more than one mesh to EquationSystems", I > want to perform fully implicit coupling(without operator splitting) and > use the NewtonKrylov method to solve conjugate heat transfer problem, > the difference is that I am not using stagger mesh, only one mesh > departed to domain A and domain B, the variables in domain A are > rho,u,v,w,E,k,w and in domain B only T, and I want to assemble the > Jacobian matrix and the rhs together, can I using only one > EquationSystems and one mesh to implement this? At the moment I think the answer is "not efficiently". Although our meshes can be flagged with subdomain ids, our DofMap still assumes that every subdomain in the mesh has the same variables defined on it. What we need is an API for the user to say "this variable only exists on subdomains 1, 5, and 13", as well as the DofMap code to respect those requests. Unless you want to dig into the library source code and add that feature (for which a patch would be much appreciated, naturally), I think the best you can do for a fully coupled solve is define all variables everywhere, then manually restrict T to be 0 on domain A and all the other variables to be 0 on domain B.  Roy 
From: Roy Stogner <roy@st...>  20080731 12:57:54

On Thu, 31 Jul 2008, Shengli Xu wrote: > Roy, Could you tell me what specific profiling information should be > gotten? I have to solve this problem. Just this: "Exactly where is the delay occurring?" If you're using our PerfLog objects, for example, you could create one in the assembly, activate it right before the matrix adds, and deactivate it right after; if that ends up being responsible for most of your runtime then you've verified that my "bad matrix assembly" hypothesis was correct. If not, then something else in your assembly is taking way too long (calling FE::reinit inside the quadrature loop?); you can use finegrained PerfLog objects to test that out too. Or use whatever profiler you're comfortable with, of course. I like oprofile; other people I know prefer Tau. http://oprofile.sourceforge.net/ http://www.cs.uoregon.edu/research/tau/home.php  Roy 
From: luyi <luyi06@ma...>  20080731 08:01:32

hello,ben, Some one had asked you about the multiphysical problems using libmesh, and you tell us you are working the conjugate heat transfer problem. As the question "Associating more than one mesh to EquationSystems", I want to perform fully implicit coupling(without operator splitting) and use the NewtonKrylov method to solve conjugate heat transfer problem, the difference is that I am not using stagger mesh, only one mesh departed to domain A and domain B, the variables in domain A are rho,u,v,w,E,k,w and in domain B only T, and I want to assemble the Jacobian matrix and the rhs together, can I using only one EquationSystems and one mesh to implement this? Best regards! Luyi  Gas Turbine Research Center email: luyi06@... 
From: Shengli Xu <shengli.xu@gm...>  20080731 07:38:54

2008/7/30 Roy Stogner <roy@...> > > On Wed, 30 Jul 2008, Shengli Xu wrote: > > But in next iteration the refinement level is 2, The process of system >> assembling is very very slowly. It took more than 12 hours when only >> assembled 30000 elements. The system and mesh information is : >> > > n_dofs()=253785 >> > > Is the system too large for only one processor? >> > > Large enough that you can't quickly solve many time steps on one > processor, maybe... but large enough that one assembly should take 12 > hours? Definitely not. There's some sort of bug here. If you could > any more specific profiling information, it would help. Roy, Could you tell me what specific profiling information should be gotten? I have to solve this problem. The only culprit I've heard of that can destroy your assembly speed is if > you > try to assemble a bunch of matrices with entries outside PETSc's > precalculated sparsity pattern, but before we figure out why that > might be happening to you it would be a good idea to verify that > that's what's happening. >  > Roy >  Yours Sincerely Shengli Xu 
From: Roy Stogner <roy@st...>  20080731 03:16:47

On Wed, 30 Jul 2008, Shengli Xu wrote: > But in next iteration the refinement level is 2, The process of system > assembling is very very slowly. It took more than 12 hours when only > assembled 30000 elements. The system and mesh information is : > n_dofs()=253785 > Is the system too large for only one processor? Large enough that you can't quickly solve many time steps on one processor, maybe... but large enough that one assembly should take 12 hours? Definitely not. There's some sort of bug here. If you could any more specific profiling information, it would help. The only culprit I've heard of that can destroy your assembly speed is if you try to assemble a bunch of matrices with entries outside PETSc's precalculated sparsity pattern, but before we figure out why that might be happening to you it would be a good idea to verify that that's what's happening.  Roy 
From: Shengli Xu <shengli.xu@gm...>  20080731 01:45:00

Hi, All The fem system is a 3D elastic structure. The element is 3D brick element Hex8. Mesh refinement is used in this system. The system assembling is quickly when maximum refinement level is 0 and 1. The system information and mesh information are as below: (1) refinement level is 0 EquationSystems n_systems()=1 System "beam_analysis" Type "LinearImplicit" Variables="u" "v" "w" Finite Element Types="LAGRANGE" "LAGRANGE" "LAGRANGE" Approximation Orders="FIRST" "FIRST" "FIRST" n_dofs()=8316 n_local_dofs()=8316 n_constrained_dofs()=0 n_vectors()=2 Mesh Information: mesh_dimension()=3 spatial_dimension()=3 n_nodes()=2772 n_elem()=1920 n_local_elem()=1920 n_active_elem()=1920 n_subdomains()=1 n_processors()=1 processor_id()=0 (2) refinement level is 1 EquationSystems n_systems()=1 System "beam_analysis" Type "LinearImplicit" Variables="u" "v" "w" Finite Element Types="LAGRANGE" "LAGRANGE" "LAGRANGE" Approximation Orders="FIRST" "FIRST" "FIRST" n_dofs()=37185 n_local_dofs()=37185 n_constrained_dofs()=6708 n_vectors()=2 Mesh Information: mesh_dimension()=3 spatial_dimension()=3 n_nodes()=12395 n_elem()=10336 n_local_elem()=10336 n_active_elem()=9284 n_subdomains()=1 n_processors()=1 processor_id()=0 But in next iteration the refinement level is 2, The process of system assembling is very very slowly. It took more than 12 hours when only assembled 30000 elements. The system and mesh information is : (3) refinement level is 2 EquationSystems n_systems()=1 System "beam_analysis" Type "LinearImplicit" Variables="u" "v" "w" Finite Element Types="LAGRANGE" "LAGRANGE" "LAGRANGE" Approximation Orders="FIRST" "FIRST" "FIRST" n_dofs()=253785 n_local_dofs()=253785 n_constrained_dofs()=30726 n_vectors()=2 Mesh Information: mesh_dimension()=3 spatial_dimension()=3 n_nodes()=84595 n_elem()=82048 n_local_elem()=82048 n_active_elem()=72032 n_subdomains()=1 n_processors()=1 processor_id()=0 Is the system too large for only one processor?  Yours Sincerely ShengliXu Department of Engineering Mechanics State Key Laboratory of Structural Analysis for Industrial Equipment Dalian University of Technology Dalian, 116024, P. R. China Email: shengli.xu.xu@... ========================== 