February 2012 - petsc-users - mailman3.cels.anl.gov

Re: [petsc-users] Starting point for Stokes fieldsplit
by Max Rudolph 26 Feb '12

26 Feb '12

Hi Dave, Thanks for your help. Max > Hey Max, > > Without knowing anything about the specific application related to > your Stokes problem, or information about the mesh you are using, I > have a couple of questions and suggestions which might help. The test case that I am working with is isoviscous convection, benchmark case 1a from Blankenbach 1989. > 1) If A, is your stokes operator A = ( K,B ; B^T, 0 ), what is your > precondition operator? > Specifically, what is in the (2,2) slot in the precondioner? - i.e. > what matrix are you you applying -stokes_fieldsplit_1_pc_type jacobi > -stokes_fieldsplit_1_ksp_type preonly to? > Is it the identity as in the SpeedUp notes? I think that this is the problem. The (2,2) slot in the LHS matrix is all zero (pressure does not appear in the continuity equation), so I think that the preconditioner is meaningless. I am still confused as to why this choice of preconditioner was suggested in the tutorial, and what is a better choice of preconditioner for this block? Should I be using one of the Schur complement methods instead of the additive or multiplicative field split? > 2) This choice > -stokes_fieldsplit_0_pc_type ml -stokes_fieldsplit_0_ksp_type preonly > may simply not be a very effective and degrade the performance of the > outer solver. > I'd make the solver for the operator in the (1,1) slot much stronger, > for example > -stokes_fieldsplit_0_ksp_type gmres > -stokes_fieldsplit_0_ksp_rtol 1.0e-4 > -stokes_fieldsplit_0_mg_levels_ksp_type gmres > -stokes_fieldsplit_0_mg_levels_pc_type bjacobi > -stokes_fieldsplit_0_mg_levels_ksp_max_it 4 > > Add a monitor on this solver (-stokes_fieldsplit_0_ksp_XXX) to see how > ML is doing. > > 3) Using -stokes_pc_fieldsplit_type MULTIPLICATIVE should reduce the > number of outer iterations by a factor of two, but it will use more > memory. > 4) You should use a flexible Krylov method on the outer most solve > (-stokes_ksp_XXX) as the preconditioner is varying between each outer > iteration. Use -stokes_ksp_type fgmres or -stokes_ksp_type gcr Thanks for pointing this out. I made that change. > 5) Depending on how the physical problem is scaled > (non-dimensionalised), the size of the residuals associated with the > momentum and continuity equation make be quite different. You are > currently use the entire residual from (u,p) to determine when to stop > iterating. You might want to consider writing a monitor which examines > the these residuals independently. I think that I have scaled the problem correctly. I (slowly) obtain a sufficiently accurate solution using as options only: -stokes_ksp_atol 1e-5 -stokes_ksp_rtol 1e-5 -stokes_ksp_monitor_true_residual -stokes_ksp_norm_type UNPRECONDITIONED > > > Cheers, > Dave

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Re: [petsc-users] [petsc-maint #107250] VecAssemblyBegin/End()
by Mark F. Adams 26 Feb '12

26 Feb '12

yes On Feb 26, 2012, at 11:43 AM, saturday luis wrote: > Hi: > > Is it necessary to use VecAssemblyBegin/End between INSERT_VALUES and > ADD_VALUES mode of VecSetValues function call? > > Luis > >

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VecAssemblyBegin/End()
by saturday luis 26 Feb '12

26 Feb '12

Hi: Is it necessary to use VecAssemblyBegin/End between INSERT_VALUES and ADD_VALUES mode of VecSetValues function call? Luis

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Matrix format mpiaij does not have a built-in PETSc XXX!
by Aron Roland 26 Feb '12

26 Feb '12

Dear All, I hope somebody can help us on this or give at least some clearance. We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme. The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem. All others give the error msg. of the mail subject, where XXX are the different PC tried. The manual is a bit diffuse on this e.g. http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework. I guess we just not understanding the concept or have some other difficulties of understanding of all this. Any comments help is welcome Aron

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Important Petsc header files to include
by Mengda Wu 25 Feb '12

25 Feb '12

Hi all, I am trying to select a set of important petsc header files to included in my installation of Petsc. Basically, I would like the header and library files to be outside of Petsc source directory. I found there are many headers under PETSC_DIR/include. Are these all necessary for a program to just use PETSC functions? Thanks, Mengda

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testing scalability for ksp/ex22.c
by Francis Poulin 24 Feb '12

24 Feb '12

Hello, I am learning to use PetSc but am just a notice. I have a rather basic question to ask and couldn't not find it on the achieves. I am wanting to test the scalability of a Multigrid solver to the 3D Poisson equation. I found ksp/ex22.c that seems to solve the problem that I'm interested in. I ran it on a large server using different processors. The syntax that I use to run using MPI was ./ex22 -da_grid_x 64 -da_grid_y 64 -da_grid_z 32 I tested it using 2, 4, 8, 16 cpus and found that the time increases. See below. Clearly there is something that I don't understand since the time should be reduced. n wtime --------------------- 2 3m58s 4 3m54s 8 5m51s 16 7m23s Any advice would be greatly appreciated. Best regrads, Francis

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Accessing Vector's ghost values
by Bojan Niceno 24 Feb '12

24 Feb '12

Hi all, I've never used a mailing list before, so I hope this message will reach PETSc users and experts and someone might be willing to help me. I am also novice in PETSc. I have developed an unstructured finite volume solver on top of PETSc libraries. In sequential, it works like a charm. For the parallel version, I do domain decomposition externally with Metis, and work out local and global numberings, as well as communication patterns between processor. (The latter don't seem to be needed for PETSc, though.) When I run my program in parallel, it also works, but I miss values in vectors' ghost points. I create vectors with command: VecCreate(PETSC_COMM_WORLD, &x); Is it possible to get the ghost values if a vector is created like this? I have tried to use VecCreateGhost, but for some reason which is beyond my comprehension, PETSc goes berserk when it reaches the command: VecCreateGhost(PETSC_COMM_WORLD, n, PETSC_DECIDE, nghost, ifrom, &x) Can anyone help me? Either how to reach ghost values for vector created by VecCreate, or how to use VecCreateGhost properly? Kind regards, Bojan

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how to pass complex scalar in command line
by Hui Zhang 23 Feb '12

23 Feb '12

I know PetscOptionsGetScalar(), but do not know how to write the complex number in command line. I tried to write it in some forms but all did not work. Say, the options is -acomplex. I tried -acomplex 1.0+1.0i, or -acomplex 1.0+1.0*i, or -acomplex 1.0+1.0*I ... no one works. thank you, Hui

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Oscillations in finite difference solution
by Patrick Alken 22 Feb '12

22 Feb '12

Hi all, I have been trying to track down a problem for a few days with solving a linear system arising from a finite differenced PDE in spherical coordinates. I found that PETSc managed to converge to a nice solution for my matrix at small grid sizes and everything looks pretty good. But when I try larger more realistic grid sizes, PETSc fails to converge. After trying with another direct solver library, I found that the direct solver found a solution which exactly solves the matrix equation, but when plotting the solution, I see that it oscillates rapidly between the grid points and therefore isn't a satisfactory solution. (At smaller grids the solution is nice and smooth) I was wondering if this phenomenon is common in PDEs? and if there is any way to correct for it? I am currently using 2nd order centered differences for interior grid points, and 1st order forward/backward differences for edge points. Would it be worthwhile to try moving to 4th order differences instead? Or would that make the problem worse? I've even tried smoothing the parameters which go into the matrix entries using moving averages...which doesn't seem to help too much. Any advice from those who have experience with this phenomenon would be greatly appreciated! Thanks, Patrick

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AO
by Mohammad Mirzadeh 22 Feb '12

22 Feb '12

Hi, Should I be worried about function call overhead if make calls like AOXXXXToYYYY(ao, 1, &node) for each node when setting up the linear system? If so, is there an array where AO internally saves the mapping information that I can access or do I need to first save the mapping once and reuse it? Thanks, Mohammad

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