[petsc-users] Mat_CheckInode

[Matthew Knepley]

On Mon, Dec 5, 2011 at 8:46 AM, Debao Shao <Debao.Shao at brion.com> wrote:

>  DA,
>
> 1, Will check_inode affect the runtime performance? For example, in my
> case, there are such different logs:****
>
>      [0] Mat_CheckInode(): Found 18602 nodes out of 18609 rows. Not using
> Inode routines****
>
>      [0] Mat_CheckInode(): Found 0 nodes of 0. Limit used: 5. Using Inode
> routines****
>
>      [0] Mat_CheckInode(): Found 14020 nodes out of 14020 rows. Not using
> Inode routines
>

This is intended to "discover" block structure. If you have it, MatMult
should be faster.


> 2, Here is the log_summary, looks like PCSetup is big time-consuming
> function, the method I’m using is ILU(1) & GMRES, may I improve it?****
>
>      MatMult            30733 1.0 8.9553e+01 1.0 3.41e+10 1.0 0.0e+00
> 0.0e+00 0.0e+00  2  4  0  0  0   2  4  0  0  0   380****
>
>      MatMultAdd          9552 1.0 6.6610e+00 1.0 2.42e+09 1.0 0.0e+00
> 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0   363****
>
>      MatSolve           36236 1.0 2.4699e+02 1.0 9.44e+10 1.0 0.0e+00
> 0.0e+00 0.0e+00  6 10  0  0  0   6 10  0  0  0   382****
>
>      MatLUFactorNum      2838 1.0 2.4328e+03 1.0 7.65e+11 1.0 0.0e+00
> 0.0e+00 0.0e+00 61 85  0  0  0  61 85  0  0  0   315****
>
>      MatILUFactorSym      173 1.0 1.3486e+02 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00  3  0  0  0  0   3  0  0  0  0     0****
>
>      MatAssemblyBegin    5787 1.0 2.0547e-03 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0****
>
>      MatAssemblyEnd      5787 1.0 5.3559e+00 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0****
>
>      KSPGMRESOrthog     30679 1.0 5.5968e+00 1.0 4.06e+09 1.0 0.0e+00
> 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0   725****
>
>      KSPSetup            2838 1.0 1.8219e-02 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0****
>
>      KSPSolve            5503 1.0 2.9136e+03 1.0 8.99e+11 1.0 0.0e+00
> 0.0e+00 0.0e+00 73100  0  0  0  73100  0  0  0   308****
>
>      PCSetUp             2838 1.0 2.5682e+03 1.0 7.65e+11 1.0 0.0e+00
> 0.0e+00 0.0e+00 64 85  0  0  0  64 85  0  0  0   298****
>
>      PCApply            36236 1.0 2.4709e+02 1.0 9.44e+10 1.0 0.0e+00
> 0.0e+00 0.0e+00  6 10  0  0  0   6 10  0  0  0   382     ****
>
> The matrix size is around 50000*50000, nnz is ~2000000
>

ILU is expensive, and levels make it much more expensive. Maybe try AMG?

> 3, Will the fill of ilu affect the runtime performance?****
>
>      [0] MatILUFactorSymbolic_SeqAIJ(): Reallocs 0 Fill ratio:given 1
> needed 1.11111****
>
>      [0] MatILUFactorSymbolic_SeqAIJ(): Reallocs 1 Fill ratio:given 1
> needed 5.05****
>
>      [0] MatILUFactorSymbolic_SeqAIJ(): Reallocs 1 Fill ratio:given 1
> needed 8.3410****
>
> How to set a proper value for fill, >8?
>

http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/PC/PCFactorSetFill.html

Use -pc_factor_fill

  Matt


> Thanks,****
>
> Debao****
>
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