[petsc-users] Using matrix-free with KSP

[Barry Smith]

> On Sep 8, 2022, at 1:47 PM, Tu, Jiannan <Jiannan_Tu at uml.edu> wrote:
> 
> Barry,
>  
> Thank you very much.
>  
> DMDASetBlockFills() needs two input arrays specifying sparsity pattern. In my case, I have 26 components at each grid. Is it correct that I need to have two arrays of 26x26 elements with value 1 for coupling and 0 for no coupling?

   Exactly

> Also how to determine when the value should be 1 or 0?

  That is problem dependent. Given paper-and-pencil you know for your stencil which components are coupled with other components at each grid point and which components are coupled with components at neighboring grid points. 

  Note the second array contains information about all the neighboring grid points. Above, below, right, left, front back. Normally the coupling is symmetric so the nonzero structures of those 6 blocks are identical. If, for you particular problem, the nonzero structures of the six are not identical you use the union of the nonzero structures of the six of them.


  2d example     say you have x,y,z at each grid point and the inter-point coupling is x is connected to y and y is connect to x then the first array is

[ 1 1 0 ; 1 1; 0 ; 0 0 1]; the zeros are because x is not coupled to z and y is not coupled to z.

For intra grid points, say x is coupled to z and itself, z is coupled to x and itself and y is not coupled to itself then

[1 0 1; 0 0 0; 1 0 1]; the middle row is zero because y is not coupled to anything and the zeros in the first and last are because x and z are not coupled to y.


  
> Each component involves 7 stencils (i-1, j, k), (I, j, k), (i+1, j, k), (I, j-1, k), (I, j+1, k), (I, j, k-1), and (I, j, k+1), and couples with several other components.
>  
> Jiannan
>  
>  
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
>  
> From: Barry Smith <mailto:bsmith at petsc.dev>
> Sent: Wednesday, September 7, 2022 11:53 AM
> To: Tu, Jiannan <mailto:Jiannan_Tu at uml.edu>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>
> Subject: Re: [petsc-users] Using matrix-free with KSP
>  
> CAUTION: This email was sent from outside the UMass Lowell network.
>  
>  
> DMDASetBlockFills() or DMDASetBlockFillsSparse() (they are just different ways of providing the same information) will help you here enormously, your type of case is exactly what they were designed for.
>  
>  Barry
>  
> 
> 
> On Sep 7, 2022, at 10:47 AM, Tu, Jiannan <Jiannan_Tu at uml.edu <mailto:Jiannan_Tu at uml.edu>> wrote:
>  
> Barry and Hong,
>  
> Thank you. 
>  
> There are 26 components at each grid and there are not fully coupled in terms of stiff functions. Mutual coupling is among about 6 components. 
>  
> I would prefer not using matrix-free since the Jacobina is not difficult to calculate and only up to 10 non-zeros at each row. I'll try DMDASetBlockFills() or DMDASetBlockFillsSparse() and see how they can reduce the memory usage.
>  
> Jiannan
> <E6340AADF8494DB7861EA4659E7713CE.png>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Sent: Tuesday, September 6, 2022 11:33 PM
> To: Tu, Jiannan <Jiannan_Tu at uml.edu <mailto:Jiannan_Tu at uml.edu>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] Using matrix-free with KSP
>  
> CAUTION: This email was sent from outside the UMass Lowell network.
>  
>  
> 
> 
> On Sep 6, 2022, at 11:00 PM, Tu, Jiannan <Jiannan_Tu at uml.edu <mailto:Jiannan_Tu at uml.edu>> wrote:
>  
> I am using TS IMEX to solve a large DAE system. The DAE is obtained by applying finite FV method to 3-D multi-specie ion/neutral fluids equations with magnetic induction equation. The Jacobian for stiff part is formed by using MatSetValuesStencil(). The Jacobian matrix is very sparse, no more than 10 non-zeros on each row. MatSetValuesStencil requires local to global mapping by calling ISLocaltoGlobalMapping(). Could you please instruct me how to use local to global mapping? 
>  
>    DMDA automatically sets up the ISLocaltoGlobalMapping() so you should not need to.
>  
> I also tried using DMCreateMatrix() to create the Jacobian. While local to global mapping is not necessary, the matrix takes too much memory and requires 64-bit indices. I would prefer to take the advantage of sparsity of the Jacobian, pre-allocate the matrix to use as less as possible memory so that the code can be run on a multi-core desktop.
>  
>   If using matrix-free does not work for you because the linear solves do not converge or converge too slowly. Then you might be able to decrease the memory used in the matrix. The DMCreateMatrix() does take advantage of sparsity and tries to preallocate only what it needs. Often what it preallocates is the best possible,  but for multicomponent problems it has to assume there is full coupling within all the degrees of freedom that live at each at each grid point. How many components live at each grid point in your model and are they not all coupled to each other in the equations? If they are not fully coupled you can use either DMDASetBlockFills() or DMDASetBlockFillsSparse() to indicate the reduced coupling that actually exists for you model.
>  
>   Barry
> 
> 
>  
> Thank you very much for your advice.
>  
> Jiannan

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