[petsc-users] Incomplete Cholesky Factorization in petsc

[Wenlong Gong]

Hong, Thank you for the clarification!
Is there a function to get row/col indices and non-zeros vector of the
factored matrix , instead of extracting the elements one by one?

-Wendy

On Tue, Dec 5, 2017 at 9:50 AM, Hong <hzhang at mcs.anl.gov> wrote:

> Wendy,
> Petsc factor matrix as
> A = U^T * U, U: upper triangular matrix.
> When A is stored in seqaij format, we store U as
> /*
>    icc() under revised new data structure.
>    Factored arrays bj and ba are stored as
>      U(0,:),...,U(i,:),U(n-1,:)
>
>    ui=fact->i is an array of size n+1, in which
>    ui+
>      ui[i]:  points to 1st entry of U(i,:),i=0,...,n-1
>      ui[n]:  points to U(n-1,n-1)+1
>
>   udiag=fact->diag is an array of size n,in which
>      udiag[i]: points to diagonal of U(i,:), i=0,...,n-1
>
>    U(i,:) contains udiag[i] as its last entry, i.e.,
>     U(i,:) = (u[i,i+1],...,u[i,n-1],diag[i])
> */
>
> see petsc/src/mat/impls/aij/seq/aijfact.c: MatICCFactorSymbolic_SeqAIJ()
>
> Petsc matrix factors only work for Petsc MatSolve().
>
> Hong
>
> On Tue, Dec 5, 2017 at 9:32 AM, Wenlong Gong <wenlonggong at gmail.com>
> wrote:
>
>> Barry, Thank you for the reply! It makes sense If two IC() function
>> returns slightly different factored matrix. But the IC factor matrix from
>> PETSc is not even close to what I get from ichol in Matlab.
>> Ultimately I need this incomplete cholesky factorization function wrapped
>> in R once it gives correct result. Not sure if I used the easiest way to
>> get IC so I also seek for help on getting a concise version of IC().
>>
>> -Wendy
>>
>>
>> On Mon, Dec 4, 2017 at 10:07 PM, Smith, Barry F. <bsmith at mcs.anl.gov>
>> wrote:
>>
>>>
>>>   I'm not sure what your goal is. In general two different IC(0) codes
>>> might produce slightly different factorizations based on implementation
>>> details even if they claim to run the same algorithm so I don't think there
>>> is a reason to try to compare the factors they produce.
>>>
>>>   In addition PETSc, as well as most IC/ILU/LU  codes store the factored
>>> matrices in a "non-conventional" form that is optimized for performance so
>>> it is not easy to just pull out the "factors" to look at them or compare
>>> them.
>>>
>>>     Barry
>>>
>>>
>>> > On Dec 4, 2017, at 9:07 PM, Wenlong Gong <wenlonggong at gmail.com>
>>> wrote:
>>> >
>>> > Hello,
>>> >
>>> > I'm trying to use the Incomplete Cholesky Factorization for a sparse
>>> matrix in petsc. I started with a 10*10 matrix and used ksp and pc in order
>>> to get the ICC(0) factor, with no fill-in, natural ordering. However, the
>>> returned factor matrix does not match with the answer I got from matlab
>>> ichol() function.
>>> >
>>> > The code with the hard-coded data is attached here. I would appreciate
>>> if anyone could help check if I did anything wrong.Please let me know if
>>> there is easier way to get this incomplete cholesky factor. Thanks!
>>> >
>>> > Best regards,
>>> > Wendy
>>> >
>>> > <repex.c>
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20171205/b01e7aa8/attachment.html>