[petsc-users] Incomplete Cholesky Factorization in petsc

[Hong]

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/20171205/1a610a4d/attachment-0001.html>