[petsc-users] matrix reordering

[Mohammad Mirzadeh]

Awesome. Thanks for doing this Jed.

On Sat, Oct 20, 2012 at 5:38 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> On Fri, Oct 19, 2012 at 6:03 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote:
>
>> Cool. Jed, could you please point me to an example/tutorial for this? I'm
>> going to give it a shot.
>>
>
> This works for SeqAIJ:
>
>   ierr = MatGetOrdering(A,ordering,&rowperm,&colperm);CHKERRQ(ierr);
>   ierr = MatPermute(A,rowperm,colperm,&Aperm);CHKERRQ(ierr);
>   ierr = VecPermute(b,colperm,PETSC_FALSE);CHKERRQ(ierr);
>
>   ierr =
> KSPSetOperators(ksp,Aperm,Aperm,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
>   ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
>   ierr = VecPermute(x,rowperm,PETSC_TRUE);CHKERRQ(ierr);
>
> Now x is the solution back in the original ordering.
>
>
> There is an example in petsc-dev now.
>
>
> https://bitbucket.org/petsc/petsc-dev/src/tip/src/ksp/ksp/examples/tutorials/ex18.c
>
> It should work with petsc-3.3 in serial, but you need petsc-dev for
> parallel MatPermute.
>
>
>
>>
>> Thanks
>>
>>
>> On Fri, Oct 19, 2012 at 3:57 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>>
>>> _You_ can compute a MatOrdering, MatPermute and VecPermute, solve, and
>>> permute back. Profile and if the solve is faster, go ahead and lift the
>>> ordering code back into your mesh.
>>>
>>>
>>> On Fri, Oct 19, 2012 at 5:48 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote:
>>>
>>>> Thanks Barry. I think I agree with you that right way to do it is
>>>> through mesh setup. As a matter of fact I have done that for some of my
>>>> problems. Yet, I can think of situations where that kind of support might
>>>> be beneficial, especially if someone (a.k.a me in this case!) is looking
>>>> for a 'dirty and fast' fix.
>>>>
>>>> Anyway, I still believe that in long term, one should do the
>>>> partitioning in a pre-processing step anyways and so there may not be much
>>>> incentive for adding such a support.
>>>>
>>>> Thanks again,
>>>> Mohammad
>>>>
>>>>
>>>> On Fri, Oct 19, 2012 at 3:00 PM, Barry Smith <bsmith at mcs.anl.gov>wrote:
>>>>
>>>>>
>>>>>    Mohammad,
>>>>>
>>>>>      We've thought about adding this kind of support this over the
>>>>> years but always came to the conclusion that "the right way to do it" is
>>>>> during the mesh setup step.
>>>>>
>>>>>    Barry
>>>>>
>>>>>
>>>>> On Oct 19, 2012, at 4:16 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>
>>>>> wrote:
>>>>>
>>>>> > Hi guys,
>>>>> >
>>>>> > Quick question. *After* the matrix is setup, is it possible to ask
>>>>> PETSc to renumber the nodes internally in the KSPSolve phase to minimize
>>>>> communications for MatMul inside the solver? Can I use the MatPartitioning
>>>>> object for this or is that only intended to partition the mesh as a
>>>>> pre-processing step?
>>>>> >
>>>>> > Thanks
>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20121020/ee30dd89/attachment.html>