[petsc-users] Conversion between AIJ & BAIJ
Chung-Kan Huang
ckhuangf at gmail.com
Wed Jan 21 16:21:34 CST 2015
On Wed, Jan 21, 2015 at 4:03 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Jan 21, 2015 at 3:16 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
>
>>
>> On Wed, Jan 21, 2015 at 2:36 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Wed, Jan 21, 2015 at 2:29 PM, Chung-Kan Huang <ckhuangf at gmail.com>
>>> wrote:
>>>
>>>>
>>>> On Wed, Jan 21, 2015 at 2:15 PM, Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Wed, Jan 21, 2015 at 2:07 PM, Chung-Kan Huang <ckhuangf at gmail.com>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> On Wed, Jan 21, 2015 at 2:01 PM, Matthew Knepley <knepley at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> On Wed, Jan 21, 2015 at 1:55 PM, Chung-Kan Huang <ckhuangf at gmail.com
>>>>>>> > wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Jan 21, 2015 at 1:44 PM, Matthew Knepley <knepley at gmail.com
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> On Wed, Jan 21, 2015 at 1:40 PM, Chung-Kan Huang <
>>>>>>>>> ckhuangf at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Then A & AB are not longer the same matrix. They become complete
>>>>>>>>>> two individuals aren't they?
>>>>>>>>>> If I do whatever to AB after AB is created the A is still the
>>>>>>>>>> same old A and not going to be affected by the operations I do to AB.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Yes.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> What I am really looking for is a way to create two interfaces
>>>>>>>>>> (one as AIJ and one as BAIJ) but they both refer to the same matrix.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Why would you ever want this? Why not just using BAIJ?
>>>>>>>>>
>>>>>>>> As I mentioned in the beginning. There are parts of the code gets
>>>>>>>> benifit when AIJ is used and the other part gets benifit if BAIJ is used.
>>>>>>>>
>>>>>>>> For instance,
>>>>>>>>
>>>>>>>> I'd like to use MatSetValuesBlocked but I also want to use ilu
>>>>>>>> constructed by AIJ instead of BAIJ (our experience found ilu from BAIJ
>>>>>>>> behaves funny sometimes.
>>>>>>>>
>>>>>>>
>>>>>>> If the blocks truly are dense, then ILU(0) is identical on both.
>>>>>>>
>>>>>>
>>>>>> Unfortunately the life is not that easy. The blocks are spares and
>>>>>> we found ILU(1) works better for our case.
>>>>>> And besides that is not the only reason I want to have AIJ & BAIJ
>>>>>> interfaces, we have some code management issue and I am looking for short
>>>>>> cut to unite them.
>>>>>>
>>>>>> So go back to the original question the short answer is no way?
>>>>>>
>>>>>
>>>>> Yes, it would not make sense.
>>>>>
>>>>> What problem are you using ILU(1) for?
>>>>>
>>>>
>>>> I am using it for flow simulation for reservoir problems.
>>>>
>>>
>>> Have you considered trying algebraic multigrid?
>>>
>>
>> I am solving PDE fully implicitly and as far as I know algebraic
>> multigrid only good for pressure equations
>> I will need 2 stages PC while AMG is for pressure stage but I will still
>> need something like ILU for second stage.
>>
>
> So you are using a mixed-formulation of Darcy? What equations do you have?
>
After some steps of reduction, the system equation solved in linear solver
is basically the convervations of masses and energy.
Together I am solving the equations with natrual variables (pressure,
temperature, saturations and molar fractions) .
It might have variable block size depend on local state and physics that
considered. For instant, I can skip mass transfer if it is impermeable to
fluid locally but I still need to solve for conduction in energy balance
equations. I might also have some zones do not have some components so I
can skip them as well. Ideally I should have used variable size of block
but I used the same size anyway in my previous BAIJ configuration as you
pointed out some optimization can be done with the same size blocked matrix.
I switched to AIJ for reason related to ILU that I explained already. I
didn't see the same problem in AIJ.
I am looking for room to improve linear solver performance in all aspects
including CPU time to assemble the matrix and also good PC that are
provided by PETSc.
Currently I am using AIJ + ILU(1) + overlay(1) +BCGS. I am not so happy
about scalbility but that is not in the scope of the problem I brought
initially. But I am interested if you have any good suggestions that I
should test.
Thanks,
Kan
>
> Thanks,
>
> MAtt
>
>
>>
>>>
>>>> Some issues we found is that
>>>> 1) for a * x = 0 it doesn't return x = 0
>>>>
>>>
>>> This is impossible. There must be a bug in the code.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> 2) After compared ILU(1) with BAIJ against with ILU(1) with AIJ I found
>>>> latter one is better. I could not find anything wrong with my BAIJ version
>>>> though. However, experiences suggested that BAIJ's ILU(1) should be better.
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Kan
>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Kan
>>>>>>
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Kan
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Matt
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Kan
>>>>>>>>>> On Wed, Jan 21, 2015 at 1:20 PM, Matthew Knepley <
>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> On Wed, Jan 21, 2015 at 12:56 PM, Chung-Kan Huang <
>>>>>>>>>>> ckhuangf at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> So if I do
>>>>>>>>>>>>
>>>>>>>>>>>> Mat A, AB;
>>>>>>>>>>>> MatCreateAIJ(comm,m,n,M,N,d_nz, d_nnz,o_nz, o_nnz, &A);
>>>>>>>>>>>> MatConvert(A, MATBAIJ, MAT_INITAL_MATRIX, &AB);
>>>>>>>>>>>> MatSetBlockSize(AB, bs)
>>>>>>>>>>>> I can create AB as a BAIJ with block size of bs from A which is
>>>>>>>>>>>> a AIJ matrix.
>>>>>>>>>>>>
>>>>>>>>>>>> So from this point I can use both A and AB and they will mean
>>>>>>>>>>>> the same matrix. Am I right?
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Yes
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> At the end of the program do I only destory one of them or both?
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Both
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Do I need to worry about anything in terms of memory penalty?
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> It is twice the memory. Its another matrix.
>>>>>>>>>>>
>>>>>>>>>>> Did you catch when Jed said you could jsut create the BAIJ up
>>>>>>>>>>> front?
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Matt
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Kan
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Jan 20, 2015 at 4:39 PM, Barry Smith <
>>>>>>>>>>>> bsmith at mcs.anl.gov> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> You can do a MatConvert() (requires another copy of the
>>>>>>>>>>>>> matrix) for the parts that benefit from BAIJ.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Barry
>>>>>>>>>>>>>
>>>>>>>>>>>>> > On Jan 20, 2015, at 4:33 PM, Chung-Kan Huang <
>>>>>>>>>>>>> ckhuangf at gmail.com> wrote:
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Hi,
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Does PETSc provide means for conversion between AIJ & BAIJ.
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > My matrix is created as AIJ because it makes life easy for
>>>>>>>>>>>>> most part of the applications but some part of applications actually get
>>>>>>>>>>>>> some benefits with BAIJ. So I wonder if a matrix can exist as two
>>>>>>>>>>>>> idenfities and I can use either format depend on which one is more
>>>>>>>>>>>>> convenient at run time.
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > So in my case the block size is fixed and identical for all
>>>>>>>>>>>>> blocks.
>>>>>>>>>>>>> >
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Thanks,
>>>>>>>>>>>>> >
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Kan
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>> *Cheers*
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>>>>> experiments lead.
>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>>> *Cheers*
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>>> experiments lead.
>>>>>>>>> -- Norbert Wiener
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> *Cheers*
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> What most experimenters take for granted before they begin their
>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>> experiments lead.
>>>>>>> -- Norbert Wiener
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> *Cheers*
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their
>>>>> experiments is infinitely more interesting than any results to which their
>>>>> experiments lead.
>>>>> -- Norbert Wiener
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> *Cheers*
>>>>
>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>
>>
>>
>> --
>>
>> *Cheers*
>>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
--
*Cheers*
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