[petsc-dev] plans for preconditioners for SeqSELL
Richard Tran Mills
rtmills at anl.gov
Mon Jun 25 20:12:53 CDT 2018
Hi Hong,
On Mon, Jun 25, 2018 at 2:52 PM, Zhang, Hong <hongzhang at anl.gov> wrote:
>
>
> On Jun 25, 2018, at 4:09 PM, Mills, Richard Tran <rtmills at anl.gov> wrote:
>
> Hi Hong,
>
> Thanks for your reply. Yes, I was just looking at what goes on in
> MatConvert_Basic() and I see the problem. I note that my AIJSELL code seems
> to always work correctly when the matrix block size is one -- I guess that
> this is because MatSeqSELLSetPreallocation() is called in this case.
>
> Are you saying that the
>
> if (A->rmap->bs > 1) {
> ierr = MatConvert_Basic(A,newtype,reuse,newmat);CHKERRQ(ierr);
> PetscFunctionReturn(0);
> }
>
> lines in sell.c should be removed and then things should work?
>
>
> If your conversion function for AIJSELL calls MatConvert_SeqAIJ_SeqSELL(),
> then yes. Otherwise you might want to copy some code from the link I
> attached (sell.c).
>
I've tried to construct things so that there is as little code duplication
as possible, so I am just calling MatConvert_SeqAIJ_SeqSELL().
> If so, I'll remove this, test on my machine, and then merge this change
> into 'next'. Or is more code needed to make SELL work properly with a block
> size > 1?
>
>
> I don't think we need more code.
>
Alright, sounds like the presence of the code path that sends things down
MatConvert_Basic() should be considered a bug, then. I'll start a fix off
of 'maint', test things locally, and then (if things pass) merge into
'next' for testing.
If removing the code in question still doesn't fix things, well, then it's
still a bug, but will need some more work to fix.
Thanks,
Richard
> Thanks,
> Hong (Mr.)
>
>
> --Richard
>
> On Mon, Jun 25, 2018 at 2:04 PM, Zhang, Hong <hongzhang at anl.gov> wrote:
>
>> Hi Richard,
>>
>> MatConvert_Basic() does not work for most cases when converting AIJ to
>> SELL because SELL may require padding and being preallocated based on the
>> nonzeros per row.
>> See the correct conversion in https://bitbucket.org/petsc
>> /petsc/src/master/src/mat/impls/sell/seq/sell.c?fileview
>> er=file-view-default%20#sell.c-251
>>
>> You were probably mislead by the code
>>
>> if (A->rmap->bs > 1) {
>> ierr = MatConvert_Basic(A,newtype,reuse,newmat);CHKERRQ(ierr);
>> PetscFunctionReturn(0);
>> }
>> which should be removed.
>>
>> Thanks,
>> Hong (Mr.)
>>
>>
>> On Jun 25, 2018, at 3:06 PM, Richard Tran Mills <rtmills at anl.gov> wrote:
>>
>> Hi Everyone (especially Herr Doktor Hong Zhang),
>>
>> It sure took me a while to get around to it, but I coded up (in branch
>> rmills/feature-add-mataijsell) the skeleton of what I'm currently calling
>> the 'AIJSELL' matrix type, which is a "meta" matrix type that inherits from
>> AIJ but maintains a "shadow" MATSEQSELL copy of the matrix for use when
>> that is appropriate. This works similarly to how AIJMKL works, insofar as
>> the PetscObjectState is tracked and used to determine when the SELL
>> "shadow" copy needs to be updated before an operation like MatMult() is
>> applied. (Note that what I have so far only does MatMult, but it should be
>> easy to add other operations once I've verified that my implementation is
>> working.) I decided on the approach of using a MATSEQSELL instance inside
>> an AIJ-derived matrix type because I still want to be able to support
>> standalone SELL matrices when there really isn't a need for any of the
>> AIJ-only operations.
>>
>> My AIJSELL implementation seems to work fine in many cases, but I've
>> spent several hours chasing some bugs that crop up in certain cases. I now
>> think that the bugs are not a problem with my AIJSELL implementation
>> (though I'd welcome another pair of eyes to help me verify this), but are
>> lurking somewhere in the SELL code and haven't been hit before because
>> AIJSELL makes it easier to exercise the SELL class on more problems.
>>
>> I've been using the well-loved SNES ex19 example (that is used for 'make
>> check') for some of my debugging. I've found that everything works great
>> when I size the problem grid such that the resulting matrices have a row
>> count that is evenly divisible by 8 (when using double precision scalars).
>> So
>>
>> ./ex19 -ksp_type gmres -pc_type none -snes_monitor -ksp_monitor
>> -da_grid_x 4 -da_grid_y 5 -mat_seqaij_type seqaijsell -snes_max_it 1
>> -ksp_monitor
>>
>> which results in an 80x80 Jacobian (since there are 4 degrees of freedom
>> per grid point) runs fine, but
>>
>> ./ex19 -ksp_type gmres -pc_type none -snes_monitor -ksp_monitor
>> -da_grid_x 3 -da_grid_y 5 -mat_seqaij_type seqaijsell -snes_max_it 1
>> -ksp_monitor
>>
>> results in either a segfault or the GMRES(30) solve terminating at 10,000
>> iterations because the residual norm just keeps bouncing up and down.
>>
>> Sticking some MatView() calls in, it appears that the MatMult() results
>> inside the KSP solve are incorrect because the SELL copy of the matrix
>> generated by my MatConvert() call is incorrect when the row count isn't
>> evenly divisible by eight. In the case of SNES ex19, MatConvert_Basic() is
>> currently used because the block size is greater than unity. So I think
>> something is going wrong either in the MatSetValues() or (my guess)
>> MatAssemblyBegin()/End().
>>
>> Poking around with a debugger, I see that the column index array
>> ("colidx") that is part of the SEQSELLHEADER ends up with nonsense values,
>> and the segfaults I see tend to occur when indexing into the x vector with
>> this.
>>
>> I'm not familiar enough with the internals of SELL to look further into
>> debugging this without a lot of effort. Hong, can you help me look at this?
>>
>> Best regards,
>> Richard
>>
>> On Tue, Mar 6, 2018 at 3:59 AM, Karl Rupp <rupp at iue.tuwien.ac.at> wrote:
>>
>>>
>>> > Karl, are you thinking of a matrix subclass that has everything that
>>> an
>>> > AIJ matrix does, but also keeps a SELL copy around for operations like
>>> > MatMult()? Would it make sense to just keep another Mat inside (like
>>> how
>>> > MPIAIJ keeps multiple Mat instances) that *is* of type MATSELL, that
>>> > gets built/updated as needed? Would this involve carrying too much
>>> > baggage around, associated with a complete Mat instance?
>>>
>>> What I have in mind is to put the SELL datastructures into a A->spptr,
>>> very much like you did for AIJMKL.
>>>
>>>
>>> > I like the idea
>>> > of having a MATSELL type available that is lean (insofar as not having
>>> > storing an AIJ matrix) for those cases when a user really knows that
>>> the
>>> > AIJ stuff will not be needed. But maybe it makes sense to be able to
>>> use
>>> > that inside another matrix class. Perhaps we could have something,
>>> > called, say, MATAIJMUTABLE that uses AIJ but might also create copies
>>> in
>>> > SELL (or other formats, potentially) when appropriate -- perhaps based
>>> > on a some performance model indicating which format is fastest for
>>> > MatMult() or whatever.
>>>
>>> The actual overhead of also storing a SELL datastructure in terms of
>>> memory footprint is at most 2x. When you keep in mind that extra memory
>>> during the matrix assembly is also needed in the stash, then the impact
>>> on overall memory consumption is about 50 percent extra. Given that SELL
>>> is a performance optimization for SpMV (and hence the SELL datastructure
>>> is only populated if you call MatMult on the particular matrix), I'm not
>>> too worried about the increased memory footprint at this time.
>>>
>>>
>>> > Having a class that's an AIJ but can also use SELL is more convenient
>>> > than adding a fallback to AIJ format inside MATSELL. I wonder if the
>>> > latter option might be preferable in some circumstances, however,
>>> > because it can avoid the extra memory footprint of also keeping the
>>> > matrix in AIJ -- maybe AIJ operations are rarely needed and the AIJ
>>> > conversion can just happen on a lazy basis.
>>>
>>> I advocate an 'optimize as needed' approach here. Let's first make SELL
>>> compatible with the full range of AIJ operations and preconditioners.
>>>
>>> Best regards,
>>> Karli
>>>
>>>
>>>
>>> >
>>> > --Richard
>>> >
>>> > On 3/4/18 2:58 AM, Karl Rupp wrote:
>>> >> Hi all,
>>> >>
>>> >> I'm getting increasingly concerned about SELL not being a subclass of
>>> >> AIJ. As such, we have to deal with all these fallback operations now,
>>> >> whereas as a subclass of AIJ we could just selectively make use of
>>> the
>>> >> SELL format where we really benefit from it. "Use AIJ by default
>>> >> unless we have something optimized for SELL" is just much more
>>> >> appropriate for the few use cases of SELL than the current "SELL has
>>> >> to implement everything and usually this means to manually convert
>>> >> back to AIJ".
>>> >>
>>> >> If there are no objections I'd like to clean this up. (Subclassing
>>> AIJ
>>> >> was unfortunately not available at the time Hong started his great
>>> >> work on SELL)
>>> >>
>>> >> Best regards,
>>> >> Karli
>>> >>
>>> >>
>>> >>
>>> >> On 03/03/2018 07:52 AM, Richard Tran Mills wrote:
>>> >>> Resurrecting a few weeks old thread:
>>> >>>
>>> >>> Stefano, did you get around to coding something up to do an
>>> automatic
>>> >>> conversion to SeqAIJ for operations unsupported by SELL format? I
>>> did
>>> >>> some hacking the other day to try to get PCGAMG to use SELL inside
>>> >>> the smoothers and this turns out to be way more complicated than I'd
>>> >>> like and very bug prone (I haven't found all of mine, anyway). I
>>> >>> think it may be preferable to be able to pass a SELL matrix to
>>> PCGAMG
>>> >>> and have an internal conversion happen in the SELL matrix to AIJ
>>> >>> format for doing the MatPtAP and LU solves. Support for this would
>>> >>> certainly make it easier for users in a lot other cases as well, and
>>> >>> might make the use of SELL much more likely. If no one has already
>>> >>> done some work on this, I'll take a stab at it.
>>> >>>
>>> >>> --Richard
>>> >>>
>>> >>> On Mon, Feb 12, 2018 at 10:04 AM, Richard Tran Mills <
>>> rtmills at anl.gov
>>> >>> <mailto:rtmills at anl.gov>> wrote:
>>> >>>
>>> >>> On Mon, Feb 12, 2018 at 8:47 AM, Smith, Barry F. <
>>> bsmith at mcs.anl.gov
>>> >>> <mailto:bsmith at mcs.anl.gov>> wrote:
>>> >>>
>>> >>>
>>> >>>
>>> >>> > On Feb 12, 2018, at 10:25 AM, Stefano Zampini
>>> >>> <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>>
>>> wrote:
>>> >>> >
>>> >>> > Barry,
>>> >>> >
>>> >>> > for sure Amat,Pmat is the right approach; however, with
>>> >>> complicated user codes, we are not always in control of having a
>>> >>> different Jacobian matrix.
>>> >>> > Since Mat*SELL does not currently support any
>>> >>> preconditioning except PCSOR and PCJACOBI, we ask the user to put
>>> >>> codes like
>>> >>> >
>>> >>> > if (type is SELL)
>>> >>> > create two matrices (and maybe modify the code in many
>>> >>> other parts)
>>> >>> > else
>>> >>> > ok with the previous code
>>> >>>
>>> >>> I don't disagree with what you are saying and am not
>>> opposed
>>> >>> to the proposed work.
>>> >>>
>>> >>> Perhaps we need to do a better job with making the
>>> mat,pmat
>>> >>> approach simpler or better documented so more people use it
>>> >>> naturally in their applications.
>>> >>>
>>> >>>
>>> >>> I wrote some code like that in some of the Jacobian/function
>>> >>> routines in PFLOTRAN to experiment with MATSELL, and it works,
>>> but
>>> >>> looks and feels pretty hacky. And if I wanted to support it for
>>> all
>>> >>> of the different systems that PFLOTRAN can model, then I'd have
>>> to
>>> >>> reproduce that it in many different Jacobian and function
>>> evaluation
>>> >>> routines. I also don't like that it makes it awkward to play with
>>> >>> the many combinations of matrix types and preconditioners that
>>> PETSc
>>> >>> allows: The above pseudocode should really say "if (type is SELL)
>>> >>> and (preconditioner is not PCSOR or PCJACOBI)". I do think that
>>> >>> Amat,Pmat is a good approach in many situations, but it's easy to
>>> >>> construct scenarios in which it falls short.
>>> >>>
>>> >>> In some situations, what I'd like to have happen is what Stefano
>>> is
>>> >>> talking about, with an automatic conversion to AIJ happening if
>>> SELL
>>> >>> doesn't support an operation. But, ideally, I think this sort of
>>> >>> implicit format conversion shouldn't be something hard-coded into
>>> >>> the workings of SELL. Instead, there should be some general
>>> >>> mechanism by which PETSc recognizes that a particular operation
>>> is
>>> >>> unsupported for a given matrix format, and then it can
>>> (optionally)
>>> >>> copy/convert to a different matrix type (probably default to AIJ,
>>> >>> but it shouldn't have to be AIJ) that supports the operation.
>>> This
>>> >>> sort of implicit data rearrangement game may actually become more
>>> >>> important if future computer architectures strongly prefer
>>> different
>>> >>> data layouts different types of operations (though let's not get
>>> >>> ahead of ourselves).
>>> >>>
>>> >>> --Richard
>>> >>>
>>> >>>
>>> >>> Barry
>>> >>>
>>> >>> >
>>> >>> > Just my two cents.
>>> >>> >
>>> >>> >
>>> >>> > 2018-02-12 19:10 GMT+03:00 Smith, Barry F.
>>> >>> <bsmith at mcs.anl.gov <mailto:bsmith at mcs.anl.gov>>:
>>> >>> >
>>> >>> >
>>> >>> > > On Feb 12, 2018, at 9:59 AM, Stefano Zampini
>>> >>> <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com
>>> >>
>>> >>> wrote:
>>> >>> > >
>>> >>> > > FYI, I just checked and MatSOR_*SELL does not use any
>>> >>> vectorized instruction.
>>> >>> > > Why just not converting to SeqAIJ, factor and then use
>>> the
>>> >>> AIJ implementation for MatSolve for the moment?
>>> >>> >
>>> >>> > Why not use the mat, pmat feature of the solvers to
>>> pass in
>>> >>> both matrices and have the solvers handle using two formats
>>> >>> simultaneously instead of burdening the MatSELL code with
>>> tons
>>> >>> of special code for automatically converting to AIJ for
>>> >>> solvers etc?
>>> >>> >
>>> >>> >
>>> >>> > >
>>> >>> > > 2018-02-12 18:06 GMT+03:00 Stefano Zampini
>>> >>> <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com
>>> >>:
>>> >>> > >
>>> >>> > >
>>> >>> > > 2018-02-12 17:36 GMT+03:00 Jed Brown <jed at jedbrown.org
>>> >>> <mailto:jed at jedbrown.org>>:
>>> >>> > > Karl Rupp <rupp at iue.tuwien.ac.at
>>> >>> <mailto:rupp at iue.tuwien.ac.at>> writes:
>>> >>> > >
>>> >>> > > > Hi Stefano,
>>> >>> > > >
>>> >>> > > >> Is there any plan to write code for native ILU/ICC
>>> etc
>>> >>> for SeqSELL, at least to have BJACOBI in parallel?
>>> >>> > > >
>>> >>> > > > (imho) ILU/ICC is a pain to do with SeqSELL.
>>> Point-Jacobi
>>> >>> should be
>>> >>> > > > possible, yes. SELL is really just tailored to
>>> MatMults
>>> >>> and a pain for
>>> >>> > > > anything that is not very similar to a MatMult...
>>> >>> > >
>>> >>> > > There is already MatSOR_*SELL. MatSolve_SeqSELL wouldn't
>>> >>> be any harder.
>>> >>> > > I think it would be acceptable to convert to SeqAIJ,
>>> >>> factor, and convert
>>> >>> > > the factors back to SELL.
>>> >>> > >
>>> >>> > > Yes, this was my idea. Today I have started coding
>>> >>> something. I'll push the branch whenever I have anything
>>> working
>>> >>> > >
>>> >>> > >
>>> >>> > >
>>> >>> > > --
>>> >>> > > Stefano
>>> >>> > >
>>> >>> > >
>>> >>> > >
>>> >>> > > --
>>> >>> > > Stefano
>>> >>> >
>>> >>> >
>>> >>> >
>>> >>> >
>>> >>> > --
>>> >>> > Stefano
>>> >>>
>>> >>>
>>> >>>
>>> >
>>>
>>
>>
>>
>
>
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