[petsc-users] PCGASMSetLocalSubdomains

[Dmitry Karpeev]

Hui,
There appears to be a bug in MatGetSubMatrices() which inserts submatrix
column indices in the same order
as they appeared in the original matrix.  If a column IS has an inversion
--  IS[2] = 8 and IS[6] = 4,
as in your case --  then the submatrix column index 2 will appear after the
submatrix column index 4, since that's
how they were ordered in the original matrix (4 < 8, and the column indices
were properly sorted). This violates
the ordering of column indices, which prevents binary search from finding
column index 2.  That results in an
apparent new nonzero insertion, which is in turn caught, since by default
no new nonzeros are allowed.

I'm looking into this, and I'm not sure that there is an easy workaround
for you at this time: if you sort the IS indices,
it will violate the implicit local-to-global submatrix mapping you are
using in your ModifySubMatrices().

Thanks.
Dmitry.

On Mon, May 21, 2012 at 2:33 PM, Hui Zhang <mike.hui.zhang at hotmail.com>wrote:

> Hi,
>
> It might be unclear.  The error here is that the submat[1] does have a
> (1,2) entry,
> but MatSetValues at (1,2) gives an error message.  GASM and ASM give the
> same error.
>
> Thanks!
>
> On May 21, 2012, at 9:11 PM, Hui Zhang wrote:
>
> Sorry, I uses PCASMSetSortIndices for GASM. Now, I correct it and the
> output becomes the
> same as PCASM. See attached.
>
> <GASM_test.zip>
>
>
> On May 21, 2012, at 8:59 PM, Hui Zhang wrote:
>
> Dmitry,
>
> finally, I am able to make a simple program and reproduce the error. Since
> I had moved to
> petsc-dev (before I used petsc-3.2), the error is a little different.
>
> Download the program attached and run the run.sh.  You will see the output
> from PCASM.
> There is a submatrix (submat[1] on rank 0) which has a row like
>
>    row 1: (0, -1)  (1, 0 + 0.4 i) (4, -1)  (2, -1)
>
> Note that the column 2 is placed in the last and the column numbers are
> not in the normal order.
> Following that, we can also see the error message like
>
>    [0]PETSC ERROR: New nonzero at (1,2) caused a malloc!
>
> You can also try with GASM, use
>
>     mpirun -np 2 ./gasm_test -dd_type gasm -n 4 -px 1 -py 2 -sx 2 -sy 1
>
> which partitions the domain to 1 * 2 and mapped to the two processors, and
> for each processor
> we further partition its local domain to 2 * 1 subdomains.
>
> Then, you will see that the row 1 of submat[1] on rank 1 becomes
>
>    row 1: (0, -1)  (1, 0 + 0.4 i) (3, -1)  (6, -1)
>
> which is totally wrong because from the IS for this overlapping subdomain
> and the big matrix A,
> row 1 should have non-zeros like the output from PCASM.
>
> I guess the problem is due to that we set PCASMSetSortIndices to FALSE and
> something goes wrong
> in asm.c and gasm.c.
>
> Thanks!
> Hui
>
>
> <GASM_test.zip>
>
>
>
>
>
> On Sun, May 20, 2012 at 5:06 AM, Hui Zhang <mike.hui.zhang at hotmail.com>wrote:
>
>> I have the following MatView output:
>>
>> row 0: (0, -0.0351719 - 0.638814 i) (1, -0.517586 - 0.617823 i) (4,
>> -0.517586 - 0.617823 i) (1, -1.03517)  (5, -0.508793)
>>
>> Note that there are two values for the column 1, is this normal?
>>
>> The above matrix is obtained from PCASMGetSubKSP(pc,subksp) and
>> KSPGetOperators(subksp[0], ...).
>>
>
> This is odd. Can you explain a bit more what leads up to this, so we can
> try and reproduce the problem?
> Thanks.
> Dmitry.
>
>>
>> Thanks!
>>
>>
>>
>> On May 11, 2012, at 7:17 PM, Dmitry Karpeev wrote:
>>
>> You can call PCSetUp(pc) on either ASM or GASM, and that will destroy and
>> recreate the matrices (including calling
>> your modification subroutine), but not the subdomains or the subdomain
>> solvers.
>> If you just want to modify the submatrices, you can call
>> PC(G)ASMGetSubmatrices() and modify the matrices it returns
>> (in the same order as the subdomains were set). That's a bit of a
>> hack, since you will essentially be modifying the PC's internal data
>> structures.  As long as you are careful, you should be okay, since you
>> already effectively have the same type of access to the submatrices through
>> the Modify callback.
>>
>> Dmitry.
>>
>> On Fri, May 11, 2012 at 11:52 AM, Hui Zhang <mike.hui.zhang at hotmail.com>wrote:
>>
>>> I just have a question about reuse of PCASM or PCGASM.
>>> Suppose I have seted up the PCASM and related KSP and I solved one time.
>>> Next for the same linear system (matrix and RHS), I just want PCASM
>>> modify the submatrices (PCSetModifySubmatrices) in a different way, using
>>> the same routine for modifying but with
>>> different user context for the modifying routine.
>>>
>>> What can I do for this task?  Currently, I destroy the KSP and
>>> re-construct it. I guess
>>> even for PCASM I can re-use it because the partition of subdomains
>>> remain the same.
>>>
>>> Thanks!
>>>
>>>
>>> On May 10, 2012, at 6:37 PM, Dmitry Karpeev wrote:
>>>
>>> Hui,
>>> There've been several changes to PCGASM ahead of the new release.
>>> Let me go back and see if it affected the convergence problem.
>>> Dmitry.
>>>
>>> On Thu, May 10, 2012 at 4:16 AM, Hui Zhang <mike.hui.zhang at hotmail.com>wrote:
>>>
>>>> Hi Dmitry,
>>>>
>>>> is there any news about PCGASM?
>>>>
>>>> thanks,
>>>> Hui
>>>>
>>>> On Feb 20, 2012, at 6:38 PM, Dmitry Karpeev wrote:
>>>>
>>>> Okay, thanks.
>>>> I'll take a look.
>>>>
>>>> Dmitry.
>>>>
>>>> On Mon, Feb 20, 2012 at 11:30 AM, Hui Zhang <mike.hui.zhang at hotmail.com
>>>> > wrote:
>>>>
>>>>> For reference, my results are attached.
>>>>>
>>>>> asm1.txt for asm with 1 process,
>>>>> asm2.txt for asm with 2 processes,
>>>>> gasm1.txt for gasm with 1 process, (with the iteration numbers
>>>>> different from others)
>>>>> gasm2.txt for gasm with 2 processes
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> thank you,
>>>>> Hui
>>>>>
>>>>> On Feb 20, 2012, at 3:06 PM, Dmitry Karpeev wrote:
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Feb 20, 2012 at 12:59 AM, Hui Zhang <
>>>>> mike.hui.zhang at hotmail.com> wrote:
>>>>>
>>>>>>
>>>>>> On Feb 20, 2012, at 12:41 AM, Dmitry Karpeev wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sun, Feb 19, 2012 at 3:08 PM, Hui Zhang <
>>>>>> mike.hui.zhang at hotmail.com> wrote:
>>>>>>
>>>>>>> I have a new problem: the results from ASM and GASM are different
>>>>>>> and it seems
>>>>>>> GASM has something wrong with SetModifySubMatrices. Numerical tests
>>>>>>> are with
>>>>>>> each subdomain supported only by one subdomain. There are no
>>>>>>> problems when
>>>>>>> I did not modify submatrices.  But when I modify submatrices, there
>>>>>>> are problems
>>>>>>> with GASM but no problems with ASM.
>>>>>>>
>>>>>>> For example, I use two subdomains. In the first case each subdomain
>>>>>>> is supported by
>>>>>>> one processor and there seems no problem with GASM. But when I use
>>>>>>> run my program
>>>>>>> with only one proc. so that it supports both of the two subdomains,
>>>>>>> the iteration
>>>>>>> number is different from the first case and is much larger.  On the
>>>>>>> other hand
>>>>>>> ASM has no such problem.
>>>>>>>
>>>>>>
>>>>>> Are the solutions the same?
>>>>>> What problem are you solving?
>>>>>>
>>>>>>
>>>>>> Yes, the solutions are the same. That's why ASM gives the same
>>>>>> results with one or
>>>>>> two processors. But GASM did not.
>>>>>>
>>>>> Sorry, I wasn't clear: ASM and GASM produced different solutions in
>>>>> the case of two domains per processor?
>>>>>
>>>>>> I'm solving the Helmholtz equation.  Maybe
>>>>>> I can prepare a simpler example to show this difference.
>>>>>>
>>>>> That would be helpful.
>>>>> Thanks.
>>>>>
>>>>> Dmitry.
>>>>>
>>>>>>
>>>>>>
>>>>>> Dmitry.
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Feb 15, 2012, at 6:46 PM, Dmitry Karpeev wrote:
>>>>>>>
>>>>>>> You should be able to.
>>>>>>> This behavior is the same as in PCASM,
>>>>>>> except in GASM the matrices live on subcommunicators.
>>>>>>> I am in transit right now, but I can take a closer look in Friday.
>>>>>>>
>>>>>>> Dmitry
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Feb 15, 2012, at 8:07, Hui Zhang <mike.hui.zhang at hotmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>> On Feb 15, 2012, at 11:19 AM, Hui Zhang wrote:
>>>>>>>
>>>>>>> Hi Dmitry,
>>>>>>>
>>>>>>> thanks a lot! Currently, I'm not using ISColoring. Just comes
>>>>>>> another question
>>>>>>> on PCGASMSetModifySubMatrices(). The user provided function has the
>>>>>>> prototype
>>>>>>>
>>>>>>> func (PC pc,PetscInt nsub,IS *row,IS *col,Mat *submat,void *ctx);
>>>>>>>
>>>>>>> I think the coloumns from the parameter 'col' are always the same as
>>>>>>> the rows
>>>>>>> from the parameter 'row'. Because PCGASMSetLocalSubdomains() only
>>>>>>> accepts
>>>>>>> index sets but not rows and columns. Has I misunderstood something?
>>>>>>>
>>>>>>>
>>>>>>> As I tested, the row and col are always the same.
>>>>>>>
>>>>>>> I have a new question. Am I allowed to SetLocalToGlobalMapping() for
>>>>>>> the submat's
>>>>>>> in the above func()?
>>>>>>>
>>>>>>> thanks,
>>>>>>> Hui
>>>>>>>
>>>>>>>
>>>>>>> thanks,
>>>>>>> Hui
>>>>>>>
>>>>>>>
>>>>>>> On Feb 11, 2012, at 3:36 PM, Dmitry Karpeev wrote:
>>>>>>>
>>>>>>> Yes, that's right.
>>>>>>> There is no good way to help the user assemble the subdomains at the
>>>>>>> moment beyond the 2D stuff.
>>>>>>> It is expected that they are generated from mesh subdomains.
>>>>>>> Each IS does carry the subdomains subcomm.
>>>>>>>
>>>>>>> There is ISColoringToList() that is supposed to convert a "coloring"
>>>>>>> of indices to an array of ISs,
>>>>>>> each having the indices with the same color and the subcomm that
>>>>>>> supports that color. It is
>>>>>>> largely untested, though.  You could try using it and give us
>>>>>>> feedback on any problems you encounter.
>>>>>>>
>>>>>>> Dmitry.
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Feb 11, 2012 at 6:06 AM, Hui Zhang <<mike.hui.zhang at hotmail.com>
>>>>>>> mike.hui.zhang at hotmail.com> wrote:
>>>>>>>
>>>>>>>> About PCGASMSetLocalSubdomains(), in the case of one subdomain
>>>>>>>> supported by
>>>>>>>> multiple processors, shall I always create the arguments 'is[s]'
>>>>>>>> and 'is_local[s]'
>>>>>>>> in a subcommunicator consisting of processors supporting the
>>>>>>>> subdomain 's'?
>>>>>>>>
>>>>>>>> The source code of PCGASMCreateSubdomains2D() seemingly does so.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Hui
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
>
>
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