[petsc-dev] MatMatMult gives different results

Wed Feb 8 10:45:40 CST 2012

Alexander :
I can repeat the crash, and am working on it.
I'll let you know after the bug is fixed.

Thanks for your patience,
Hong

>
> It seems now I know why I used MAT_REUSE_MATRIX and preallocated matrix.
> I removed MatCreateMPIAIJ() and use just MatTranspose with
> MAT_INITIAL_MATRIX.
> As a consequence I get hundreds of errors like:
>
> [30]PETSC ERROR: MatSetValues_MPIAIJ() line 538 in
> /home/mt/agrayver/lib/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
> [30]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 653 in
> /home/mt/agrayver/lib/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
> [30]PETSC ERROR: MatAssemblyEnd() line 4978 in
> /home/mt/agrayver/lib/petsc-dev/src/mat/interface/matrix.c
> [30]PETSC ERROR: MatTranspose_MPIAIJ() line 2061 in
> /home/mt/agrayver/lib/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
> [30]PETSC ERROR: MatTranspose() line 4397 in
> /home/mt/agrayver/lib/petsc-dev/src/mat/interface/matrix.c
> [31]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [31]PETSC ERROR: Argument out of range!
> [31]PETSC ERROR: New nonzero at (1659,53337) caused a malloc!
>
> Ans this is the lastest petsc-dev revision.
> I know there were some changes in petsc-dev concerning this issue.
> Can you give me a hint how to avoid this?
>
> As for why I need C=A^T*B. This product is used further as a system matrix
> for LSQR solver. The largest dimension is on the order of 10^6
> Since I form A and B myself I can, of course, form A^T explicitly, but I
> thought I would first implement everything as it is written down on paper
> and then optimize once it works (I thought it's easier way).
>
>
> On 07.02.2012 20:44, Hong Zhang wrote:
>
> Alexander,
> I'm curious about why do you need parallel C=A^T*B?
> How large your matrices are?
>
>  In petsc-dev, we have MatTransposeMatMult() for mpiaij and mpiaij, but
> not mpiaij and mpidense.
> We may add support of MatTransposeMatMult_MPIAIJ_MPIDense() if there is
> such need.
>
>  Hong
>
>
> On Tue, Feb 7, 2012 at 1:18 PM, agrayver at gfz-potsdam.de <
> agrayver at gfz-potsdam.de> wrote:
>
>> Hong,
>>
>> Thanks for explanation. I will try this tomorrow. Good to have this stuff
>> in the help now.
>>
>> And sorry for misleading you initially.
>>
>> Regards,
>> Alexander
>>
>>
>> ----- Reply message -----
>> From: "Hong Zhang" <hzhang at mcs.anl.gov>
>> To: "For users of the development version of PETSc" <
>> petsc-dev at mcs.anl.gov>
>> Subject: [petsc-dev] MatMatMult gives different results
>> Date: Tue, Feb 7, 2012 19:09
>>
>>
>> Alexander :
>>
>>>
>>> There is something I didn't get yet, I hope you could clarify it.
>>>
>>> So, when I use flag MAT_INITIAL_MATRIX in test program it works fine.
>>>
>> Good to know :-)
>>
>>
>>>  If I put this flag in my original program I get dozens of exceptions
>>> like:
>>> [42]PETSC ERROR: Argument out of range!
>>> [42]PETSC ERROR: New nonzero at (1336,153341) caused a malloc!
>>>
>> You cannot do
>>  MatCreateMPIAIJ()
>> MatTranspose(A,MAT_INITIAL_MATRIX,&AT);
>>
>>  MatCreateMPIAIJ() creates AT and preallocates approximate nonzeros,
>> which does not match exactly the nonzeros in
>> MatTranspose(A,MAT_INITIAL_MATRIX,&AT);
>> MatTranspose(A,MAT_INITIAL_MATRIX,&AT) creates matrix AT and sets correct
>> nonzero pattern and values in AT.
>> MatTranspose() only takes in "MAT_INITIAL_MATRIX" - for a new AT,
>> and "MAT_REUSE_MATRIX" when AT is created with
>> MatTranspose(A,MAT_INITIAL_MATRIX,&AT)
>> and reuse for updating its values (not nonzero patten).
>>
>>  I'm updating petsc help menu on MatTranspose(). Thanks for the report.
>>
>>  Hong
>>
>>
>>> I changed this flag to MAT_REUSE_MATRIX and exceptions disappeared, but
>>> result is incorrect again (same as for MAT_IGNORE_MATRIX)
>>> I tried test program with MAT_REUSE_MATRIX and it also gives different
>>> matrix product.
>>>
>>> Since there is no description of MatReuse structure for MatTranspose
>>> it's a bit confusing what to expect from it.
>>>
>>>
>>>>  Do you mean 'Cm = A'*B;'?
>>>> 'Cm = A.'*B;' gives component-wise matrix product, not matrix product.
>>>>
>>>>
>>>>  .' operator means non-Hermitian transpose. That is what I get with
>>>> MatTranspose (in contrast with MatHermitianTranspose)
>>>> component-wise matrix product would be .*
>>>>
>>> You are correct.
>>>
>>>  Hong
>>>
>>>>
>>>>
>>>>
>>>>  Hong
>>>>
>>>>
>>>>
>>>>>  C = PetscBinaryRead('C.dat','complex',true);
>>>>>
>>>>> Matrix C is different depending on number of cores I use.
>>>>> My PETSc is:
>>>>> Using Petsc Development HG revision:
>>>>> 876c894d95f4fa6561d0a91310ca914592527960  HG Date: Tue Jan 10 19:27:14 2012
>>>>> +0100
>>>>>
>>>>>
>>>>> On 06.02.2012 17:13, Hong Zhang wrote:
>>>>>
>>>>> MatMatMult() in petsc is not well-tested for complex - could be buggy.
>>>>> Can you send us the matrices A and B in petsc binary format for
>>>>> investigation?
>>>>>
>>>>>  Hong
>>>>>
>>>>> On Mon, Feb 6, 2012 at 5:55 AM, Alexander Grayver <
>>>>> agrayver at gfz-potsdam.de> wrote:
>>>>>
>>>>>> Dear PETSc team,
>>>>>>
>>>>>> I try to use:
>>>>>> call
>>>>>> MatMatMult(A,B,MAT_INITIAL_MATRIX,PETSC_DEFAULT_DOUBLE_PRECISION,C,ierr);CHKERRQ(ierr)
>>>>>>
>>>>>> Where both A and B are rectangular, but A is sparse and B is dense.
>>>>>> Both are double complex and distributed.
>>>>>> The product PETSc gives me contains some errors in some part of the
>>>>>> matrix.
>>>>>> I output A, B and C then computed product in matlab.
>>>>>>
>>>>>> Attached you see figure plotted as:
>>>>>> imagesc(log10(abs(C-Cm)))
>>>>>>
>>>>>> Where Cm -- product computed in matlab.
>>>>>>
>>>>>> The pattern and amplitude vary depending on the number of cores I
>>>>>> use. This picture is obtained for 48 cores (I've tried 12, 64 cores as
>>>>>> well).
>>>>>>
>>>>>> Where should I look for possible explanation?
>>>>>>
>>>>>> --
>>>>>> Regards,
>>>>>> Alexander
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>   --
>>>>> Regards,
>>>>> Alexander
>>>>>
>>>>>
>>>>
>>>>
>>>>   --
>>>> Regards,
>>>> Alexander
>>>>
>>>>
>>>
>>>
>>>   --
>>> Regards,
>>> Alexander
>>>
>>>
>>
>
>
> --
> Regards,
> Alexander
>
>
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