[petsc-users] New nonzero caused a malloc

[George Pau]

Hi Matt,

Thanks, redividing between diagonal and off-diagonal solves the malloc
issue.

George



On Thu, Apr 4, 2013 at 2:02 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, Apr 5, 2013 at 7:05 AM, George Pau <gpau at lbl.gov> wrote:
>
>> Hi
>>
>> Just a follow up on the previous email which was sent accidentally.  The
>> info during assembly indicates there is no mallocs (typo in previous
>> email).  In addition, mncon is 18 and so the total nonzero column blocks
>> per row block is greater than the nonzero blocks shown.  If I use a single
>> processor, I do not see the above error.
>>
>
> Then this is likely you are not dividing the nonzeros between the diagonal
> and off-diagonal blocks correctly.
>
>     Matt
>
>
>> Thanks,
>> George
>>
>>
>>
>> On Thu, Apr 4, 2013 at 1:01 PM, George Pau <gpau at lbl.gov> wrote:
>>
>>> Hi,
>>>
>>> I am trying to determine where there is malloc when I am doing a
>>> MatSetValuesBlocked.  The following is the error:
>>>
>>> [1]PETSC ERROR: --------------------- Error Message
>>> ------------------------------------
>>> [1]PETSC ERROR: Argument out of range!
>>> [1]PETSC ERROR: New nonzero at (69216,95036) caused a malloc!
>>>
>>> However, when I look at the info during the assembly, I have
>>>
>>> [0] MatAssemblyBegin_MPIBAIJ(): Stash has 0 entries,uses 0 mallocs.
>>> [0] MatAssemblyBegin_MPIBAIJ(): Block-Stash has 0 entries, uses 0
>>> mallocs.
>>> [1] MatAssemblyEnd_SeqBAIJ(): Matrix size: 381300 X 381300, block size
>>> 4; storage space: 14143776 unneeded, 10259424 used
>>> [1] MatAssemblyEnd_SeqBAIJ(): Number of mallocs during MatSetValues is 0
>>> [1] MatAssemblyEnd_SeqBAIJ(): Most nonzeros blocks in any row is 16
>>> [0] MatAssemblyEnd_SeqBAIJ(): Matrix size: 381300 X 381300, block size
>>> 4; storage space: 13696176 unneeded, 10707024 used
>>> [0] MatAssemblyEnd_SeqBAIJ(): Number of mallocs during MatSetValues is 0
>>> [0] MatAssemblyEnd_SeqBAIJ(): Most nonzeros blocks in any row is 11
>>>
>>> which indicates there is mallocs.
>>>
>>> The following is how I set up the matrix:
>>>
>>> call MatCreate(PETSC_COMM_WORLD,petsc_obj%jacmat, pierr)
>>> call
>>> MatSetSizes(petsc_obj%jacmat,PETSC_DECIDE,PETSC_DECIDE,nel*neq,nel*neq,pierr)
>>> call MatSetFromOptions(petsc_obj%jacmat,pierr)
>>> call MatSetBlockSize(petsc_obj%jacmat,neq,pierr)
>>> call MatSetType(petsc_obj%jacmat,MATBAIJ,pierr)
>>> call
>>> MatSeqBAIJSetPreallocation(petsc_obj%jacmat,neq,(mncon+1)*neq*neq,PETSC_NULL_INTEGER,pierr)
>>> call MatMPIBAIJSetPreallocation(petsc_obj%jacmat,
>>> neq,neq*neq,PETSC_NULL_INTEGER,mncon*neq*neq,PETSC_NULL_INTEGER,pierr)
>>>     call
>>> MatSetOption(petsc_obj%jacmat,MAT_ROW_ORIENTED,PETSC_FALSE,pierr) !because
>>> of how aval is stored.
>>>
>>> --
>>> George Pau
>>> Earth Sciences Division
>>> Lawrence Berkeley National Laboratory
>>> One Cyclotron, MS 74-120
>>> Berkeley, CA 94720
>>>
>>> (510) 486-7196
>>> gpau at lbl.gov
>>> http://esd.lbl.gov/about/staff/georgepau/
>>>
>>
>>
>>
>> --
>> George Pau
>> Earth Sciences Division
>> Lawrence Berkeley National Laboratory
>> One Cyclotron, MS 74-120
>> Berkeley, CA 94720
>>
>> (510) 486-7196
>> gpau at lbl.gov
>> http://esd.lbl.gov/about/staff/georgepau/
>>
>
>
>
> --
> 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
>



-- 
George Pau
Earth Sciences Division
Lawrence Berkeley National Laboratory
One Cyclotron, MS 74-120
Berkeley, CA 94720

(510) 486-7196
gpau at lbl.gov
http://esd.lbl.gov/about/staff/georgepau/
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