[petsc-users] New nonzero caused a malloc

[George Pau]

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.

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/
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