sparsity pattern setup

Ryan Yan vyan2000 at
Mon Sep 21 16:35:30 CDT 2009

Hi Fredrik,
If I understand correctly, I have the same issue as what you have here.

I do not have the code yet(It is also depends on how your store your matrix
data.).  But I can forward Barry's idea to you.  Hope this is helpful to


    Simply read through the ASCII file(s) twice. The first time count the
number of blocks per row, then preallocate then read through the ASCII file
again reading and setting the values. This will be very fast.

  Barry- Hide quoted text -

On Sep 20, 2009, at 10:20 AM, Ryan Yan wrote:

 Hi All,
> I have a large size application. Mesh size is 30000 nodes, with dof 25 on
> each vertex. And it's 3d unstructured,  Tet, and Hex mesh. In the following
> I will denote blksize=25
> I am testing how to build up a PETSc matrix object quick and fast.
> The data I have is Block Compressed Sparse Row(BCSR) files. And my
> objective is to read BCSR files and generate PETSc Binaries
> Firstly, I choose the MATMPIAIJ, I opened the BCSR data files on each
> processor, and set up the preallocation use
> MatMPIAIJSetPreallocation(A,blksize,PETSC_NULL,blksize,PETSC_NULL); The
> reason why I choose 25 as the number for d_nz and o_nz is that I do not have
> access to the ordering of the vertices. So it's the worst case set up, and
> it takes about 7 minutes on 30 MIPS node(180 processors) to write the output
> into PETSc binaries.
> Secondly, I choose the MatMPIBAIJ, and same procedure as above, but also
> set up
> MatMPIBAIJSetPreallocation(A,blksize,blksize,PETSC_NULL,blksize,PETSC_NULL),
> here blksize = 25 and it's also the worst case; This experiments takes
> forever and could not generate the PETSc binaries.
> I guess the reason why it takes so long in the MATMPIBAIJ case is that I
> did not set up the preallocation accurately. Alougth I think the
> preallocation is also not accurate in the MATMPIAIJ case, but it seems like
> the preallocation effect is not as serious as for the MPIBAIJ. Correct me
> please, if there are other reasons.
> Can I anyone please give a hint on how to set up the preallocation right
> for a unstructured mesh without knowing the mesh ordering?
> Thank you very much in advance,
> Yan

On Mon, Sep 21, 2009 at 4:24 PM, Fredrik Bengzon <
fredrik.bengzon at> wrote:

> Hi,
> This is probably the wrong forum to ask, but does anyone have a piece of
> code for computing the correct ndnz and nodnz vectors needed for assembly of
> the stiffness (MPIAIJ) matrix on an unstructured tetrahedral mesh given the
> node-to-element adjacency?
> Thanks,
> Fredrik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the petsc-users mailing list