Barry Smith bsmith at
Sun Sep 20 10:36:53 CDT 2009


      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  


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

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