[petsc-users] Slepc SVDCyclicSetExplicitMatrix does not prealloc memory?

[Jose E. Roman]

On 01/04/2011, Gong Ding wrote:

> Hi,
> I am stiall dealing with the ill conditioned problem. :-(
> Yesderday, I installed slepc-3.1-p6 for SVD calculation of my matrix.
> 
> The SVD solver works well for the largest singualr value calculation.
> But for the smallest singualr value, all most all the methods fail.
> 
> Finally, I chosen the most inefficient way. 
> That build the cyclic matrix explicitly with 
> shift-and-invert spectral transformation.
> And solve the eigen value problem by LU preconditioned GMRES.
> The preconditioner should be superlu rather than others.
> I guess the reason is superlu use static pivot. 
> Because solver with partial pivot such as mumps can not work.
> Anyway, slepc solved my problem. 
> 
> However, the explicit building cyclic matrix takes too long to finish.
> The log info says 
> 
> [0] MatSetUpPreallocation(): Warning not preallocating matrix storage
> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 35038 X 35038; storage space: 325302 unneeded,482948 used
> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 42204
> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 33
> [0] Mat_CheckInode(): Found 26800 nodes of 35038. Limit used: 5. Using Inode routines
> 
> It seems no preallocation for cyclic matrix. Is it a bug or I forgot something?
> 

Yes, you are right. No preallocation is done in this case within SLEPc. This is a problem also in SLEPc's QEPLINEAR. This is pending, my intention is to get it fixed for the next release.

Thanks.
Jose