MatTranspose Question

[Toby D. Young]

> I'll start out by saying I'm a new user to PETSc.  I'm actually using
> SLEPc

Me too.   :-)

> I have a very large, very sparse matrix with dimensions on the order
> of 3 million by 1 million.  I created my matrix using MatCreateMPIAIJ
> and it seems to be evenly distributed across my machines.  I've hit a
> bottleneck when running some code to compute the SVD of the matrix
> and the bottleneck seems to be using the MatTranspose operation on my
> matrix.

I can not directly help you with your questions Sarah, sorry. Out of
sheer academic interest in your problem (I had a similar problem once and
found a work-around): Have you tried to run your code for very small
matrices (say, 300x100)? Just to check that the bottleneck problem is in
fact not something else!

Transposing a HUGE matrix such as the one you have is an expensive
operation in anyone's book. As far as I know, PETSc does not store
zero-components of a matrix but uses a sparsity pattern to "remember"
them... (Someone please correct me if I am wrong).

Hope that is somehow helpful for you.

Best,
	Toby


-----

Toby D. Young - Adiunkt (Assistant Professor)
Department of Computational Science
Institute of Fundamental Technological Research
Polish Academy of Sciences
Room 206, ul. Swietokrzyska 21
00-049 Warszawa, Polska

+48 22 826 12 81 ext. 184
http://rav.ippt.gov.pl/~tyoung