Re: [Libmesh-users] Re: libmesh eigenproblem and pysparse

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I wrote a python script that loads the matrices exported in matllab
and converts them to matrix market coordinate format that is required
by spmatrix.ll_mat_from_mtx routine. Since the matlab output is almost
identical to MM format, the conversion is easy and fast. I tested on
two 70000x70000 matrices A and B (180MB each in file size). The
conversion and loading finished in 5s. The JDSYM solver call took
about 30~45s.

Next I will see if I can implement JDSYM into my libmesh code.

By the way, the print function in SparseMatrix/DenseMatrix class can
only output to screen. I was wondering how you managed to export to
file?

David

On 3/6/06, Ondrej Certik <on...@ce...> wrote:
> I checked it again - so it's only 38000x38000 matrix, it took around 60s =
to
> load the element matrices (I assemble the big matrix in python, so it's p=
retty
> slow), and the solver ran for 22s. On smaller matrices the assembling is
> faster. And of course it would be much faster if I clever renumbered the =
nodes.
>
> Ondrej
>
> On Mon, Mar 06, 2006 at 01:41:33PM +0100, Ondrej Certik wrote:
> > A few minutes on a fast amd64 comp. Loading the matrices takes around 1=
0% or
> > 20% of the total time. It could be optimized more, but I just need it t=
o work
> > somehow now.
> >
> > On Mon, Mar 06, 2006 at 04:37:44AM -0800, David Xu wrote:
> > > How long did it take for pysparse to solve the 300 000x300 000 matrix=
?
> > > In my case, most of the time is wasted on loading the large matrices
> > > into matlab. How long did it take for your python code to reassemble
> > > the 300 000x300 000 matrices into pysparse required format? I'd love
> > > to get pysparse working on my system and try it out.
> > >
> > > David
> > >
> > > On 3/6/06, Ondrej Certik <on...@ce...> wrote:
> > > > I think I tried even something like 300 000 x 300 000 matrix with p=
ysparse, and
> > > > it was ok. the pysparse compiles without errors at my computer. For=
 my
> > > > problems, the time spent assembling the matrices is negligible comp=
ared to the
> > > > solving time, so for me it's really no big deal to solve the matric=
es
> > > > elsewhere, I mainly use libmesh for the assembly and for that purpo=
se the
> > > > libmesh is a really, really great library.
> > > >
> > > > As to the solvers in libmesh - it's good they have one interface to=
 many
> > > > solvers, because I believe one has to find the best method for each=
 equation
> > > > one tries to solve with libmesh, maybe even for each problem. I pre=
fer to
> > > > have 2 programs, one for assembling, the other for solving, but tha=
t's just my
> > > > personal choice. Maybe it would be good to integrate pysparse to li=
bmesh
> > > > directly, but if it works that way, I really don't have the need.
> > > >
> > > > Ondrej
> > > >
> > > >
> > > > On Sun, Mar 05, 2006 at 07:31:04PM -0800, David Xu wrote:
> > > > > Ondrej,
> > > > >
> > > > > Thanks for tips. I tried to compile pysparse, but the program had
> > > > > problems. So I instead used libmesh sparsematrix print_matlab opt=
ion
> > > > > and export the matrices A and B directly to matlab sparse matrix =
file
> > > > > format. The files can be directly loaded to matlab, which is very
> > > > > convenient. Then the matrices A and B can be solved by matlab's e=
igs
> > > > > (using ARPACK) or jdcg_gep (a Jacobi-Davidson matlab routine).
> > > > >
> > > > > eigs is actually pretty fast, the only problem is it can't handle
> > > > > large matrix. I tried 10201x10201. it gives me error. But jdcg_ge=
p
> > > > > solves the large matrix without problem and quite fast. I don't k=
won
> > > > > if the performance is comparable to jdsym in pysparse, but it's q=
uite
> > > > > good for me.
> > > > >
> > > > > I wish the libmesh team had implement the J-D algorithm in the co=
de.
> > > > > That would be very nice.
> > > > >
> > > > > Regards,
> > > > >
> > > > > David
> > > > >
> > > > >
> > > > >
> > > > > On 3/3/06, Ondrej Certik <on...@ce...> wrote:
> > > > > > David, why don't you look in the documentation first?
> > > > > >
> > > > > > http://libmesh.sourceforge.net/doxygen/classDenseMatrixBase.htm=
l
> > > > > >
> > > > > > void    print (std::ostream &os) const
> > > > > > void    print_scientific (std::ostream &os) const
> > > > > >
> > > > > > Ondrej
> > > > > >
> > > > > > On Fri, Mar 03, 2006 at 01:12:18AM -0800, David Xu wrote:
> > > > > > > Which class/functionof libmesh did you use to export the matr=
ices. I
> > > > > > > couldn't figure it out. Would you send me a piece of sample c=
ode
> > > > > > > please?
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > > David
> > > > > > >
> > > > > > > On 3/1/06, Ondrej Certik <on...@ce...> wrote:
> > > > > > > > Export them how you want, then read them in the python scri=
pt.
> > > > > > > > Ondrej
> > > > > > > >
> > > > > > > > On Wed, Mar 01, 2006 at 09:34:09AM -0800, David Xu wrote:
> > > > > > > > > Dear Ondrej,
> > > > > > > > >
> > > > > > > > > Thanks for sending the python code. Could you elaborate t=
he procedures
> > > > > > > > > of exporting the matrices to disk? Which libmesh function=
 should I
> > > > > > > > > use? An example will be greatly appreciated.
> > > > > > > > >
> > > > > > > > > Best wishes,
> > > > > > > > >
> > > > > > > > > David
> > > > > > > > >
> > > > > > > > > On 3/1/06, Ondrej Certik <on...@ce...> wrote:
> > > > > > > > > > here is the python code which solves it. you need to ex=
port the matrices to
> > > > > > > > > > disk from your c++ code. also extract boundary nodes. I=
t gives you both
> > > > > > > > > > eigenvalues and eigenvectors.
> > > > > > > > > > Ondrej
> > > > > > > > > >
> > > > > > > > > > On Tue, Feb 28, 2006 at 11:22:21PM -0800, David Xu wrot=
e:
> > > > > > > > > > > Dear Ondrej,
> > > > > > > > > > >
> > > > > > > > > > > I read your previous emails and know you've figured o=
ut a way
> > > > > > > > > > > calculating the eigenvalues using pysparse. I'm new t=
o libmesh and in
> > > > > > > > > > > desperate need of someone enlightening me on how to u=
se libmesh to
> > > > > > > > > > > solve generalized eigen value problems. Would you ple=
ase send me a
> > > > > > > > > > > simple example of your working code? I also have a qu=
estion, will
> > > > > > > > > > > pysparse also solve the linear system and calculate t=
he function
> > > > > > > > > > > values after the eigen values are calcuated? If not, =
what would you do
> > > > > > > > > > > to get the eigen states that are corresponding to the=
 eigen values
> > > > > > > > > > > calculated?
> > > > > > > > > > >
> > > > > > > > > > > Thanks a lot in advance!
> > > > > > > > > > >
> > > > > > > > > > > David
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> >
> >
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