petsc and matlab

[Barry Smith]

  Alejandro,

    That is really weird, the convergence usually does
not depend much on exactly what the right hand side is.

Are you using a nonzero initial guess with Matlab?
With PETSc? (With PETSc call KSPSetInitialGuessNonzero().

Can you run the PETSc one with -ksp_monitor so that 
you see how many iterations are needed each time, and get that
information from Matlab to compare?

   Barry


On Tue, 21 Aug 2007, Alejandro Garzon wrote:

> Yes, the "A" matrix is the same.
> --
> Alejandro
> 
> 
> Quoting Barry Smith <bsmith at mcs.anl.gov>:
> 
> >
> >   Is the matrix "A" the same for all groups (and the only thing
> > different for each group is b)?
> >
> >    Barry
> >
> >
> > On Mon, 20 Aug 2007, Alejandro Garzon wrote:
> >
> > > Hi, I wrote a code for solving a time dependent pde. In each time step
> > > I have to solve a linear system. I first wrote a prototype in matlab
> > > and then a C version using Petsc. To my surprise for some input
> > > parameters the matlab version runs faster than the Petsc code (on the
> > > same single processor). I did
> > > the performance comparison by timing 20 groups of 40 iterations. The
> > > times for Petsc and matlab are shown bellow
> > >
> > > group        Petsc        matlab
> > >
> > >     1       0.244981     1.110283
> > >     2       0.244995     1.112919
> > >     3       0.241305     1.113608
> > >     4       0.244542     1.114669
> > >     5       7.534417     1.112450
> > >     6       0.242212     1.115867
> > >     7       0.246327     1.111135
> > >     8       0.241105     1.113442
> > >     9       0.244468     1.111215
> > >    10       0.241113     1.111334
> > >    11       0.244541     1.112467
> > >    12       0.241400     1.113525
> > >    13       0.245020     1.114077
> > >    14       0.241303     1.113409
> > >    15       0.244380     1.116238
> > >    16       0.241372     1.109931
> > >    17       0.244108     1.100667
> > >    18       0.240419     1.096030
> > >    19       0.244337     1.096293
> > >    20      17.139999     1.097120
> > >            ---------     --------
> > > total      29.0523       22.1967
> > > time
> > >
> > > As can be seen in the table, although in most of the groups the time
> > > spent by the Petsc code is lower than that of matlab
> > > (0.24 compared to 1.1) there are two groups (5 and 20) in the Petsc column
> > that
> > > take a long time and make the total for the Petsc code bigger than
> > > that for matlab.
> > >
> > > In Petsc and matlab the method used is bicg and the relative residual
> > > is the same: 1e-8. The preconditioners are different, though. In petsc
> > > I used the default preconditioner and in matlab I used incomplete LU
> > > decomposition  with drop tolerance. The code that solves the linear
> > > system in matlab is
> > >
> > > [L,U] = luinc(A,droptol); <---- this is done only once before the
> > >                                  first iteration, droptol = 1e-12
> > >
> > > x = bicg(A,b,relres,maxsteps,L,U);
> > >
> > > I know incomplete LU decomposition as a preconditioner is available in
> > > Petsc but in order to use it one must provide two arguments in
> > > addition to the drop tolerance and I didn't know what values to give
> > > to them.
> > >
> > > My question is this: what options should be chosen so that the
> > > preconditioner and method use by Petsc are the same as those shown in
> > > the two lines of matlab code above? (could you contact the authors of the
> > > matlab functions?) A comparison of the performace of Petsc and matlab
> > > makes sense only if they are using the exact same methods.
> > >
> > >
> > > Thanks.
> > >
> > > --
> > > Alejandro
> > >
> > >
> > >
> > >
> > >
> >
> >
> 
>