petsc and matlab

[Barry Smith]

  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
> 
> 
> 
> 
>