fenics team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Sun, Dec 18, 2005 at 04:12:50PM -0800, Theodore Omtzigt wrote:
> I have two questions that pertain to whether or not my sw stack is working
> properly.
> 
>  
> 
> QUESTION #1
> 
>  
> 
> The first one is relatively simple. I have PETSc configured with the standard
> GCC compiler set but without MPI. When building the poisson demo, I am
> generating the attached poisson.m file. The question is whether or not the
> plotsolution.m and associated Octave specific M-files work for others. On two
> different Linux boxes, for me, Octave goes to lala land and takes the cpu with
> it to never return either with a plot or with a completion. MATLAB does a
> little better but the pdemesh visualization produces an empty plot although
> pdesurf does produce a plot.

For Octave, you need to have ivview installed. In Debian, this is in
the inventor-clients package.

Did you try to do the visualization with ParaView or MayaVi? We have
just moved to VTK as the default output format, since MATLAB is not
free and the visualization support in Octave is rather sparse.

The solution poisson.m lookes correct. I get the same solution
with DOLFIN 0.5.11 if I switch to MATLAB format.

> QUESTION #2
> 
>  
> 
> The second question is more confusing. Since I am trying to get the whole
> FEniCS/PETSc stack running under MSVC7, I was experimenting with different
> configurations that would build given the tools I have. I was able to
> successfully build PETSc with the MS compilers using the following
> configuration:
> 
>  
> 
> --with-vendor-compilers=microsoft
> 
> --with-fc=0
> 
> --download-c-blas-lapack=1
> 
> --with-mpi=0
> 
>  
> 
> Here is the top of configure.log:
> 
>  
> 
> Starting Configure Run at Sun Dec 18 11:39:57 2005
> 
> Configure Options: --with-vendor-compilers=microsoft -with-fc=0
> --download-c-blas-lapack=1 --with-mpi=0 --useThreads=0 --with-shared=0
> -configModules=PETSc.Configure
> 
> Working directory: /home/Theo/petsc-2.3.0
> 
> Python version:
> 
> 2.4.1 (#1, May 27 2005, 18:02:40)
> 
> [GCC 3.3.3 (cygwin special)]
> 
>  
> 
> And the tail:
> 
>  
> 
> Compilers:
> 
>   C Compiler:         /home/Theo/petsc-2.3.0/bin/win32fe/win32fe cl  -MT -Z7
> 
> PETSc:
> 
>   PETSC_ARCH: cygwin
> 
>   PETSC_DIR: /home/Theo/petsc-2.3.0
> 
>   Scalar type:real
> 
>   Clanguage: C
> 
> BLAS/LAPACK: -L/home/Theo/petsc-2.3.0/externalpackages/f2cblaslapack/cygwin -L/
> home/Theo/petsc-2.3.0/externalpackages/f2cblaslapack/cygwin -lf2clapack -L/home
> /Theo/petsc-2.3.0/externalpackages/f2cblaslapack/cygwin -L/home/Theo/
> petsc-2.3.0/externalpackages/f2cblaslapack/cygwin -lf2cblas
> 
>  
> 
> Since I don’t have the rest of FEniCS running under MSDev, I figured I’ll use
> the same configuration on a linux box, that is, using GNU but without Fortran,
> to see what FEniCS does on that configuration. And Murphy’s law applied: the
> poisson demo won’t complete due to GMRES not converging. Here is the log for
> that failure:
> 
>  
> 
> [tomtzigt@p4-28G-512M-ws1 poisson]$ ./dolfin-poisson
> 
> Computing mesh connectivity:
> 
>   Found 289 nodes
> 
>   Found 512 cells
> 
>   Created 800 edges
> 
>   Created 0 faces
> 
>   Sorting mesh entities locally.
> 
> Initializing PETSc (ignoring command-line arguments).
> 
> Assembling system (matrix and vector) of size 289 x 289.
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |-----------------------------------------------------------------| 0.0%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |======|----------------------------------------------------------| 10.2%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |=============|---------------------------------------------------| 20.3%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |===================|---------------------------------------------| 30.5%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |==========================|--------------------------------------| 40.6%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |=================================|-------------------------------| 50.8%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |=======================================|-------------------------| 60.9%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |==============================================|------------------| 71.1%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |====================================================|------------| 81.2%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |===========================================================|-----| 91.4%
> 
> | Assembling matrix and vector (interior contributions)           |
> 
> |=================================================================| 100.0%
> 
> Maximum number of nonzeros in each row is 7 (estimated 21).
> 
> Applying Dirichlet boundary conditions.
> 
> Computing boundary:
> 
>   Found 64 edges on the boundary.
> 
>   Found 64 nodes on the boundary.
> 
> Boundary condition applied to 17 degrees of freedom on the boundary.
> 
> Setting up PETSc GMRES solver: (rtol, atol, dtol, maxiter) = (1.0e-05, 1.0e-50,
> 1.0e+04, 10000).
> 
> *** Error: GMRES solver did not converge. [GMRES.cpp:71: solve()]
> 
>  
> 
> My postulate would be that PETSc with the above configuration somehow gets put
> into single precision mode and the atol=1.0e-50 doesn’t stand a change.
> However, I can’t find this information (yet) in the PETSc log.
> 
>  
> 
> So, any known issues that explain the two issues here?

I have no idea what goes wrong. Since you managed to run the demo in
one configuration, try comparing the systems you solve on the two
configurations to see if they are the same. In the Poisson demo, do

    A.disp();
    b.disp();

to print out the matrix and vector. If they agree on both
configurations, there's something wrong with the GMRES solver.

> Theo
> 
>  
> 
> P.S. Both PETSc and FEniCS are a joy to work in. I love scripts that give you
> enough feedback to resolve issues that the script ran into. So kudos to all
> those who put in the sweat and tears.  If I can just get over the initial hump,
> then I can start contributing too.

That would be great.

/Anders


>  
> 

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> 
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> 186 187 204 
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> 193 211 210 
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> 270 288 287 
> 271 272 289 
> 271 289 288 ]';
> 
> edges = [1;2;0;0;0;0;0];
> 
> u = [ 0.068508108463468 0.068331656343913 0.067787751802850 0.066842946337859 0.065453911247884 0.063571630686899 0.061144621166713 0.058121745108905 0.054454905180132 0.050101860283095 0.045029360637377 0.039216843732185 0.032661084700093 0.025382417919178 0.017433711813898 0.008914840610784 0.000000000000000 0.068682019070932 0.068511567288807 0.067981845618438 0.067056164060138 0.065689097618680 0.063830018692588 0.061426037890154 0.058424667334030 0.054776406221804 0.050437445914348 0.045372682116936 0.039559232390031 0.032990768751642 0.025683132959532 0.017681951251288 0.009073439456833 0.000000000000000 0.069189212589894 0.069032967207812 0.068538881900727 0.067662512923766 0.066352808468410 0.064554582235563 0.062210881660364 0.059265275909529 0.055664154432242 0.051359142689576 0.046309762391092 0.040486468622373 0.033874221634198 0.026476759656031 0.018321653315124 0.009465851305391 0.000000000000000 0.069996233164266 0.069859263842080 0.069414843912414 0.068608423467629 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0.000000000000000 0.083388474300208 0.083483412574669 0.083653379071895 0.083730255683655 0.083550238765157 0.082952248127509 0.081776220790100 0.079861379373164 0.077044480088628 0.073157965615598 0.068027926091677 0.061471914022489 0.053296495516936 0.043294583472588 0.031242751573747 0.016898765465604 0.000000000000000 0.084117351619882 0.084226646695219 0.084433967999928 0.084563824385137 0.084446143196030 0.083914191228833 0.082802533475431 0.080945038831062 0.078172891810310 0.074312472850533 0.069182990882559 0.062593942079586 0.054342224327528 0.044208743943881 0.031954347680548 0.017315486612892 0.000000000000000 0.084563600609706 0.084682947448735 0.084915863217287 0.085081515184752 0.085005638096565 0.084517871730675 0.083449420065282 0.081630845352855 0.078889867420766 0.075049046395770 0.069923282807568 0.063317045877094 0.055020949706306 0.044807735867490 0.032427022120972 0.017598180772988 0.000000000000000 0.084704097454380 0.084827485869462 0.085070195165615 0.085249234592995 0.085188821797707 0.084717359837415 0.083664909179017 0.081860877935198 0.079131809750569 0.075299003275924 0.070175863232324 0.063565113721141 0.055255227329406 0.045016024705603 0.032592949048255 0.017698727956244 0.000000000000000; ]';
> 

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-- 
Anders Logg
Research Assistant Professor
Toyota Technological Institute at Chicago
http://www.tti-c.org/logg/