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two questions

To: "'Discussion of FEniCS development'" <fenics-dev@xxxxxxxxxx>
From: "Theodore Omtzigt" <tomtzigt@xxxxxxxxxxx>
Date: Sun, 18 Dec 2005 16:12:50 -0800
Thread-index: AcYEMPKWTp+JikS4Q7WeuS9vBW29BQ==

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.

 

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?

 

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.

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edges = [1;2;0;0;0;0;0];

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Follow ups

Re: two questions
From: Anders Logg, 2005-12-19