dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On 07/04/10 02:54, Nathan Borggren wrote:
> Hello,
>      I'm trying a 3D analogue of the advection-diffusion demo with a
> few other modifications and am having a couple troubles that I'm
> hoping to resolve.
>
> Say I have:
>
> u0 = Function(Q)
> v0 = Expression("exp(-x[0]*x[0]-x[1]*x[1]-x[2]*x[2])")
> u0.interpolate(v0)
>
> and would like to normalize u0 without changing the expression.  What
> is the best way to do this?  I would like to be able to insure at each
> time step that the function is positive everywhere and integrates over
> the mesh to 1.  the normalize() command seems to require a vector.
>
> also when I ask for to large of a mesh I get an out of memory error as
> below.  I didn't manage to find a solution in the suggested documents.
>   I'd like to still run everything on my humble intel Duo Core on my
> desk.  Is there away to make it just take longer rather then all out
> crashing?

Try using an iterative linear solver. There are different ways to do 
this, depending in which linear solver interface you're using. If using 
the free function 'solve', just do

    solve(A, u1.vector(), b, "gmres")

Garth

> Thanks,
>     Nathan Borggren
>
> error message:
>
> Applying boundary conditions to linear system.
> Solving linear system of size 110592 x 110592 (PETSc LU solver, umfpack).
>
> UMFPACK V5.2.0 (Nov 1, 2007): ERROR: out of memory
>
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Error in external library!
> [0]PETSC ERROR: umfpack_UMF_numeric failed!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 8, Fri Aug 21
> 14:02:12 CDT 2009
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Libraries linked from /home/nborggren/Work/FEniCS/build/lib
> [0]PETSC ERROR: Configure run at Thu Feb  4 10:30:23 2010
> [0]PETSC ERROR: Configure options COPTFLAGS=-O3 --with-debugging=0
> --with-shared=1 --with-clanguage=cxx --download-umfpack=1
> --prefix=/home/nborggren/Work/FEniCS/build
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: MatLUFactorNumeric_UMFPACK() line 176 in
> src/mat/impls/aij/seq/umfpack/umfpack.c
> [0]PETSC ERROR: MatLUFactorNumeric() line 2396 in src/mat/interface/matrix.c
> [0]PETSC ERROR: PCSetUp_LU() line 222 in src/ksp/pc/impls/factor/lu/lu.c
> [0]PETSC ERROR: PCSetUp() line 794 in src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c
>
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