[petsc-users] sieve-dev Unstructured meshes in PETSC using Sieve

[Chris Eldred]

Thanks for the info!- I will modify my code to use DMComplex instead of
DMMesh (and migrate to the latest version of petsc-dev/slepc-dev). I'll let
you know if that does not get rid of the Segfault as well.

On Wed, Jul 25, 2012 at 11:34 AM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Jul 24, 2012 at 12:31 PM, Chris Eldred <chris.eldred at gmail.com>wrote:
>
>> Hey PETSC/Sieve Developers,
>>
>> I am building a nonlinear shallow water testbed model (along with an
>> associated eigensolver for the linear equations) intended to work on
>> unstructured Voronoi meshes and cubed-sphere grids (with arbitrary
>> block-structured refinement)- it will be a 2-D code. There will NOT be any
>> adaptive mesh refinement- the mesh is defined once at the start of the
>> application. It will support finite difference, finite volume and finite
>> element-type (spectral elements and Discontinuous Galerkin) schemes- so
>> variables will be defined on edges, cells and vertexes. I would like to use
>> PETSC/SLEPC (currently limited to v3.2 for both since that is the latest
>> version of SLEPC) for the spare linear algebra and eigenvalue solvers. This
>> is intended as a useful tool for researchers in atmospheric model
>> development- it will allow easy inter-comparison of different grids and
>> schemes under a common framework.
>>
>
> Cool. Use slepc-dev.
>
>
>> Right now I have a serial version (written in Fortran 90) that implements
>> a few different finite-difference schemes (along with a multigrid solver
>> for square and hexagonal meshes) on unstructured Voronoi meshes and I would
>> like to move to a parallel version (also using Fortran 90). The Sieve
>> framework seems like an excellent fit for defining the unstructured mesh,
>> managing variables defined on edges/faces/vertices and handling
>> scatter/gather options between processes. I was planning on doing parallel
>> partitioning using ParMetis.
>>
>
> That is definitely what it is for.
>
>
>> My understanding is that DMMesh handles mesh topology (interconnections,
>> etc) while Sections define variables and mesh geometry (edge lengths,
>> areas, etc.). Sections can be created over different depths/heights (chains
>> of points in Sieve) in order to define variables on vertices/edges/cells.
>>
>
> Yes.
>
>
>> I am looking for documentation and examples of code use. I found:
>>
>> http://www.mcs.anl.gov/petsc/petsc-dev/src/snes/examples/tutorials/ex62.c.html
>>
>> http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex12.c.html
>>
>> Are there other examples/documentation available?
>>
>
> Here is my simple tutorial:
>
> Building and Running ex62
> --------------------------------------
>
> First, configure with FEM stuff turned on:
>
>     '--download-triangle',
>     '--download-ctetgen',
>     '--download-fiat',
>     '--download-generator',
>     '--download-chaco',
>     '--download-metis',
>     '--download-parmetis',
>     '--download-scientificpython',
>
> I also use
>
>     '--with-dynamic-loading',
>     '--with-shared-libraries',
>     '--download-mpich',
>     '--download-ml',
>
> and if you want to try GPU stuff
>
>     '--with-cuda',
>     '--with-cuda-arch=sm_10',
>     '--with-cuda-only',
>     '--with-cudac=nvcc -m64',
>
> Then build PETSc with the Python make:
>
>    python2.7 ./config/builder2.py clean
>    python2.7 ./config/builder2.py build    <This rebuilds only changed
> things correctly as well>
>
>   python2.7 ./config/builder2.py --help <This is useful>
>   python2.7 ./config/builder2.py build --help <This is too>
>   python2.7 ./config/builder2.py check --help <And this>
>
> Once you have this, you should be able to build and run ex62
>
>    python2.7 ./config/builder2.py check src/snes/examples/tutorials/ex62.c
> --testnum=0
>
> which runs the first test. You can run them all with no argument. All the
> options are listed
> at the top of ./config/builder.py.
>
>
>
>> Also, I was wondering what the difference is between DMMesh and
>> DMComplex- it appears that they both implement the Sieve framework?
>>
>
> DMMesh is the old DMComplex. I decided that C++ is a blight upon mankind
> and templates are its Furies, so
> I rewrite all of DMMesh in C, used Jed's new communication stuff, got rid
> of iterators, and made things integrate
> with the solvers much better.
>
>    Thanks,
>
>       Matt
>
>
>> Thanks,
>> Chris Eldred
>>
>> --
>> Chris Eldred
>> DOE Computational Science Graduate Fellow
>> Graduate Student, Atmospheric Science, Colorado State University
>> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
>> chris.eldred at gmail.com
>>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>



-- 
Chris Eldred
DOE Computational Science Graduate Fellow
Graduate Student, Atmospheric Science, Colorado State University
B.S. Applied Computational Physics, Carnegie Mellon University, 2009
chris.eldred at gmail.com
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