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

[Matthew Knepley]

On Wed, Jul 25, 2012 at 2:30 PM, Chris Eldred <chris.eldred at gmail.com>wrote:

> Where are the Fortran include files for DMComplex - I checked
> ${PETSC_DIR}/include/finclude but they are not there. The C/C++ headers are
> in ${PETSC_DIR}/include/ though.
>

You are the first Fortran user :) Added them. Will test later.

   Matt


> On Wed, Jul 25, 2012 at 11:48 AM, Chris Eldred <chris.eldred at gmail.com>wrote:
>
>> 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
>>
>
>
>
> --
> 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
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