- sieve-dev - mailman3.cels.anl.gov

Issues with DMComplexSetCone
by Chris Eldred 24 Aug '12

24 Aug '12

The following code snippet does not appear to be working: PetscInt, dimension(4) :: EC EC(1) = 1 EC(2) = 2 EC(3) = 3 EC(4) = 4 write(*,*) 'cell',EC call DMComplexSetCone(model_mesh, lcell , EC, ierr) CHKERRQ(ierr) call DMComplexGetCone(model_mesh, lcell , EC, ierr) CHKERRQ(ierr) write(*,*) 'cell', EC I get the following as output: cell 1 2 3 4 cell 18673792 0 -1 -1 DMComplexGetConeSize returns 4 as expected. I am using the latest version of petsc-dev. Later on there is a segmentation fault violation, probably related to this issue. Any ideas? -- 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(a)gmail.com

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Ghost values in sieve
by Chris Eldred 17 Aug '12

17 Aug '12

I was wondering how ghost values were handled when creating a distributed (global) vector from a specific PetscSection over a DMComplex object- ie what defines the stencils used to figure out which values need to be ghosted? What about local vs. global indexes? -Chris -- 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(a)gmail.com

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Fortran bindings for additional Sieve specific functions
by Chris Eldred 14 Aug '12

14 Aug '12

Could fortran bindings for the following functions be added? DMPrintCellVector() DMComplexSetCoordinateSection() DMComplexGetCoordinateSection() DMComplexGetCoordinateVec() DMComplexCreateSection() DMComplexGetHeightStratum() DMComplexGetDepthStratum() DMComplexComputeCellGeometry() DMComplexJoinPoints() DMComplexMeetPoints() VecGetValuesSection() VecSetValuesSection() PetscSectionCreate() PetscSectionGetNumFields() PetscSectionSetNumFields() PetscSectionGetFieldComponents() PetscSectionSetFieldComponents() PetscSectionGetChart() PetscSectionSetChart() PetscSectionGetDof() PetscSectionSetDof() PetscSectionAddDof() PetscSectionGetFieldDof() PetscSectionSetFieldDof() PetscSectionGetOffset() PetscSectionGetFieldOffset() PetscSectionGetOffsetRange() 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(a)gmail.com

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Fortran bindings for PetscSectionSetFieldName
by Chris Eldred 03 Aug '12

03 Aug '12

Can a Fortran binding for PetscSectionSetFieldName be added? Also, is it possible to get a brief explanation of exactly what this does and what the different arguments are for? 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(a)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(a)gmail.com

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Fortran bindings for DMComplexCreateSection
by Chris Eldred 01 Aug '12

01 Aug '12

Can a Fortran binding fro DMComplexCreateSection be added? Also, is it possible to get a brief explanation of exactly what this does and what the different arguments are for? 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(a)gmail.com

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Missing DMComplex routines for Fortran
by Chris Eldred 26 Jul '12

26 Jul '12

As far as I can tell (I get linking errors), the following DMComplex routines that exist in the DM Manual Pages are not yet implemented for Fortran: DMComplexDistribute DMComplexGetStratumSize DMComplexGetStratumIS DMComplexGetLabelSize DMComplexGetLabelIdIS DMComplexSetLabelValue DMComplexHasLabel DMComplexVecSetClosure DMComplexGetCone DMComplexGetConeOrientation DMComplexGetSupport DMComplexGetTransitiveClosure -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(a)gmail.com

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Support for Fortran versions of DMComplexGetCone, DMComplexGetConeOrientation
by Chris Eldred 26 Jul '12

26 Jul '12

Is there a plan to implement support for Fortran versions of DMComplexGetCone and DMComplexGetConeOrientation? -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(a)gmail.com

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DMComplex Output
by Chris Eldred 26 Jul '12

26 Jul '12

I was wondering how to output a sieve DAG to a file- I tried to use an HDF5 viewer with DMView and it does not seem to be working. 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(a)gmail.com

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Unstructured meshes in PETSC using Sieve
by Chris Eldred 25 Jul '12

25 Jul '12

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. 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. 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. 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.h… http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex12… Are there other examples/documentation available? Also, I was wondering what the difference is between DMMesh and DMComplex- it appears that they both implement the Sieve framework? 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(a)gmail.com

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Data shared between points in a Sieve DAG
by Chris Eldred 25 Jul '12

25 Jul '12

I was wondering if it was possible to have fields that are shared between points in a sieve DAG: For example, I would like to have data that is connected to both an edge and a cell (instead of just tied to a Section). Consider a cell with three edges (ie a triangular cell). Before I was just using a length 3 array attached to the cell with the convention that the ordering of the array matched the ordering of the edge list associated with the cell. Now, I would like an implementation that does not assume anything about the ordering of the edge list (since I am getting that from cones/supports). 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(a)gmail.com

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