[petsc-users] Understanding DMPlexDistribute overlap

[Francesco Caimmi]

Hi Michael,

thanks for the prompt reply!

While I am happy I mostly got it right, this means I have some kind of problem 
I cannot solve on my own. :(

I have this very simple 2D mesh I am experimenting with: a rectangle with  64 
vertexes and 45 cells (attached in exodus format as cantilever.e); I am using 
in this very simple petsc4py program to read it, define a section and output a 
vector. The overlay value can be controlled by the -o command line switch. The 
program is executed as:
mpiexec -np 2 python overlay-test.py -o <overlap_value> -log_view.


Everything works smoothly for <overlap_value> = 0 or to 1, but for values >2 
the program fails with the error message captured in the attached file 
error.log. Changing the number of processors does not alter the behavior. Note 
also that the same holds if I use a mesh generated by DMPlexCreateBoxMesh.

I would really appreciate hints on how to solve this issue and I will of 
course provide any needed additional information.

Thank you very much,
FC

On mercoledì 5 aprile 2017 10:50:59 CEST you wrote:
> Hi Francesco,
> 
> Your description is almost correct: the overlap defines the topological
> depth of shared entities as counted in "neighboring cells", where a cell
> counts as a neighbor of an owned cell according to the defined adjacency
> style. So for overlap=0 only facets, edges and vertices may be shared
> along the partition boundary, whereas for overlap=1 you can expect one
> additional "layer" of cells around each partition (the partitioning is
> done based on cell connectivity). For second neighbors, however, you
> need overlap=2. And yes, there is conceptually no upper bound on the
> overlap.
> 
> Hope this helps,
> 
> Michael
> 
> On 05/04/17 10:27, Francesco Caimmi wrote:
> > Dear all,
> > 
> > I was playing with DMPlex objects and I was trying to exactly figure out
> > what the `overlap` parameter in DMPlexDistribute does.
> > 
> >  From the tutorial "Flexible, Scalable Mesh and Data Management
> > 
> > using PETSc DMPlex" (slide 10) and from the work by Knepley et al.
> > "Unstructured Overlapping Mesh Distribution in Parallel" I somehow got the
> > idea that it should control the "depth" of the mesh overlap.
> > That is, given the partition boundary, if overlay is set to 0 only the
> > entities adjacent (in the DMPlex topological sense and with the "style"
> > defined by the AdjacencyUse routines) to entities at the boundary are
> > shared, if overlay is 1 the first and the second neighbors (always in the
> > DMPlex topological sense) are shared and so on, up to the point were we
> > have a full duplicate of the mesh on each process (i.e. there is no upper
> > bound on `overlap`).
> > 
> > Is this correct or am I -totally- misunderstanding the meaning of the
> > parameter?
> > 
> > I am asking this because I see some behavior I cannot explain at varying
> > the value of the overlap, but before going into the details I would like
> > to be sure to understand  exactly what the overlap parameter is supposed
> > to do.
> > 
> > Many thanks,


-- 
Francesco Caimmi
 
Laboratorio di Ingegneria dei Polimeri
http://www.chem.polimi.it/polyenglab/

Politecnico di Milano - Dipartimento di Chimica,
Materiali e Ingegneria Chimica “Giulio Natta”

P.zza Leonardo da Vinci, 32
I-20133 Milano
Tel. +39.02.2399.4711
Fax +39.02.7063.8173

francesco.caimmi at polimi.it
Skype: fmglcaimmi (please arrange meetings by e-mail)
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