[petsc-dev] DMPLEX cannot support two different edges for the same two vertices, hence DMPLEX cannot?

Wed Dec 1 17:12:13 CST 2021

Here is a specific example. I have 10 global edges and 10 global vertices. The vertices and edges represent neurons and synapses in the brain, respectively. Vertices 0-7  and 7-9 have excitation and depression effect on the target vertices. The first rank owns 5 edges (0-4) and 6 vertices ( 0-4 local and 8 ghost). The second rank owns 5 edges (5-9) and 6 vertices (5-9 local and 4 ghost). Note that edges 4 (neuron 8 depresses neuron 4) and 8 (neuron 4 excite neuron 8) that share the same vertices on different ranks. The generated Plex is correct based on the cone and support outputs. However, the SF object is completely wrong as shown below. The first rank supposed to have 10 roots and one leaf (vertex 8), and the second rank suppose to have the same number of roots and leaf (vertex 4) as the first rank. My guess is something went wrong in sfPoint when determining the shared local vertices. I can provide more outputs from DMPlex if it helps, please let me know.

DM Object: 2 MPI processes
  type: network
  NSubnets: 1; NEdges: 10; NVertices: 10; NSharedVertices: 0.
  [0] nEdges: 5; nVertices: 6; nSharedVertices: 0
     Subnet 0: nEdges 5, nVertices(include shared vertices) 6
       edge 0: 4 ----> 0
       edge 1: 4 ----> 1
       edge 2: 4 ----> 2
       edge 3: 4 ----> 3
       edge 4: 8 ----> 4
  [1] nEdges: 5; nVertices: 6; nSharedVertices: 0
     Subnet 0: nEdges 5, nVertices(include shared vertices) 6
       edge 5: 4 ----> 5
       edge 6: 4 ----> 6
       edge 7: 4 ----> 7
       edge 8: 4 ----> 8
       edge 9: 4 ----> 9

Cones:
[0] Max cone size: 2
[0]: 0 <---- 9 (0)
[0]: 0 <---- 5 (0)
[0]: 1 <---- 9 (0)
[0]: 1 <---- 6 (0)
[0]: 2 <---- 9 (0)
[0]: 2 <---- 7 (0)
[0]: 3 <---- 9 (0)
[0]: 3 <---- 8 (0)
[0]: 4 <---- 10 (0)
[0]: 4 <---- 9 (0)
[1] Max cone size: 2
[1]: 0 <---- 5 (0)
[1]: 0 <---- 6 (0)
[1]: 1 <---- 5 (0)
[1]: 1 <---- 7 (0)
[1]: 2 <---- 5 (0)
[1]: 2 <---- 8 (0)
[1]: 3 <---- 5 (0)
[1]: 3 <---- 9 (0)
[1]: 4 <---- 5 (0)
[1]: 4 <---- 10 (0)

PetscSF Object: 2 MPI processes
  type: basic
  [0] Number of roots=11, leaves=2, remote ranks=1
  [0] 9 <- (1,5)
  [0] 10 <- (1,9)
  [1] Number of roots=11, leaves=0, remote ranks=0
  [0] Roots referenced by my leaves, by rank
  [0] 1: 2 edges
  [0]    9 <- 5
  [0]    10 <- 9
  [1] Roots referenced by my leaves, by rank
  MultiSF sort=rank-order

________________________________
From: Abhyankar, Shrirang G <shrirang.abhyankar at pnnl.gov>
Sent: Wednesday, December 1, 2021 4:17 PM
To: Knepley, Matthew G (VISIT) <knepley at gmail.com>; Barry Smith <bsmith at petsc.dev>
Cc: petsc-dev <petsc-dev at mcs.anl.gov>; Zhang, Hong <hzhang at mcs.anl.gov>; Betrie, Getnet <gbetrie at anl.gov>
Subject: Re: DMPLEX cannot support two different edges for the same two vertices, hence DMPLEX cannot?

“You can certainly have many fields on a given edge, but I don't know what it would mean to have two edges since no topological query could tell the difference.”

The two edges in a power grid represent two parallel power lines that are connected between two locations (vertices). There are line ids (stored in the component data) to distinguish the two lines.

Thanks,

Shri

From: Matthew Knepley <knepley at gmail.com>
Date: Wednesday, December 1, 2021 at 4:07 PM
To: Barry Smith <bsmith at petsc.dev>
Cc: "Abhyankar, Shrirang G" <shrirang.abhyankar at pnnl.gov>, PETSc Development <petsc-dev at mcs.anl.gov>, "Zhang, Hong" <hzhang at mcs.anl.gov>, Getnet Betrie <gbetrie at anl.gov>
Subject: Re: DMPLEX cannot support two different edges for the same two vertices, hence DMPLEX cannot?

On Wed, Dec 1, 2021 at 4:51 PM Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>> wrote:

  It may not happen with one rank. Or it may.

  With more than one rank one may run a code and think it is working correctly but that does not mean the PetscSF is correct. It is generating "extra" degrees of freedom for these vertices each associated with a different edge and not properly connecting them. You can tell by doing a full DMView on the dmplex and PetscSF and seeing more roots than there should be listed. Hence the numerics will be wrong even though it does not crash or complain.

Okay, I think we need specific tests to see what is going on.

Theoretically, having multiple edges between vertices does not make sense since the edge _means_ (v_i, v_j) topologically. You can certainly have many fields on a given edge, but I don't know what it would mean to have two edges since no topological query could tell the difference.

However, you can certainly tell Plex anything you want to tell it. DMPlexBuildFromCellListParallel() gets only cells and vertices, so you are saying that there is a duplicate cell. That is allowed and should work properly, EXCEPT if you wanted to identify a cell only by its cone (then you could not tell them apart). I do this for faces, but I did not think I ever did it for cells.

  Thanks,

     Matt

On Dec 1, 2021, at 4:37 PM, Abhyankar, Shrirang G <shrirang.abhyankar at pnnl.gov<mailto:shrirang.abhyankar at pnnl.gov>> wrote:

Barry,

“Is there anything we can do to support having multiple edges between the same two vertices”

Some of my power grid datasets have multiple edges between the same two vertices and I’ve not faced an issue with DMNetwork. However, all the data was read on rank 0 only (and then distributed).

Maybe the issue is with the edges being passed on different ranks?

Thanks,

Shri

From: Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>>
Date: Wednesday, December 1, 2021 at 3:19 PM
To: "Knepley, Matthew G (VISIT)" <knepley at gmail.com<mailto:knepley at gmail.com>>, PETSc Development <petsc-dev at mcs.anl.gov<mailto:petsc-dev at mcs.anl.gov>>, "Abhyankar, Shrirang G" <shrirang.abhyankar at pnnl.gov<mailto:shrirang.abhyankar at pnnl.gov>>, "Zhang, Hong" <hzhang at mcs.anl.gov<mailto:hzhang at mcs.anl.gov>>, Getnet Betrie <gbetrie at anl.gov<mailto:gbetrie at anl.gov>>
Subject: DMPLEX cannot support two different edges for the same two vertices, hence DMPLEX cannot?

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   Matt,

     If DMPlexBuildFromCellListParallel() is called with two edges that have the same two vertices what will happen? It looks like it ends up with an incorrect PetscSF if the two edges are passed on different ranks. Hence the DMPLEX is not valid and produces garbage.

     Neurons can be connected to themselves which seems to be breaking DMPLEX and hence DMNETWORK.

     Is there anything we can do to support having multiple edges between the same two vertices? If not is there a way we can have DMPlexBuildFromCellListParallel() generate an error automatically if there are such extra edges in the input data.

   Thanks

  Barry

In this work, the neurons are represented by vertices in the network and each synapse is a graph edge.

--

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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