[petsc-users] specifying vertex coordinates using DMPlexCreateFromCellListParallel

Thu Jun 29 09:57:37 CDT 2017

On Thu, Jun 29, 2017 at 9:52 AM, Hassan Raiesi <
Hassan.Raiesi at aero.bombardier.com> wrote:

> That would great if it allows elements with mixed faces,
>

Note that if you really needed this, you can always input the information
by hand using DMPlexCreateDAG(), but
its laborious.

   Matt

>
>
> Thank you
>
> -Hassan
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Thursday, June 29, 2017 10:36 AM
> *To:* Hassan Raiesi <Hassan.Raiesi at aero.bombardier.com>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] specifying vertex coordinates using
> DMPlexCreateFromCellListParallel
>
>
>
> On Thu, Jun 29, 2017 at 9:32 AM, Hassan Raiesi <Hassan.Raiesi at aero.
> bombardier.com> wrote:
>
> Ok,
>
>
>
> The problem is that the faceSizes varies for pyramids and prisms, they
> have faces with variable number of nodes (i.e for pyramids, four triangular
> faces and one quad face, this I don’t see how to specify?
>
> What if I report all faces as quad faces, for triangular faces, there
> would be a repeated vertex, would it make any problem?
>
>
>
> No, you are right, that will not work. The whole interpolation code would
> have to be rewritten to allow faces with
>
> variable size. Its not hard, but it is time-consuming. Since I am moving
> this summer, this will not be done in a timely
>
> manner unfortunately.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
> Thank you
>
> -Hassan
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Thursday, June 29, 2017 10:12 AM
> *To:* Hassan Raiesi <Hassan.Raiesi at aero.bombardier.com>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] specifying vertex coordinates using
> DMPlexCreateFromCellListParallel
>
>
>
> On Thu, Jun 29, 2017 at 8:59 AM, Hassan Raiesi <Hassan.Raiesi at aero.
> bombardier.com> wrote:
>
> Matthew,
>
>
>
> Not sure if I understood completely, I have the ordering according to the
> CGNS standard for all cells in the mesh, or I can change it if needed, but
> I don’t understand what you mean by reporting all faces as ordered
> vertices? Do you mean I just define the face connectivity?Could you explain
> a bit more?
>
>
>
> For a triangular prism, you would add the case in GetRawFaces() for dim 3,
> coneSize 6. Lets look at a triangle (dim 2, coneSize 3)
>
>
>
>   https://bitbucket.org/petsc/petsc/src/5ebd2cd705b0ffa5a27aee8a08f867
> 95d413b548/src/dm/impls/plex/plexinterpolate.c?at=master&
> fileviewer=file-view-default#plexinterpolate.c-63
>
>
>
> You see that it returns 3 groups of 2 vertices, which are the edges. For a
> tetrahedron
>
>
>
>   https://bitbucket.org/petsc/petsc/src/5ebd2cd705b0ffa5a27aee8a08f867
> 95d413b548/src/dm/impls/plex/plexinterpolate.c?at=master&
> fileviewer=file-view-default#plexinterpolate.c-101
>
>
>
> it returns 4 groups of 3 vertices, which are the faces. Note that all
> faces should be oriented such that the normal is outward.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
>
>
> Thank you
>
> -Hassan
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Tuesday, June 27, 2017 1:54 PM
> *To:* Hassan Raiesi <Hassan.Raiesi at aero.bombardier.com>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] specifying vertex coordinates using
> DMPlexCreateFromCellListParallel
>
>
>
> On Tue, Jun 27, 2017 at 11:30 AM, Hassan Raiesi <Hassan.Raiesi at aero.
> bombardier.com> wrote:
>
> I meant the interpolation,
>
> DMPlex supports those element shapes, however, there are two problems,
> one, “DMPlexBuildFromCellList_Parallel” does not take mixed elements
> (numCorners must be constant for all elements in current implementation),
> that was easy to fix,
>
> I already extended DMPlexBuildFromCellList_Parallel_Private to take
> elements with different shapes,  then I realized the interpolation does not
> work when the mesh has elements other than tets and hex.
>
>
>
> Okay, here is what is needed. You need to
>
>
>
>   a) prescribe an order for the vertices in a prism/pyramid (all input
> cells must have this order)
>
>
>
>   b) report all faces as sets of ordered vertices
>
>     - You have to order them matching the Plex vertex order for the lower
> dimensional shape
>
>     - They should be oriented as to have outward facing normal
>
>
>
> Regarding the interpolation, I also noticed that the memory requirement is
> huge if I load the whole mesh on one core and interpolate (I cannot
> interpolate a mesh with 9M tets on a machine with 128GB of memory, it ran
> out of memory, I’ll try to run with petsc memory logs and send).
>
>
>
> I am not sure what the upper limit is, but in a 3D mesh you could have
> many times the number of cells in faces and edges. Note that
>
> you would need --with-64-bit-indices to go beyond 4GB.
>
>
>
> is there anyways to interpolate the mesh after  DMPlexdistribute? The code
> crashes if I move DMPlexInterpolate to after calling DMPlexdistribute., I
> guess what is needed is a DMPlexInterpolate on already distributed meshes.
>
>
>
> This should work. Maybe try a small example? If that crashes, just send it.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
> Thank you
>
> -Hassan
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Tuesday, June 27, 2017 11:53 AM
> *To:* Hassan Raiesi <Hassan.Raiesi at aero.bombardier.com>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] specifying vertex coordinates using
> DMPlexCreateFromCellListParallel
>
>
>
> On Tue, Jun 27, 2017 at 10:08 AM, Hassan Raiesi <Hassan.Raiesi at aero.
> bombardier.com> wrote:
>
> Great, It’s clear now J,
>
> One more question, any plan to support other element shapes (prism and
> pyramid) in 3D?,  DMPlexGetRawFaces_Internal only supports tets and hexs
> in 3D, can prisms and pyramids be used as degenerate hexahedrons?
>
>
>
> It depends on what you mean "support". Right now, we can represent these
> shapes in Plex. However, if you
>
> want mesh interpolation to work, then yes you need to extend GetRawFaces()
> to understand that shape. If
>
> you want them read out of a file format, other than Gmsh, we would likely
> have to extend that as well. These
>
> are straightforward once I understand what exactly you want to do.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
> Thank you
>
> -Hassan
>
>
>
>
>
>
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Tuesday, June 27, 2017 10:17 AM
> *To:* Hassan Raiesi <Hassan.Raiesi at aero.bombardier.com>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] specifying vertex coordinates using
> DMPlexCreateFromCellListParallel
>
>
>
> On Tue, Jun 27, 2017 at 9:12 AM, Hassan Raiesi <Hassan.Raiesi at aero.
> bombardier.com> wrote:
>
> Thanks for your reply,
>
>
>
> Is there any example where each rank owns more than 1 element, i.e for the
> simple mesh here(attached png file), how should I pack and pass the
> coordinates of the vertices owned by rank0, rank1
>
>
>
> Rank0:numcells = 2; num nodes=4, cells=[154 245] , nodes=[1 5 2 4]
>
> nodes = 1245
>
> vertex coords: in what node order ?
>
> [coords_n1 coords_n2 coords_n4 coords_n5] or
>
> [coords_n2 coords_n4 coords_n1 coords_n5] or …..?
>
>
>
>
>
> rank1: numcells = 2; num nodes=2, cells=[532 635], nodes=[6 3]
>
> vertexcoords [how to pack the nodes coords here?]
>
> should it be  [x6y6 x3y3] or [x3y3 x6y6]? In what order?
>
>
>
> I think there is a misunderstanding here.
>
>
>
> There is NO connection between the cell order and the vertex order. Each
> process gets a contiguous
>
> set of cells (in the global numbering) and a contiguous set of vertices
> (in the global numbering). These
>
> two are NOT related. We then move the vertices to the correct processes.
> In this way, we can load
>
> completely in parallel, without requiring any setup in the mesh file.
>
>
>
> If you are worried, you can always arrange the order of vertices to
> "match" the order of cells.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
> thanks
>
>
>
>
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Sunday, June 25, 2017 1:04 PM
> *To:* Hassan Raiesi <Hassan.Raiesi at aero.bombardier.com>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] specifying vertex coordinates using
> DMPlexCreateFromCellListParallel
>
>
>
> On Tue, Apr 11, 2017 at 9:21 AM, Hassan Raiesi <Hassan.Raiesi at aero.
> bombardier.com> wrote:
>
> Hello,
>
>
>
> I’m trying to use DMPlexCreateFromCellListParallel to create a DM from an
> already partitioned mesh,
>
> It requires an array of numVertices*spaceDim numbers, but how should one
> order the coordinates of the vertices?
>
>
>
> Global order. Here is the idea. You must read the file in chunks so that
> each proc can read its own chunk in parallel
>
> without talking to anyone else.
>
>
>
> we only pass the global vertex numbers using ‘const int cells[]’ to define
> the cell-connectivity, so passing the vertex coordinates in local ordering
> wouldn’t make sense?
>
>
>
> Yes.
>
>
>
> If it needs to be in global ordering, should I sort the global index of
> the node numbers owned by each rank (as they wont be continuous).
>
>
>
> Nope.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
>
>
> Thank you
>
>
>
> Hassan Raiesi,
>
> Bombardier Aerospace
>
> www.bombardier.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
>
>
>
> http://www.caam.rice.edu/~mk51/
>
>
>
>
>
> --
>
> 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
>
>
>
> http://www.caam.rice.edu/~mk51/
>
>
>
>
>
> --
>
> 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
>
>
>
> http://www.caam.rice.edu/~mk51/
>
>
>
>
>
> --
>
> 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
>
>
>
> http://www.caam.rice.edu/~mk51/
>
>
>
>
>
> --
>
> 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
>
>
>
> http://www.caam.rice.edu/~mk51/
>
>
>
>
>
> --
>
> 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
>
>
>
> http://www.caam.rice.edu/~mk51/
>

-- 
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

http://www.caam.rice.edu/~mk51/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20170629/0d815a71/attachment-0001.html>