[petsc-users] Uninterpolating DMLabels?
Justin Chang
jchang27 at uh.edu
Fri Apr 10 01:01:27 CDT 2015
Matt,
I am not sure I follow what you're saying here. Currently I am working with
3D simplex elements so if the variable numSubcells is what you're referring
to in CellRefinerGetAffineTransforms_Internal(), there's no example for
REFINER_SIMPLEX_3D. What would it be in that case, 7?
What I am looking for is a function and/or a set of algorithms where given
a sieve point m from the original coarse mesh, I can obtain the
corresponding set of (fine mesh) sieve points. I am assuming c_f \in [C
c_c, C (c_c + 1) ) describes just that?
Is there an existing DMPlex related function that implements this directly?
Because I don't see how CellRefinerGetAffineTransforms_Internal() will help.
Thanks,
On Thu, Apr 9, 2015 at 8:20 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Thu, Apr 9, 2015 at 8:14 PM, Justin Chang <jchang27 at uh.edu> wrote:
>
>> Matt, thank you for the clarification. One more question somewhat on a
>> related note.
>>
>> I have auxiliary data corresponding to the permeability of a reservoir
>> (for instance, the SPE10 benchmark problem). The data is cell-wise and read
>> from a binary file. I want to refine both the DM and this data. Is there a
>> way to obtain the mapping from the coarse mesh to the fine mesh? What I
>> mean is, given a coarse cell, can I somehow get the transitive closure of
>> the fine cells it created during the refinement process? This would allow
>> me to copy the value of the coarse cell data onto it's children.
>>
>
> If you are doing regular refinement, there is a simple formula:
>
> c_f \in [ C c_c, C (c_c +1) )
>
> where C is the number of cells created from each cell. You can get C from
>
> CellRefinerGetAffineTransforms_Internal()
>
> which I could promote to a real interface function.
>
> Thanks,
>
> Matt
>
>
>> Thanks,
>>
>> On Thu, Apr 9, 2015 at 7:52 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Thu, Apr 9, 2015 at 7:21 PM, Justin Chang <jchang27 at uh.edu> wrote:
>>>
>>>> 1) I did what you had suggested and it works very well thanks.
>>>>
>>>
>>> Cool.
>>>
>>>
>>>> 2) In my case, calling uninterpolate does make a difference, just not
>>>> necessarily in the solver step (I am using Tao's BLMVM). I attached two
>>>> output files, one containing the timings and summaries with uninterpolating
>>>> and one without uninterpolating. And the source code if you wanted to
>>>> verify the "correctness" of my implementation. Namely, the biggest
>>>> difference I see is in setting up the PetscSection. When uninterpolating
>>>> the data this steps takes 8.64039 seconds but when I do not uninterpolate
>>>> the data it takes 61.2977 seconds. Is this "significant" enough, or is it
>>>> unimportant given the fact that this step occurs only once during any
>>>> simulation?
>>>>
>>>
>>> That is significant. Most of that time is in the operator preallocation
>>> routine. It was cleaner to first gather the point
>>> adjacency information, and then push the dof information on top. If I
>>> aggressively merged the dof data, I could have
>>> pruned a bunch of the work here and gotten much closer to the first
>>> time, at the expense of more complicated code.
>>> I guess this is the right pattern if you know that you will only have
>>> unknowns on cells and vertices.
>>>
>>>
>>>> 3) Also, about DMPlexDistribute(...). Right now it still seems
>>>> extremely slow, hence why I am distributing a coarse mesh and having each
>>>> processor refine its local portion of the mesh. In my current
>>>> implementation, I have rank 0 distribute the mesh via ParMETIS. Will there
>>>> eventually be a methodology to do parallel I/O then redistribution for load
>>>> balancing or does it already exist?
>>>>
>>>
>>> Redistribution for load balancing already exists. The stumbling block
>>> right now is parallel mesh import. However,
>>> the group at ICL (Michael Lange and Gerard Gorman) is working on this,
>>> and we expect to have it working by
>>> the end of summer. Until then, I recommend exactly what you are doing.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Thanks,
>>>>
>>>> On Tue, Apr 7, 2015 at 8:37 PM, Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Tue, Apr 7, 2015 at 7:18 PM, Justin Chang <jchang27 at uh.edu> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> So I am interpolating/uninterpolating my DMPlex mesh. This is the
>>>>>> mesh information for a cell-vertex mesh only:
>>>>>>
>>>>>> DM Object: 1 MPI processes
>>>>>> type: plex
>>>>>> DM_0x84000000_0 in 3 dimensions:
>>>>>> 0-cells: 159
>>>>>> 3-cells: 592
>>>>>> Labels:
>>>>>> marker: 1 strata of sizes (100)
>>>>>> depth: 2 strata of sizes (159, 592)
>>>>>>
>>>>>> I am interpolating the mesh with the following lines:
>>>>>>
>>>>>> ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
>>>>>> ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr);
>>>>>> ierr = DMPlexCopyLabels(*dm, idm);CHKERRQ(ierr);
>>>>>> ierr = DMPlexGetLabel(idm, "marker", &label);CHKERRQ(ierr);
>>>>>> ierr = DMPlexMarkBoundaryFaces(idm,label);CHKERRQ(ierr);
>>>>>> ierr = DMDestroy(dm);CHKERRQ(ierr);
>>>>>> *dm = idm;
>>>>>>
>>>>>> And the resulting mesh:
>>>>>>
>>>>>> DM Object: 1 MPI processes
>>>>>> type: plex
>>>>>> DM_0x84000000_1 in 3 dimensions:
>>>>>> 0-cells: 159
>>>>>> 1-cells: 845
>>>>>> 2-cells: 1280
>>>>>> 3-cells: 592
>>>>>> Labels:
>>>>>> marker: 1 strata of sizes (292)
>>>>>> depth: 4 strata of sizes (159, 845, 1280, 592)
>>>>>>
>>>>>> The reason I did this is so that incase I decide to refine the mesh
>>>>>> with "-dm_refine <number>" the DM will be sure to include the "marker"
>>>>>> points in the refinement process. Now, if I decide to uninterpolate the
>>>>>> mesh with the following lines:
>>>>>>
>>>>>> ierr = DMPlexUninterpolate(*dm, &idm);CHKERRQ(ierr);
>>>>>> ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr);
>>>>>> ierr = DMPlexCopyLabels(*dm, idm);CHKERRQ(ierr);
>>>>>> ierr = DMDestroy(dm);CHKERRQ(ierr);
>>>>>> *dm = idm;
>>>>>>
>>>>>> I end up with this mesh:
>>>>>>
>>>>>> DM Object: 1 MPI processes
>>>>>> type: plex
>>>>>> DM_0x84000000_2 in 3 dimensions:
>>>>>> 0-cells: 159
>>>>>> 3-cells: 592
>>>>>> Labels:
>>>>>> marker: 1 strata of sizes (292)
>>>>>> depth: 2 strata of sizes (159, 592)
>>>>>>
>>>>>> The problem is that although the cells and vertices have gone back to
>>>>>> the original number, the "marker" label still includes face/edge points.
>>>>>> This gives me an error once I invoke DMCreateGobalVector(...).
>>>>>>
>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>> --------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Argument out of range
>>>>>> [0]PETSC ERROR: Section point 755 should be in [0, 751)
>>>>>> [0]PETSC ERROR: See
>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>>>> shooting.
>>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2528-gbee642f
>>>>>> GIT Date: 2015-03-29 20:36:38 -0500
>>>>>> [0]PETSC ERROR: ./cube_with_hole on a arch-linux2-c-debug named
>>>>>> pacotaco by justin Tue Apr 7 19:09:12 2015
>>>>>> [0]PETSC ERROR: Configure options --download-chaco
>>>>>> --download-exodusii --download-fblaslapack --download-hdf5 --download-metis
>>>>>> --download-mpich --download-mumps --download-netcdf --download-parmetis
>>>>>> --download-scalapack --download-triangle --with-cc=gcc --with-cmake=cmake
>>>>>> --with-cxx=g++ --with-debugging=1 --with-fc=gfortran --with-valgrind=1
>>>>>> PETSC_ARCH=arch-linux2-c-debug
>>>>>> [0]PETSC ERROR: #1 PetscSectionGetDof() line 499 in
>>>>>> /home/justin/petsc-dev/src/vec/is/utils/vsectionis.c
>>>>>> [0]PETSC ERROR: #2 DMPlexGetConeSize() line 841 in
>>>>>> /home/justin/petsc-dev/src/dm/impls/plex/plex.c
>>>>>> [0]PETSC ERROR: #3 DMPlexGetTransitiveClosure() line 1342 in
>>>>>> /home/justin/petsc-dev/src/dm/impls/plex/plex.c
>>>>>> [0]PETSC ERROR: #4 DMPlexLabelComplete() line 88 in
>>>>>> /home/justin/petsc-dev/src/dm/impls/plex/plexsubmesh.c
>>>>>> [0]PETSC ERROR: #5 DMCreateDefaultSection_Plex() line 5605 in
>>>>>> /home/justin/petsc-dev/src/dm/impls/plex/plex.c
>>>>>> [0]PETSC ERROR: #6 DMGetDefaultSection() line 3035 in
>>>>>> /home/justin/petsc-dev/src/dm/interface/dm.c
>>>>>> [0]PETSC ERROR: #7 DMGetDefaultGlobalSection() line 3266 in
>>>>>> /home/justin/petsc-dev/src/dm/interface/dm.c
>>>>>> [0]PETSC ERROR: #8 DMCreateGlobalVector_Section_Private() line 13 in
>>>>>> /home/justin/petsc-dev/src/dm/interface/dmi.c
>>>>>> [0]PETSC ERROR: #9 DMCreateGlobalVector_Plex() line 1170 in
>>>>>> /home/justin/petsc-dev/src/dm/impls/plex/plexcreate.c
>>>>>> [0]PETSC ERROR: #10 DMCreateGlobalVector() line 698 in
>>>>>> /home/justin/petsc-dev/src/dm/interface/dm.c
>>>>>> [0]PETSC ERROR: #11 main() line 363 in
>>>>>> /home/justin/Dropbox/Research_Topics/Code_PETSc/Nonneg/cube_with_hole.c
>>>>>>
>>>>>>
>>>>>> From this error, it seems it's trying to access sieve points that non
>>>>>> longer exist. And I think it has to do with the label "marker" still
>>>>>> contains data from the interpolated mesh. Is there a way to "uninterpolate"
>>>>>> or remove such points? Or is there a better way of approaching this whole
>>>>>> thing?
>>>>>>
>>>>>
>>>>> 1) It would be easy to write a small function to throw out the points
>>>>> in the label that do not exist in the DM. You
>>>>> would just extract each stratumIS and then Clear each invalid
>>>>> point.
>>>>>
>>>>> 2) However, I do not understand the rationale for this above. You
>>>>> could just call MarkBoundaryFaces on the final mesh.
>>>>> If you are really trying to preserve a label across regular
>>>>> refinement AND you really do not want an interpolated mesh,
>>>>> then code up 1). I have yet to see a case where the extra memory
>>>>> for edges and faces makes a difference, but it may exist.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Justin Chang
>>>>>> PhD Candidate, Civil Engineering - Computational Sciences
>>>>>> University of Houston, Department of Civil and Environmental
>>>>>> Engineering
>>>>>> Houston, TX 77004
>>>>>> (512) 963-3262
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Justin Chang
>>>> PhD Candidate, Civil Engineering - Computational Sciences
>>>> University of Houston, Department of Civil and Environmental Engineering
>>>> Houston, TX 77004
>>>> (512) 963-3262
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> Justin Chang
>> PhD Candidate, Civil Engineering - Computational Sciences
>> University of Houston, Department of Civil and Environmental Engineering
>> Houston, TX 77004
>> (512) 963-3262
>>
>
>
>
> --
> 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
>
--
Justin Chang
PhD Candidate, Civil Engineering - Computational Sciences
University of Houston, Department of Civil and Environmental Engineering
Houston, TX 77004
(512) 963-3262
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