[petsc-users] Uninterpolating DMLabels?
Matthew Knepley
knepley at gmail.com
Fri Apr 10 13:21:23 CDT 2015
On Fri, Apr 10, 2015 at 12:58 PM, Justin Chang <jchang27 at uh.edu> wrote:
> Sorry I am a little confused here. I understand that each refinement of a
> 3D simplex element yields 8 subcells, but give the expression c_f \in [C
> c_c, C (c_c + 1) ) what exactly are these and/or what do they mean:
>
There are 8 fine cells created in each coarse cell. If the coarse cell
number is c_c, then the fine cells numbers are
C c_c, C c_c + 1, ..., C (c_c + 1) -1
So, if the coarse cell number is 3, then the fine cells inside are
24, 25, 26, 27, 28, 29, 30, 31
Thanks,
Matt
> c_f \in [... )
> C
> c_c
> (c_c + 1)
>
> Originally I was thinking the functions DMPlexGetTransitiveClosure(...)
> and/or DMPlexGetCoarseDM(...) need to be invoked somehow. Do they?
>
> Again thanks for your help
>
> --
> Justin Chang
> PhD Candidate, Civil Engineering - Computational Sciences
> University of Houston, Department of Civil and Environmental Engineering
> Houston, TX 77004
> (512) 963-3262
>
> On Fri, Apr 10, 2015 at 11:38 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Fri, Apr 10, 2015 at 1:01 AM, Justin Chang <jchang27 at uh.edu> wrote:
>>
>>> 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?
>>>
>>
>> Its 8. There are 8 fine cells for every coarse cell.
>>
>>
>>> 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?
>>>
>>
>> Yes, C = 8.
>>
>>
>>> Is there an existing DMPlex related function that implements this
>>> directly? Because I don't see how CellRefinerGetAffineTransforms_Internal()
>>> will help.
>>>
>>
>> I would just give you C. Yes, I would just write it. It should be 1 line.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>>
>>> 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
>>>
>>
>>
>>
>> --
>> 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
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