[petsc-users] Uninterpolating DMLabels?
Justin Chang
jchang27 at uh.edu
Fri Apr 10 15:39:32 CDT 2015
That makes a lot of sense now. So if I understand this correctly, with
-dm_refine 2, all of the fine cells for coarse cell number 3 would be:
192 193 ... 255
-dm_refine 3 for the same cell would be:
1536 1537 .... 2047
and so on. And this would hold true even for distributed meshes?
Thanks,
On Fri, Apr 10, 2015 at 1:21 PM, Matthew Knepley <knepley at gmail.com> wrote:
> 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
>
--
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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