[petsc-dev] [petsc4py] Broken tests for DMStag

Tue Jun 18 14:44:44 CDT 2019

  Ah


> On Jun 18, 2019, at 2:24 PM, Patrick Sanan <patrick.sanan at gmail.com> wrote:
> 
> It's for domains of any width on one processor + periodic boundary conditions in a given direction.
> 
> Am Di., 18. Juni 2019 um 21:19 Uhr schrieb Smith, Barry F. <bsmith at mcs.anl.gov>:
> 
>   Is it only for super skinny domains when periodic or any size domain when periodic? If only super skinny you can still develop and run with one processor right, just not super skinny. 
> 
>   I don't think it is worth the time and extra code but that's, of course, up to you.
> 
>    Barry
> 
>   DMDA actually had an entire other scatter for doing the local to global that worked for all cases but I threw it away a few years ago figuring the small failed special case as not important enough to keep around all that extra infrastructure.
> 
> 
> > On Jun 18, 2019, at 2:05 PM, Patrick Sanan <patrick.sanan at gmail.com> wrote:
> > 
> > 
> > 
> > Am Di., 18. Juni 2019 um 20:30 Uhr schrieb Smith, Barry F. <bsmith at mcs.anl.gov>:
> > 
> >   Patrick,
> > 
> >     I understand the problem with DMDA and periodicity with only a single  skinny processor in one direction, local to global won't work without lots of additional code. I don't care because PETSc is for big problems and that problem is not big. 
> > 
> > Agreed, as far as performance is concerned, but I also very much value being able to run and debug small problems, in serial at first, on my laptop. This skinny-periodic case doesn't matter much for DMDA, because you don't really need to do a lot of local->global scatters with INSERT_VALUES (just access the global vector directly). The way DMStag is right now, I use this to construct coordinates and to do data migration, because of the regular blocking of the local vectors.
> > 
> >     Could you please explain to me the problem with Stag unrelated to a skinny domain with one processor and periodic boundary conditions? 
> > 
> >     Each unknown in the global vector presumably has an unknown on the local vector that "lives" at the same point. For insert why can't the local to global just use the value from that location? Meanwhile for ADD_VALUES why can't you just use the reverse of the global to local?
> > I don't think there's a way to know (from the point of view of the VecScatter) which of several local unknowns is the right one to map to a given global unknown. Usually you saying "it's the one coming from this rank", but that breaks down for the skinny periodic case. 
> > 
> > 
> >     If the problem is just with skinny domain periodic one process in that direction just generate the error and remove any test cases for that situation. It seems absurd to me to waste time worrying about a totally irrelevant special case and introducing all kinds of special constructs for it is just making a mountain out of a mole hill.
> > Potential users have noticed and complained, so I need to fix it somehow : ( Sounds like playing with higher-level DM stuff isn't worth the churn, so I should focus on solutions internal to DMStag.
> > 
> > 
> >    Barry
> > 
> > 
> > > On Jun 18, 2019, at 10:51 AM, Patrick Sanan via petsc-dev <petsc-dev at mcs.anl.gov> wrote:
> > > 
> > > Sorry about the delay on this - I'm still trying to decide on what's an elegant solution. I'll attempt to describe the issue and potential solutions, in case anyone has interest/ideas:
> > > 
> > > My understanding of the way things work now
> > > - DMLocalToGlobal() sends data from "local" vectors to "global" vectors. 
> > > - This "l2g" map is in general surjective (onto) but not injective (into) because local subdomains can overlap.
> > > - When DMLocalToGlobal() is called with INSERT_VALUES, there needs to be some mechanism to resolve this non-injectivity.
> > > - The mechanism is to ignore the parts of the l2g map that aren't rank-local. 
> > > - This usually works very well because "local" vectors can usually be constructed to consist of degrees of freedom consisting of rank-local dof in the global representation (I like to call these "native"), plus additional dof corresponding to other dof, which are either on other ranks or not part of the global representation at all (ghosted boundaries).
> > > - This breaks down for a DMDA with a single rank in a given coordinate direction, and periodic boundary conditions. You'll get an error trying due to the non-injectivity of the map, even after excluding off-rank communication (since the ghost region maps to native dof, which never happens otherwise)
> > > - However, this isn't an issue in practice, because with DMDA you can just operate directly on a global vector. Local-to-global inserts aren't very useful in general.
> > > 
> > > Issue related to DMStag
> > > - With DMStag, the same issue occurs as with DMDA (and this is the topic of this thread).
> > > - However, operating directly on a global vector isn't currently convenient with DMStag, because global vectors aren't regularly blocked, while local vectors are. 
> > > - This is perhaps a design flaw to be addressed with DMStag, because the local representation is being used for two orthogonal purposes: padding out to obtain regular blocking, and padding out to include ghost regions.
> > > 
> > > Potential solutions
> > > I can think of a few avenues to pursue, including
> > > 1. Whenever this could potentially arise, pad all local vectors with the necessary 0's and use ADD_VALUES [gross]
> > > 2. Add a dedicated "padded global" representation for DMStag, and tools for working with it. [elegant in that it resolves the design flaw above, but adds quite a lot of code]
> > > 
> > > but here's the idea  that I'm also intrigued by:
> > > - It's an abuse of notation to use INSERT_VALUES for DMLocalToGlobal() in the first place
> > > - Rather, it'd be more meaningful to use a new InsertMode value, INSERT_VALUES_LOCAL, deprecating the use of INSERT_VALUES for DMLocalToGlobal()*
> > > - This name corresponds to SCATTER_REVERSE_LOCAL which gets called in e.g. DMLocalToGlobalBegin_DA(), or the equivalent logic in DMLocalToGlobalBegin() using PetscSection
> > > - In most cases, this works just as before, but now the error message is more accurate - you can't use INSERT_VALUES_LOCAL when the l2g map isn't injective, even when ignoring parallel communication
> > > - Add another new InsertMode value, INSERT_VALUES_INJECTIVE, which asks the DM implementation to resolve the non-injectivity of the l2g map
> > > - In most cases, this would behave just like INSERT_VALUES_LOCAL and most users wouldn't know or care
> > > - However, for the case of interest here, the implementation would be free to use its implementation-dependent data to "do the right thing"
> > > - For DMStag, the right thing would be to behave consistently with the case with 2 or more ranks in the periodic direction (ignoring dof on ghost elements).
> > > - This could be done by setting up another VecScatter during DMSetUp_Stag(), and using it with INSERT_VALUES_INJECTIVE
> > > 
> > > * eventually this could become an error if the l2g map was non-injective, but probably not for a long time if ever
> > > 
> > > Am Do., 13. Juni 2019 um 15:09 Uhr schrieb Patrick Sanan <patrick.sanan at gmail.com>:
> > > I will attempt to just fix the underlying issue here, that is allow DMStagSetUniformCoordinates() to work for period boundary conditions with a single rank in the corresponding dimension.
> > > 
> > > Am Mi., 12. Juni 2019 um 19:10 Uhr schrieb Patrick Sanan <patrick.sanan at gmail.com>:
> > > Ah, okay, so unless something weird is going on, that probably should never have passed (if it's asking for periodic BCs with one rank in a given direction, and INSERT_VALUES, so it's not well-defined which of the multiple local dof mapping to a given global dof should be used). I'll try to reproduce and fix it and/or talk to Chris.
> > > 
> > > Am Mi., 12. Juni 2019 um 18:27 Uhr schrieb Balay, Satish via petsc-dev <petsc-dev at mcs.anl.gov>:
> > > On Wed, 12 Jun 2019, Lisandro Dalcin via petsc-dev wrote:
> > > 
> > > > $ python test/runtests.py -v -i dmstag TestDMStag_2D_PXY
> > > > [0 at kl-18232] Python 2.7 (/usr/local/opt/python at 2/bin/python2.7)
> > > > [0 at kl-18232] PETSc 3.11.2 development (conf: 'arch-darwin-c-debug')
> > > > [0 at kl-18232] petsc4py 3.11.0 (build/lib.macosx-10.14-x86_64-2.7/petsc4py)
> > > > testCoordinates (test_dmstag.TestDMStag_2D_PXY) ... ERROR
> > > > testDMDAInterface (test_dmstag.TestDMStag_2D_PXY) ... ERROR
> > > > testDof (test_dmstag.TestDMStag_2D_PXY) ... ok
> > > > testGetOther (test_dmstag.TestDMStag_2D_PXY) ... ok
> > > > testGetVec (test_dmstag.TestDMStag_2D_PXY) ... ERROR
> > > > testMigrateVec (test_dmstag.TestDMStag_2D_PXY) ... ERROR
> > > 
> > > I get:
> > > 
> > > ======================================================================
> > > ERROR: testCoordinates (test_dmstag.TestDMStag_2D_PXY)
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > >   File "test/test_dmstag.py", line 39, in testCoordinates
> > >     self.da.setUniformCoordinates(0,1,0,1,0,1)
> > >   File "PETSc/DMStag.pyx", line 255, in petsc4py.PETSc.DMStag.setUniformCoordinates
> > > Error: error code 56
> > > [0] DMStagSetUniformCoordinates() line 1077 in /home/balay/petsc.z/src/dm/impls/stag/stagutils.c
> > > [0] DMStagSetUniformCoordinatesExplicit() line 1118 in /home/balay/petsc.z/src/dm/impls/stag/stagutils.c
> > > [0] DMStagSetUniformCoordinatesExplicit_2d() line 135 in /home/balay/petsc.z/src/dm/impls/stag/stag2d.c
> > > [0] DMLocalToGlobalBegin() line 2614 in /home/balay/petsc.z/src/dm/interface/dm.c
> > > [0] DMLocalToGlobalBegin_Stag() line 230 in /home/balay/petsc.z/src/dm/impls/stag/stag.c
> > > [0] No support for this operation for this object type
> > > [0] Local to Global scattering with INSERT_VALUES is not supported for single rank in a direction with boundary conditions (e.g. periodic) inducing a non-injective local->global map. Either change the boundary conditions, use a stencil width of zero, or use more than one rank in the relevant direction (e.g. -stag_ranks_x 2)
> > > 
> > > Satish
> > > 
> > 
>