[petsc-dev] Soliciting suggestions for linear solver work under SciDAC 4 Institutes

[Hong]

Efficient and scalable MatGetSubmatrix() and assemble submatrices into a
matrix -- used for multiphysic simulation, e.g., wash project we are doing
now.

Hong

On Sat, Jul 2, 2016 at 2:46 AM, Patrick Sanan <patrick.sanan at gmail.com>
wrote:

> Maybe a general class of opportunities for PETSc could be wrapped up
> under "good abstractions for memory space awareness". That is, all
> these topics have been discussed recently:
>
> 1.  Re Jeff's excellent suggestion about OpenMP, it would be nice if
> more were done to promote the alternative, MPI-based shared memory
> capability. It's quite clear that this is a good way to go, but this
> doesn't mean that people (who often equate shared memory parallelism
> with threads) will use it, so the more that can be done to make the
> internals of the library use this approach and the more that the
> classes (DM in particular) can make it easy to do things "the right
> way", the better.
>
> 2. As we saw from Richard's talk on KNL, that device will feature
> (when used a certain way) one NUMA domain which can provide much
> greater memory bandwidth. As in the discussions here before on the
> topic, it's a real challenge to figure out how to to make something
> like this usable via PETSc, and an even greater one to pick defaults
> in a way that won't sometimes produce bewildering performance results.
> Nevertheless, there's a good chance this is the kind of hardware that
> people will be running PETSc on, and given that this is something
> which attacks memory bandwidth bottlenecks, something that could speed
> up a lot of PETSc code.
>
> 3. People will likely also be running on machines with
> coprocessors/accelerators/etc for a while, and there needs to be
> plumbing to deal with the fact that each device may provide an extra
> memory space which needs to be managed properly in the flat MPI
> environment. This is of course related to point 1, as good use of
> MPI-3 shared memory seems like a reasonable way forward.
>
> 4. Related topics re MPI-4/endpoints and how PETSc really could be
> used properly from an existing multi-threaded environment. Karl has
> talked about the challenges of doing this the right way a lot
> recently.
>
> With all of these, introducing some clever abstractions to allow these
> sorts of things to be as transparent/automatic/encapsulated as
> possible might be very valuable and well-used additions to the
> library.
>
> On Sat, Jul 2, 2016 at 1:13 AM, Jeff Hammond <jeff.science at gmail.com>
> wrote:
> > Obviously, holistic support for OpenMP is critical to the future of PETSc
> > :-D
> >
> > On a more serious note, Matt and I have discussed the use of PETSc for
> > sparse multidimensional array computations for dimensions greater than 2,
> > also known as tensor computations. The associated paper describing
> previous
> > work with dense arrays is
> > http://www.eecs.berkeley.edu/Pubs/TechRpts/2012/EECS-2012-210.html.
> There
> > was even an unsuccessful SciDAC application proposal that described how
> > PETSc could be used for that domain when sparsity is important.  To
> start,
> > all we'd need is sparse matrix x sparse matrix multiplication, which I
> hear
> > the multigrid folks also need.  Sparse times dense is also important.
> > Sparse tensor factorization would also help, but I get that there are
> enough
> > open math questions there that it might be impractical to try to
> implement
> > something in PETSc in the near future.
> >
> > Maybe I am just biased because I spend all of my time reading
> > www.nextplatform.com, but I hear machine learning is becoming an
> important
> > HPC workload.  While the most hyped efforts related to running
> inaccurate -
> > the technical term is half-precision - dense matrix multiplication as
> fast
> > as possible, I suspect that more elegant approaches will prevail.
> > Presumably there is something that PETSc can do to enable machine
> learning
> > algorithms.  As most of the existing approaches use silly programming
> models
> > based on MapReduce, it can't be too hard for PETSc to do better.
> >
> > Jeff
> >
> > On Fri, Jul 1, 2016 at 2:32 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >>
> >>
> >>    The DOE SciDAC institutes have supported PETSc linear solver
> >> research/code development for the past fifteen years.
> >>
> >>     This email is to solicit ideas for linear solver research/code
> >> development work for the next round of SciDAC institutes (which will be
> a 4
> >> year period) in PETSc. Please send me any ideas, no matter how crazy, on
> >> things you feel are missing, broken, or incomplete in PETSc with regard
> to
> >> linear solvers that we should propose to work on. In particular, issues
> >> coming from particular classes of applications would be good. Generic
> "multi
> >> physics" coupling types of things are too general (and old :-)) while
> work
> >> for extreme large scale is also out since that is covered under another
> call
> >> (ECP). But particular types of optimizations etc for existing or new
> codes
> >> could be in, just not for the very large scale.
> >>
> >>     Rough ideas and pointers to publications are all useful. There is an
> >> extremely short fuse so the sooner the better,
> >>
> >>     Thanks
> >>
> >>       Barry
> >>
> >>
> >>
> >
> >
> >
> > --
> > Jeff Hammond
> > jeff.science at gmail.com
> > http://jeffhammond.github.io/
>
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