[petsc-users] Matvecs and KSPSolves with multiple vectors

[Sreeram R Venkat]

The reason for the large number of RHS's is that the problem originally
comes from having to do one solve with 1e10 size matrix. If we make some
extra assumptions on our problem, that 1e10 matrix becomes block diagonal
with blocks of size 1e6 and all the blocks are the same. The 1e6 is a
spatial discretion dimension and the 1e4 is the number of time steps. So
that's why we wanted to do the batched solve like this.

Thanks,
Sreeram

On Fri, Dec 22, 2023, 1:56 AM Pierre Jolivet <pierre at joliv.et> wrote:

>
>
> On 21 Dec 2023, at 7:38 PM, Junchao Zhang <junchao.zhang at gmail.com> wrote:
>
>
>
>
> On Thu, Dec 21, 2023 at 5:54 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Thu, Dec 21, 2023 at 6:46 AM Sreeram R Venkat <srvenkat at utexas.edu>
>> wrote:
>>
>>> Ok, I think the error I'm getting has something to do with how the
>>> multiple solves are being done in succession. I'll try to see if there's
>>> anything I'm doing wrong there.
>>>
>>> One question about the -pc_type lu -ksp_type preonly method: do you know
>>> which parts of the solve (factorization/triangular solves) are done on host
>>> and which are done on device?
>>>
>>
>> For SEQDENSE, I believe both the factorization and solve is on device. It
>> is hard to see, but I believe the dispatch code is here:
>>
> Yes, it is correct.
>
>
> But Sreeram matrix is sparse, so this does not really matter.
> Sreeram, I don’t enough about the internals of CHOLMOD (and its interface
> in PETSc) to know which part is done on host and which part is done on
> device.
> By the way, you mentioned a very high number of right-hand sides (> 1E4)
> for a moderately-sized problem (~ 1E6).
> Is there a particular reason why you need so many of them?
> Have you considered doing some sort of deflation to reduce the number of
> solves?
>
> Thanks,
> Pierre
>
>
>>
>> https://gitlab.com/petsc/petsc/-/blob/main/src/mat/impls/dense/seq/cupm/matseqdensecupm.hpp?ref_type=heads#L368
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thanks,
>>> Sreeram
>>>
>>> On Sat, Dec 16, 2023 at 10:56 PM Pierre Jolivet <pierre at joliv.et> wrote:
>>>
>>>> Unfortunately, I am not able to reproduce such a failure with your
>>>> input matrix.
>>>> I’ve used ex79 that I linked previously and the system is properly
>>>> solved.
>>>> $ ./ex79 -pc_type hypre -ksp_type hpddm -ksp_hpddm_type cg
>>>> -ksp_converged_reason -ksp_view_mat ascii::ascii_info -ksp_view_rhs
>>>> ascii::ascii_info
>>>> Linear solve converged due to CONVERGED_RTOL iterations 6
>>>> Mat Object: 1 MPI process
>>>>   type: seqaijcusparse
>>>>   rows=289, cols=289
>>>>   total: nonzeros=2401, allocated nonzeros=2401
>>>>   total number of mallocs used during MatSetValues calls=0
>>>>     not using I-node routines
>>>> Mat Object: 1 MPI process
>>>>   type: seqdensecuda
>>>>   rows=289, cols=10
>>>>   total: nonzeros=2890, allocated nonzeros=2890
>>>>   total number of mallocs used during MatSetValues calls=0
>>>>
>>>> You mentioned in a subsequent email that you are interested in systems
>>>> with at most 1E6 unknowns, and up to 1E4 right-hand sides.
>>>> I’m not sure you can expect significant gains from using GPU for such
>>>> systems.
>>>> Probably, the fastest approach would indeed be -pc_type lu -ksp_type
>>>> preonly -ksp_matsolve_batch_size 100 or something, depending on the memory
>>>> available on your host.
>>>>
>>>> Thanks,
>>>> Pierre
>>>>
>>>> On 15 Dec 2023, at 9:52 PM, Sreeram R Venkat <srvenkat at utexas.edu>
>>>> wrote:
>>>>
>>>> Here are the ksp_view files.  I set the options
>>>> -ksp_error_if_not_converged to try to get the vectors that caused the
>>>> error. I noticed that some of the KSPMatSolves converge while others don't.
>>>> In the code, the solves are called as:
>>>>
>>>> input vector v --> insert data of v into a dense mat --> KSPMatSolve()
>>>> --> MatMatMult() --> KSPMatSolve() --> insert data of dense mat into output
>>>> vector w -- output w
>>>>
>>>> The operator used in the KSP is a Laplacian-like operator, and the
>>>> MatMatMult is with a Mass Matrix. The whole thing is supposed to be a solve
>>>> with a biharmonic-like operator. I can also run it with only the first
>>>> KSPMatSolve (i.e. just a Laplacian-like operator). In that case, the KSP
>>>> reportedly converges after 0 iterations (see the next line), but this
>>>> causes problems in other parts of the code later on.
>>>>
>>>> I saw that sometimes the first KSPMatSolve "converges" after 0
>>>> iterations due to CONVERGED_RTOL. Then, the second KSPMatSolve produces a
>>>> NaN/Inf. I tried setting ksp_min_it, but that didn't seem to do anything.
>>>>
>>>> I'll keep trying different options and also try to get the MWE made
>>>> (this KSPMatSolve is pretty performance critical for us).
>>>>
>>>> Thanks for all your help,
>>>> Sreeram
>>>>
>>>> On Fri, Dec 15, 2023 at 1:01 AM Pierre Jolivet <pierre at joliv.et> wrote:
>>>>
>>>>>
>>>>> On 14 Dec 2023, at 11:45 PM, Sreeram R Venkat <srvenkat at utexas.edu>
>>>>> wrote:
>>>>>
>>>>> Thanks, I will try to create a minimal reproducible example. This may
>>>>> take me some time though, as I need to figure out how to extract only the
>>>>> relevant parts (the full program this solve is used in is getting quite
>>>>> complex).
>>>>>
>>>>>
>>>>> You could just do -ksp_view_mat binary:Amat.bin -ksp_view_pmat
>>>>> binary:Pmat.bin -ksp_view_rhs binary:rhs.bin and send me those three files
>>>>> (I’m guessing your are using double-precision scalars with 32-bit PetscInt).
>>>>>
>>>>> I'll also try out some of the BoomerAMG options to see if that helps.
>>>>>
>>>>>
>>>>> These should work (this is where all “PCMatApply()-ready” PC are being
>>>>> tested):
>>>>> https://petsc.org/release/src/ksp/ksp/tutorials/ex79.c.html#line215
>>>>> You can see it’s also testing PCHYPRE + KSPHPDDM on device (but not
>>>>> with HIP).
>>>>> I’m aware the performance should not be optimal (see your comment
>>>>> about host/device copies), I’ve money to hire someone to work on this but:
>>>>> a) I need to find the correct engineer/post-doc, b) I currently don’t have
>>>>> good use cases (of course, I could generate a synthetic benchmark, for
>>>>> science).
>>>>> So even if you send me the three Mat, a MWE would be appreciated if
>>>>> the KSPMatSolve() is performance-critical for you (see point b) from above).
>>>>>
>>>>> Thanks,
>>>>> Pierre
>>>>>
>>>>> Thanks,
>>>>> Sreeram
>>>>>
>>>>> On Thu, Dec 14, 2023, 1:12 PM Pierre Jolivet <pierre at joliv.et> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On 14 Dec 2023, at 8:02 PM, Sreeram R Venkat <srvenkat at utexas.edu>
>>>>>> wrote:
>>>>>>
>>>>>> Hello Pierre,
>>>>>>
>>>>>> Thank you for your reply. I tried out the HPDDM CG as you said, and
>>>>>> it seems to be doing the batched solves, but the KSP is not converging due
>>>>>> to a NaN or Inf being generated. I also noticed there are a lot of
>>>>>> host-to-device and device-to-host copies of the matrices (the non-batched
>>>>>> KSP solve did not have any memcopies). I have attached dump.0 again. Could
>>>>>> you please take a look?
>>>>>>
>>>>>>
>>>>>> Yes, but you’d need to send me something I can run with your set of
>>>>>> options (if you are more confident doing this in private, you can remove
>>>>>> the list from c/c).
>>>>>> Not all BoomerAMG smoothers handle blocks of right-hand sides, and
>>>>>> there is not much error checking, so instead of erroring out, this may be
>>>>>> the reason why you are getting garbage.
>>>>>>
>>>>>> Thanks,
>>>>>> Pierre
>>>>>>
>>>>>> Thanks,
>>>>>> Sreeram
>>>>>>
>>>>>> On Thu, Dec 14, 2023 at 12:42 AM Pierre Jolivet <pierre at joliv.et>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello Sreeram,
>>>>>>> KSPCG (PETSc implementation of CG) does not handle solves with
>>>>>>> multiple columns at once.
>>>>>>> There is only a single native PETSc KSP implementation which handles
>>>>>>> solves with multiple columns at once: KSPPREONLY.
>>>>>>> If you use --download-hpddm, you can use a CG (or GMRES, or more
>>>>>>> advanced methods) implementation which handles solves with multiple columns
>>>>>>> at once (via -ksp_type hpddm -ksp_hpddm_type cg or KSPSetType(ksp,
>>>>>>> KSPHPDDM); KSPHPDDMSetType(ksp, KSP_HPDDM_TYPE_CG);).
>>>>>>> I’m the main author of HPDDM, there is preliminary support for
>>>>>>> device matrices, but if it’s not working as intended/not faster than column
>>>>>>> by column, I’d be happy to have a deeper look (maybe in private), because
>>>>>>> most (if not all) of my users interested in (pseudo-)block Krylov solvers
>>>>>>> (i.e., solvers that treat right-hand sides in a single go) are using plain
>>>>>>> host matrices.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Pierre
>>>>>>>
>>>>>>> PS: you could have a look at
>>>>>>> https://www.sciencedirect.com/science/article/abs/pii/S0898122121000055 to
>>>>>>> understand the philosophy behind block iterative methods in PETSc (and in
>>>>>>> HPDDM), src/mat/tests/ex237.c, the benchmark I mentioned earlier, was
>>>>>>> developed in the context of this paper to produce Figures 2-3. Note that
>>>>>>> this paper is now slightly outdated, since then, PCHYPRE and PCMG (among
>>>>>>> others) have been made “PCMatApply()-ready”.
>>>>>>>
>>>>>>> On 13 Dec 2023, at 11:05 PM, Sreeram R Venkat <srvenkat at utexas.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Hello Pierre,
>>>>>>>
>>>>>>> I am trying out the KSPMatSolve with the BoomerAMG preconditioner.
>>>>>>> However, I am noticing that it is still solving column by column (this is
>>>>>>> stated explicitly in the info dump attached). I looked at the code for
>>>>>>> KSPMatSolve_Private() and saw that as long as ksp->ops->matsolve is
>>>>>>> true, it should do the batched solve, though I'm not sure where that gets
>>>>>>> set.
>>>>>>>
>>>>>>> I am using the options -pc_type hypre -pc_hypre_type boomeramg when
>>>>>>> running the code.
>>>>>>>
>>>>>>> Can you please help me with this?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Sreeram
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Dec 7, 2023 at 4:04 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>
>>>>>>>> N.B., AMGX interface is a bit experimental.
>>>>>>>> Mark
>>>>>>>>
>>>>>>>> On Thu, Dec 7, 2023 at 4:11 PM Sreeram R Venkat <
>>>>>>>> srvenkat at utexas.edu> wrote:
>>>>>>>>
>>>>>>>>> Oh, in that case I will try out BoomerAMG. Getting AMGX to build
>>>>>>>>> correctly was also tricky so hopefully the HYPRE build will be easier.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Sreeram
>>>>>>>>>
>>>>>>>>> On Thu, Dec 7, 2023, 3:03 PM Pierre Jolivet <pierre at joliv.et>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 7 Dec 2023, at 9:37 PM, Sreeram R Venkat <srvenkat at utexas.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> Thank you Barry and Pierre; I will proceed with the first option.
>>>>>>>>>>
>>>>>>>>>> I want to use the AMGX preconditioner for the KSP. I will try it
>>>>>>>>>> out and see how it performs.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Just FYI, AMGX does not handle systems with multiple RHS, and
>>>>>>>>>> thus has no PCMatApply() implementation.
>>>>>>>>>> BoomerAMG does, and there is a PCMatApply_HYPRE_BoomerAMG()
>>>>>>>>>> implementation.
>>>>>>>>>> But let us know if you need assistance figuring things out.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Pierre
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Sreeram
>>>>>>>>>>
>>>>>>>>>> On Thu, Dec 7, 2023 at 2:02 PM Pierre Jolivet <pierre at joliv.et>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> To expand on Barry’s answer, we have observed repeatedly that
>>>>>>>>>>> MatMatMult with MatAIJ performs better than MatMult with MatMAIJ, you can
>>>>>>>>>>> reproduce this on your own with
>>>>>>>>>>> https://petsc.org/release/src/mat/tests/ex237.c.html.
>>>>>>>>>>> Also, I’m guessing you are using some sort of preconditioner
>>>>>>>>>>> within your KSP.
>>>>>>>>>>> Not all are “KSPMatSolve-ready”, i.e., they may treat blocks of
>>>>>>>>>>> right-hand sides column by column, which is very inefficient.
>>>>>>>>>>> You could run your code with -info dump and send us dump.0 to
>>>>>>>>>>> see what needs to be done on our end to make things more efficient, should
>>>>>>>>>>> you not be satisfied with the current performance of the code.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Pierre
>>>>>>>>>>>
>>>>>>>>>>> On 7 Dec 2023, at 8:34 PM, Barry Smith <bsmith at petsc.dev> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Dec 7, 2023, at 1:17 PM, Sreeram R Venkat <
>>>>>>>>>>> srvenkat at utexas.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>> I have 2 sequential matrices M and R (both MATSEQAIJCUSPARSE of
>>>>>>>>>>> size n x n) and a vector v of size n*m. v = [v_1 , v_2 ,... , v_m] where
>>>>>>>>>>> v_i has size n. The data for v can be stored either in column-major or
>>>>>>>>>>> row-major order.  Now, I want to do 2 types of operations:
>>>>>>>>>>>
>>>>>>>>>>> 1. Matvecs of the form M*v_i = w_i, for i = 1..m.
>>>>>>>>>>> 2. KSPSolves of the form R*x_i = v_i, for i = 1..m.
>>>>>>>>>>>
>>>>>>>>>>> From what I have read on the documentation, I can think of 2
>>>>>>>>>>> approaches.
>>>>>>>>>>>
>>>>>>>>>>> 1. Get the pointer to the data in v (column-major) and use it to
>>>>>>>>>>> create a dense matrix V. Then do a MatMatMult with M*V = W, and take the
>>>>>>>>>>> data pointer of W to create the vector w. For KSPSolves, use KSPMatSolve
>>>>>>>>>>> with R and V.
>>>>>>>>>>>
>>>>>>>>>>> 2. Create a MATMAIJ using M/R and use that for matvecs directly
>>>>>>>>>>> with the vector v. I don't know if KSPSolve with the MATMAIJ will know that
>>>>>>>>>>> it is a multiple RHS system and act accordingly.
>>>>>>>>>>>
>>>>>>>>>>> Which would be the more efficient option?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Use 1.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> As a side-note, I am also wondering if there is a way to use
>>>>>>>>>>> row-major storage of the vector v.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> No
>>>>>>>>>>>
>>>>>>>>>>> The reason is that this could allow for more coalesced memory
>>>>>>>>>>> access when doing matvecs.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>   PETSc matrix-vector products use BLAS GMEV matrix-vector
>>>>>>>>>>> products for the computation so in theory they should already be
>>>>>>>>>>> well-optimized
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Sreeram
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> <dump.0>
>>>>>>>
>>>>>>>
>>>>>>> <dump.0>
>>>>>>
>>>>>>
>>>>>>
>>>>> <Pmat.bin><Amat.bin><rhs.bin>
>>>>
>>>>
>>>>
>>
>> --
>> 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
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20231222/ccb88e11/attachment-0001.html>